ABSTRACT Title of Thesis: THE ECOLOGY OF URBANIZATION: A STUDY OF SOIL MICROBIAL COMMUNITY RESPONSE Dietrich Jonathan Epp Schmidt, Master of Science, 2016 Thesis Directed By: Assistant Professor, Stephanie Yarwood, Environmental Science and Technology Department Urbanization is associated with global biodiversity loss of macrophauna and flora through direct and indirect mechanisms, but to date few studies have examined urban soil microbes. Although there are numerous studies on the influence of agricultural management on soil microbial community composition, there has been no global- scale study of human control over urban soil microbial communities. This thesis extends the literature of urban ecology to include soil microbial communities by analyzing soils that are part of the Global Urban Soil Ecology and Education Network (GLUSEEN). Chapter 1 sets the context for urban ecology; Chapters 2 addresses patterns of community assembly, biodiversity loss, and the phylogenetic relationships among community members; Chapter 3 addresses the metabolic pathways that characterize microbial communities existing under different land-uses across varying geographic scales; and Chapter 4 relates Chapter 2 and 3 to one another and to evolutionary theory, tackling assumptions that are particular to microbial ecology. THE ECOLOGY OF URBANIZATION: A STUDY OF SOIL MICROBIAL COMMUNITY RESPONSE by Dietrich Jonathan Epp Schmidt Thesis submitted to the Faculty of the Graduate School of the University of Maryland, College Park, in partial fulfillment of the requirements for the degree of Master of Science 2016 Advisory Committee: Professor Stephanie Yarwood, Chair Professor Wendy Ann Peer Richard Pouyat, PhD Jude Maul, PhD © Copyright by Dietrich Jonathan Epp Schmidt 2016 ii iii Dedication I dedicate this thesis to my grandparents, Robert and Amelia Epp, and Melvin and Charlotte Schmidt, who have each committed substantial portions of their lives towards caring for society’s vulnerable people, and protecting the environment. I am proud of the ethos of stewardship that they have cultivated, and I am honored to be a part of their legacies. iv Acknowledgements First and foremost I must thank Stephanie Yarwood, without whom I would not have had the opportunity to embark on such an invigorating quest. She has been supportive of my many whims, and patient as I have slowly, laboriously, overcome the various roadblocks along the way. This research has been a truly collaborative project and I am indebted to the many GLUSEEN collaborators, all of whom are amazing people, inspiring scientists, and have provided invaluable feedback and mentorship along the way (in no particular order): Kathy Szlavecz, Ian Yesilonis, Richard Pouyat, Heikki Setälä, Johan Kotzé, Eszerbeth Hornung, Sarel Cilliers, and Miklós Dumbos. Special thanks go to my parents, Tim Epp and Heidi Schmidt, for raising me right; and to my entire family for providing emotional support on the occasions when my aspirations feel out of reach and the demands of life are overwhelming. To all the members past and present of the Yarwood lab: Christine Maietta, Glade Dlott, Holly Bowen, Martina Gonzalez-Mateu, Tammy Walski, Ashley Robey, Zach Bernstein, and Zack Berry; in addition to being super helpful in all portions of the scientific process, each of you have contributed to an amazingly cohesive working environment that feels as much like a home as it does a place of work. I could not have asked for a better experience. The same goes for the lost residents of the HJP hermitage: Barret Wessel, Sara Mack, (Robert) Kyle Derby, Sarah Hirsch, and Natalia Salazar. I always look forward to our coffee-break musings on life, liberty, and the great pursuit. This research was funded by NSF-ACI 1244820; I have been supported financially through the ENST department. v Table of Contents Dedication .................................................................................................................... iii   Acknowledgements ...................................................................................................... iv   Table of Contents .......................................................................................................... v   List of Tables .............................................................................................................. vii   List of Figures ............................................................................................................ viii   Chapter 1: Humans as Ecosystem Engineers and the Convergence Paradigm ............. 1   A Brief History ......................................................................................................... 1   Mechanisms and Outcomes of Cultural Control ....................................................... 3   GLUSEEN ................................................................................................................ 4   Unique Energetic Controls on Soil Microbial Ecology ............................................ 6   Urban Soils................................................................................................................ 7   The Questions Considered ........................................................................................ 9   Chapter 2: Urbanization Leads to a loss of Ectomycorrhizal Fungal Diversity and the Convergence of Archaeal and Fungal Soil Communities ........................................... 12   Introduction ............................................................................................................. 12   The Global Urban Soil Ecology Education Network ............................................. 13   Biogeography and Urbanization ............................................................................. 15   Urban Soil Convergence ......................................................................................... 19   Evidence for Global Biodiversity Loss? ................................................................. 25   Conclusions ............................................................................................................. 27   Methods: ................................................................................................................. 28   Soil Sampling ...................................................................................................... 28   DNA Extraction and Preparation: ....................................................................... 31   Microbial Community Analysis: ......................................................................... 31   Bioinformatics and Statistical Analyses: ............................................................ 32   Chapter 3: A Metagenomics Approach to Inferring Microbial Function: Functions Differ Due to Geography and Land Use, but do not Converge due to Urbanization . 35   Introduction ............................................................................................................. 35   Methods................................................................................................................... 38   Site Description: .................................................................................................. 38   DNA Preparation: ............................................................................................... 39   Data Analysis: ..................................................................................................... 40   vi Results ..................................................................................................................... 41   Discussion ............................................................................................................... 54   Summary ................................................................................................................. 56   Chapter 4: Conclusions ............................................................................................... 58   Discussion ............................................................................................................... 58   Summary ................................................................................................................. 66   Appendices .................................................................................................................. 68   Appendix A: Anova Tables .................................................................................... 68   Amplicon ............................................................................................................. 68   Appendix B: R Scripts ............................................................................................ 83   Appendix C: Qiime Scripts ................................................................................... 105   16s Library: ....................................................................................................... 105   ITS Library: ...................................................................................................... 148   Appendix D: Funguilds: ........................................................................................ 204   Bibliography ............................................................................................................. 205   vii List of Tables 1.1 A summary of the four site categories defined along a disturbance management spectrum from low disturbance and low management to high disturbance or high management. 2.1 A summary of the four site categories defined along a disturbance management spectrum from low disturbance and low management to high disturbance or high management 2.2 Primer information for all laboratory techniques employed. 2.3 Raw and adjusted gene quantities, and sequence depths for each sample. 3.1 Significant indicator subsystems classifications for each site category across the globe viii List of Figures Figure 2.1: A) Geographic distribution of cities: 1) Baltimore, USA; 2) Helsinki, Finland; 3) Lahti, Finland; 4) Budapest, Hungary; 5) Potchefstroom, South Africa. Pie charts represent the average abundance of phyla across all samples for a given city (n=20). The top pie charts show the six most abundant archaeal class. The middle pie charts show the seven most abundant bacterial phyla. The bottom pie chart shows distribution of the most abundant fungal classes. B) The heat map represents the R-squared values of correlations between edaphic factors and community composition of each community. Figure 2.2: Non-metric multidimensional scaling ordinations of archaea (A), bacteria (D), and fungi (G). Gene quantities per gram of soil for archaea (B), bacteria (E), and fungi (H). Average species richness for archaea (C), bacteria (F), and fungi (I). In all cases, error bars represent standard error. Figure 2.3: Euclidian distance from centroid, representing within-group variance. Points are the average of all cities. Groups were defined as A) Group 1 is reference, Group 2 is remnant, Group 3 is turf, Group 4 is ruderal B) Group 1 is reference and remnant sites, and Group 2 is turf and ruderal; C) Group 1 is reference sites and Group 2 is all other sites. Lowercase letters indicate significant difference between groups. Figure 2.4: A) NMS ordination of the ectomycorrhizal community showing both land-use (P=0.004) and city effects (P=0.001). B) the average sequence abundance within each site category, measured after rarefying the fungal community to 20,000 OTU’s. C) Average OTU richness of the ectomycorrhizal community, grouped according to land-use category. Error bars represent standard error. D) Within group variance, using groups defined by land-use categories, of the OTU richness. Figure 2.5: Shows a significant divergence of richness values (P>0.001) in the archaeal turf site. Convergence of Richness values has an implicit impact on biodiversity; The values shown above, along with a significant increase in gene quantity per gram of soil (shown in text, table 2.3), increase in richness value, and a convergence of bray-curtis dissimilarity indices among turf sites in particular, together points to an enrichment of archaeal community without exclusion (i.e. a few winners, and no losers). Figure 2.6: Rarefaction curve of A) archaea, B) bacterial and C) fungal sequence abundances. Figure 3.1: NMS ordinations representing the similarity of A) the functional composition of sites at level 3 ontology. Each symbol represents the centroid of all cites falling in the given land use category and city. B) taxonomy assignments of communities. Each symbol represents the centroid of all cities falling in the given land use category and city. ix Figure 3.2: The relative abundance of A) zinc resistance genes and B) relative zinc transport genes determined by metagenomic annotation. Figure 3.3: Metal Resistance genes for A) Mercury B) Cadmium C) Cobalt-Zinc- Cadmium D) Arsenic. Relative abundance determined using metagenomics annotation in MG-Rast Figure 3.4: Relative abundance of metal transport genes for A) nickel and B) manganese and cobalt. Figure 3.5: Relative abundance of A) Transport genes, and B) combined siderophores. Figure 3.6: relative abundance of sulfur oxidation genes Figure 3.7: Relative abundance of A) methanogenesis genes, B) Particulate methane monooxygenase C) Carbon monoxide dehydrogenase. Figure 3.8: N metabolism Relative abundance of A) N fixation, B) nitrite/nitrate ammonification, C) ammonia assimilation, D) Nitrosative stress, E) actual abundance of ammonia oxidizing genes measured by QPCR, in each site category F) correlation between ammonia oxidizing genes and taxa identified using 16s amplicon sequencing, which are putatively identified to engage in ammonia oxidation. Figure 3.9: Relative abundance of stress response genes: A) universal stress protein, B) osmotic stress, C) oxidative stress, D) periplasmic acid stress response in enterobacteria, E) sugar-phosphate stress regulation, and F) SigmaB stress regulation. Figure 3.10: Pathogens Relative abundance of A) Staphylococcus pathogenicity island, B) Listeria pathogenicity island, C) Vibrio pathogenicity island. Figure 4.1: Taxonomic coherence of the global phylogenetic convergence pattern in A) archaea; B) bacteria; C) fungi. The dotted line represents the P-value at each taxonomic level. Solid circle is reference, open circle is remnant, open triangle is turf, closed circle is ruderal. If needed. 1 Chapter 1: Humans as Ecosystem Engineers and the Convergence Paradigm A Brief History Humans are supremely effective at altering the environment to fit our needs; our species dominates global ecological processes1. In the last ten-thousand years we have given rise to entirely new ecosystems, which we called cities. Cities developed concomitantly with an agricultural system that was simultaneously intensive2 and extensive in nature3,4. These cities, and their agricultural support system, exert new controls and represent a new ecological regime across the landscape5. In the last two hundred years, cities have transformed in scale, in structure, and in chemical signature, with the effect of vastly increasing their regional impact6. The move towards globalization of our economy has had direct impacts on the dispersal of plant and animal material, and has connected the human behavioral controls on ecological function across the globe, in what has been referred to as the tele-coupling of ecosystem services7. Our function as a keystone species and ecological engineer has evolved; we began with a propensity to encourage plants that provisioned us. But our ecological manipulations grew as we domesticated plant and animal varieties, harnessed water and shaped its flow across the landscape, and demolished entire mountains and laid down vast impervious surfaces. We have even exerted our control over the very chemical composition of the atmosphere and perturbed our planet’s long-term climactic cycles8,9. 2 Western tradition has traditionally held human activity apart from the natural world, as the “unnatural” yang to the yin of nature. As such, ecologists have at times struggled to place human ecology as a part of the natural landscape in ecological framework. This cultural phenomena is covered extensively in the conservation biology literature10 as conservation biologists and ecologists have been forced to wrestled with our widespread cultural value system. But we have made great strides as we have embraced both the role of keystone species and ecological engineers in ecosystem processes, and our particular efficacy in this role. In this philosophy, we have created various frameworks for human control in ecological processes. In one instance, this has been conceptualized as the biotic homogenization hypothesis11. This hypothesis posits that human behavior is a dominant control on ecosystem process across a human-influenced landscape by intentionally and unintentionally promoting organisms better adapted to human disturbance over those sensitive to human impact12. This construct has been particularly applied in urban ecology13, in agricultural landscapes14, and to forests15 in order to connect local management behavior with global ecological patterns. A shortcoming of the biotic homogenization hypothesis is its implicit focus on active transport and promotion, of species as the driving force behind community ecology, and the de-emphasis of other indirect human impacts and interactions. Work in urban ecology has led to the reformulation of the biotic homogenization hypothesis as the urban convergence hypothesis. This approach focuses on the diverse set of human behaviors that structure the interaction between physicochemical alterations imposed on the landscape by urbanization and the adaptive responses of individual organisms16. These include such 3 properties as human transport and cultivation, but are not limited by them. According to the urban convergence hypothesis, the aggregate of these behavior-environment feedback interactions across the landscape lead to a convergence of urban community ecology and ecosystem process towards similar states across the globe. Mechanisms and Outcomes of Cultural Control Urban centers represent only about 2 percent of the human-occupied land area5, but have far reaching implications on global biogeochemical cycles and biodiversity6. Urban centers control land-use via their pattern of consumption. Some resources, such as drinking water, must be captured at local-regional scales. On the other hand, food may be traded globally. In such a way, local environmental services such as water provisioning become tele-coupled at regional and global scales by urban living and global trade7. A fundamental feature of the human managed landscape is patchiness17; driven by land-use partitioning18. Humans meet the urban resource demands by partitioning the landscape at local, regional, and global scales, to maximize the production of the required resources to support cities19. Physical infrastructure, such as road and rail systems, have direct impacts on local topography, and also catalyze global trade in resource-use, effectively coupling local land-use decisions with global-scale resource partitioning. These multi- scalar interactions are fundamental to the understanding of human ecology. For example, crop diversity hotspots (regions in the United States that maintain unusually high crop diversity, particularly heirloom varieties) such as Appalachia, maintain a deep cultural heritage celebrating local crop varieties and are generally isolated from market opportunities20. To fully understand human impacted ecology, we must acknowledge and 4 incorporate cultural and economic knowledge so as to understand the complex landscapes that humans create and to also make practical and feasible management decisions. GLUSEEN The Global Urban Soil Ecology Education Network (GLUSEEN) is an international collaboration among urban ecologists to use a common methodology to understand soil ecosystem process in urban centers. GLUSEEN primarily seeks to test the urban convergence hypothesis, which posits that urbanization creates a habitat suitable for humans, and thus urban habitats tend to converge towards one another relative to their historic state. GLUSEEN has treated urbanization as an intensification of human impact in two categories: management, and disturbance. The framework of urban centers as a patchwork of land-use decisions is central to the experiments of GLUSEEN. Within this experiment, seven land-use categories are defined with the intention to capture a range of human impacts along management-disturbance spectrums; however this pilot study uses only four of the GLUSEEN categories (Table 1.1). The categories used in this study are defined as follows: reference sites are unmanaged sites that represent the historic state of the ecosystem. Remnant sites are similarly unmanaged sites reflecting the historic state of the ecosystem, but are located within the urban matrix. They are intended to capture the influences of anthropologically influenced floral and faunal communities (including human use), and to capture the array of chemical influences of urbanization (atmospheric N deposition, elevated CO2 concentrations, heavy metal deposition etc.). The turf site category is intended to represent a characteristically human ecosystem: lawns. This is our management category, and is intended to capture the array of behaviors that humans leverage to keep their lawns presentable by cultural standards. The ruderal site category is 5 the disturbance category, representing substantial disruption of the soil profile through demolition or development work, and also representing a shorter time since disturbance. Table 1.1: A summary of the four site categories defined along a disturbance management spectrum from low disturbance and low management to high disturbance or high management. Site Within City Disturbed soil Unmanaged Reference ✔ Remnant ✔ ✔ Turf ✔ ✔ Ruderal ✔ ✔ ✔ In my definition of management, I do not treat human intervention per se as a disturbance event; rather we treat human management as imposing a new homeostatic condition that persists through time. It is, however, important to acknowledge that much of the urban landscape is significantly disturbed early in the urbanization process, and therefore most management conditions within urbanization are applied after a disturbance event. Thus, greater time since disturbance is an implied feature of the management category. At each sampling location, GLUSEEN protocols stipulate the collection of edaphic data, including data on physiochemical properties of soils (texture, pH, SOM; available N, P, and K etc.), and biological features (decomposition rates and microbial community composition). These sampling protocols were replicated across five urban centers that were distributed across the globe: Baltimore, USA; Helsinki and Lahti, Finland; Budapest, Hungary; and Potchefstroom, South Africa. Each site category was 6 replicated five times within each city. Data on physicochemical properties of urban soils have been reported separately16, and are used as explanatory variables for interpreting the microbial community data reported in this thesis. A key objective of GLUSEEN is to provide a proof of concept for including citizen science in soil ecology. In view of that objective, the microbial dataset presented in this thesis is a supporting dataset that will be used in interpreting the decomposition data that is part of a related citizen science project Unique Energetic Controls on Soil Microbial Ecology Carbon (C) availability, soil pH and redox potential (eH) contribute to determining which metabolic strategies provide positive energetic returns for microbes. The factors affecting microbial community assembly are thoroughly reviewed by Nemergut et al., (2013)21. Among the typical cadre of factors that are studied in community ecology (such as dispersal and life history), the unusual diversity of metabolic strategies among microbes is a prominent feature that defines our understanding of microbial community assembly. In brief: microbial energy capture can be broadly divided into two strategies: autotrophy and heterotrophy. Although autotrophy linked to photosynthesis is common in plants, microbes engage in a wider range of autotrophic strategies that include the oxidation of ammonium, hydrogen, iron, and sulfur. Heterotrophy is dominant in most microbial communities, however, and relies on sufficient carbon (C) inputs. Under anaerobic conditions, some microbes can carry out fermentation reactions and others use alternative electron donor-acceptor pairs. Landscape features, such as water saturation or the mineralogy of the soil thus influence community composition and metabolic activity. 7 Urban Soils A recent publication by the Global Urban Soil Ecology Network (GLUSEEN) have drawn attention to some “universal” impacts of urbanization on soils. Particularly, GLUSEEN documented a convergence of soil pH, soil organic matter (SOM) concentration, and total soil nitrogen (N)16. SOM and pH were inversely related, with highest pH and lowest SOM generally occurring in turf and ruderal sites across cities, and the greatest similarity across cities (convergence) in soil pH and SOM occurred in ruderal sites. However, they also found that available potassium and phosphorous diverged within land-use categories among cities, with the greatest divergence occurring in turf sites. It was not clear whether this was due to an interaction with parent material or fertilization; however, it is worth noting the phosphorous and potassium are each common in fertilizers. An assumption of this research is that similar ecological processes across urban environments leads to the similar outcomes. If we consider the five factors of soil formation (climate, organisms, time, topography, parent materials), urbanization either directly or indirectly impacts each factor. Aspects of climate such as temperature (via the heat island effect22), and moisture regime (through irrigation and drainage17) are influenced by urbanization. The macrofloral and faunal communities are certainly altered by urbanization12,13,23, and this thesis will show that the microbes are as well. Microbes in particular have been shown to contribute to mineral transformations, contributing to soil weathering24–26. The grading and drainage that occurs in development and the installation of new roads can alter local topography, effectively changing the landscape position of soils. Particularly at early stages in soil development, parent material is an 8 important factor in soil formation; urbanization introduces entirely new parent material (concrete, asphalt, gravel etc.) onto the landscape27. It has been argued that in the cases where we bury soils under anthropogenic material (as opposed to transported soil material)27 that we reset the clock for pedogenesis and thereby also impact the time factor of soil formation28. Logically, if urbanization impacts each of the five important factors in pedogenesis, then it must be true that the processes of pedogenesis are altered by urbanization. These well-known anthropogenic changes to local hydrology, pH, and carbon inputs23,29,30 impact the energetic potential on which microbial life is dependent. For example, while elevated N inputs in the urban setting may prime the microbial community for greater dominance by N-cycling organisms, the transformations that take place depend on the form of N input, C availability, and redox potential of the system. While ammonium might be oxidized by ammonium oxidizing archaea, if the inputs are primarily oxygenated N species (such as nitrate), ammonium oxidation is not available as a metabolic pathway. Denitrification may occur, but only if soils become sufficiently anaerobic and sufficient C substrate exists to fuel the reaction. Therefore, the convergence of various landscape features will shape the microbial community. We may expect that if humans are imposing a consistent environmental filter via our various impacts, then ecological communities, ecological function, and ecosystem processes should converge in accordance with the type of impact. There is a modest literature13 documenting the phylogenetic convergence of plant communities 31, insect communities32, and bird communities33 in urban environments. However, I am only aware of one study that explicitly considers land-use on the convergence of microbial 9 community composition, and that on bacterial community structure in a single agricultural system in Brazil14. The Questions Considered Microbial ecologists have been challenged to justify the study of soil microbial communities with arguments which claim that microbial community composition is not a necessary factor in predicting soil ecosystem function34. Yet soil microbes are important: loss in soil microbial diversity has been shown to significantly impact N cycling35, and there is a general recognition that large portions of the plant community (including some important agricultural cultivars) depend on fungal symbionts for nutrient capture36. Meanwhile, certain groups of microbes, such as fungal root symbionts, are more likely to act as keystone species (e.g. the presence or absence of ectomycorrhizal fungal networks may impact seedling success and thereby control plant succession37). In recognition of their importance, microbial ecologists have studied microbial community dynamics; the literature available on microbial community stability would suggest that structural disruption of soils significantly increases the vulnerability of the microbial community to other forms of disturbance38. The richness of a community (or biodiversity), which is often incorporated into beta diversity metrics in microbial ecology, may not always be a good predictor of ecosystem response because dominant, minor, and keystone species each play different roles in determining a given stability domain39–41. In an urban center, however, where soils are regularly and significantly disturbed, a sharp decrease in species richness may relate to the loss of specific functions42. Both direct and indirect human management may influence local ecology; the four GLUSEEN site categories are intended to capture a range of effects including direct 10 disturbance effects (ruderal), direct management effects (turf), indirect effects of anthropogenic dispersal and atmospheric deposition (remnant), and also includes minimally affected sites (reference). This thesis seeks to answer the broad question: Do defined urban land uses have a characteristic impact on soil microbial community composition and functional potential? If so do these common land use features lead to convergence among urban microbial communities (i.e. what is the interaction between urbanization and microbial biogeography on a global scale)? Chapters 2 and Chapter 3 represent two different molecular approaches to understanding microbial community response to land-use regimes. Chapter 2 uses amplicon sequencing to ask: do the microbial communities in all cities experience a phylogenetic convergence, leading to a uniquely urban soil microbial community? I hypothesize that land use will cause microbial communities to converge relative to the “historic” proxy category (e.g. “reference”), and that the convergence will be driven by a unique interaction between land-use and the ecology of the specific microbes making up the community. Chapter 3 uses shotgun sequencing to generate a microbial metagenome. This approach allowed me to identify metabolic pathways that reflect adaptations to the new environmental conditions. Microbial metagenomic functional annotations have been shown to be sensitive enough to detect biome-scale differences in community function pathways using the same techniques employed in chapter 343. I address three major questions: 1) Are the distribution of soil microbial functions driven by geographic differences among cities? 2) Do land-use categories structure microbial metabolic pathways? 3) Does land-use drive a convergence of functional profiles on a global scale? 11 I hypothesize that there will be detectable differences in the abundance and composition of functional DNA pathways according to city (geography) and to land use. Furthermore, there will be a convergence of functional pathways under globally similar management schemes. In my concluding chapter, I compare the metagenomics approach to the amplicon sequencing approach, and discuss some biases associated with annotating the shotgun library sequences. 12 Chapter 2: Urbanization Leads to a loss of Ectomycorrhizal Fungal Diversity and the Convergence of Archaeal and Fungal Soil Communities Introduction We are in an era of unprecedented human impact5, as modified landscapes alter ecosystem function44,45 and shift the local physical, chemical, and biotic environments46,47,23. Urban ecosystems favor species that are well-adapted to a variety of anthropogenic processes such as frequent disturbance, increased nutrients, landscape fragmentation, and facilitated dispersal11,12,48. Thus, the impact of urbanization on global species distribution has been characterized as Biotic Homogenization (BH) 12,23,13. It has been suggested that BH is a major mechanism of global biodiversity loss11. There is conflict within the literature, however, as BH is often interpreted to mean that particular species are expected to appear across all urban areas and exclude endemic populations49. Although it is possible that urbanization leads to cosmopolitan species such as Columba livia domestica (pigeons) or Festuca arundinacea (tall fescue grass); it is also possible for two urban centers to contain different species, for example F. arundiacea and Poa pratensis (Kentucky blue grass), but converge in terms of functional traits 50. Such convergence can nonetheless lead to biodiversity loss if it results in the exclusion of one guild in favor of another (e.g. opportunists over competitors)48. Diversity metrics that are used by community ecologists capture positive occurrence patterns; because these metrics do not measure extinction directly, 13 biodiversity loss is determined based on inferences made from those metrics51. The techniques used to make these inferences depend on the species, tools available, and question being asked. In This case, I considered global biodiversity loss to be likely only if the microbial community exhibited a strong pattern of biogeography (representing the “average” degree of endemism, and thus vulnerability to extinction), exhibited a convergence in community composition similarity (implying a decreased prevalence of unique taxa), and a decrease in both community richness and abundance (demonstrating site specific decreases in biodiversity)51,52. Thus, I compared the communities from five cities on three continents to explore the relationship between urbanization, community convergence, and global biodiversity in soil microbes. The Global Urban Soil Ecology Education Network Soils were sampled from five cities: Baltimore, USA; Helsinki and Lahti, Finland; Budapest, Hungary; and Potchefstroom, South Africa (Figure 2.1). These cities are all part of the Global Urban Soil Ecology and Education Network47, a distributed network of urban ecologist using agreed upon protocols to investigate urban soils. 14 Figure 2.1: A) Geographic distribution of cities: 1) Baltimore, USA; 2) Helsinki, Finland; 3) Lahti, Finland; 4) Budapest, Hungary; 5) Potchefstroom, South Africa. Pie charts represent the average abundance of phyla across all samples for a given city (n=20). The top pie charts show the six most abundant archaeal class. The middle pie charts show the seven most abundant bacterial phyla. The bottom pie chart shows distribution of the most abundant fungal classes. B) The heat map represents the R-squared values of correlations between edaphic factors and community composition of each community. The GLUSEEN experiment defined seven land-use categories that are designed to represent a range of disturbance and management impacts of the urban landscape; this portion of the pilot study employs four of these categories (Table 2.1). In our definition, disturbance is an event that substantially, physically disrupts the soil, which results in an undifferentiated soil profile (e.g. soils are massive). Foot traffic across a site, for example, would not be considered to be a disturbance event because the soil remains intact. Management is defined as an intentional alteration to the ecosystem state that persists through time. Our four land-uses were: reference, remnant, turf, and ruderal 15 (Table 2.1). Reference sites were unmanaged, undisturbed sites located outside the urban matrix that had similar soil characteristics to those found in the city47. Remnant sites are reflective of the historic ecosystem type, but are located within the city. Turf sites included park, residential, and municipal lawns maintained in a homeostatic state due to mowing and other management. Ruderal sites were chosen based on a recent history of substantial disturbance to the soil profile. Typically, ruderal sites were recent construction or demolition sites. Each land-use category was replicated five times within each city, totaling 100 sites in the study. Table 1.1: A summary of the four site categories defined along a disturbance management spectrum from low disturbance and low management to high disturbance or high management. Site Within City Disturbed soil Unmanaged Reference ✔ Remnant ✔ ✔ Turf ✔ ✔ Ruderal ✔ ✔ ✔ Biogeography and Urbanization An important indicator of a community’s vulnerability to biodiversity loss is the degree of endemism among its members53; cosmopolitan organisms are less vulnerable to extinction given a local habitat alteration. In the case of microbial communities, I interpret the strength of biogeographic patterns as indicative of the average degree of endemism among community taxa. I clustered microbes at 97% sequence similarity into Operational Taxonomic Units (OTU); analyses at other taxonomic resolution were 16 clustered according to putative taxonomy. The relative abundance of putatively defined groups across all the site categories were averaged, and separate abundance distributions were created for archaea, bacteria, and fungi (Figure 2.1A). The abundance of major taxonomic groups differed across cities for all three domains, but they were more pronounced in bacteria and fungi, compared to archaea. In the bacterial community, the two Finnish cities were more similar and Baltimore, USA was the most distinct (Figure 2.1A). For example, Planctomycetes averaged 17% in Baltimore soils, but made up less than 7% of all sequences in the other four cities (Figure 2.1A). Proteobacteria were most abundant in the two Finnish cities and was the lowest in Baltimore. Thus, the bacteria exhibited a strong pattern of global biogeography (P<0.001), as cities generally separated from one another. Nested within each city, bacterial communities in the reference and remnant sites did tend to separate from turf and ruderal sites, but the turf and ruderal sites for the individual cities remained distinct (Figure 2.2D; P<0.001). This was especially true for Baltimore soils. Along with composition, bacterial gene quantity was determined by multiplying Q-PCR determined 16s gene copy numbers to the percent abundance of sequences matching bacterial OTUs. This multiplication was necessary, because I used the same primers for both Q-PCR and sequencing (Table 2.1), a primer set that simultaneously amplifies both archaea and bacteria (archaea discussed below). Bacterial gene copies numbers were lower in all three within city sites compared to the reference (Figure 2.2E: P=0.011) and did not differ in terms of species richness (Figure 2.2F). 17 Figure 2.2: Non-metric multidimensional scaling ordinations of archaea (A), bacteria (D), and fungi (G). Gene quantities per gram of soil for archaea (B), bacteria (E), and fungi (H). Average species richness for archaea (C), bacteria (F), and fungi (I). In all cases, error bars represent standard error. 18 Table 2.1: Primer information for all analyses. Target Sequence Gene-info Use 5.8S CGC-TGC-GTT-CTT-CAT-CG Intergenic-spacer-region-fungi QPCR ITS1F CTTGGTCATTTAGAGGAAGTA Intergenic-spacer-region-fungi QPCR ITS1f+adapter TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGACTTGGTCATTTAGAGGAAGTAA Overhang-adapter+ITS-primer-ITS1F Sequencing ITS2r+adapter GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAGCTGCGTTCTTCATCGATGC Overhang-adapter+ITS-primer-ITS2R Sequencing F515 GTGCCAGCMGCCGCGGTAA 16s-rRNA QPCR R806 GGACTACVSGGGTATCTAAT 16s-rRNA QPCR F515+adapter TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTGCCAGCMGCCGCGGTAA Overhang-adapter+16s-primer-ITS1F Sequencing R806+adapter GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGACTACVSGGGTATCTAAT Overhang-adapter+16s-primer-ITS2R Sequencing Similar to the bacteria, fungal communities, , showed a strong pattern of land-use (P<0.001) nested within a pattern of biogeography among fungal OTUs (P<0.001;Figure 2.2G), but unlike the bacteria, turf and ruderal sites contained significantly fewer fungal ITS gene copy numbers (Figure 2.2H; P=0.01). Species richness did not change between the four site categories (Figure 2.2I). The relative proportions of Ascomycota to Basidiomycota drove global differences in the fungal biogeography (Figure 2.1A). And similarly to bacteria, the fungal ordinations showed that in each site category, Baltimore sites separated from similar categories of the other four cities (Figures 2.2D and 2.2G). In contrast, the archaeal communities had limited evidence for biogeographic distribution. Although there was some variation in the abundance of some phyla among cities, a PerMANOVA analysis shows no significant effect of city among archaeal genera (Figure 2.2A; P=0.17). More detailed abundance distribution is provided in the Supplementary Materials. Along with composition, archaeal gene quantity was determined by multiplying Q-PCR determined 16s gene copy numbers to the percent abundance of sequences matching archaeal OTUs. Surprisingly, turf sites contained the most archaeal 16S rRNA gene copy numbers (2.34E+9 gene copies g-1 of soil; P=0.034), with fewer archaeal sequences detected in both the reference and remnant (Figure 2.2B). Likewise, archaeal species richness was also higher in the turf sites (Figure 2.2C; 19 P<<0.001). These data suggest that management practices such as increased nutrients may favor a larger, more diverse archaeal population (see Figure 2.5 for more detail). Microbial community composition was correlated to a number of physiochemical parameters to further elucidate distribution patterns. Global bacterial and fungal community compositions were found to be highly correlated with soil pH, % organic matter, and organic C (Figure 2.1B). Physicochemical properties of these soils have been reported seperately47. Soil pH strongly correlated with the bacterial community (R2 =0.61; Figure 2.1B) and fungal community (R2=0.57; Figure 2.1B), a phenomena that has been reported in the literature previously 54,55 ,56. The archaeal community composition also correlated with pH (R2=0.51; Figure 2.1B), but had lower correlation coefficients with % organic matter and organic C compared to bacteria and fungi (Figure 2.1B). These data suggest that archaeal distribution does not necessarily correspond to bacterial or fungal distribution, and in particular archaea appear to be less impacted by soil Urban Soil Convergence Convergence of microbial communities represents a decrease in dominance of site-specific species, which may result in a loss of biodiversity. I measured convergence as a reduction of between-site variance through time, and regarded the reference sites as a proxy for the historic state of each city. I used Bray-Curtis dissimilarity index to compare site similarity. If microbial communities were converging, I expected to see dispersed reference sites for each city, but clustered (e.g. more similar) urban sites. The archaeal communities exhibited this relationship well; the reference and remnant sites were more variable especially from Baltimore, Helsinki, and Lahti, but the turf and ruderal sites were very similar (Figure 2.2A; P<<0.001); thus a PerMANOVA analysis of archaeal 20 genera found no significant effect of city on community composition (e.g. no biogeography), but a significant effect of landuse (P<0.001). I tested for convergence using the betadisper function in the vegan57 statistical package in R (version 3.1.3), a multivariate analogue of the Levene’s test of homogeneity of variances. I analyzed variance according to three site groupings (Figure 2.3); first I compared the four groups according to their land-use category, then I categorized sites into high or low impact groups (discussed below), and finally I categorized sites into groups based on whether they fall inside or outside of the urban matrix. These groupings were applied to the global dataset (Figure 2.3), and within each individual city (data not shown) in order to elucidate potential drivers of convergence. With the exception of archaeal (P=0.037) and fungal (P=0.004) communities in Baltimore, there were equal category-wise (land-use) variances of community composition in each individual city, indicating that generally convergence is not detectable at local scales. 21 Figure 2.3: Euclidian distance from centroid, representing within-group variance. Points are the average of all cities. Groups were defined as A) Group 1 is reference, Group 2 is remnant, Group 3 is turf, Group 4 is ruderal B) Group 1 is reference and remnant sites, and Group 2 is turf and ruderal; C) Group 1 is reference sites and Group 2 is all other sites. Lowercase letters indicate significant difference between groups. When I analyzed group variance according to site category, archaeal community converged (P<0.001); turf and ruderal site were less variable relative to reference and 22 remnant sites (Figure 2.3A). The fungal community also converged (P=0.047); ruderal sites were less variable relative to reference sites. The bacterial community differed in variance between site categories (P=0.023); however, a post hoc TukeyHSD indicated that this was driven by a slight increase in variance among remnant sites and slight decrease in variance among turf sites relative to reference. Thus, while the variance of remnant and turf sites differed, neither the variance of turf nor ruderal sites differed significantly from the reference (Figure 2.3A). Using the same approach, I explored whether microbial communities converge simply because they exist within the urban matrix, or whether direct management and disturbance led to a greater degree of convergence. Thus, I conducted two tests to investigate the effect of management and disturbance on convergence. First, I grouped all reference and remnant sites together (Low impact), and compared them to a grouping of all turf and ruderal (High impact; Figure 2.3B). In this case, all three microbial communities converged (archaea P<0.001; bacteria P=0.002; and fungi P=0.014). To test difference due to being within the city, reference sites were compared to a grouping of remnant, turf, and ruderal (Figure 2.3C). In this case, only the archaea converged (P<0.001). These results suggest that human processes such as soil disturbance, and direct management of the flora, alter microbial communities more than other changes such as air temperature or atmospheric N deposition within an urban center. Thus, distinct human processes define each of the high impact sites, and yet when grouped together they have lower variation than the reference and remnant sites across all three domains, suggesting that there is either a common set of organisms that is able to exploit 23 these new environments, or as has been reported elsewhere in the BH literature, there is a consistent suppression of certain guilds48. To answer whether urbanization suppresses organisms of certain metabolic strategies (or functions), I assigned functional guilds to our identified OTUs, using publicly available databases. Attempts to characterize bacterial and archaeal functional differences were hampered due to database limitations. I explore bacterial function using a metagenomics approach in Chapter 3. In the case of fungi, the fungal database program FUNGuilds was used to assign putative function to identified OTUs58. The majority of my fungal sequence data was binned into a functional category using this approach. The resulting data pointed to a loss of ectomycorrhizal fungi (ECM) as the main driver for convergence and differences between land-uses. When ECM sequences were examined at the family level, turf and ruderal sites significantly converged compared to reference and remnant (P=0.016). At the OTU level, the turf and ruderal sites also converged (Figure 2.4A). There was also a significant decrease in sequence abundance (P=0.003, Figure 2.4B) and on OTU richness (P>0.001, Figure 2.4C) within the turf and ruderal sites. This supports previous research that also reported lower ECM colonization in disturbed urban soils59; to my knowledge ours is the first paper to report this trend across multiple cities. 24 Figure 2.4: A) NMS ordination of the ectomycorrhizal community showing both land-use (P=0.004) and city effects (P=0.001). B) the average sequence abundance within each site category, measured after rarefying the fungal community to 20,000 OTU’s. C) Average OTU richness of the ectomycorrhizal community, grouped according to land-use category. Error bars represent standard error. D) Within group variance, using groups defined by land-use categories, of the OTU richness. 25 0" 500" 1000" 1500" 2000" 2500" 3000" 3500" 4000" 4500" Reference" Remnant" Turf" Ruderal" Va ria nc e( Site(Category( Figure 2.5: Shows a significant divergence of richness values (P>0.001) in the archaeal turf site. Convergence of Richness values has an implicit impact on biodiversity; The values shown above, along with a significant increase in gene quantity per gram of soil (shown in text, table 2.3), increase in richness value, and a convergence of bray-curtis dissimilarity indices among turf sites in particular, together points to an enrichment of archaeal community without exclusion (i.e. a few winners, and no losers). Evidence for Global Biodiversity Loss? A major concern of urbanization is that BH will lead to global biodiversity loss. However, the pattern of convergence among urban biotic communities does not inherently imply a loss in biodiversity51. My fungal, archaeal, and bacterial datasets demonstrate how BH may be associated with biodiversity loss in some communities, but not others. My most compelling evidence for biodiversity loss was found in the fungal dataset, where I found evidence of endemism (biogeography) and an urban filter effect; the convergence of ruderal sites relative to reference shows that this filter is consistent 26 across cities globally. Likely many factors contribute to this observed change, including soil factors such as pH and nutrient concentration, but also the presence of particular host plants 60. I found that the convergence of urban sites was associated with a precipitous loss of ectomycorrhizal fungi, which declined in abundance and richness. This data supports previous literature demonstrating that loss of diversity may be an important factor driving convergence48,51, and provides evidence supporting the connection between BH and global biodiversity loss11. The convergence of the archaeal communities provides a contrasting scenario in which communities may converge without losing biodiversity. Archaeal communities converged in turf and ruderal sites, suggesting that urbanization is an environmental filter that increases community similarity. But there was little evidence of endemism, and my richness and abundance data suggests that urbanization enriches the archaeal community without necessarily excluding diversity. Thus I observe that if an introduced cosmopolitan species does not compete with endemic taxa, as is likely given archaeal metabolic strategy and the soil medium in which they grow21,61, then the community may experience convergence in composition without experiencing competitive exclusion and loss of biodiversity. The bacterial community presents yet a third possibility. Even though the bacterial communities do exhibit strong pattern of biogeography and urbanization does appear to impact bacterial abundance, urbanization does not appear to impact bacterial diversity per se; there was little evidence for convergence and no change in richness. In such cases where decreased bacterial abundance and shifts in community composition do reflect an increased likelihood that some bacterial lineages are extirpated locally, the rapid rate of 27 bacterial evolution62,63 and horizontal transfer of genetic materials64 allow that bacterial diversity and function may nonetheless remain intact. This highlights the important interaction between time and evolutionary process, and raises intriguing questions about the impact of human management on global biodiversity at a geologic time-scale, should human management persist. Conclusions My study represents one of the first comparisons of microbial community composition between different cities and across all three domains of microbial life. Although several previous studies have examined microbial communities within a single city, those studies could not infer global diversity loss, due to a lack of information concerning regional variation. I have shown that although urbanization leads to community composition changes across a wide range of microbes, that there were differences in specific interactions between land-use and community composition among the three microbial domains. I also found that ectomycorrhizal fungi may be the only group that experiences significant diversity loss due to urbanization. Because ECM are dependent on woody host plants that are often limited in cities compared to the surrounding environment, future city planning should include remnant sites that will help to support these microbes. Even if the host plant is present, large amounts of nutrients such as nitrogen65 can further discourage ectomycorrhizal colonization. Nutrient management within urban centers and planting of host species will assist in remediating the loss of these valuable organisms. 28 Methods: Soil Sampling In each city, we took special care to ensure that soil type was consistent across all selected site categories (Table 1.1). In particular, we favored well-drained upland soils, avoiding riparian zones, and soils that are often saturated. Each sample consisted of five- 2.5 x 10 cm deep soil cores, excluding the O horizon, that were homogenized in a sterile plastic bag using a sterile scoopula. A soil sample from each homogenized bag, weighing ~2 g, was preserved in 4 mL Lifeguard™ preservation solution (MoBio, Carlsbad, CA). This procedure was repeated at 5 locations per site category, resulting in 100 samples total (n=5). Illumina amplicon sequencing returned 12.5 million archaeal and bacterial 16S rRNA sequences and 6.2 million fungal ITS sequences. By comparing 16S rRNA sequences to the Greengenes database at 97% similarity, 270,000 OTUs were identified across all samples. This included 3,700 archaeal OTUs; 255,481 bacterial OTUs; and 17,439 unassigned OTUs. Rarefaction analysis did not result in plateaued curves, suggesting additional sequencing would yield even more OTUs. On average, 62,132 sequences per sample were generated for the fungi and a total of 12,620 OTU’s were identified by matching to the UNITE database66. Rarefaction curves of the fungal sequences indicted that this sequencing was sufficient to accurately sample fungal diversity. Rarefaction curves and sequences for each sample can be found in Figure 2.6, and Table 2.2 respectively. I document an OTU diversity in my global dataset that is approximately two times greater than the diversity documented in a recent study claiming 29 that soil biodiversity in New York’s Central Park was equivalent to biodiversity found in global sampling67. In my analysis I used similar sequencing methods and clustering thresholds, but had one fifth the sampling depth (100 samples vs. 500 samples) and sequencing depth (12.5 million sequence reads vs. 50 million sequence reads). Figure 2.6: Rarefaction curve of A) archaea, B) bacterial and C) fungal sequence abundances. 30 Table 2.2: Raw and adjusted gene quantities, and sequence depths for each sample 31 Each sample consisted of five-2.5 x 10 cm deep soil cores, excluding the O horizon, that were homogenized in a sterile plastic bag using a sterile scoopula. A soil sample from each homogenized bag, weighing ~2 g, was preserved in 4 mL Lifeguard™ preservation solution (MoBio, Carlsbad, CA). This was procedure was repeated at 5 locations per site category, resulting in 100 samples total (n=5). DNA Extraction and Preparation: Soils were extracted following the MOBIO Laboratories inc. Powerlyzer™ Powersoils® DNA isolation kit protocol (MoBio, Carlsbad, CA, USA), with two exceptions. First, instead of adding 0.25 g of dry soil to the bead beating tubes in step two, 750 uL of soil suspended in Lifeguard™ solution was added to each tube. Second, a Fastprep®-24 set to 3.5 m/s for 45 s was used in cell lysis (MP Biomedical, Santa Ana, CA, USA). The exact weight of each soil sample used for extraction was calculated based on the measured weight of a 0.5 mL aliquot of soil slurry dried at 60º C for one week. Extracted DNA was quantified using a QuBit® 2.0 Flourometer (Invitrogen, Carlsbad, CA). DNA extracts were diluted to 1.25 ng/uL for sequencing amplification and QPCR. DNA samples are stored at -20º C between each analysis. Microbial Community Analysis: Amplicon sequencing targeted a section of the 16S rRNA using primers 515F+adapter and 806R+adapter (Table 2.2) and the ITS1 region in fungi using primers ITS1F+adapter and ITS2+adapter (Table 2.2). Adapters were ligated to the forward and reverse strands, and the libraries were indexed using the Nextera XT 96 index kit 32 (Illumina, San Diego, CA, USA). Samples were sequenced using an Illumina MiSeq 2000 (Illumina, San Diego, CA, USA) at the Oregon State University Center for Genome Research and Biocomputing. The sequencing kit produced 250 bp, paired-end read, and was run with a 10% Phix. Q-PCR for the combined bacterial and archaeal community was performed using the primers F515 and 806R (Table 2.2). Fungal community were quantified by targeting the ITS region using ITS1F and 5.8S (Table 2.2). The master mix for each QPCR reaction was as follows: 16 uL of Kicqstart Sybr Green Readymix With Rox (Sigma, St. Louis, MO), 1.0 uL of 10 uM forward and reverse primers, and 2 uL DNA diluted to 1.25 ng/mL. The standard curve was a 1:10 serial dilution of 2.5 ug/ml DNA, and concentrations are calculated based on the size of the plasmid containing an insert. An inhibition correction was applied using the following strategy: 2 uL of each sample was pooled and quantified using the flourometer; a soil standard curve consisted of 1:10 serial dilutions. I calculated a soil efficiency standard correction according to previously reported protocol68, but rejected this correction because it applied a more significant correction to samples with higher gene counts rather than lower gene counts. Bioinformatics and Statistical Analyses: The QIIME pipeline69 was used in processing sequence libraries, with a few variations between the 16S and ITS sequence analysis. For ITS samples, the number of allowable homopolymer repeats in the split-libraries were increased from 6 to 8, because at the default of 6, 80% of the sequences were eliminated. The RDP70 classifier was used to assign fungal taxonomy against the UNITE database66; and I used uclust to cluster the 16s OTUs against the Greengenes database71. Both datasets were clustered at 97% 33 similarity, followed by open-reference OTU-picking. The reverse primers were removed in the split-libraries step and the minimum overlap in joining the paired end reads (ea- utils72, fastq-join.py) was increased from 6 to 50 bases in both amplicon libraries. All other functions in the QIIME pipeline were run on default settings. Our QIIME pipeline workflow went as follows: fastq-join.py; convert_fastqual_Fastq.py; split-libraries.py; cat; pick-otus.py; pick_rep_set.py; assign_taxonomy.py; make_otu_table.py; biom convert; and summarize_taxa.py. I used outputs from the make_otu_table and summarize_taxa functions in our downstream data analysis in R and PC-ORD. Full scripts can be found in the supplemental information. Alpha diversity was calculated based on Shannon-Weiner diversity indices in each sample and Pielou’s J was used to calculate evenness indices. Both R and PC-ORD platforms were used to construct Bray-Curtis distance matrices. PC-ORD73 was used to run a nested Permanova to compare differences in community composition and the betadisper function (of the vegan package57) in R74 (version 3.1.3) was used to test for difference in within group variance among site categories. The envfit (vegan package) function in R was used to generate correlations between microbial communities and environmental parameters. I also used the vegan stat package to run blocked one-way ANOVAs and Tukey post-hoc analyses for differences in gene abundances between site categories. All R scripts can be found in the supplemental material. For all ECM analysis, the fungal communities were rarefied to 20,000 OTU’s. R scripts for rarefaction and downstream statistics are available in the supplemental material. I used the R statistical packages vegan, stats74 and lawstat75 (scripts in supplemental; citations). 10 sites falling under 20,000 sequences were omitted from all 34 analyses, while an additional 13 sites were omitted from my community composition analysis because they lacked any ECM. Because I rarefied the community to equal sampling depth, I treat sequence abundance as accurately representing relative ECM abundance in the environment. Richness values were calculated as the total number of distinct OTU’s at each site. Convergence was identified by comparing within-group variances among land-use categories, and tested using levene’s test of equality of variances. The NMS ordination was constructed in PC-ORD73, with Beals smoothing applied to the distance matrix, accounting for the high incidence of zeroes within the ECM community. 35 Chapter 3: A Metagenomics Approach to Inferring Microbial Function: Functions Differ Due to Geography and Land Use, but do not Converge due to Urbanization Introduction Amplicon sequencing has been most commonly used to investigate soil microbial communities. Many studies have used 16S rRNA to reconstruct evolutionary history and infer phylogenetic relationships. However, a major shortcoming of amplicon sequencing is the absence of information on the metabolic characteristics of the organisms, and therefor also the inability to assess the potential function of the aggregate community. There have been a few attempts at addressing this issue; databases such as PICRUSt76, and FUNGuilds58 attempt to predict metabolism or ecological function from 16S or other ribosomal RNA genes either using whole sequenced genomes of known organisms, or by applying literature reviews of representative taxa within a phylogeny. Because programs like PICRUSt leverage sequenced genomes to predict function, these models are limited in accuracy and breadth by organismal groups for which a representative genome has been sequenced. Another issue with using phylogenetic markers to infer function, is that difference in rRNA may not provide sufficient resolution to distinguish between strains. We know that in the case of E. coli, strains can have radically different ecological function77 and up to one-third of the genome may differ within cells that are all considered the same species. Shotgun metagenomic sequencing offers a complimentary approach to examine the functional capacity of the soil microbial community. Unlike, amplicon sequencing 36 that relies on targeting a specific gene of interest through PCR amplification, metagenomic sequencing does not use PCR, and random fragments of DNA are sequenced. Following the amplicon sequencing that was described in Chapter 2, I used metagenomic sequencing to further investigate the urban soil microbial communities, in this case focusing on differences in function. The metagenomic sequence dataset can be analyzed by assigning metabolic pathways, or subsystems, to metagenomic datasets. Urban soil microbial data were analyzed using Metagenomic Rapid Assignment using Subsystems Technology (mg- RAST78) from Argon National Lab to make assignments based on the SEED database79. MG-RAST operates in three steps: 1) quality control filtering selected by the user; 2) assigning sequences to a likely protein via a database search (such as blast); and 3) annotating the sequences using the assigned subsystem. Subsystems are collections of genes that make up a metabolic pathway79 and are curated manually, meaning they can change as more information about organismal metabolism becomes available. The shotgun sequencing approach primarily captures bacterial genes because of their dominant presence in bulk soils; therefore it should be considered a complimentary analysis to the bacterial 16S rRNA amplicon library from Chapter 2. A number of edaphic factors are known to correlate to microbial community composition, including: soil texture, SOM concentration, C availability and pH. Previous research has shown that soil pH is perhaps the most significant variable correlated to landscape-level changes in community composition80. This is not surprising as soil pH controls nutrient availability and likely contributes to a host of microbial adaptations. Soil mineralogy has likewise been shown to strongly correlate to shifts in microbial 37 community composition81. One caveat of these studies, however, is that most are based on 16S rRNA. The 16S rRNA composition could appear different due to differences in environmental filtering caused by pH or mineralogy, but these factors may not necessarily lead to differences in functional pathways. Likewise, two soils may have similar communities based on 16S rRNA, but environmental variables may lead to the selection of strains that differ in functional composition82. My study is therefore one of the first to assess the role of these soil factors on soil metagenome composition. For this study, the relationship between geographic distribution of edaphic properties such as mineralogy and pH is complicated by anthropogenic modification. Notably, carbon (C) concentration and pH of northern soils are significantly affected by urbanization. The increase in soil pH within cities has been attributed to the introduction of alkaline inputs in the form of concrete83 (calcium carbonates and calcium). Management of the urban plant community23 in combination with the physical disturbance of the soils, may result in C loss or accumulation84; my turf and ruderal site categories are consistent with land uses that may decrease soil carbon. The global convergence of soil pH and C content in urban soils has already been confirmed in these sites47. In this study, I used a metagenomics to assign potential function profiles and taxonomic community profiles to microbial communities sampled in five cities on three continents. I hypothesize that given predictable changes in urban soils such as increase pH and decreased C, the microbial communities within cities will converge in terms of functional characteristics, even if they do not converge in terms of community composition. 38 Methods Site Description: The Global Urban Soil Ecology Education Network (GLUSEEN) is a diffuse network of scientists using common methodology to answer basic questions about the ecology of urban ecosystems. Five cities distributed across three continents participated in this study: Baltimore, USA; Helsinki and Lahti, Finland; Budapest, Hungary; and Potchefstroom, South Africa. In each of these cities, four habitat types were defined: reference, remnant, turf, and ruderal47. These habitat types represent a range of disturbance and management inputs in soils. Reference sites are defined as undisturbed and unmanaged soils that are located outside of the urban matrix. Remnant sites are defined as undisturbed and unmanaged sites that are located within the urban matrix. Turf sites are defined as sites that are not recently disturbed (grading, soil transport etc. may have occurred at some point in the past), but are under management to maintain a turf ecosystem; typical examples include park lawns, municipal lawns, and residential lawns. Finally, ruderal sites are defined as having recently endured substantial disturbance to the soils structure, and include vacant lots and other abandoned properties. Soils for this study were sampled using a 2.5 cm diameter core to a depth of 10 cm; five separate cores were taken, and organic material was removed from the top leaving the mineral soil and in some cases an Oa horizon. These cores were homogenized in a sterile plastic bag, and a 2 g subsample was placed in a LifeGuard preservation solution. The soils differ significantly in pH, organic matter concentration, and mineralogy among the various cities. For example, the soils of Lahti and Helsinki were spodosols47, 39 and have a higher organic fraction (our analysis included the Oa with the A mineral horizon) which represents a greater availability of organic C and N. Spodosols are acidic due to their high organic acid content, whereas the alphasols of Baltimore are buffered at around a pH of 5.2 by aluminum redox in the mineral matrix; arid soils such as those found around Potchefstroom are typically more alkaline, and Budapest sits on calcareous parent material, buffering soils to a more alkaline state47. DNA Preparation: DNA was extracted using the MoBIO (Carlsbad, California) Powersoils Powerlyzer DNA extraction kit. Q-PCR for the Ammonia oxidizing archaea and bacteria were quantified by targeting the ammonia monooxygenase gene, using previously published primer sets that were unique for each of the archaeal85 and the bacterial86 homologues. The master mix for each QPCR reaction was as follows: 16 uL of Kicqstart Sybr Green Readymix With Rox (Sigma, St. Louis, MO), 1.0 uL of 10 uM forward and reverse primers, and 2 uL DNA diluted to 1.25 ng/mL. The standard curve was a 1:10 serial dilution of 2.5 ug/ml DNA, and concentrations are calculated based on the size of the plasmid containing an insert. I only used QPCR data for which the run had 95-105% amplification efficiency, and an R-squared above 0.995. The DNA library was prepared using the Nextera XT Tagmentation kit to prepare 96 samples, which were indexed using the Nextera XT 96 sample index. I followed Illumina recommended protocols (Part# 15044223 Rev. B). The resulting fragments ranged in size from 0.2 to 2.0 kb, determined by Bioanalyzer using the Agilent high sensitivity DNA assay at the University of Oregon Center of Genome Research and Biocomputing (Corvalis, OR). The initial objective of shotgun sequencing was to test a 40 new algorithm for detecting pathogens; our 16s rRNA library sequences indicated that I had Yersinia sp. (Figure 2.4) and I was looking to confirm the presence of Y. pestis. Therefore, I chose to omit four samples from Baltimore (samples 2 and 4 were ruderal sites, sample 1 was remnant, and sample 5 was turf) which had no Yersinia calls in the previous sequencing run. Paired-end sequencing, with 150bp reads, was conducted on an Illumina Hiseq 3000 platform, using the Nextera XT 96 sample indexes, at the University of Oregon Center of Genome Research and Biocomputing (Corvalis, OR). Data Analysis: Sequence annotation was done on the MG-RAST server (Argon National Lab, Chicago, IL); with no host filters applied, and no filter for PCR replication. I chose to use the SEED database79 for function annotations in my analysis because this is the most robust database. Function and taxonomy data was downloaded using the matR package87 in R (version 3.1.1), at two levels of ontology (level one and level three), and three levels of taxonomy (genus, family, and order; assigned based on the Greengenes database). Cutoff e-values were left at default (1e-5) for this analysis. The annotation data was then used to create a function matrix, which was the basis of my statistical analyses. I assessed the convergence of community function profiles using the betadisper function of the Vegan57 package in R (version 3.1.1). Scripts can be found in the Appendix B. Beta diversity in the function profiles was assessed using a nested PerMANOVA analysis in PCORD73, and using the Vegan package in R. 41 Results At both ontology categorization levels, functional profiles were significantly affected by geography (e.g. City; P=0.007, P<0.0001) and land-use category (P=0.0004, P<0.0001). These effects are clearly visible on an NMS ordination (Figure 3.1). As in the 16s library, Baltimore sites clustered away from other cities and show a clear separation between site categories (Figure 2.2; Figure 3.1); Helsinki and Lahti also clustered together with distinctions among their constituent land-use categories, and Budapest and Potchefstroom cluster together. Although there were significantly different functional gene profiles present in each site category, there was no difference among the variances of each site category (i.e. there was no convergence; P=0.95, P=0.99). 42 Figure 3.1: NMS ordinations representing the similarity of A) the functional composition of sites at level 3 ontology. Each symbol represents the centroid of all cites falling in the given land use category and city. B) taxonomy assignments of communities. Each symbol represents the centroid of all cities falling in the given land use category and city. For the level one ontology group, the indicator categories in reference sites were: “Virulence, disease and defense”; and “Potassium metabolism.” Level one ontology groups with the highest abundance in remnant sites were: “sulfur metabolism”; “Metabolism of Aromatic Compounds”; “Fatty Acids, Lipids, and Isoprenoids”; 43 “Secondary Metabolism”; and “Photosynthesis.” In ruderal sites the most abundant categories were: “Nitrogen Metabolism”; and “Iron Acquisition and Metabolism.” There were no indicators of turf at level one ontology. At level three ontology, which is higher resolution, the functions that strongly indicate each site category are genes that encode for maintenance, and metabolism (Table 3.1). There were a total of 1155 level 3 subsystems identified across all 96 samples. Of those, 902 subsystems were significant indicators for at least one city (P<0.05). This is due to the strong geographic structure of this dataset. Across all cities, there were fewer indicators of site category. Ruderal sites had 69 significant indicator functions, turf sites had only one indicator function. Intermediate to these sites, 11 indicators were associated with remnant and 16 indicators were associated with reference. Though there were few statistically significant indicators of land use category, many of the functions had different expression patterns based on city and land use category. Resistance to some metals, such as zinc, arsenic and cobalt-zinc-cadmium, had geographic structure. For example, zinc resistance was higher in Baltimore (Figure 3.2) than in any other city (P<0.001). In contrast, arsenic resistance was highest in Helsinki ruderal sites (Figure 3.3; P<0.001). Interestingly, some resistance pathways such as mercury, cadmium, and arsenic, exhibited as much variation within cities as among cities; in every city arsenic resistance was highest in turf or ruderal sites, as was mercury resistance (Figure 3.3, panel A; P<0.001). Meanwhile, Zinc-Cobalt-Cadmium resistance was lowest in turf and ruderal sites in all cities (P<0.001), and had the greatest abundance and differences among sites in northern cities (P<0.001). The abundance of zinc transporters was negatively correlated with zinc resistance (R=-0.559). This may be 44 related to zinc availability and toxicity; zinc is a necessary micronutrient, but is also toxic at elevated levels. When it is scarce, I expect microbes to need genes that engage in active zinc transport into the cell, whereas when it is abundant microbes will need mechanisms for avoiding toxicity. Thus, genes for transport and resistance should be negatively correlated with one another. 45 Figure 3.3: Metal Resistance genes for A) Mercury B) Cadmium C) Cobalt-Zinc-Cadmium D) Arsenic. Relative abundance determined using metagenomics annotation in MG-Rast 46 With the exception of Baltimore sites, Nickel and Cobalt transport was most abundant in turf and ruderal sites (figure 3.4). This is corroborated by the indicator analysis that found arsenic resistance was a strong indicator of ruderal sites(P=0.003), as were copper homeostasis genes (p=0.001), and Nickel and cobalt transport genes (P=0.004). Manganese transport, on the other hand, was expressed least in turf and ruderal sites (P<0.001). There was a significant land use effect on siderophore gene abundance (Figure 3.5), with gene abundance being on average highest in ruderal sites (P<0.001). Iron metabolism exhibited a similar pattern, with Baltimore having the lowest abundance of these genes (P<0.001), and ruderal sites having the highest average abundance. Iron metabolism was highly correlated with Iron transport (Figure 3.8; R=0.869), and siderophore presence (Figure 3.8; R=0.899). 47 Figure 3.4: Relative abundance of metal transport genes for A) nickel and B) manganese and cobalt. Figure 3.5: Relative abundance of A) iron transport genes, and B) combined siderophores. Sulfur oxidation also exhibited a geographic pattern; Baltimore sites exhibited the highest abundance of Sulfur oxidation genes (Figure 3.6; P<0.001). Across land use, turf exhibited the highest number of annotations, and ruderal exhibited the lowest. Methanogenesis exhibited a significant geographic expression pattern (P<0.001), but no relationship to landuse (Figure 3.7;P=0.116). This pattern was mirrored in the particulate methane mono-oxygenase patterns (P=0.007; P=0.305, geography and land use respectively). In both cases, abundance was highest in Baltimore. Carbon monoxide dehydrogenase, a gene involved in in methane oxidation as well as a diverse array of other carbon-oxidation metabolic pathways, was most abundant in Baltimore sites 48 (P<0.001) and remnant sites (Figure 3.7; P<0.001). Nitrogen metabolism was a significant ontology level 1 indicator of ruderal sites. The level-three ontology indicated that the functions driving this annotation were nitrate and nitrite ammonification genes. Ammonia assimilation, an essential cell function for all life, exhibited no difference in expression profiles based on land use, but was significantly higher in Baltimore than all other cities (Figure 3.8; P<0.001). Expression of N fixation genes were again, highest in Baltimore (P<0.001), and exhibited no response to landuse (P=0.243). N fixation was weakly and negatively correlated to nitrate and nitrite ammonification (R=-0.172), and was most expressed in ruderal sites and in Helsinki and Lahti. Ammonia oxidation genes, a function which were not annotated to any sequences, were significantly more abundant in turf sites (P=0.004), and were positively correlated with the number of putatively identified ammonia oxidizing archaea in my the 16s amplicon dataset presented in Chapter 2 (R=0.797, Figure 3.8). 0" 0.0001" 0.0002" 0.0003" 0.0004" 0.0005" 0.0006" 0.0007" 0.0008" 0.0009" Re fe re nc e" Re m na nt " Tu rf " Ru de ra l" Re fe re nc e" Re m na nt " Tu rf " Ru de ra l" Re fe re nc e" Re m na nt " Tu rf " Ru de ra l" Re fe re nc e" Re m na nt " Tu rf " Ru de ra l" Re fe re nc e" Re m na nt " Tu rf " Ru de ra l" Bal;more" Helsinki" Lah;" Budapest" Potchefstroom" Re la %v e' Ab un da nc e' Sulfur'Oxida%on' Figure 3.6: relative abundance of sulfur oxidation genes 49 Figure 3.7: Relative abundance of A) methanogenesis genes, B) Particulate methane monooxygenase C) Carbon monoxide dehydrogenase. 50 Figure 3.8: N metabolism Relative abundance of A) N fixation, B) nitrite/nitrate ammonification, C) ammonia assimilation, D) Nitrosative stress, E) actual abundance of ammonia oxidizing genes measured by QPCR, in each site category F) correlation between 51 ammonia oxidizing genes and taxa identified using 16s amplicon sequencing, which are putatively identified to engage in ammonia oxidation. Nitrosative stress markers were found mostly in turf and ruderal sites (Figure 3.8, P<0.001), with Baltimore containing the fewest sequence matches. Other stress responses, such as osmotic stress (respectively, land use and city; P=0.0147; P<0.001), had similar patterns, while total stress response differed by geography (Figure 3.9; P<0.001), but not land use. Oxidative stress responses was not different across cities or landuse types. Periplasmic stress response was significantly different among cities (P<0.001) but not significantly different among land use (P=0.06), though it was generally highest in reference and remnant sites, with the exception of Baltimore and Potchefstroom. Genes associated with carbon starvation and biofilm adhesin production were prevalent in ruderal sites (P=0.012, and P=0.002, respectively). 52 Figure 3.9: Relative abundance of stress response genes: A) universal stress protein, B) osmotic stress, C) oxidative stress, D) periplasmic acid stress response in enterobacteria, E) sugar-phosphate stress regulation, and F) SigmaB stress regulation. Two diseases were annotated to indicate turf sites in particular cities: Diphtheria in Potchefstroom, and Staphylococcal pathogenicity islands in Baltimore. Pathogenicity hotspots for staphylococcus, vibrio and listeria each exhibited a different geographic expression pattern (Figure 3.10); Listeria was concentrated in Budapest (P<0.001), while vibrio pathogenicity island was in greater abundance in Helsinki, Lahti and Budapest (P<0.001). Neither pathogen exhibited a significant relationship to land use. 53 Staphylococcus was most abundant in Baltimore ruderal sites (P=0.008); across all cities, it was most abundant in turf sites. Helsinki and Lahti had the lowest proportion of Staphyloccocus pathogenicity hotspot SaPI (P<0.001). Figure 3.10: Pathogens Relative abundance of A) Staphylococcus pathogenicity island, B) Listeria pathogenicity island, C) Vibrio pathogenicity island. 54 Discussion The metagenomic data significantly differed based on geography and land-use, however, there was no significant convergence of function profiles according to land use. These results suggest that urbanization is not leading to functional convergence of the bacterial community. Previous research has shown that there may be a strong influence of local geology on the mineralogy of urban soils83. Many functions that were significantly different among cities were functions thought to be affected by mineralogy or climate. For example, Baltimore receives approximately twice the annual rainfall than any of the other cities, and its soils often have a seasonally high water table during the winter (I sampled the 14th and 15th of November). Thus these soils are more likely to periodically have lower redox potential. In addition, the moist climate may cause soluble nutrients such as nitrate to leach out. Functions such as methanogenesis, N fixation, and sulfur oxidation were highest in Baltimore. Conversely, functions related to the capture and transport of iron were least abundant. This may happen if iron is reduced, making it soluble and easily available. At the global scale, N fixation is negatively correlated with nitrate and nitrite ammonification. This suggests that in some areas, N recycling is more important to microbial communities in fixation. Some of the differences in function may be driven by soil mineralogy. For example, resistance, uptake, and transport pathways for some metals, such as zinc, arsenic and cobalt-zinc-cadmium show distinct geographic distributions. Zinc resistance was higher in Baltimore than in any other city, while arsenic resistance was highest in 55 Helsinki ruderal sites (Figure 3.3). Genes responsible for cobalt, zinc and cadmium resistance were indicators of reference sites in Baltimore. This may be a result of the proximity of Baltimore reference sites to the “serpentine barrens,” a prairie ecosystem that is characterized by serpentine soils, which are ultramafic, with low Ca:Mg ratios, and are sometimes associated with higher concentrations of heavy metals88. The availability of these metals, may have been further modified by human intervention such as tillage and development that increases air and water deposition of these sediments. Human alteration of pH and moisture content may mediate the availability of micronutrients. For example, oxidized iron is insoluble and not readily available to plants, whereas reduced iron is highly soluble and mobile in soils, and humans have a long history of manipulating local hydrology. Most metal micronutrients are most available at a pH between 6.2 and 6.8 (Brady and Weil, 2010); thus agricultural fields are limed to increase the availability of these micronutrients. However in the urban environment, in addition to parent material, heavy metals can be enriched in soils by industrial activity. Particularly, zinc enrichment occurs in close proximity to roadways89. The modification of soil pH may further enhance the bioavailability of zinc, and thus increase the abundance of genes. Altough resistance and uptake pathways for metals varied according to city, they were also significantly impacted by urbanization. Arsenic resistance was a strong indicator of ruderal sites(P=0.003), as were copper homeostasis genes (p=0.001), as well as nickel and cobalt transport genes. These functions could be related to either a concentrating of heavy metal in ruderal soils, or an increased biological availability of heavy metal species. 56 Humans have other impacts as well. The widespread combustion of fossil fuels in industrialized nations is associated with higher concentrations of reactive nitrogen species in the atmosphere90. These reactive species may induce nitrosative stress. However, the nitrosative stress responses in the bacterial community is an indicator of greater oxidative stress that could be produced as a byproduct of denitrification, due to exposure to nitric oxide generated in the process. Bacterial DNA repair mechanisms were also more abundant in ruderal sites, which indirectly supports the observation that urban soil bacteria are responding to some sort of oxidative stress. While it is not possible to determine the driving mechanism exposing soil organisms to greater oxidative stress, this example illustrates that it is conceivable that soil microbial community respond to atmospheric pollutants even if there is no physical disruption of soil structure. This raises the interesting possibility that urban microbes may also be impacted by days with high ground-level ozone concentrations. Further research is needed to elucidate these interactions. Summary I hypothesized that microbial function profiles would reflect differences that are adaptive to global patterns in the soil environment, such as parent material and climate. I hypothesized additionally that urban land use would modify those geographic patterns to reflect the new soil conditions imposed by land use. I also hypothesized that this interaction would cause highly modified environments, such as turf and ruderal sites, to converge relative to the historic state. In this dataset, I have shown that microbial functional gene profiles do reflect broad geographic and climactic patterns, while land 57 use effects were detectable nested within the geographic blocks (i.e. cities). However, I rejected my hypothesis that there would be a convergence of functional gene profiles. The differences I found in function profiles indicate the microbes are particularly responding to different mineral abundance of metals, nutrient status, and redox potential of the soil. In addition to the mineralogy of the parent material, moisture regime and pH are factors that interact to induce changes to redox potential and mineral solubility, and explain many of the global-scale and city-scale patterns I found in functional genes. 58 Chapter 4: Conclusions Discussion An important, but often unstated, assumption of the convergence and biotic homogenization hypotheses, is that closely related species are functionally similar. This is an assumption that is particularly important in interpreting amplicon sequencing, where there is no measure of function. In contrast, the metagenomics analysis assigns putative function to genes; putative function assignment is possible in amplicon libraries for organisms that are known to have high coherence of traits to phylogeny. To predict a convergence of community composition implies that similar functions among closely related organisms will cause them to become more abundant in the environment, driving convergence. I compared the detectability of a convergence pattern at each level of taxonomic assignment within each domain of life in this study (Figure 4.1) to determine how tightly coupled the traits under convergent selection are to phylogeny. What I found was that the ability to detect phylogenetic convergence patterns followed closely predictions we might make based on what we know about metabolic coherence of lineages within each domain, and what we know about our ability to accurately assign taxonomy. For example, certain metabolic traits, such as photosynthesis and methanogenesis, can be coherent to the phylum level91. In contrast, heterotrophic strategies (carbon oxidation) vary at finer taxonomy, sometimes to the order or class level34. Although I did not test functional traits of any of the organisms in this study, there were remarkable parallels between expected outcomes and coherence patterns. For 59 example, the archaeal community, which was dominated by methanogens and ammonium oxidizers, are generally known to have functional coherence to the class level. I observed that significant phylogenetic convergence also occurred at the class level. Similarly, the bacterial community, which has a greater proportion of members that use metabolic strategies with lower degrees of phylogenetic coherence, only exhibited a detectable convergence pattern at the family level or finer (Figure 4.1). Previous research has shown that bacterial niche parameters are randomly distributed at the class level82. My data agrees with these findings and suggest that community assembly should be studied at taxonomic resolution fine enough to distinguish metabolic strategies. Although there are still many unknowns, the archaeal and bacterial databases have considerably improved in recent years. The pattern of phylogenetic coherence in fungal community (Figure 4.1), however, suggests that unresolved taxonomy does not accurately represent true functional or phylogenetic relationships. I expect that once taxonomy can accurately be assigned, fungal convergence pattern will be similar to bacterial community patterns. Whether we expect community function, or community composition to converge, depends on a relationship between dispersal rate of organisms, rate of evolutionary change within organisms, and crucially, the distribution of functional traits across lineages. 60 Figure 4.1: Taxonomic coherence of the global phylogenetic convergence pattern in A) archaea; B) bacteria; C) fungi. The dotted line represents the P-value at each taxonomic level. Solid circle is reference, open circle is remnant, open triangle is turf, closed circle is ruderal. 61 A key question driving the metagenomics approach was to ascertain whether there was a functional convergence within the bacterial community even when there was only weak evidence of convergence in community composition. My chapter three clearly demonstrates that there was not; there were significant effects of land-use and geography on function profiles, but these functional profiles did not converge. Furthermore, the metagenomics approach does also allow us to assign taxonomic profiles to the most abundant organisms. The patterns within the metagenome-derived community composition closely match those found in the functional profiles. Together, they also tell a similar story to the amplicon-derived community composition: that the bacterial community is structured by geography, and by landuse. But I find that the convergence of urban characteristics (pH, SOM etc.) is not associated with a convergence of bacterial community composition or potential function. This may be the result of unique interactions between different parent material and pH and SOM of soils. There are a number of reasons why convergence might not be detectable, or may not have occurred, in the function dataset. There is a pervasive database bias in metagenomic annotations; annotations primarily derived of medical research, or agronomy (e.g. plant pathology). For example, campylobacter is a genus that the world health organization describes as causing intestinal infections (WHO Fact Sheet #255; published October, 2011), and according to my metagenomics annotations is responsible for pathways identified in iron metabolism, adhesion, and antibacterial drug resistance. And yet, there were no sequences identified as belonging to the campylobacter genus in my 16s community dataset. In fact, many of the annotated functions, including siderophore expression, biofilm formation, and antibacterial resistance pathways, are 62 derived from medical model organisms. For example, annotations of siderophores are associated with pathogens such as Yersinia, Enterobactin, and campylobacter (all engage in some pathogenicity); annotations of biofilms are nearly all related to pathogenesis pathways in campylobacter and staphylococcus; many drug resistance annotations are based on resistance to specific market antibiotics such as Erythromycin or Fosfomycin (though there are a few “broad-range” anti-bacterial resistance loci annotations), and the list goes on. In my preceding analysis, I have assumed that many of these annotations do represent accurately the functions, if perhaps not the specific organism from which they are derived. It is possible, however, that some functions are simply not annotated yet. For example, I used the PICRUSt tool to predict the functional potential of our 16s amplicon library to investigate the presence of ammonium oxidizing archaea and bacteria in turf site categories. Quite to my surprise, PICRUSt predicted no ammonium oxidation. I collected QPCR data on Ammonium oxidizing archaeal genes and ammonium oxidizing bacterial genes using the ammonium monooxigenase subunit A. My data shows a significant correlation between AMOA genes and the identification of archaeal taxa that are generally known to engage in ammonium oxidation (Figure 3.8, Panel E and F). Therefore, I am confident that ammonium oxidizing archaea are a part of the community. In exploring the metagenomics data, which uses some of the same databases as PICRUSt while employing a different annotation algorithm, I discovered that ammonium oxidation and methane oxidation are binned together because the enzymes are closely related. Thus, not only are some functions not annotated, the relationships between other annotations and environmental parameters may be obscured by the confounding effect of 63 inappropriate binning of enzymes. Potentially further obscuring these relationships, it is also possible that many enzymes that engage in homologous activity are not yet known. And, if pH is a master variable controlling microbial survival, then the proteins for some common cell functions are likely to have homologues that are optimized to operate under different pH environments; if these functions are binned together as homologues contributing to the same function, then the overall community function profile may not appear to converge even if the community becomes enriched with genes for resistant homologues of that enzyme. Thus, if the database is not curated in such a way as to be sensitive to the environmental performance of genes, we will not be able to detect a relationship between the expression of certain homologues and the environment from which they were sampled. And finally, lack of convergence may be due to the nature of the similarity indices themselves. If the majority of genes identified are house-keeping genes that are expected to be present in some form in all samples, then the large body of genes that should not converge might mask the smaller fraction of those that should. Moreover, previous research has shown that the richness component of the index is highly correlated with convergences; that much of convergence is actually the richness of sites becoming more similar51. This is an irrelevant metric in metagenomics as the vast diversity of bacterial metabolic genes and housekeeping genes, means that it is highly unlikely that our sampling will detect a decrease in functional diversity even if a couple functional groups are indeed lost. It is also possible that there was truly no convergence in function profiles. Changes in edaphic factors are certainly going to increase the expression of certain genes 64 relative to others. However, increased expression can occur without increasing the concentration of genes themselves. And reciprocally, cells will not express every gene they contain all the time. This is crucially important because in a given gram of soil, there will certainly exist many microsites for which the conditions differ dramatically from the average state, and the states of these microsites will vary through time. Thus, it is reasonable to assert that many genes coding for diverse functions may be maintained, and expressed when they are necessary. It is also important to consider that the scale at which we measure edaphic factors is much broader than the micro-site scale at which microbes face environmental selection, thus we certainly will not detect the existence of deviant microsite conditions; given our methodology, it is not possible to determine the variance in pH of the distribution of microsite pH conditions. Because we have no ability to quantify the variation of microsite conditions in situ, the relationship between annotated functions and the measured soil conditions may be obscured by the existence of divergent microsites. Widely divergent microsites that vary through time may maintain a broad functional diversity in the collective genome, in spite of an average state that converges on a global scale. Thus, while relatively broad scale measurements may be sufficient to predict aggregate functions across many grams of soil, they may not be sufficient to predict whether microsites will maintain selection on a diversity of facultative response genes. The function of the urban ecosystem is a product of interacting physical, chemical and biotic alterations made by humans. Previous research indicates that mycorrhizal fungi can have a dramatic influence on seedling establishment37,92. The opposite effect is also true: the suppression of host species leads to a dramatic loss in ectomycorrhizal fungi. 65 This is a feedback that may make it harder for myccorhizal plants to persist in urban areas. The suppression of ectomycorrhizal hosts also suppresses a mutualism that is particularly effective at capturing and cycling nutrient resources, and may contribute to the increased rate of nutrient loss in urban areas. In terms of the bacterial community, research indicates that landscape features are more useful in predicting denitrification activity than is community composition42, but this does not preclude disturbance from sufficiently altering the community composition to induce changes in function. It is also likely that within an urban center, disruption of past hydrology and community composition are not independent events. The “leakiness” of urban centers is likely due to a combination of altered landscape features, substantial N enrichment, and simultaneous disruption of nutrient cycling mechanisms. The loss of ectomycorrhizal fungi itself is a symptom of the larger problem: substantial nutrient enrichment and suppression of the native plant community. Remediating this situation necessarily means restructuring the landscape, selecting for the plant community, and substantially reducing nutrient inputs. But there are also opportunities; recent modeling work has shown that ectomycorrhizal fungi play an important role in carbon sequestration. In N-limited ecosystems with abundant ectomycorrhizal fungi, the fungi outcompete other decomposers for access to N, and carbon cycling in the soil is slowed leading to accumulating C in the soil93,94. By mitigating nutrient inputs, we may be able to engineer urban landscapes that are effective in capturing carbon. Since atmospheric N deposition represents a large portion of urban N flux95,96, converting to a fossil fuel-free transport infrastructure would have the synergistic effect of tilting the soil community towards one that more efficiently captures carbon, and reducing urban emissions. In order to create an environment where urban 66 areas are in equilibrium with the surrounding landscape, we must understand how microbial communities respond to our management, and be able to predict the likely biogeochemical outcomes of those responses. This thesis represents one small step towards generating the knowledge necessary to complete such a project. Summary In each data chapter, I used a different molecular technique to address the microbial community response to urbanization. This provided me the opportunity to directly compare shotgun sequencing to amplicon sequencing techniques in terms of the patterns they are capable of detecting, and the information they provide. In Chapter 2, I argue that the archaeal community has the strongest convergence effect but that this effect is driven by the dominance of just a few common lineages without evidence for biodiversity loss; the fungal communities are strongly structured by biogeography, and converge due to a loss in ectomycorrhizal fungi. The bacterial community provides strong evidence of a geographic distribution, but weak evidence of convergence. In fact, the global patterns discovered in Chapter 3 correspond well to bacterial distribution patterns found in Chapter 2; both analyses found significant differences among cities in community composition or function profiles, and significant differences among land-use categories within each city. And, in neither analysis was there a significant convergence of ruderal or turf sites relative to the reference. While Chapter 3 focused on the assigned functional traits, metagenomics can also be used to assign taxonomy; I compared amplicon and shotgun generated taxonomic profiles directly. The taxonomy assignments generated from mg-RAST show the exact same patterns as the functional assignments; geographic structure, land-use filter, and no convergence. Amplicon sequencing gives better 67 resolution (more taxa identified per sample); the remarkable congruence between these two approaches gives me confidence that the patterns are real. Patterns among mineral transport and resistance genes suggest that urban impacted sites are affected by the local mineralogy. The lack of convergence of functional profiles suggests one of three things: that our test is not sensitive to changes in function; or it indicates that real variation is driven either by a persistence of native edaphic factors in spite of urbanization, or that certain human impacts increase the variability of soil conditions. assembly. 68 Appendices Appendix A: Anova Tables Amplicon Convergence Bacteria Phylum   Class   Order a. Family   Genus OTU 69 Convergence Archaea Phylum Class Order Family Genus     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)  Groups   3   2.7342   0.9114   19.31   7.06E-­‐10  Residuals   96   4.5311   0.0472           OTU     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)  Groups   3   0.78984   0.26328   19.078   8.75E-­‐10  Residuals   96   1.3248   0.0138           70 Convergence Fungi Phylum     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)  Groups   3   0.258   0.085992   1.7333   0.1653  Residuals   96   4.7628   0.049612           Class     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)  Groups   3   0.0162   0.005396   0.0607   0.9803  Residuals   96   8.5314   0.088869           Order     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)  Groups   3   0.021   0.006992   0.0716   0.975  Residuals   96   9.3795   0.097703           Family     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)  Groups   3   0.1086   0.036187   0.7532   0.5232  Residuals   96   4.6125   0.048047           Genus     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)  Groups   3   0.0212   0.00708   0.1504   0.9292  Residuals   96   4.5181   0.047064           OTU     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)  Groups   3   0.2369   0.078967   2.7335   0.04792  Residuals   96   2.7733   0.028888           71 Convergence of Function Convergence Function Level1     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)  Groups   3   0.00005   1.59E-­‐05   0.11   0.95  Residuals   92   0.01296   1.41E-­‐04                      Convergence Function Level 3     Df   Sum  Sq   Mean  Sq  F   value   Pr(>F)  Groups   3   0.0001   0.000035   0.04   0.99  Residuals   92   0.0795   0.000864             Biogeography Permanova Bacteria Permanova Archaea Permanova Fungi 72 Permanova Function1 Permanova Function 3 Metagenome Functions Fatty  Acid  Regulation             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.17E-­‐05   7.22E-­‐06   14.185   1.98E-­‐07   CITY   4   3.31E-­‐05   8.28E-­‐06   16.273   1.14E-­‐09   TRT:CITY   12   2.21E-­‐05   1.84E-­‐06   3.618   0.00027   Residuals   76   3.87E-­‐05   5.09E-­‐07                   Pyruvate  Metabolism/acetyl  CoA  acetogenesis  from  pyruvate       Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.26E-­‐06   7.53E-­‐07   8.75   4.68E-­‐05   CITY   4   5.15E-­‐06   1.29E-­‐06   14.962   4.61E-­‐09   TRT:CITY   12   1.55E-­‐06   1.29E-­‐07   1.496   0.144   Residuals   76   6.54E-­‐06   8.61E-­‐08                               Universal  GTPases             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   73 TRT   3   3.46E-­‐07   1.15E-­‐07   0.641   0.59085   CITY   4   8.43E-­‐06   2.11E-­‐06   11.714   1.84E-­‐07   TRT:CITY   12   6.37E-­‐06   5.31E-­‐07   2.95   0.00205   Residuals   76   1.37E-­‐05   1.80E-­‐07                   Methionine   Biosynthesis             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.28E-­‐07   7.61E-­‐08   1.207   0.31291   CITY   4   1.11E-­‐06   2.78E-­‐07   4.408   0.00294   TRT:CITY   12   1.27E-­‐06   1.06E-­‐07   1.674   0.0895   Residuals   76   4.79E-­‐06   6.31E-­‐08                               Glutamine/Glutamate  and  Aspartamine/Aspartamate  biosynthesis     Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   5.57E-­‐07   1.86E-­‐07   2.259   0.08839   CITY   4   4.66E-­‐06   1.17E-­‐06   14.163   1.11E-­‐08   TRT:CITY   12   2.44E-­‐06   2.03E-­‐07   2.469   0.00882   Residuals   76   6.25E-­‐06   8.22E-­‐08                   Peptidoglycan  Biosynthesis           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.50E-­‐06   4.99E-­‐07   6.972   0.000331   CITY   4   7.80E-­‐06   1.95E-­‐06   27.228   4.96E-­‐14   TRT:CITY   12   1.69E-­‐06   1.41E-­‐07   1.968   0.039074   Residuals   76   5.44E-­‐06   7.16E-­‐08                               TCA  Cycle               Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.24E-­‐06   4.12E-­‐07   2.156   0.1002   CITY   4   2.18E-­‐05   5.44E-­‐06   28.516   1.78E-­‐14   TRT:CITY   12   4.31E-­‐06   3.59E-­‐07   1.879   0.0503   Residuals   76   1.45E-­‐05   1.91E-­‐07                   PROSC               Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.24E-­‐07   7.48E-­‐08   2.304   0.0836   CITY   4   9.23E-­‐07   2.31E-­‐07   7.113   6.42E-­‐05   TRT:CITY   12   8.04E-­‐07   6.70E-­‐08   2.065   0.0294   74 Residuals   76   2.47E-­‐06   3.25E-­‐08                   tRNA  modification  in  Bacteria           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   7.90E-­‐06   2.63E-­‐06   13.936   2.50E-­‐07   CITY   4   9.96E-­‐06   2.49E-­‐06   13.185   3.32E-­‐08   TRT:CITY   12   5.61E-­‐06   4.67E-­‐07   2.473   0.00874   Residuals   76   1.44E-­‐05   1.89E-­‐07                   DNA  Replication             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   3.90E-­‐06   1.30E-­‐06   16.045   3.57E-­‐08   CITY   4   1.60E-­‐05   4.00E-­‐06   49.375   <  2e-­‐16   TRT:CITY   12   1.02E-­‐06   8.50E-­‐08   1.045   0.418   Residuals   76   6.16E-­‐06   8.10E-­‐08                   Sugar  Utilization  in  thermotogales           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.41E-­‐06   8.04E-­‐07   1.75   0.16389   CITY   4   2.13E-­‐05   5.33E-­‐06   11.617   2.06E-­‐07   TRT:CITY   12   1.40E-­‐05   1.16E-­‐06   2.536   0.00722   Residuals   76   3.49E-­‐05   4.59E-­‐07                   YgfZ               Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   8.41E-­‐07   2.80E-­‐07   0.902   0.4444   CITY   4   2.81E-­‐05   7.01E-­‐06   22.549   2.64E-­‐12   TRT:CITY   12   7.75E-­‐06   6.46E-­‐07   2.078   0.0283   Residuals   76   2.36E-­‐05   3.11E-­‐07                   Serine  glyoxelate  cycle             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.58E-­‐05   5.25E-­‐06   7.719   0.000144   CITY   4   7.95E-­‐05   1.99E-­‐05   29.196   1.04E-­‐14   TRT:CITY   12   2.57E-­‐05   2.14E-­‐06   3.146   0.00113   Residuals   76   5.17E-­‐05   6.80E-­‐07                   Photosystem  1             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.42E-­‐11   4.74E-­‐12   1.871   0.14166   75 CITY   4   8.67E-­‐11   2.17E-­‐11   8.558   9.34E-­‐06   TRT:CITY   12   8.08E-­‐11   6.74E-­‐12   2.661   0.00494   Residuals   76   1.92E-­‐10   2.53E-­‐12                   photosystem  II             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.06E-­‐11   3.52E-­‐12   4.02   0.0104   CITY   4   2.28E-­‐12   5.69E-­‐13   0.651   0.628   TRT:CITY   12   2.36E-­‐11   1.96E-­‐12   2.244   0.0174   Residuals   76   6.65E-­‐11   8.75E-­‐13                   Photosystem  II  type  photosynthetic  reaction   center         Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.26E-­‐10   4.19E-­‐11   3.138   0.0302   CITY   4   3.09E-­‐11   7.72E-­‐12   0.578   0.6798   TRT:CITY   12   1.45E-­‐10   1.21E-­‐11   0.904   0.5467   Residuals   76   1.02E-­‐09   1.34E-­‐11                   Bacteria  light  harvesting  proteins           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   3.90E-­‐12   1.30E-­‐12   1.786   0.157   CITY   4   2.78E-­‐12   6.95E-­‐13   0.954   0.438   TRT:CITY   12   1.21E-­‐11   1.01E-­‐12   1.38   0.194   Residuals   76   5.54E-­‐11   7.28E-­‐13                   Particulate  methane  monooxygenase           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   3.50E-­‐12   1.17E-­‐12   1.228   0.30525   CITY   4   1.46E-­‐11   3.65E-­‐12   3.848   0.00669   TRT:CITY   12   1.54E-­‐11   1.29E-­‐12   1.355   0.20659   Residuals   76   7.21E-­‐11   9.49E-­‐13                   CO  dehydrogenase             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   6.21E-­‐06   2.07E-­‐06   11.201   3.63E-­‐06   CITY   4   1.78E-­‐05   4.46E-­‐06   24.115   6.67E-­‐13   TRT:CITY   12   3.61E-­‐06   3.01E-­‐07   1.628   0.101   Residuals   76   1.41E-­‐05   1.85E-­‐07                   Methanogenesis           76   Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.09E-­‐08   3.62E-­‐09   2.038   0.115576   CITY   4   1.54E-­‐07   3.85E-­‐08   21.724   5.57E-­‐12   TRT:CITY   12   7.11E-­‐08   5.92E-­‐09   3.339   0.000628   Residuals   76   1.35E-­‐07   1.77E-­‐09                   Methanogenesis  from  methylated  compounds         Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.06E-­‐09   3.54E-­‐10   6.337   0.000681   CITY   4   1.07E-­‐09   2.68E-­‐10   4.795   0.001673   TRT:CITY   12   5.43E-­‐10   4.52E-­‐11   0.81   0.63927   Residuals   76   4.24E-­‐09   5.58E-­‐11                   Siderophore   Enterobactin             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   4.04E-­‐06   1.35E-­‐06   9.061   3.35E-­‐05   CITY   4   9.85E-­‐06   2.46E-­‐06   16.578   8.31E-­‐10   TRT:CITY   12   4.56E-­‐06   3.80E-­‐07   2.562   0.00667   Residuals   76   1.13E-­‐05   1.49E-­‐07                   Siderophore  Desferroxamine           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.02E-­‐10   6.75E-­‐11   0.992   0.40121   CITY   4   1.37E-­‐09   3.43E-­‐10   5.044   0.00117   TRT:CITY   12   5.20E-­‐10   4.33E-­‐11   0.637   0.80449   Residuals   76   5.17E-­‐09   6.80E-­‐11                   Iron  Chelation  (all  siderophores)           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.84E-­‐05   6.12E-­‐06   6.467   0.000588   CITY   4   8.25E-­‐05   2.06E-­‐05   21.787   5.26E-­‐12   TRT:CITY   12   2.97E-­‐05   2.47E-­‐06   2.614   0.005703   Residuals   76   7.19E-­‐05   9.46E-­‐07                   Sulfur  Oxidation             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.27E-­‐07   7.58E-­‐08   9.325   2.53E-­‐05   CITY   4   1.78E-­‐06   4.45E-­‐07   54.742   <  2e-­‐16   TRT:CITY   12   1.32E-­‐07   1.10E-­‐08   1.355   0.207   77 Residuals   76   6.18E-­‐07   8.10E-­‐09                   Campylobacter  Iron  metabolism           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   7.00E-­‐07   2.33E-­‐07   9.363   2.43E-­‐05   CITY   4   1.85E-­‐06   4.63E-­‐07   18.579   1.10E-­‐10   TRT:CITY   12   7.51E-­‐07   6.26E-­‐08   2.512   0.00776   Residuals   76   1.89E-­‐06   2.49E-­‐08                   Pyruvateferredoxinoxidoreductase           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   3.86E-­‐07   1.29E-­‐07   10.52   7.26E-­‐06   CITY   4   5.17E-­‐07   1.29E-­‐07   10.572   7.30E-­‐07   TRT:CITY   12   5.79E-­‐07   4.83E-­‐08   3.944   0.000102   Residuals   76   9.30E-­‐07   1.22E-­‐08                   Nitrate  and  Nitrite  ammonification           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   3.00E-­‐05   1.00E-­‐05   34.091   4.57E-­‐14   CITY   4   1.41E-­‐05   3.52E-­‐06   11.98   1.34E-­‐07   TRT:CITY   12   1.24E-­‐05   1.04E-­‐06   3.524   0.00036   Residuals   76   2.23E-­‐05   2.94E-­‐07                   N  fixation               Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   4.81E-­‐08   1.60E-­‐08   1.421   0.243   CITY   4   3.59E-­‐07   8.97E-­‐08   7.956   2.06E-­‐05   TRT:CITY   12   8.26E-­‐08   6.88E-­‐09   0.611   0.827   Residuals   76   8.57E-­‐07   1.13E-­‐08                   Dissimilatory  nitrite  reductase           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.25E-­‐08   7.49E-­‐09   3.411   0.02165   CITY   4   1.30E-­‐07   3.25E-­‐08   14.799   5.50E-­‐09   TRT:CITY   12   6.90E-­‐08   5.75E-­‐09   2.618   0.00563   Residuals   76   1.67E-­‐07   2.20E-­‐09                   Nitriliase               Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   4.44E-­‐11   1.48E-­‐11   0.485   0.694   78 CITY   4   2.21E-­‐10   5.53E-­‐11   1.812   0.135   TRT:CITY   12   5.01E-­‐10   4.18E-­‐11   1.368   0.2   Residuals   76   2.32E-­‐09   3.05E-­‐11                   Ammonia  assimilation             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   3.50E-­‐07   1.17E-­‐07   1.364   0.26   CITY   4   3.98E-­‐06   9.95E-­‐07   11.644   2.00E-­‐07   TRT:CITY   12   1.49E-­‐06   1.24E-­‐07   1.452   0.162   Residuals   76   6.50E-­‐06   8.55E-­‐08                   Urea  decomposition             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.08E-­‐06   3.61E-­‐07   6.493   0.00057   CITY   4   4.01E-­‐06   1.00E-­‐06   18.052   1.85E-­‐10   TRT:CITY   12   1.17E-­‐06   9.75E-­‐08   1.755   0.07152   Residuals   76   4.22E-­‐06   5.56E-­‐08                   NiFe  hydrogenase  maturation           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.83E-­‐08   9.44E-­‐09   0.736   0.53355   CITY   4   3.16E-­‐07   7.90E-­‐08   6.158   0.00024   TRT:CITY   12   1.20E-­‐07   1.00E-­‐08   0.78   0.66864   Residuals   76   9.75E-­‐07   1.28E-­‐08                   Putative  hemin  transporter           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   8.69E-­‐08   2.90E-­‐08   1.63   0.18943   CITY   4   1.54E-­‐06   3.85E-­‐07   21.66   5.93E-­‐12   TRT:CITY   12   5.91E-­‐07   4.92E-­‐08   2.77   0.00354   Residuals   76   1.35E-­‐06   1.78E-­‐08                   Transport  of  Iron             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   3.46E-­‐06   1.15E-­‐06   10.942   4.72E-­‐06   CITY   4   6.86E-­‐06   1.72E-­‐06   16.254   1.16E-­‐09   TRT:CITY   12   2.87E-­‐06   2.39E-­‐07   2.265   0.0163   Residuals   76   8.02E-­‐06   1.06E-­‐07                   Transport  of   Manganese           79   Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   3.69E-­‐07   1.23E-­‐07   14.341   1.71E-­‐07   CITY   4   6.00E-­‐07   1.50E-­‐07   17.514   3.18E-­‐10   TRT:CITY   12   3.25E-­‐07   2.71E-­‐08   3.158   0.00109   Residuals   76   6.51E-­‐07   8.57E-­‐09                   Transport  of   Molybdenum             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.15E-­‐08   3.85E-­‐09   1.392   0.2517   CITY   4   1.15E-­‐07   2.88E-­‐08   10.411   8.90E-­‐07   TRT:CITY   12   6.93E-­‐08   5.77E-­‐09   2.09   0.0274   Residuals   76   2.10E-­‐07   2.76E-­‐09                   Transport  of  Nickel  and  Cobalt           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   7.21E-­‐07   2.40E-­‐07   13.928   2.52E-­‐07   CITY   4   3.67E-­‐07   9.17E-­‐08   5.311   0.000796   TRT:CITY   12   5.00E-­‐07   4.17E-­‐08   2.416   0.010369   Residuals   76   1.31E-­‐06   1.73E-­‐08                   Transport  of  Zinc             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.00E-­‐07   3.33E-­‐08   2.941   0.03838   CITY   4   9.09E-­‐07   2.27E-­‐07   20.038   2.68E-­‐11   TRT:CITY   12   3.56E-­‐07   2.97E-­‐08   2.619   0.00561   Residuals   76   8.61E-­‐07   1.13E-­‐08                   Potassium  homeostasis             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.20E-­‐06   4.00E-­‐07   2.33   0.081   CITY   4   3.43E-­‐05   8.56E-­‐06   49.866   <2e-­‐16   TRT:CITY   12   5.26E-­‐06   4.38E-­‐07   2.551   0.0069   Residuals   76   1.31E-­‐05   1.72E-­‐07                   Zinc  Resistance             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.42E-­‐08   4.70E-­‐09   0.756   0.522   CITY   4   2.96E-­‐06   7.41E-­‐07   118.005   <2e-­‐16   TRT:CITY   12   9.46E-­‐08   7.90E-­‐09   1.256   0.263   80 Residuals   76   4.77E-­‐07   6.30E-­‐09                   Arsenic  Resistance             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.46E-­‐06   4.88E-­‐07   22.05   2.26E-­‐10   CITY   4   1.03E-­‐06   2.56E-­‐07   11.58   2.15E-­‐07   TRT:CITY   12   7.43E-­‐07   6.19E-­‐08   2.8   0.00323   Residuals   76   1.68E-­‐06   2.21E-­‐08                   Cadmium  Resistance             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.69E-­‐09   8.96E-­‐10   1.351   0.26425   CITY   4   1.02E-­‐08   2.55E-­‐09   3.841   0.00676   TRT:CITY   12   7.29E-­‐09   6.08E-­‐10   0.917   0.53476   Residuals   76   5.04E-­‐08   6.63E-­‐10                   Cobalt-­‐zinc-­‐cadmium  resistance           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   7.60E-­‐05   2.53E-­‐05   39.77   1.47E-­‐15   CITY   4   2.23E-­‐04   5.57E-­‐05   87.435   <  2e-­‐16   TRT:CITY   12   4.91E-­‐05   4.09E-­‐06   6.427   9.78E-­‐08   Residuals   76   4.84E-­‐05   6.40E-­‐07                   Mercury  resistance  operon           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.71E-­‐08   9.02E-­‐09   8.923   3.89E-­‐05   CITY   4   1.42E-­‐08   3.54E-­‐09   3.501   0.0112   TRT:CITY   12   1.08E-­‐08   8.96E-­‐10   0.887   0.5635   Residuals   76   7.68E-­‐08   1.01E-­‐09                   Resistance  to  chromium  compounds           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.09E-­‐08   6.97E-­‐09   2.641   0.0554   CITY   4   1.94E-­‐07   4.85E-­‐08   18.375   1.35E-­‐10   TRT:CITY   12   3.70E-­‐08   3.09E-­‐09   1.17   0.3195   Residuals   76   2.00E-­‐07   2.64E-­‐09                   Acid  resistance  mechanisms           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.15E-­‐07   3.84E-­‐08   2.278   0.0863   81 CITY   4   1.60E-­‐06   4.00E-­‐07   23.68   9.73E-­‐13   TRT:CITY   12   4.44E-­‐07   3.70E-­‐08   2.192   0.0202   Residuals   76   1.28E-­‐06   1.69E-­‐08                   Mercuric  reductase             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.04E-­‐07   6.79E-­‐08   13.036   5.91E-­‐07   CITY   4   5.52E-­‐07   1.38E-­‐07   26.507   8.91E-­‐14   TRT:CITY   12   2.13E-­‐07   1.78E-­‐08   3.411   0.000505   Residuals   76   3.96E-­‐07   5.21E-­‐09                   Multidrug  resistance  efflux  pump           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   5.90E-­‐06   1.97E-­‐06   8.47   6.33E-­‐05   CITY   4   2.93E-­‐05   7.32E-­‐06   31.505   1.81E-­‐15   TRT:CITY   12   4.30E-­‐06   3.59E-­‐07   1.544   0.127   Residuals   76   1.77E-­‐05   2.32E-­‐07                   Themdt  ABCD  mutidrug  ressitance  cluster         Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   4.50E-­‐07   1.50E-­‐07   3.137   0.0302   CITY   4   3.71E-­‐06   9.26E-­‐07   19.367   5.10E-­‐11   TRT:CITY   12   1.11E-­‐06   9.28E-­‐08   1.94   0.0423   Residuals   76   3.64E-­‐06   4.78E-­‐08                   lipid  AAra4N  pathway  polymyxine  resistance         Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.44E-­‐07   4.81E-­‐08   3.366   0.0229   CITY   4   1.37E-­‐06   3.43E-­‐07   23.99   7.43E-­‐13   TRT:CITY   12   9.92E-­‐08   8.30E-­‐09   0.578   0.8532   Residuals   76   1.09E-­‐06   1.43E-­‐08                   Nitrosative  stress             Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.24E-­‐06   4.14E-­‐07   14.988   9.35E-­‐08   CITY   4   2.69E-­‐06   6.71E-­‐07   24.316   5.61E-­‐13   TRT:CITY   12   1.12E-­‐06   9.29E-­‐08   3.365   0.000581   Residuals   76   2.10E-­‐06   2.76E-­‐08                   SigmaB  stress  response  regulation           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   82 TRT   3   6.28E-­‐08   2.10E-­‐08   3.346   0.02344   CITY   4   7.64E-­‐07   1.91E-­‐07   30.519   3.79E-­‐15   TRT:CITY   12   2.05E-­‐07   1.71E-­‐08   2.727   0.00404   Residuals   76   4.76E-­‐07   6.26E-­‐09                   Periplasmic  Stress  response           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.70E-­‐07   8.99E-­‐08   2.47   0.0682   CITY   4   2.16E-­‐06   5.40E-­‐07   14.832   5.31E-­‐09   TRT:CITY   12   8.29E-­‐07   6.90E-­‐08   1.897   0.0478   Residuals   76   2.77E-­‐06   3.64E-­‐08                   Osmotic  cluster  regulation           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   5.32E-­‐08   1.77E-­‐08   3.729   0.0147   CITY   4   2.73E-­‐07   6.82E-­‐08   14.345   9.05E-­‐09   TRT:CITY   12   1.30E-­‐07   1.08E-­‐08   2.28   0.0156   Residuals   76   3.61E-­‐07   4.75E-­‐09                   total  stress  (all  stress  indicators  combined)         Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   2.08E-­‐07   6.92E-­‐08   0.332   0.802118   CITY   4   4.96E-­‐06   1.24E-­‐06   5.954   0.000319   TRT:CITY   12   2.78E-­‐06   2.32E-­‐07   1.112   0.362931   Residuals   76   1.58E-­‐05   2.08E-­‐07                   Listeria  Pathogenicity  island  LIPI1           Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   1.32E-­‐10   4.38E-­‐11   1.475   0.228154   CITY   4   6.30E-­‐10   1.57E-­‐10   5.297   0.000812   TRT:CITY   12   6.91E-­‐10   5.76E-­‐11   1.937   0.042709   Residuals   76   2.26E-­‐09   2.97E-­‐11                   Staphylococcal  pathogenicity  island  SaPI         Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   4.35E-­‐07   1.45E-­‐07   4.204   0.00832   CITY   4   2.87E-­‐06   7.18E-­‐07   20.799   1.31E-­‐11   TRT:CITY   12   6.66E-­‐07   5.55E-­‐08   1.608   0.10717   Residuals   76   2.62E-­‐06   3.45E-­‐08                   Vibrio  pathogenicity  Island         83   Df   Sum  Sq   Mean  Sq   F  value   Pr(>F)   TRT   3   3.77E-­‐09   1.26E-­‐09   2.414   0.073141   CITY   4   1.11E-­‐08   2.78E-­‐09   5.335   0.000769   TRT:CITY   12   1.71E-­‐08   1.43E-­‐09   2.744   0.003841   Residuals   76   3.96E-­‐08   5.21E-­‐10       Appendix B: R Scripts Shannon Weiner Index library(vegan) Bacteria=read.csv(‘Desktop/Thesis/AlphaDiversity/Bacteria_OTU.csv’) attach(Bacteria) diversity(Bacteria, index’”Shannon”, MARGIN=1, base=exp(1)) Archaea=read.csv(‘Desktop/Thesis/AlphaDiversity/ArchaeaOTUtable.csv’) attach(Archaea) diversity(Archaea, index’”Shannon”, MARGIN=1, base=exp(1)) Fungi=read.csv(‘Desktop/Thesis/AlphaDiversity/Fungal_OTU.csv’) attach(Fungal) diversity(Fungal, index’”Shannon”, MARGIN=1, base=exp(1)) Pielou’s J library(asbio) Bacteria=read.csv(‘Desktop/Thesis/AlphaDiversity/Bacteria_OTU.csv’) Archaea=read.csv(‘Desktop/Thesis/AlphaDiversity/ArchaeaOTUtable.csv’) Fungi=read.csv(‘Desktop/Thesis/AlphaDiversity/Fungal_OTU.csv’) evenness(Bacteria) evenness(Archaea) evenness(Fungi) Convergence Archaea: ArchaealCommunity_Phylum=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_07311 5/PCOA/Archaea/Archaea_CommunityData_Phylum_101915.csv') ArchaeaPhylum_DistanceMatrix=vegdist(ArchaealCommunity_Phylum, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_Data=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/SecondMa trix.csv') 84 attach(Sup_Data) GroupA=BLK2 GroupB=BLK GroupC=TRT ArchaeaPhylum_modA=betadisper(ArchaeaPhylum_DistanceMatrix, GroupA, type=c("median")) ArchaeaPhylum_modB=betadisper(ArchaeaPhylum_DistanceMatrix, GroupB, type=c("median")) ArchaeaPhylum_modC=betadisper(ArchaeaPhylum_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaPhylum_modA) anova(ArchaeaPhylum_modB) anova(ArchaeaPhylum_modC) permutest(ArchaeaPhylum_modA) permutest(ArchaeaPhylum_modB) permutest(ArchaeaPhylum_modC) ArchaeaPhylum_modA ArchaeaPhylum_modB ArchaeaPhylum_modC #####CLASS###### ArchaeaCommunity_Class=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/P COA/Archaea/Archaea_CommunityData_Class_101915.csv') ArchaeaClass_DistanceMatrix=vegdist(ArchaeaCommunity_Class, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) ArchaeaClass_modA=betadisper(ArchaeaClass_DistanceMatrix, GroupA, type=c("median")) ArchaeaClass_modB=betadisper(ArchaeaClass_DistanceMatrix, GroupB, type=c("median")) ArchaeaClass_modC=betadisper(ArchaeaClass_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaClass_modA) anova(ArchaeaClass_modB) anova(ArchaeaClass_modC) permutest(ArchaeaClass_modA) permutest(ArchaeaClass_modB) 85 permutest(ArchaeaClass_modC) ArchaeaClass_modA ArchaeaClass_modB ArchaeaClass_modC #####ORDER###### ArchaeaCommunity_Order=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/ PCOA/Archaea/Archaea_CommunityData_Order_101915.csv') ArchaeaOrder_DistanceMatrix=vegdist(ArchaeaCommunity_Order, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) ArchaeaOrder_modA=betadisper(ArchaeaOrder_DistanceMatrix, GroupA, type=c("median")) ArchaeaOrder_modB=betadisper(ArchaeaOrder_DistanceMatrix, GroupB, type=c("median")) ArchaeaOrder_modC=betadisper(ArchaeaOrder_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaOrder_modA) anova(ArchaeaOrder_modB) anova(ArchaeaOrder_modC) permutest(ArchaeaOrder_modA) permutest(ArchaeaOrder_modB) permutest(ArchaeaOrder_modC) ArchaeaOrder_modA ArchaeaOrder_modB ArchaeaOrder_modC #####FAMILY##### ArchaeaCommunity_Family=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115 /PCOA/Archaea/Archaea_CommunityData_Family_101915.csv') 86 ArchaeaFamily_DistanceMatrix=vegdist(ArchaeaCommunity_Family, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) ArchaeaFamily_modA=betadisper(ArchaeaFamily_DistanceMatrix, GroupA, type=c("median")) ArchaeaFamily_modB=betadisper(ArchaeaFamily_DistanceMatrix, GroupB, type=c("median")) ArchaeaFamily_modC=betadisper(ArchaeaFamily_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaFamily_modA) anova(ArchaeaFamily_modB) anova(ArchaeaFamily_modC) permutest(ArchaeaFamily_modA) permutest(ArchaeaFamily_modB) permutest(ArchaeaFamily_modC) ArchaeaFamily_modA ArchaeaFamily_modB ArchaeaFamily_modC #########GENUS####### ArchaeaCommunity_Genus=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/ PCOA/Archaea/Archaea_CommunityData_Genus_073115.csv') ArchaeaGenus_DistanceMatrix=vegdist(ArchaeaCommunity_Genus, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) ArchaeaGenus_modA=betadisper(ArchaeaGenus_DistanceMatrix, GroupA, type=c("median")) ArchaeaGenus_modB=betadisper(ArchaeaGenus_DistanceMatrix, GroupB, type=c("median")) ArchaeaGenus_modC=betadisper(ArchaeaGenus_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaGenus_modA) anova(ArchaeaGenus_modB) anova(ArchaeaGenus_modC) permutest(ArchaeaGenus_modA) permutest(ArchaeaGenus_modB) 87 permutest(ArchaeaGenus_modC) ArchaeaGenus_modA ArchaeaGenus_modB ArchaeaGenus_modC ############Archaea OTU######### ArchaeaOTU=read.csv('Desktop/Thesis/R/AlphaDiversity/ArchaeaOTUtable.csv') ArchaeaOTU_DistanceMatrix=vegdist(ArchaeaOTU, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) ArchaeaOTU_modA=betadisper(ArchaeaOTU_DistanceMatrix, GroupA, type=c("median")) ArchaeaOTU_modB=betadisper(ArchaeaOTU_DistanceMatrix, GroupB, type=c("median")) ArchaeaOTU_modC=betadisper(ArchaeaOTU_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaOTU_modA) anova(ArchaeaOTU_modB) anova(ArchaeaOTU_modC) permutest(ArchaeaOTU_modA) permutest(ArchaeaOTU_modB) permutest(ArchaeaOTU_modC) ArchaeaOTU_modA ArchaeaOTU_modB ArchaeaOTU_modC ################################################# Treatment by City ##################################################### Baltimore Archaea_Baltimore=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/ Archaea/Archaea_PCOA_Genus_Baltimore.csv') 88 ArchaeaBaltimore_DistanceMatrix=vegdist(Archaea_Baltimore, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataBaltimore=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/ Second_Baltimore.csv') GroupC=TRT ArchaeaBaltimore_modC=betadisper(ArchaeaBaltimore_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaBaltimore_modC) permutest(ArchaeaBaltimore_modC) ArchaeaBaltimore_modC ###############BY CITY################# #####Baltimore####### Archaea_Baltimore=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/ Archaea/Archaea_PCOA_Genus_Baltimore.csv') ArchaeaBaltimore_DistanceMatrix=vegdist(Archaea_Baltimore, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataBaltimore=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/ Second_Baltimore.csv') attach(Sup_DataBaltimore) GroupC=TRT ArchaeaBaltimore_modC=betadisper(ArchaeaBaltimore_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaBaltimore_modC) permutest(ArchaeaBaltimore_modC) ArchaeaBaltimore_modC #####helsinki########## Archaea_Helsinki=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Ar chaea/Archaea_PCOA_Genus_Helsinki.csv') 89 ArchaeaHelsinki_DistanceMatrix=vegdist(Archaea_Helsinki, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataHelsinki=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Se cond_Helsinki.csv') attach(Sup_DataHelsinki) GroupC=TRT ArchaeaHelsinki_modC=betadisper(ArchaeaHelsinki_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaHelsinki_modC) permutest(ArchaeaHelsinki_modC) ArchaeaHelsinki_modC ####Lahti##### Archaea_Lahti=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Archa ea/Archaea_PCOA_Genus_Lahti.csv') ArchaeaLahti_DistanceMatrix=vegdist(Archaea_Lahti, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataLahti=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Seco nd_Lahti.csv') attach(Sup_DataLahti) GroupC=TRT ArchaeaLahti_modC=betadisper(ArchaeaLahti_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaLahti_modC) permutest(ArchaeaLahti_modC) ArchaeaLahti_modC ####Budapest#### Archaea_Budapest=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/A rchaea/Archaea_PCOA_Genus_Budapest.csv') 90 ArchaeaBudapest_DistanceMatrix=vegdist(Archaea_Budapest, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataBudapest=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/S econd_Budapest.csv') attach(Sup_DataBudapest) GroupC=TRT ArchaeaBudapest_modC=betadisper(ArchaeaBudapest_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaBudapest_modC) permutest(ArchaeaBudapest_modC) ArchaeaBudapest_modC ####Potchefstroom##### Archaea_Potchefstroom=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PC OA/Archaea/Archaea_PCOA_Genus_Potchefstroom.csv') ArchaeaPotchefstroom_DistanceMatrix=vegdist(Archaea_Potchefstroom, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataPotchefstroom=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PC OA/Second_Potchefstroom.csv') attach(Sup_DataPotchefstroom) GroupC=TRT ArchaeaPotchefstroom_modC=betadisper(ArchaeaPotchefstroom_DistanceMatrix, GroupC, type=c("median")) anova(ArchaeaPotchefstroom_modC) permutest(ArchaeaPotchefstroom_modC) ArchaeaPotchefstroom_modC Convergence Bacteria BacterialCommunity_Phylum=read.csv('/Volumes/Seagate/R/BetaDiversityAnalysis_073 115/PCOA/Bacteria_CommunityData_Phylum.csv') 91 BacteriaPhylum_DistanceMatrix=vegdist(BacterialCommunity_Phylum, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_Data=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/SecondMa trix.csv') attach(Sup_Data) GroupA=BLK2 GroupB=BLK GroupC=TRT BacteriaPhylum_modA=betadisper(BacteriaPhylum_DistanceMatrix, GroupA, type=c("median")) BacteriaPhylum_modB=betadisper(BacteriaPhylum_DistanceMatrix, GroupB, type=c("median")) BacteriaPhylum_modC=betadisper(BacteriaPhylum_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaPhylum_modA) anova(BacteriaPhylum_modB) anova(BacteriaPhylum_modC) permutest(BacteriaPhylum_modA) permutest(BacteriaPhylum_modB) permutest(BacteriaPhylum_modC) BacteriaPhylum_modA BacteriaPhylum_modB BacteriaPhylum_modC #####CLASS###### BacterialCommunity_Class=read.csv('/Volumes/Seagate/R/BetaDiversityAnalysis_07311 5/PCOA/Bacteria_CommunityData_Class.csv') BacteriaClass_DistanceMatrix=vegdist(BacterialCommunity_Class, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) BacteriaClass_modA=betadisper(BacteriaClass_DistanceMatrix, GroupA, type=c("median")) BacteriaClass_modB=betadisper(BacteriaClass_DistanceMatrix, GroupB, type=c("median")) BacteriaClass_modC=betadisper(BacteriaClass_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaClass_modA) 92 anova(BacteriaClass_modB) anova(BacteriaClass_modC) permutest(BacteriaClass_modA) permutest(BacteriaClass_modB) permutest(BacteriaClass_modC) BacteriaClass_modA BacteriaClass_modB BacteriaClass_modC #####ORDER###### BacterialCommunity_Order=read.csv('/Volumes/Seagate/R/BetaDiversityAnalysis_0731 15/PCOA/Bacteria_CommunityData_Order.csv') BacteriaOrder_DistanceMatrix=vegdist(BacterialCommunity_Order, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) BacteriaOrder_modA=betadisper(BacteriaOrder_DistanceMatrix, GroupA, type=c("median")) BacteriaOrder_modB=betadisper(BacteriaOrder_DistanceMatrix, GroupB, type=c("median")) BacteriaOrder_modC=betadisper(BacteriaOrder_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaOrder_modA) anova(BacteriaOrder_modB) anova(BacteriaOrder_modC) permutest(BacteriaOrder_modA) permutest(BacteriaOrder_modB) permutest(BacteriaOrder_modC) BacteriaOrder_modA BacteriaOrder_modB BacteriaOrder_modC #####FAMILY##### 93 BacterialCommunity_Family=read.csv('/Volumes/Seagate/R/BetaDiversityAnalysis_073 115/PCOA/Bacteria_CommunityData_Family.csv') BacteriaFamily_DistanceMatrix=vegdist(BacterialCommunity_Family, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) BacteriaFamily_modA=betadisper(BacteriaFamily_DistanceMatrix, GroupA, type=c("median")) BacteriaFamily_modB=betadisper(BacteriaFamily_DistanceMatrix, GroupB, type=c("median")) BacteriaFamily_modC=betadisper(BacteriaFamily_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaFamily_modA) anova(BacteriaFamily_modB) anova(BacteriaFamily_modC) permutest(BacteriaFamily_modA) permutest(BacteriaFamily_modB) permutest(BacteriaFamily_modC) BacteriaFamily_modA BacteriaFamily_modB BacteriaFamily_modC #########GENUS####### BacterialCommunity_Genus=read.csv('/Volumes/Seagate/R/BetaDiversityAnalysis_0731 15/PCOA/Bacteria_CommunityData_Genus_073115.csv') BacteriaGenus_DistanceMatrix=vegdist(BacterialCommunity_Genus, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) BacteriaGenus_modA=betadisper(BacteriaGenus_DistanceMatrix, GroupA, type=c("median")) BacteriaGenus_modB=betadisper(BacteriaGenus_DistanceMatrix, GroupB, type=c("median")) BacteriaGenus_modC=betadisper(BacteriaGenus_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaGenus_modA) anova(BacteriaGenus_modB) 94 anova(BacteriaGenus_modC) permutest(BacteriaGenus_modA) permutest(BacteriaGenus_modB) permutest(BacteriaGenus_modC) BacteriaGenus_modA BacteriaGenus_modB BacteriaGenus_modC ############Bacteria OTU######### read.tcsv = function(file, header=TRUE, sep=",", ...) { n = max(count.fields(file, sep=","), na.rm=TRUE) x = readLines(file) .splitvar = function(x, sep, n) { var = unlist(strsplit(x, split=sep)) length(var) = n return(var) } x = do.call(cbind, lapply(x, .splitvar, sep=sep, n=n)) x = apply(x, 1, paste, collapse=sep) out = read.csv(text=x, sep=sep, header=header, ...) return(out) } bacteria_OTU=read.tcsv('Desktop/Thesis/R/AlphaDiversity/Bacteria_OTU.csv') BacteriaOTU_DistanceMatrix=vegdist(bacteria_OTU, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) BacteriaOTU_modA=betadisper(BacteriaOTU_DistanceMatrix, GroupA, type=c("median")) BacteriaOTU_modB=betadisper(BacteriaOTU_DistanceMatrix, GroupB, type=c("median")) BacteriaOTU_modC=betadisper(BacteriaOTU_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaOTU_modA) 95 anova(BacteriaOTU_modB) anova(BacteriaOTU_modC) permutest(BacteriaOTU_modA) permutest(BacteriaOTU_modB) permutest(BacteriaOTU_modC) BacteriaOTU_modA BacteriaOTU_modB BacteriaOTU_modC ###############BY CITY################# #####Baltimore####### Bacteria_Baltimore=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/ Bacteria/Bacteria_PCOA_Genus_Baltimore.csv') BacteriaBaltimore_DistanceMatrix=vegdist(Bacteria_Baltimore, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataBaltimore=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/ Second_Baltimore.csv') attach(Sup_DataBaltimore) GroupC=TRT BacteriaBaltimore_modC=betadisper(BacteriaBaltimore_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaBaltimore_modC) permutest(BacteriaBaltimore_modC) BacteriaBaltimore_modC #####helsinki########## Bacteria_Helsinki=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Ba cteria/Bacteria_PCOA_Genus_Helsinki.csv') BacteriaHelsinki_DistanceMatrix=vegdist(Bacteria_Helsinki, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataHelsinki=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Se cond_Helsinki.csv') attach(Sup_DataHelsinki) 96 GroupC=TRT BacteriaHelsinki_modC=betadisper(BacteriaHelsinki_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaHelsinki_modC) permutest(BacteriaHelsinki_modC) BacteriaHelsinki_modC ####Lahti##### Bacteria_Lahti=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Bacte ria/Bacteria_PCOA_Genus_Lahti.csv') BacteriaLahti_DistanceMatrix=vegdist(Bacteria_Lahti, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataLahti=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Seco nd_Lahti.csv') attach(Sup_DataLahti) GroupC=TRT BacteriaLahti_modC=betadisper(BacteriaLahti_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaLahti_modC) permutest(BacteriaLahti_modC) BacteriaLahti_modC ####Budapest#### Bacteria_Budapest=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/B acteria/Bacteria_PCOA_Genus_Budapest.csv') BacteriaBudapest_DistanceMatrix=vegdist(Bacteria_Budapest, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataBudapest=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/S econd_Budapest.csv') attach(Sup_DataBudapest) GroupC=TRT 97 BacteriaBudapest_modC=betadisper(BacteriaBudapest_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaBudapest_modC) permutest(BacteriaBudapest_modC) BacteriaBudapest_modC ####Potchefstroom##### Bacteria_Potchefstroom=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PC OA/Bacteria/Bacteria_PCOA_Genus_Potchefstroom.csv') BacteriaPotchefstroom_DistanceMatrix=vegdist(Bacteria_Potchefstroom, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataPotchefstroom=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PC OA/Second_Potchefstroom.csv') attach(Sup_DataPotchefstroom) GroupC=TRT BacteriaPotchefstroom_modC=betadisper(BacteriaPotchefstroom_DistanceMatrix, GroupC, type=c("median")) anova(BacteriaPotchefstroom_modC) permutest(BacteriaPotchefstroom_modC) BacteriaPotchefstroom_modC Convergence Fungi FungilCommunity_Phylum=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/ PCOA/Fungi/Fungal_CommunityData_Phylum_101915.csv') FungiPhylum_DistanceMatrix=vegdist(FungilCommunity_Phylum, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_Data=read.csv('Volumes/Seagate/R/BetaDiversityAnalysis_073115/PCOA/Second Matrix.csv') attach(Sup_Data) 98 GroupA=BLK2 GroupB=BLK GroupC=TRT FungiPhylum_modA=betadisper(FungiPhylum_DistanceMatrix, GroupA, type=c("median")) FungiPhylum_modB=betadisper(FungiPhylum_DistanceMatrix, GroupB, type=c("median")) FungiPhylum_modC=betadisper(FungiPhylum_DistanceMatrix, GroupC, type=c("median")) anova(FungiPhylum_modA) anova(FungiPhylum_modB) anova(FungiPhylum_modC) permutest(FungiPhylum_modA) permutest(FungiPhylum_modB) permutest(FungiPhylum_modC) FungiPhylum_modA FungiPhylum_modB FungiPhylum_modC #####CLASS###### FungiCommunity_Class=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PC OA/Fungi/Fungal_CommunityData_Class_101915.csv') FungiClass_DistanceMatrix=vegdist(FungiCommunity_Class, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) FungiClass_modA=betadisper(FungiClass_DistanceMatrix, GroupA, type=c("median")) FungiClass_modB=betadisper(FungiClass_DistanceMatrix, GroupB, type=c("median")) FungiClass_modC=betadisper(FungiClass_DistanceMatrix, GroupC, type=c("median")) anova(FungiClass_modA) anova(FungiClass_modB) anova(FungiClass_modC) permutest(FungiClass_modA) permutest(FungiClass_modB) permutest(FungiClass_modC) FungiClass_modA FungiClass_modB FungiClass_modC 99 #####ORDER###### FungiCommunity_Order=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PC OA/Fungi/Fungal_CommunityData_Order_101915.csv') FungiOrder_DistanceMatrix=vegdist(FungiCommunity_Order, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) FungiOrder_modA=betadisper(FungiOrder_DistanceMatrix, GroupA, type=c("median")) FungiOrder_modB=betadisper(FungiOrder_DistanceMatrix, GroupB, type=c("median")) FungiOrder_modC=betadisper(FungiOrder_DistanceMatrix, GroupC, type=c("median")) anova(FungiOrder_modA) anova(FungiOrder_modB) anova(FungiOrder_modC) permutest(FungiOrder_modA) permutest(FungiOrder_modB) permutest(FungiOrder_modC) FungiOrder_modA FungiOrder_modB FungiOrder_modC #####FAMILY##### FungiCommunity_Family=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/P COA/Fungi/Fungal_CommunityData_Family_101915.csv') FungiFamily_DistanceMatrix=vegdist(FungiCommunity_Family, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) FungiFamily_modA=betadisper(FungiFamily_DistanceMatrix, GroupA, type=c("median")) FungiFamily_modB=betadisper(FungiFamily_DistanceMatrix, GroupB, type=c("median")) FungiFamily_modC=betadisper(FungiFamily_DistanceMatrix, GroupC, type=c("median")) 100 anova(FungiFamily_modA) anova(FungiFamily_modB) anova(FungiFamily_modC) permutest(FungiFamily_modA) permutest(FungiFamily_modB) permutest(FungiFamily_modC) FungiFamily_modA FungiFamily_modB FungiFamily_modC #########GENUS####### FungiCommunity_Genus=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/P COA/Fungi/Fungal_CommunitData_Genus_090215.csv') FungiGenus_DistanceMatrix=vegdist(FungiCommunity_Genus, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) FungiGenus_modA=betadisper(FungiGenus_DistanceMatrix, GroupA, type=c("median")) FungiGenus_modB=betadisper(FungiGenus_DistanceMatrix, GroupB, type=c("median")) FungiGenus_modC=betadisper(FungiGenus_DistanceMatrix, GroupC, type=c("median")) anova(FungiGenus_modA) anova(FungiGenus_modB) anova(FungiGenus_modC) permutest(FungiGenus_modA) permutest(FungiGenus_modB) permutest(FungiGenus_modC) FungiGenus_modA FungiGenus_modB FungiGenus_modC ############Fungi OTU######### 101 Fungi_OTU=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Fungi/F ungal_CommunitData_OTU_073115.csv') FungiOTU_DistanceMatrix=vegdist(Fungi_OTU, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) FungiOTU_modA=betadisper(FungiOTU_DistanceMatrix, GroupA, type=c("median")) FungiOTU_modB=betadisper(FungiOTU_DistanceMatrix, GroupB, type=c("median")) FungiOTU_modC=betadisper(FungiOTU_DistanceMatrix, GroupC, type=c("median")) anova(FungiOTU_modA) anova(FungiOTU_modB) anova(FungiOTU_modC) permutest(FungiOTU_modA) permutest(FungiOTU_modB) permutest(FungiOTU_modC) FungiOTU_modA FungiOTU_modB FungiOTU_modC ###############BY CITY################# #####Baltimore####### Fungi_Baltimore=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Fun gi/Fungi_PCOA_OTU_Baltimore.csv') FungiBaltimore_DistanceMatrix=vegdist(Fungi_Baltimore, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataBaltimore=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/ Second_Baltimore.csv') attach(Sup_DataBaltimore) GroupC=TRT FungiBaltimore_modC=betadisper(FungiBaltimore_DistanceMatrix, GroupC, type=c("median")) anova(FungiBaltimore_modC) 102 permutest(FungiBaltimore_modC) FungiBaltimore_modC #####helsinki########## Fungi_Helsinki=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Fung i/Fungi_PCOA_OTU_Helsinki.csv') FungiHelsinki_DistanceMatrix=vegdist(Fungi_Helsinki, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataHelsinki=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Se cond_Helsinki.csv') attach(Sup_DataHelsinki) GroupC=TRT FungiHelsinki_modC=betadisper(FungiHelsinki_DistanceMatrix, GroupC, type=c("median")) anova(FungiHelsinki_modC) permutest(FungiHelsinki_modC) FungiHelsinki_modC ####Lahti##### Fungi_Lahti=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Fungi/F ungi_PCOA_OTU_Lahti.csv') FungiLahti_DistanceMatrix=vegdist(Fungi_Lahti, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataLahti=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Seco nd_Lahti.csv') attach(Sup_DataLahti) GroupC=TRT FungiLahti_modC=betadisper(FungiLahti_DistanceMatrix, GroupC, type=c("median")) anova(FungiLahti_modC) permutest(FungiLahti_modC) 103 FungiLahti_modC ####Budapest#### Fungi_Budapest=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/Fun gi/Fungi_PCOA_OTU_Budapest.csv') FungiBudapest_DistanceMatrix=vegdist(Fungi_Budapest, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataBudapest=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA/S econd_Budapest.csv') attach(Sup_DataBudapest) GroupC=TRT FungiBudapest_modC=betadisper(FungiBudapest_DistanceMatrix, GroupC, type=c("median")) anova(FungiBudapest_modC) permutest(FungiBudapest_modC) FungiBudapest_modC ####Potchefstroom##### Fungi_Potchefstroom=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PCOA /Fungi/Fungi_PCOA_OTU_Potchefstroom.csv') FungiPotchefstroom_DistanceMatrix=vegdist(Fungi_Potchefstroom, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm=FALSE) Sup_DataPotchefstroom=read.csv('Desktop/Thesis/R/BetaDiversityAnalysis_073115/PC OA/Second_Potchefstroom.csv') attach(Sup_DataPotchefstroom) GroupC=TRT FungiPotchefstroom_modC=betadisper(FungiPotchefstroom_DistanceMatrix, GroupC, type=c("median")) anova(FungiPotchefstroom_modC) permutest(FungiPotchefstroom_modC) FungiPotchefstroom_modC 104 Anova library(vegan) qpcr.data=read.csv('Desktop/Thesis/R/QPCR/QPCR_Data_100615.csv') attach(qpcr.data) ITS.TRT=aov(its ~ TRT + CITY, data=qpcr.data) summary(ITS.TRT) X16s.TRT=aov(X16s ~ TRT+ CITY, data=qpcr.data) summary(X16s.TRT) AOA.TRT=aov(AOA~ TRT+ CITY, data=qpcr.data) summary(AOA.TRT) logaoa.TRT=aov(logaoa ~ TRT+ CITY, data=qpcr.data) summary(logaoa.TRT) logaob.TRT=aov(logaob ~ TRT+ CITY, data=qpcr.data) summary(logaob.TRT) AOB.TRT=aov(AOB ~ TRT+ CITY, data=qpcr.data) summary(AOB.TRT) PICRUStAmoa.TRT=aov(PICRUStAmoa ~ TRT+ CITY, data=qpcr.data) summary(PICRUStAmoa.TRT) F_Pathotroph.TRT=aov(F_Pathotroph ~ TRT+ CITY, data=qpcr.data) summary(F_Pathotroph.TRT) F_Symbiotroph.TRT=aov(F_Symbiotroph ~ TRT+ CITY, data=qpcr.data) summary(F_Symbiotroph.TRT) F_Saprotroph.TRT=aov(F_Saprotroph ~ TRT+ CITY, data=qpcr.data) summary(F_Saprotroph.TRT) Archseq_Thaum=aov(Arch_Amoa~TRT + CITY, data=qpcr.data) summary(Archseq_Thaum) Archseq_Therm=aov(Arch_acid~TRT+ CITY, data=qpcr.data) summary(Archseq_Therm) Archseq_Meth=aov(Arch_Meth~TRT+ CITY, data=qpcr.data) summary(Archseq_Meth) Post-hoc Tukey HSD TukeyHSD(ITS.TRT, ordered=FALSE, conf.level=0.95) TukeyHSD(AOA.TRT, ordered=FALSE, conf.level=0.95) TukeyHSD(Logaoa.TRT, ordered=FALSE, conf.level=0.95) TukeyHSD(PICRUStAmoa.TRT, ordered=FALSE, conf.level=0.95) TukeyHSD(F_Symbiotroph.TRT, ordered=FALSE, conf.level=0.95) TukeyHSD(Archseq_Thaum, ordered=FALSE, conf.level=0.95) 105 Environmental correlation archaeacmatrix1=read.csv('Desktop/Thesis/R/MainMatrix/Archaea_Genus_Main.csv') ArchOrd1=metaMDS(archaeacmatrix1) Bacteriamatrix1=read.csv('Desktop/Thesis/R/MainMatrix/Bacteria_Genus_Main.csv') BacOrd1=metaMDS(Bacteriamatrix1) Fungimatrix1=read.csv('Desktop/Thesis/R/MainMatrix/Fungi_OTU_Main.csv') FunOrd1=metaMDS(Fungimatrix1) Data.env=read.csv('Desktop/Thesis/R/MainMatrix/Second.csv') ArchFit=envfit(ArchOrd1, Data.env) ArchFit BacFit=envfit(BacOrd1, Data.env) BacFit FunFit=envfit(FunOrd1, Data.env) FunFit Appendix C: Qiime Scripts 16s Library: fastq-join -m 50 -r /media/Seagate/QIIME/16s/Joinreport/DES_1_Joinreport Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s008-indexN708-S501-CAGAGAGG- TAGATCGC-8_S8_L001_R1_001.fastq.gz Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s008-indexN708-S501-CAGAGAGG- TAGATCGC-8_S8_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_1_Unpaired_R1 -o /media/Seagate/QIIME/16s/DES_1_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_1_Joined;fastq-join -m 50 -r /media/Seagate/QIIME/16s/Joinreport/DES_2_Joinreport Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s020-indexN708-S502-CAGAGAGG- CTCTCTAT-20_S20_L001_R1_001.fastq.gz Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s020-indexN708-S502-CAGAGAGG- CTCTCTAT-20_S20_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_2_Unpaired_R1 -o 106 /media/Seagate/QIIME/16s/DES_2_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_2_Joined;fastq-join -m 50 -r /media/Seagate/QIIME/16s/Joinreport/DES_3_Joinreport Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s032-indexN708-S503-CAGAGAGG- TATCCTCT-32_S32_L001_R1_001.fastq.gz Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s032-indexN708-S503-CAGAGAGG- TATCCTCT-32_S32_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_3_Unpaired_R1 -o /media/Seagate/QIIME/16s/DES_3_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_3_Joined;fastq-join -m 50 -r /media/Seagate/QIIME/16s/Joinreport/DES_4_Joinreport Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s044-indexN708-S504-CAGAGAGG- AGAGTAGA-44_S44_L001_R1_001.fastq.gz Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s044-indexN708-S504-CAGAGAGG- AGAGTAGA-44_S44_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_4_Unpaired_R1 -o /media/Seagate/QIIME/16s/DES_4_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_4_Joined;fastq-join -m 50 -r /media/Seagate/QIIME/16s/Joinreport/DES_5_Joinreport Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s056-indexN708-S505-CAGAGAGG- GTAAGGAG-56_S56_L001_R1_001.fastq.gz Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 8_0067_000000000-A8U60/BaseCalls/lane1-s056-indexN708-S505-CAGAGAGG- GTAAGGAG-56_S56_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_5_Unpaired_R1 -o /media/Seagate/QIIME/16s/DES_5_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_5_Joined;fastq-join -m 50 -r /media/Seagate/QIIME/16s/Joinreport/DES_6_Joinreport Illumina/Data/MiSeq_67_Sequences/files.cgrb.oregonstate.edu/Illumina/140331_M0149 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/media/Seagate/QIIME/16s/DES_97_Joined;fastq-join -m 50 -r /media/Seagate/QIIME/16s/Joinreport/DES_98_Joinreport Illumina/Data/MiSeq_78_Sequences/files.cgrb.oregonstate.edu/Illumina/140509_M0149 8_0078_000000000-A902R/BaseCalls/lane1-s070-indexN710-S506-CGAGGCTG- ACTGCATA-70_S70_L001_R1_001.fastq.gz Illumina/Data/MiSeq_78_Sequences/files.cgrb.oregonstate.edu/Illumina/140509_M0149 8_0078_000000000-A902R/BaseCalls/lane1-s070-indexN710-S506-CGAGGCTG- ACTGCATA-70_S70_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_98_Unpaired_R1 -o /media/Seagate/QIIME/16s/DES_98_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_98_Joined;fastq-join -m 50 -r 128 /media/Seagate/QIIME/16s/Joinreport/DES_99_Joinreport Illumina/Data/MiSeq_78_Sequences/files.cgrb.oregonstate.edu/Illumina/140509_M0149 8_0078_000000000-A902R/BaseCalls/lane1-s082-indexN710-S507-CGAGGCTG- AAGGAGTA-82_S82_L001_R1_001.fastq.gz Illumina/Data/MiSeq_78_Sequences/files.cgrb.oregonstate.edu/Illumina/140509_M0149 8_0078_000000000-A902R/BaseCalls/lane1-s082-indexN710-S507-CGAGGCTG- AAGGAGTA-82_S82_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_99_Unpaired_R1 -o /media/Seagate/QIIME/16s/DES_99_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_99_Joined;fastq-join -m 50 -r /media/Seagate/QIIME/16s/Joinreport/DES_100_Joinreport Illumina/Data/MiSeq_78_Sequences/files.cgrb.oregonstate.edu/Illumina/140509_M0149 8_0078_000000000-A902R/BaseCalls/lane1-s094-indexN710-S508-CGAGGCTG- CTAAGCCT-94_S94_L001_R1_001.fastq.gz Illumina/Data/MiSeq_78_Sequences/files.cgrb.oregonstate.edu/Illumina/140509_M0149 8_0078_000000000-A902R/BaseCalls/lane1-s094-indexN710-S508-CGAGGCTG- CTAAGCCT-94_S94_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_100_Unpaired_R1 -o /media/Seagate/QIIME/16s/DES_100_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_100_Joined;fastq-join -m 50 -r GLUSEEN/QIIME/Joinreport/DES_51a_Joinreport Illumina/Data/MiSeq_78_Sequences/files.cgrb.oregonstate.edu/Illumina/140509_M0149 8_0078_000000000-A902R/BaseCalls/lane1-­‐s076-­‐indexN704-­‐S507-­‐TCCTGAGC-­‐ AAGGAGTA-­‐76_S76_L001_R1_001.fastq.gz Illumina/Data/MiSeq_78_Sequences/files.cgrb.oregonstate.edu/Illumina/140509_M0149 8_0078_000000000-A902R/BaseCalls/lane1-­‐s076-­‐indexN704-­‐S507-­‐TCCTGAGC-­‐ AAGGAGTA-­‐76_S76_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_51a_Unpaired_R1 -o /media/Seagate/QIIME/16s/DES_51a_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_51a_Joined;fastq-join -m 50 -r GLUSEEN/QIIME/Joinreport/DES_51b_Joinreport Illumina/Data/MiSeq_109_Sequences/files.cgrb.oregonstate.edu/Illumina/141020_M014 98_0109_000000000-ABC6D/BaseCalls/lane1-­‐s076-­‐indexN704-­‐S507-­‐TCCTGAGC-­‐ AAGGAGTA-­‐76_S76_L001_R1_001.fastq.gz Illumina/Data/MiSeq_109_Sequences/files.cgrb.oregonstate.edu/Illumina/141020_M014 98_0109_000000000-ABC6D/BaseCalls/lane1-­‐s076-­‐indexN704-­‐S507-­‐TCCTGAGC-­‐ AAGGAGTA-­‐76_S76_L001_R2_001.fastq.gz -o /media/Seagate/QIIME/16s/DES_51b_Unpaired_R1 -o /media/Seagate/QIIME/16s/DES_51b_Unpaired_R2 -o /media/Seagate/QIIME/16s/DES_51b_Joined; cat /media/Seagate/QIIME/16s/DES_51b_Joined /media/Seagate/QIIME/16s/DES_51a_Joined > /media/Seagate/QIIME/16s/DES_51_Joined; cat /media/Seagate/QIIME/16s/DES_39b_Joined /media/Seagate/QIIME/16s/DES_39a_Joined > 129 /media/Seagate/QIIME/16s/DES_39_Joined; cat /media/Seagate/QIIME/16s/DES_40b_Joined /media/Seagate/QIIME/16s/DES_40a_Joined > /media/Seagate/QIIME/16s/DES_40_Joined; cat /media/Seagate/QIIME/16s/DES_43b_Joined /media/Seagate/QIIME/16s/DES_43a_Joined > /media/Seagate/QIIME/16s/DES_43_Joined; cat /media/Seagate/QIIME/16s/DES_53b_Joined /media/Seagate/QIIME/16s/DES_53a_Joined > /media/Seagate/QIIME/16s/DES_53_Joined; cat /media/Seagate/QIIME/16s/DES_64b_Joined /media/Seagate/QIIME/16s/DES_64a_Joined > /media/Seagate/QIIME/16s/DES_64_Joined convert_fastaqual_fastq.py  -­‐c  fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_1_Joined  -­‐ o  /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_2_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_3_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_4_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_5_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_6_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_7_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_8_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_9_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_10_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_11_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_12_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_13_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_14_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_15_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_16_Joined  -­‐o   130 /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_17_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_18_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_19_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_20_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_21_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_22_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_23_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_24_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_25_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_26_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_27_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_28_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_29_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_30_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_31_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_32_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_33_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_34_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_35_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_36_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_37_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_38_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   131 fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_39_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_40_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_41_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_42_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_43_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_44_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_45_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_46_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_47_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_48_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_49_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_50_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_51_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_52_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_53_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_54_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_55_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_56_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_57_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_58_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_59_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_60_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_61_Joined  -­‐o   132 /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_62_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_63_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_64_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_65_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_66_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_67_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_68_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_69_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_70_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_71_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/16s/DES_72_Joined  -­‐o   /media/Seagate/QIIME/16s/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   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pick_closed_reference_otus.py -r Desktop/gg_13_8_otus/rep_set/97_otus.fasta -i /media/Seagate/QIIME/16s/split_libraries_output/Combined_sequence_libraries_050115 .fna -o /media/Seagate/QIIME/16s/Pick_OTU_ClosedReference_091315/ pick_rep_set.py -i /media/Seagate/QIIME/16s/Pick_OTU_050115/Combined_sequence_libraries_050115_ otus.txt -f /media/Seagate/QIIME/16s/split_libraries_output/Combined_sequence_libraries_050115 .fna -o /media/Seagate/QIIME/16s/Rep_set/Combined_sequence_libraries_050115_repset.fna assign_taxonomy.py -i /media/Seagate/QIIME/16s/Rep_set/Combined_sequence_libraries_050115_repset.fna - o /media/Seagate/QIIME/16s/taxonomy_results/ make_otu_table.py -i /media/Seagate/QIIME/16s/Pick_OTU_050115/Combined_sequence_libraries_050115_ otus.txt -t /media/Seagate/QIIME/16s/taxonomy_results/Combined_sequence_libraries_050115_re pset_tax_assignments.txt -o /media/Seagate/QIIME/16s/OTU_Tables/Combined_sequence_libraries_050115_OTU_t able.biom biom convert -i /media/Seagate/QIIME/16s/OTU_Tables/Combined_sequence_libraries_050115_OTU_t able.biom -o /media/Seagate/QIIME/16s/OTU_Tables/OTU_Table_050115.txt -b -- header-key=”taxonomy” --output-metadata-id=”consensus_lineage”;summarize_taxa.py - i /media/Seagate/QIIME/16s/OTU_Tables/Combined_sequence_libraries_050115_OTU_t able.biom -o /media/Seagate/QIIME/16s/taxonomy_summaries/;align_seqs.py -i /media/Seagate/QIIME/16s/Rep_set/Combined_sequence_libraries_050115_repset.fna -o /media/Seagate/QIIME/16s/alignment/ 148 ITS Library: fastq-join: fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/DES_1_Joinreport Illumina/Data/MiSeq_79_Sequences/files.cgrb.oregonstate.edu/Illumina/140512_M0149 8_0079_000000000-A86D3/BaseCalls/lane1-s008-indexN708-S501-CAGAGAGG- TAGATCGC-8_S8_L001_R1_001.fastq.gz Illumina/Data/MiSeq_79_Sequences/files.cgrb.oregonstate.edu/Illumina/140512_M0149 8_0079_000000000-A86D3/BaseCalls/lane1-s008-indexN708-S501-CAGAGAGG- TAGATCGC-8_S8_L001_R2_001.fastq.gz -o 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498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s035-­‐indexN711-­‐S503-­‐AAGAGGCA-­‐ TATCCTCT-­‐35_S35_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample57_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample57_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample57_Joined fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/Joinreport_62 Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M014 98_0110_000000000-ABM1R/BaseCalls/lane1-­‐s040-­‐indexN704-­‐S504-­‐TCCTGAGC-­‐ AGAGTAGA-­‐40_S40_L001_R1_001.fastq.gz   Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M01 498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s040-­‐indexN704-­‐S504-­‐TCCTGAGC-­‐ AGAGTAGA-­‐40_S40_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample62_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample62_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample62_Joined fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/Joinreport_76 Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M014 98_0110_000000000-ABM1R/BaseCalls/lane1-­‐s054-­‐indexN706-­‐S505-­‐TAGGCATG-­‐ GTAAGGAG-­‐54_S54_L001_R1_001.fastq.gz   Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M01 498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s054-­‐indexN706-­‐S505-­‐TAGGCATG-­‐ GTAAGGAG-­‐54_S54_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample76_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample76_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample76_Joined 181 fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/Joinreport_80 Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M014 98_0110_000000000-ABM1R/BaseCalls/lane1-­‐s058-­‐indexN710-­‐S505-­‐CGAGGCTG-­‐ GTAAGGAG-­‐58_S58_L001_R1_001.fastq.gz   Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M01 498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s058-­‐indexN710-­‐S505-­‐CGAGGCTG-­‐ GTAAGGAG-­‐58_S58_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample80_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample80_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample80_Joined fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/Joinreport_81 Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M014 98_0110_000000000-ABM1R/BaseCalls/lane1-­‐s059-­‐indexN711-­‐S505-­‐AAGAGGCA-­‐ GTAAGGAG-­‐59_S59_L001_R1_001.fastq.gz   Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M01 498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s059-­‐indexN711-­‐S505-­‐AAGAGGCA-­‐ GTAAGGAG-­‐59_S59_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample81_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample81_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample81_Joined fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/Joinreport_83 Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M014 98_0110_000000000-ABM1R/BaseCalls/lane1-­‐s061-­‐indexN701-­‐S506-­‐TAAGGCGA-­‐ ACTGCATA-­‐61_S61_L001_R1_001.fastq.gz   Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M01 498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s061-­‐indexN701-­‐S506-­‐TAAGGCGA-­‐ ACTGCATA-­‐61_S61_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample83_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample83_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample83_Joined fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/Joinreport_85 Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M014 98_0110_000000000-ABM1R/BaseCalls/lane1-­‐s063-­‐indexN703-­‐S506-­‐AGGCAGAA-­‐ ACTGCATA-­‐63_S63_L001_R1_001.fastq.gz   Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M01 498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s063-­‐indexN703-­‐S506-­‐AGGCAGAA-­‐ ACTGCATA-­‐63_S63_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample85_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample85_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample85_Joined; fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/Joinreport_86 182 Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M014 98_0110_000000000-ABM1R/BaseCalls/lane1-­‐s064-­‐indexN704-­‐S506-­‐TCCTGAGC-­‐ ACTGCATA-­‐64_S64_L001_R1_001.fastq.gz   Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M01 498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s064-­‐indexN704-­‐S506-­‐TCCTGAGC-­‐ ACTGCATA-­‐64_S64_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample86_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample86_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample86_Joined fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/Joinreport_93 Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M014 98_0110_000000000-ABM1R/BaseCalls/lane1-­‐s071-­‐indexN711-­‐S506-­‐AAGAGGCA-­‐ ACTGCATA-­‐71_S71_L001_R1_001.fastq.gz   Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M01 498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s071-­‐indexN711-­‐S506-­‐AAGAGGCA-­‐ ACTGCATA-­‐71_S71_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample93_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample93_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample93_Joined; fastq-join -m 50 -r /media/Seagate/QIIME/ITS/Joinreport/Joinreport_99 Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M014 98_0110_000000000-ABM1R/BaseCalls/lane1-­‐s077-­‐indexN705-­‐S507-­‐GGACTCCT-­‐ AAGGAGTA-­‐77_S77_L001_R1_001.fastq.gz   Illumina/Data/MiSeq_110_Sequences/files.cgrb.oregonstate.edu/Illumina/141022_M01 498_0110_000000000-­‐ABM1R/BaseCalls/lane1-­‐s077-­‐indexN705-­‐S507-­‐GGACTCCT-­‐ AAGGAGTA-­‐77_S77_L001_R2_001.fastq.gz -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample99_R1_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample99_R2_Unpaired -o GLUSEEN/QIIME/Publication_Data/ITS/110/Sample99_Joined cat /media/Seagate/QIIME/ITS/Joined/DES_23b_Joined /media/Seagate/QIIME/ITS/Joined/DES_23a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_23_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_24b_Joined /media/Seagate/QIIME/ITS/Joined/DES_24a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_24_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_25b_Joined /media/Seagate/QIIME/ITS/Joined/DES_25a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_25_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_27b_Joined /media/Seagate/QIIME/ITS/Joined/DES_27a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_27_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_30b_Joined 183 /media/Seagate/QIIME/ITS/Joined/DES_30a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_30_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_31b_Joined /media/Seagate/QIIME/ITS/Joined/DES_31a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_31_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_32b_Joined /media/Seagate/QIIME/ITS/Joined/DES_32a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_32_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_33b_Joined /media/Seagate/QIIME/ITS/Joined/DES_33a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_33_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_34b_Joined /media/Seagate/QIIME/ITS/Joined/DES_34a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_34_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_36b_Joined /media/Seagate/QIIME/ITS/Joined/DES_36a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_36_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_37b_Joined /media/Seagate/QIIME/ITS/Joined/DES_37a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_37_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_39b_Joined /media/Seagate/QIIME/ITS/Joined/DES_39a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_39_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_42b_Joined /media/Seagate/QIIME/ITS/Joined/DES_42a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_42_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_44b_Joined /media/Seagate/QIIME/ITS/Joined/DES_44a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_44_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_46b_Joined /media/Seagate/QIIME/ITS/Joined/DES_46a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_46_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_47b_Joined /media/Seagate/QIIME/ITS/Joined/DES_47a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_47_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_48b_Joined /media/Seagate/QIIME/ITS/Joined/DES_48a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_48_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_50b_Joined /media/Seagate/QIIME/ITS/Joined/DES_50a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_50_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_51b_Joined /media/Seagate/QIIME/ITS/Joined/DES_51a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_51_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_52b_Joined /media/Seagate/QIIME/ITS/Joined/DES_52a_Joined > 184 /media/Seagate/QIIME/ITS/Joined/DES_52_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_54b_Joined /media/Seagate/QIIME/ITS/Joined/DES_54a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_54_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_58b_Joined /media/Seagate/QIIME/ITS/Joined/DES_58a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_58_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_59b_Joined /media/Seagate/QIIME/ITS/Joined/DES_59a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_59_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_60b_Joined /media/Seagate/QIIME/ITS/Joined/DES_60a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_60_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_61b_Joined /media/Seagate/QIIME/ITS/Joined/DES_61a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_61_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_63b_Joined /media/Seagate/QIIME/ITS/Joined/DES_63a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_63_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_64b_Joined /media/Seagate/QIIME/ITS/Joined/DES_64a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_64_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_65b_Joined /media/Seagate/QIIME/ITS/Joined/DES_65a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_65_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_66b_Joined /media/Seagate/QIIME/ITS/Joined/DES_66a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_66_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_67b_Joined /media/Seagate/QIIME/ITS/Joined/DES_67a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_67_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_68b_Joined /media/Seagate/QIIME/ITS/Joined/DES_68a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_68_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_69b_Joined /media/Seagate/QIIME/ITS/Joined/DES_69a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_69_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_70b_Joined /media/Seagate/QIIME/ITS/Joined/DES_70a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_70_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_71b_Joined /media/Seagate/QIIME/ITS/Joined/DES_71a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_71_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_72b_Joined /media/Seagate/QIIME/ITS/Joined/DES_72a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_72_Joined;cat 185 /media/Seagate/QIIME/ITS/Joined/DES_73b_Joined /media/Seagate/QIIME/ITS/Joined/DES_73a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_73_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_74b_Joined /media/Seagate/QIIME/ITS/Joined/DES_74a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_74_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_75b_Joined /media/Seagate/QIIME/ITS/Joined/DES_75a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_75_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_77b_Joined /media/Seagate/QIIME/ITS/Joined/DES_77a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_77_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_78b_Joined /media/Seagate/QIIME/ITS/Joined/DES_78a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_78_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_79b_Joined /media/Seagate/QIIME/ITS/Joined/DES_79a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_79_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_82b_Joined /media/Seagate/QIIME/ITS/Joined/DES_82a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_82_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_84b_Joined /media/Seagate/QIIME/ITS/Joined/DES_84a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_84_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_87b_Joined /media/Seagate/QIIME/ITS/Joined/DES_87a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_87_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_88b_Joined /media/Seagate/QIIME/ITS/Joined/DES_88a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_88_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_89b_Joined /media/Seagate/QIIME/ITS/Joined/DES_89a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_89_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_90b_Joined /media/Seagate/QIIME/ITS/Joined/DES_90a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_90_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_91b_Joined /media/Seagate/QIIME/ITS/Joined/DES_91a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_91_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_92b_Joined /media/Seagate/QIIME/ITS/Joined/DES_92a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_92_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_94b_Joined /media/Seagate/QIIME/ITS/Joined/DES_94a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_94_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_95b_Joined 186 /media/Seagate/QIIME/ITS/Joined/DES_95a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_95_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_96b_Joined /media/Seagate/QIIME/ITS/Joined/DES_96a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_96_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_97b_Joined /media/Seagate/QIIME/ITS/Joined/DES_97a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_97_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_98b_Joined /media/Seagate/QIIME/ITS/Joined/DES_98a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_98_Joined;cat /media/Seagate/QIIME/ITS/Joined/DES_100b_Joined /media/Seagate/QIIME/ITS/Joined/DES_100a_Joined > /media/Seagate/QIIME/ITS/Joined/DES_100_Joined convert_fastaqual_fastq.py  -­‐c  fastq_to_fastaqual  -­‐f   /media/Seagate/QIIME/ITS/Joined/Sample1_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample2_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample3_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample4_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample5_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample6_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample7_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample8_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample9_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample10_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample11_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample12_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample13_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample14_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample15_Joined  -­‐o   187 /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample16_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample17_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample18_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample19_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample20_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample21_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/Sample22_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_23_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_24_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_25_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_26_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_27_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_28_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_29_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_30_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_31_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_32_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_33_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_34_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_35_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_36_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_37_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   188 fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_38_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_39_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_40_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_41_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_42_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_43_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_44_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_45_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_46_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_47_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_48_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_49_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_50_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_51_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_52_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_53_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_54_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_55_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_56_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_57_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_58_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_59_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_60_Joined  -­‐o   189 /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_61_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_62_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_63_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_64_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_65_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_66_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_67_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_68_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_69_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_70_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_71_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_72_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_73_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_74_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_75_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_76_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_77_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_78_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_79_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_80_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_81_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_82_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   190 fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_83_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_84_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_85_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_86_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_87_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_88_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_89_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_90_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_91_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_92_Joined  -­‐o   /media/Seagate/QIIME/ITS/Joined/Fastaqual_output/;convert_fastaqual_fastq.py  -­‐c   fastq_to_fastaqual  -­‐f  /media/Seagate/QIIME/ITS/Joined/DES_93_Joined  -­‐o   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/media/Seagate/QIIME/ITS/split_libraries_output/split_library_100/seqs.fna > /media/Seagate/QIIME/ITS/split_libraries_output/Combined_sequence_libraries_050115 .fna pick_otus.py -i /media/Seagate/QIIME/ITS/split_libraries_output/Combined_sequence_libraries_050115 .fna -o /media/Seagate/QIIME/ITS/Pick_OTU_050115/ pick_rep_set pick_rep_set.py -i /media/Seagate/QIIME/ITS/Pick_OTU_050115/Combined_sequence_libraries_050115_ otus.txt -f /media/Seagate/QIIME/ITS/split_libraries_output/Combined_sequence_libraries_050115 .fna -o /media/Seagate/QIIME/ITS/Rep_set/Combined_sequence_libraries_050115_repset.fna assign_taxonomy assign_taxonomy.py -i /media/Seagate/QIIME/ITS/Rep_set/Combined_sequence_libraries_050115_repset.fna - t /media/Seagate/QIIME/ITS/sh_qiime_release_10/sh_taxonomy_qiime_ver6_dynamic_1 0.09.2014.txt -r /media/Seagate/QIIME/ITS/sh_qiime_release_10/sh_refs_qiime_ver6_dynamic_10.09.2 014.fasta -o /media/Seagate/QIIME/ITS/taxonomy_results/ -m rdp --rdp_max_memory 10000 make_otu_table.py -i /media/Seagate/QIIME/ITS/Pick_OTU_050115/Combined_sequence_libraries_050115_o tus.txt -t /media/Seagate/QIIME/ITS/taxonomy_results/Combined_sequence_libraries_050115_rep set_tax_assignments.txt -o /media/Seagate/QIIME/ITS/otu_tables/combined_seqs_otu_table_050115.biom summarize_taxa.py -i /media/Seagate/QIIME/ITS/otu_tables/combined_seqs_otu_table_050115.biom -o /media/Seagate/QIIME/ITS/taxonomy_summaries/ 204 Appendix D: Funguilds: python Guilds_v1.0.py -otu /Volumes/Seagate/FUNGuilds/Fungi_Indicators_Function.txt python Guilds_v1.0.py -otu /Volumes/Seagate/FUNGuilds/TaxonomyAssignments.txt 205 Bibliography 1. Vitousek, P. M., Mooney, H. A., Lubchenco, J. & Melillo, J. M. Human Domination of Earth’s Ecosystems. Science 277, 494–499 (1997). 2. Goldewijk, K. K. Estimating global land use change over the past 300 years: the HYDE Database. Glob. Biogeochem. Cycles 15, 417–433 (2001). 3. Tilman, D., Balzer, C., Hill, J. & Befort, B. L. Global food demand and the sustainable intensification of agriculture. Proc. Natl. Acad. Sci. 108, 20260–20264 (2011). 4. Krebs, J. R., Wilson, J. D., Bradbury, R. B. & Siriwardena, G. M. The second Silent Spring? Nature 400, 611–612 (1999). 5. Ellis, E. C. & Ramankutty, N. Putting people in the map: anthropogenic biomes of the world. Front. Ecol. Environ. 6, 439–447 (2007). 6. Wu, J. (Jingle). Making the Case for Landscape Ecology An Effective Approach to Urban Sustainability. Landsc. J. 27, 41–50 (2008). 7. Framing ecosystem services in the telecoupled Anthropocene - Liu - 2016 - Frontiers in Ecology and the Environment - Wiley Online Library. Available at: http://onlinelibrary.wiley.com/doi/10.1002/16-0188.1/full. (Accessed: 14th March 2016) 8. Johns, T. C. et al. Anthropogenic climate change for 1860 to 2100 simulated with the HadCM3 model under updated emissions scenarios. Clim. Dyn. 20, 583–612 (2003). 9. Bindoff, N. L. et al. IPCC Chapter 10: Detection and Attribution of Climate Change: from Global to Regional. 867–952 (Cambridge, UK, 2013). 206 10. Mulder, M. B. & Coppolillo, P. Conservation: Linking Ecology, Economics, and Culture. (Princeton University Press, 2004). 11. McKinney, M. L. & Lockwood, J. L. Biotic homogenization: a few winners replacing many losers in the next mass extinction. Trends Ecol. Evol. 14, 450–453 (1999). 12. Baiser, B., Olden, J. D., Record, S., Lockwood, J. L. & McKinney, M. L. Pattern and process of biotic homogenization in the New Pangaea. Proc. R. Soc. Lond. B Biol. Sci. rspb20121651 (2012). doi:10.1098/rspb.2012.1651 13. McKinney, M. L. Urbanization as a major cause of biotic homogenization. Biol. Conserv. 127, 247–260 (2006). 14. Rodrigues, J. L. M. et al. Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc. Natl. Acad. Sci. 110, 988–993 (2013). 15. Naaf, T. & Wulf, M. Habitat specialists and generalists drive homogenization and differentiation of temperate forest plant communities at the regional scale. Biol. Conserv. 143, 848–855 (2010). 16. Pouyat, R. et al. A global comparison of surface soil across five cities: a test of the urban ecosystem convergence hypothesis. Soil Sci. (2015). 17. Pickett, S. T. A. et al. Urban ecological systems: Scientific foundations and a decade of progress. J. Environ. Manage. 92, 331–362 (2011). 18. Setälä, H. et al. Urban and agricultural soils: conflicts and trade-offs in the optimization of ecosystem services. Urban Ecosyst. 17, 239–253 (2013). 19. Odum, H. T. Energy, Ecology, and Economics. Ambio 2, 220–227 (1973). 207 20. Veteto, J. R., Nabhan, G. P., Fitzsimmons, R., Routson, K. & Walker, D. Place- Based Foods of Appalachia: From Rarity to Community Restoration and Market Recovery. (Renewing America’s Food Traditions Alliance, 2011). 21. Nemergut, D. R. et al. Patterns and Processes of Microbial Community Assembly. Microbiol. Mol. Biol. Rev. 77, 342–356 (2013). 22. George, K., Ziska, L. H., Bunce, J. A. & Quebedeaux, B. Elevated atmospheric CO2 concentration and temperature across an urban–rural transect. Atmos. Environ. 41, 7654–7665 (2007). 23. Groffman, P. M. et al. Ecological homogenization of urban USA. Front. Ecol. Environ. 12, 74–81 (2014). 24. Finlay, R. et al. The role of fungi in biogenic weathering in boreal forest soils. Fungal Biol. Rev. 23, 101–106 (2009). 25. Frey, B. et al. Weathering-Associated Bacteria from the Damma Glacier Forefield: Physiological Capabilities and Impact on Granite Dissolution. Appl. Environ. Microbiol. 76, 4788–4796 (2010). 26. Balland, C., Poszwa, A., Leyval, C. & Mustin, C. Dissolution rates of phyllosilicates as a function of bacterial metabolic diversity. Geochim. Cosmochim. Acta 74, 5478– 5493 (2010). 27. Lehmann, A. & Stahr, K. Nature and significance of anthropogenic urban soils. J. Soils Sediments 7, 247–260 (2007). 28. Pouyat, R. V., Szlavecz, K., Yesilonis, I. D., Groffman, P. M. & Schwarz, K. in Urban Ecosystem Ecology 119–152 (American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, 2010). 208 29. Kaye, J. P., Groffman, P. M., Grimm, N. B., Baker, L. A. & Pouyat, R. V. A distinct urban biogeochemistry? Trends Ecol. Evol. 21, 192–199 (2006). 30. Pickett, S. T. A. et al. Beyond Urban Legends: An Emerging Framework of Urban Ecology, as Illustrated by the Baltimore Ecosystem Study. BioScience 58, 139–150 (2008). 31. Kühn, I. & Klotz, S. Urbanization and homogenization – Comparing the floras of urban and rural areas in Germany. Biol. Conserv. 127, 292–300 (2006). 32. McIntyre, N. E. Ecology of Urban Arthropods: A Review and a Call to Action. Ann. Entomol. Soc. Am. 93, 825–835 (2000). 33. van Rensburg, B. J., Peacock, D. S. & Robertson, M. P. Biotic homogenization and alien bird species along an urban gradient in South Africa. Landsc. Urban Plan. 92, 233–241 (2009). 34. Schimel, J. & Schaeffer, S. M. Microbial control over carbon cycling in soil. Terr. Microbiol. 3, 348 (2012). 35. Philippot, L. et al. Loss in microbial diversity affects nitrogen cycling in soil. ISME J. 7, 1609–1619 (2013). 36. Smith, S. E. & Read, D. J. Mycorrhizal Symbiosis. (Elsevier, 2008). 37. Nara, K. in Mycorrhizal Networks (ed. Horton, T. R.) 177–201 (Springer Netherlands, 2015). 38. Allison, S. D. & Martiny, J. B. H. Resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci. U. S. A. 105, 11512–11519 (2008). 39. Solé, R. V. & Montoya, M. Complexity and fragility in ecological networks. Proc. R. Soc. Lond. B Biol. Sci. 268, 2039–2045 (2001). 209 40. Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012). 41. Walker, B., Kinzig, A. & Langridge, J. Original Articles: Plant Attribute Diversity, Resilience, and Ecosystem Function: The Nature and Significance of Dominant and Minor Species. Ecosystems 2, 95–113 (1999). 42. Attard, E. et al. Soil environmental conditions rather than denitrifier abundance and diversity drive potential denitrification after changes in land uses. Glob. Change Biol. 17, 1975–1989 (2011). 43. Dinsdale, E. A. et al. Functional metagenomic profiling of nine biomes. Nature 452, 629–632 (2008). 44. Foster, D. et al. The Importance of Land-Use Legacies to Ecology and Conservation. BioScience 53, 77–88 (2003). 45. Rothwell, A., Ridoutt, B., Page, G. & Bellotti, W. Feeding and housing the urban population: Environmental impacts at the peri-urban interface under different land- use scenarios. Land Use Policy 48, 377–388 (2015). 46. Scheffer, M., Carpenter, S., Foley, J. A., Folke, C. & Walker, B. Catastrophic shifts in ecosystems. Nature 413, 591–596 (2001). 47. Pouyat, R. V. et al. A Global Comparison of Surface Soil Characteristics Across Five Cities: A Test of the Urban Ecosystem Convergence Hypothesis. Soil Sci. 136–145 (2015). doi:10.1097/SS.0000000000000125 48. Tabarelli, M., Peres, C. A. & Melo, F. P. L. The ‘few winners and many losers’ paradigm revisited: Emerging prospects for tropical forest biodiversity. Biol. Conserv. 155, 136–140 (2012). 210 49. Olden, J. D. & Rooney, T. P. On defining and quantifying biotic homogenization. Glob. Ecol. Biogeogr. 15, 113–120 (2006). 50. Fukami, T., Martijn Bezemer, T., Mortimer, S. R. & van der Putten, W. H. Species divergence and trait convergence in experimental plant community assembly. Ecol. Lett. 8, 1283–1290 (2005). 51. Baiser, B., Olden, J. D., Record, S., Lockwood, J. L. & McKinney, M. L. Pattern and process of biotic homogenization in the New Pangaea. Proc. R. Soc. B Biol. Sci. 279, 4772–4777 (2012). 52. Boyero, L. et al. Global patterns of stream detritivore distribution: implications for biodiversity loss in changing climates. Glob. Ecol. Biogeogr. 21, 134–141 (2012). 53. Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A. B. & Kent, J. Biodiversity hotspots for conservation priorities. Nature 403, 853–858 (2000). 54. Fierer, N., Strickland, M. S., Liptzin, D., Bradford, M. A. & Cleveland, C. C. Global patterns in belowground communities. Ecol. Lett. 12, 1238–1249 (2009). 55. Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340–1351 (2010). 56. Bru, D. et al. Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME J. 5, 532–542 (2011). 57. Oksanen, J. et al. vegan: Community Ecology Package. (2015). 58. Nguyen, N. H. et al. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. doi:10.1016/j.funeco.2015.06.006 211 59. Karpati, A. S., Handel, S. N., Dighton, J. & Horton, T. R. Quercus rubra-associated ectomycorrhizal fungal communities of disturbed urban sites and mature forests. Mycorrhiza 21, 537–547 (2011). 60. Jumpponen, A. & Egerton-Warburton, L. M. Mycorrhizal fungi in successional environments: a community assembly model incorporating host plant, environmental, and biotic filters. Mycol. Ser. 23, 139 (2005). 61. Hanson, C. A., Fuhrman, J. A., Horner-Devine, M. C. & Martiny, J. B. H. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat. Rev. Microbiol. 10, 497–506 (2012). 62. Taddei, F. et al. Role of mutator alleles in adaptive evolution. Nature 387, 700–702 (1997). 63. Tenaillon, O., Toupance, B., Nagard, H. L., Taddei, F. & Godelle, B. Mutators, Population Size, Adaptive Landscape and the Adaptation of Asexual Populations of Bacteria. Genetics 152, 485–493 (1999). 64. Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304 (2000). 65. Högberg, M. N., Yarwood, S. A. & Myrold, D. D. Fungal but not bacterial soil communities recover after termination of decadal nitrogen additions to boreal forest. Soil Biol. Biochem. 72, 35–43 (2014). 66. Abarenkov, K. et al. The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytol. 186, 281–285 (2010). 212 67. Ramirez, K. S. et al. Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proc. R. Soc. Lond. B Biol. Sci. 281, 20141988 (2014). 68. Hargreaves, S. K., Roberto, A. A. & Hofmockel, K. S. Reaction- and sample-specific inhibition affect standardization of qPCR assays of soil bacterial communities. Soil Biol. Biochem. 59, 89–97 (2013). 69. Edgar, R. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010). 70. Wang, Q., Garrity, G., Tiedje, J. & Cole, J. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007). 71. DeSantis, T. et al. Greengenes, a chimera-checked 16s rRNS gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006). 72. Aronesty, E. ea-utils: ‘Command-line tools for processing biological sequencing data’. 73. McCune, B. & Mefford, M. PC-ORD. Multivariate Analysis of Ecological Data. (MjM Software, 2011). 74. R Core Team. A language and environment for statistical computing. (R Foundation for Statistical Computing, 2015). 75. lawstat: An R Package for Law, Public Policy and Biostatistics | Hui | Journal of Statistical Software. Available at: https://www.jstatsoft.org/article/view/v028i03. (Accessed: 6th July 2016) 213 76. Langille, M. G. I. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814–821 (2013). 77. Rasko, D. A. et al. The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates. J. Bacteriol. 190, 6881–6893 (2008). 78. Meyer, F. et al. The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics (2008). 79. Overbeek, R. et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42, D206–D214 (2014). 80. Lauber, C. L., Strickland, M. S., Bradford, M. A. & Fierer, N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem. 40, 2407–2415 (2008). 81. Uroz, S., Calvaruso, C., Turpault, M.-P. & Frey-Klett, P. Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol. 17, 378–387 (2009). 82. Philippot, L. et al. The ecological coherence of high bacterial taxonomic ranks. Nat. Rev. Microbiol. 8, 523–529 (2010). 83. Pouyat, R. V., Yesilonis, I. D., Russell-Anelli, J. & Neerchal, N. K. Soil Chemical and Physical Properties That Differentiate Urban Land-Use and Cover Types. Soil Sci. Soc. Am. J. 71, 1010 (2007). 84. Pouyat, R., Groffman, P., Yesilonis, I. & Hernandez, L. Soil carbon pools and fluxes in urban ecosystems. Environ. Pollut. 116, Supplement 1, S107–S118 (2002). 214 85. Mincer, T. J. et al. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ. Microbiol. 9, 1162–1175 (2007). 86. Rotthauwe, J. H., Witzel, K. P. & Liesack, W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63, 4704–4712 (1997). 87. Braithwaite, D. & Keegan, K. matR: Metagenomics Analysis Tools for R. (2008). 88. Brady, K. U., Kruckeberg, A. R. & Bradshaw, H. D. Evolutionary Ecology of Plant Adaptation to Serpentine Soils. Annu. Rev. Ecol. Evol. Syst. 36, 243–266 (2005). 89. Pagotto, C., Rémy, N., Legret, M. & Cloirec, P. L. Heavy Metal Pollution of Road Dust and Roadside Soil near a Major Rural Highway. Environ. Technol. 22, 307–319 (2001). 90. Galloway, J. N. & Cowling, E. B. Reactive Nitrogen and The World: 200 Years of Change. AMBIO J. Hum. Environ. 31, 64–71 (2002). 91. Martiny, A. C., Treseder, K. & Pusch, G. Phylogenetic conservatism of functional traits in microorganisms. ISME J. 7, 830–838 (2013). 92. van der Heijden, M. G., Bruin, S. de, Luckerhoff, L., van Logtestijn, R. S. & Schlaeppi, K. A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment. ISME J. 10, 389–399 (2016). 93. Averill, C. & Hawkes, C. V. Ectomycorrhizal fungi slow soil carbon cycling. Ecol. Lett. 19, 937–947 (2016). 215 94. Terrer, C., Vicca, S., Hungate, B. A., Phillips, R. P. & Prentice, I. C. Mycorrhizal association as a primary control of the CO2 fertilization effect. Science 353, 72–74 (2016). 95. Baker, L. A., Hope, D., Xu, Y., Edmonds, J. & Lauver, L. Nitrogen Balance for the Central Arizona–Phoenix (CAP) Ecosystem. Ecosystems 4, 582–602 96. Fenn, M. E. et al. Ecological Effects of Nitrogen Deposition in the Western United States. BioScience 53, 404–420 (2003).