Microbial functional diversity: From concepts to applications

Escalas, Arthur; Hale, Lauren; Voordeckers, James W.; Yang, Yunfeng; Firestone, Mary K.; Alvarez‐Cohen, Lisa; Zhou, Jizhong

doi:10.1002/ece3.5670

Title: Microbial functional diversity: From concepts to applications

Journal Article · 02 October 2019 · Ecology and Evolution

DOI: https://doi.org/10.1002/ece3.5670 · OSTI ID:1568935

^[1]; Hale, Lauren ^[2]; Voordeckers, James W. ^[2]; Yang, Yunfeng ^[3]; Firestone, Mary K. ^[4]; Alvarez‐Cohen, Lisa ^[4]; Zhou, Jizhong ^[5]

Univ. of Montpellier, Montpellier Cedex (France); Univ. of Oklahoma, Norman, OK (United States)
USDA‐ARS, Parlier, CA (United States)
Tsinghua Univ., Beijing (China)
Univ. of California, Berkeley, CA (United States)
Univ. of Oklahoma, Norman, OK (United States); Tsinghua Univ., Beijing (China); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; SC0004601; SC0010570; CBET‐1336709; P42ES004705; AC02‐05CH11231

OSTI ID:: 1568935

Alternate ID(s):: OSTI ID: 1568938; OSTI ID: 1580942

Journal Information:: Ecology and Evolution, Vol. 9, Issue 20; ISSN 2045-7758

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 101 works

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References (197)

Interactions in the microbiome: communities of organisms and communities of genes Boon, Eva; Meehan, Conor J.; Whidden, Chris FEMS Microbiology Reviews, Vol. 38, Issue 1 https://doi.org/10.1111/1574-6976.12035	journal	January 2014
Phytoplankton traits predict ecosystem function in a global set of lakes Zwart, Jacob A.; Solomon, Christopher T.; Jones, Stuart E. Ecology, Vol. 96, Issue 8 https://doi.org/10.1890/14-2102.1	journal	August 2015
Fundamentals of Microbial Community Resistance and Resilience Shade, Ashley; Peter, Hannes; Allison, Steven D. Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00417	journal	January 2012
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences Langille, Morgan G. I.; Zaneveld, Jesse; Caporaso, J. Gregory Nature Biotechnology, Vol. 31, Issue 9 https://doi.org/10.1038/nbt.2676	journal	August 2013
Defining Disturbance for Microbial Ecology Plante, Craig J. Microbial Ecology, Vol. 74, Issue 2 https://doi.org/10.1007/s00248-017-0956-4	journal	March 2017
Beyond the Venn diagram: the hunt for a core microbiome: The hunt for a core microbiome Shade, Ashley; Handelsman, Jo Environmental Microbiology, Vol. 14, Issue 1 https://doi.org/10.1111/j.1462-2920.2011.02585.x	journal	October 2011
How fundamental plant functional trait relationships scale-up to trade-offs and synergies in ecosystem services: Plant traits scale to ecosystem services trade-offs Lavorel, Sandra; Grigulis, Karl Journal of Ecology, Vol. 100, Issue 1 https://doi.org/10.1111/j.1365-2745.2011.01914.x	journal	December 2011
A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning Wallenstein, Matthew D.; Hall, Edward K. Biogeochemistry, Vol. 109, Issue 1-3 https://doi.org/10.1007/s10533-011-9641-8	journal	September 2011
Concluding Remarks Hutchinson, G. E. Cold Spring Harbor Symposia on Quantitative Biology, Vol. 22, Issue 0 https://doi.org/10.1101/SQB.1957.022.01.039	journal	January 1957
Cultivation of unculturable soil bacteria Pham, Van H. T.; Kim, Jaisoo Trends in Biotechnology, Vol. 30, Issue 9 https://doi.org/10.1016/j.tibtech.2012.05.007	journal	September 2012
Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China Huang, Qiuyuan; Briggs, Brandon R.; Dong, Hailiang PLoS ONE, Vol. 9, Issue 11 https://doi.org/10.1371/journal.pone.0111681	journal	November 2014
Responses of Methanogen mcrA Genes and Their Transcripts to an Alternate Dry/Wet Cycle of Paddy Field Soil Ma, Ke; Conrad, Ralf; Lu, Yahai Applied and Environmental Microbiology, Vol. 78, Issue 2 https://doi.org/10.1128/AEM.06934-11	journal	November 2011
Disentangling biodiversity effects on ecosystem functioning: deriving solutions to a seemingly insurmountable problem Naeem, Shahid; Wright, Justin P. Ecology Letters, Vol. 6, Issue 6 https://doi.org/10.1046/j.1461-0248.2003.00471.x	journal	June 2003
Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling Wu, Linwei; Yang, Yunfeng; Wang, Shiping The ISME Journal, Vol. 11, Issue 9 https://doi.org/10.1038/ismej.2017.75	journal	May 2017
Explaining microbial phenotypes on a genomic scale: GWAS for microbes Dutilh, B. E.; Backus, L.; Edwards, R. A. Briefings in Functional Genomics, Vol. 12, Issue 4 https://doi.org/10.1093/bfgp/elt008	journal	April 2013
Microbiomes in light of traits: A phylogenetic perspective Martiny, J. B. H.; Jones, S. E.; Lennon, J. T. Science, Vol. 350, Issue 6261 https://doi.org/10.1126/science.aac9323	journal	November 2015
Partitioning of functional and taxonomic diversity in surface-associated microbial communities: Partitioning of microbial diversity Roth-Schulze, Alexandra J.; Zozaya-Valdés, Enrique; Steinberg, Peter D. Environmental Microbiology, Vol. 18, Issue 12 https://doi.org/10.1111/1462-2920.13325	journal	May 2016
In Nature, There Is Only Diversity McLaren, Michael R.; Callahan, Benjamin J. mBio, Vol. 9, Issue 1 https://doi.org/10.1128/mBio.02149-17	journal	January 2018
Loss in microbial diversity affects nitrogen cycling in soil Philippot, Laurent; Spor, Aymé; Hénault, Catherine The ISME Journal, Vol. 7, Issue 8 https://doi.org/10.1038/ismej.2013.34	journal	March 2013
Re-evaluating prokaryotic species Gevers, Dirk; Cohan, Frederick M.; Lawrence, Jeffrey G. Nature Reviews Microbiology, Vol. 3, Issue 9 https://doi.org/10.1038/nrmicro1236	journal	August 2005
Belowground biodiversity and ecosystem functioning Bardgett, Richard D.; van der Putten, Wim H. Nature, Vol. 515, Issue 7528 https://doi.org/10.1038/nature13855	journal	November 2014
Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis Yachi, S.; Loreau, M. Proceedings of the National Academy of Sciences, Vol. 96, Issue 4 https://doi.org/10.1073/pnas.96.4.1463	journal	February 1999
Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils Eichorst, Stephanie A.; Strasser, Florian; Woyke, Tanja FEMS Microbiology Ecology, Vol. 91, Issue 10 https://doi.org/10.1093/femsec/fiv106	journal	August 2015
Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets Nagpal, Sunil; Haque, Mohammed Monzoorul; Mande, Sharmila S. PLOS ONE, Vol. 11, Issue 2 https://doi.org/10.1371/journal.pone.0148347	journal	February 2016
Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information Barberán, Albert; Caceres Velazquez, Hildamarie; Jones, Stuart mSphere, Vol. 2, Issue 4 https://doi.org/10.1128/mSphere.00237-17	journal	August 2017
Which is more important for classifying microbial communities: who’s there or what they can do? Xu, Zhenjiang; Malmer, Daniel; Langille, Morgan G. I. The ISME Journal, Vol. 8, Issue 12 https://doi.org/10.1038/ismej.2014.157	journal	August 2014
High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved Turaev, Dmitrij; Rattei, Thomas Current Opinion in Biotechnology, Vol. 39 https://doi.org/10.1016/j.copbio.2016.04.011	journal	June 2016
Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy Miki, Takeshi; Yokokawa, Taichi; Matsui, Kazuaki Proceedings of the Royal Society B: Biological Sciences, Vol. 281, Issue 1776 https://doi.org/10.1098/rspb.2013.2498	journal	February 2014
Molecular biology and regulation of methane monooxygenase Murrell, J. Colin; Gilbert, Bettina; McDonald, Ian R. Archives of Microbiology, Vol. 173, Issue 5-6 https://doi.org/10.1007/s002030000158	journal	April 2000
Microbial resource utilization traits and trade-offs: implications for community structure, functioning, and biogeochemical impacts at present and in the future Litchman, Elena; Edwards, Kyle F.; Klausmeier, Christopher A. Frontiers in Microbiology, Vol. 06 https://doi.org/10.3389/fmicb.2015.00254	journal	April 2015
Patterns and Processes of Microbial Community Assembly Nemergut, D. R.; Schmidt, S. K.; Fukami, T. Microbiology and Molecular Biology Reviews, Vol. 77, Issue 3 https://doi.org/10.1128/MMBR.00051-12	journal	September 2013
Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers Chao, Anne; Chiu, Chun-Huo; Jost, Lou Annual Review of Ecology, Evolution, and Systematics, Vol. 45, Issue 1 https://doi.org/10.1146/annurev-ecolsys-120213-091540	journal	November 2014
Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints Mouchet, Maud A.; Bouvier, Corinne; Bouvier, Thierry FEMS Microbiology Ecology, Vol. 79, Issue 3 https://doi.org/10.1111/j.1574-6941.2011.01241.x	journal	December 2011
Functional trait space and the latitudinal diversity gradient Lamanna, C.; Blonder, B.; Violle, C. Proceedings of the National Academy of Sciences, Vol. 111, Issue 38 https://doi.org/10.1073/pnas.1317722111	journal	September 2014
Functional diversity: back to basics and looking forward Petchey, Owen L.; Gaston, Kevin J. Ecology Letters, Vol. 9, Issue 6 https://doi.org/10.1111/j.1461-0248.2006.00924.x	journal	June 2006
Biodiversity Loss Threatens Human Well-Being Díaz, Sandra; Fargione, Joseph; Chapin, F. Stuart PLoS Biology, Vol. 4, Issue 8 https://doi.org/10.1371/journal.pbio.0040277	journal	August 2006
Probing the active fraction of soil microbiomes using BONCAT-FACS Couradeau, Estelle; Sasse, Joelle; Goudeau, Danielle Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10542-0	journal	June 2019
Effects of biodiversity on the functioning of trophic groups and ecosystems Cardinale, Bradley J.; Srivastava, Diane S.; Emmett Duffy, J. Nature, Vol. 443, Issue 7114 https://doi.org/10.1038/nature05202	journal	October 2006
Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules: Functional diversity measures Mouchet, Maud A.; Villéger, Sébastien; Mason, Norman W. H. Functional Ecology, Vol. 24, Issue 4 https://doi.org/10.1111/j.1365-2435.2010.01695.x	journal	March 2010
GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves Bai, Shijie; Li, Jiangwei; He, Zhili Applied Microbiology and Biotechnology, Vol. 97, Issue 15 https://doi.org/10.1007/s00253-012-4496-z	journal	November 2012
Biodiversity effects on ecosystem functioning: emerging issues and their experimental test in aquatic environments S. Giller, Paul; Hillebrand, Helmut; Berninger, Ulrike-G. Oikos, Vol. 104, Issue 3 https://doi.org/10.1111/j.0030-1299.2004.13253.x	journal	March 2004
Function and functional redundancy in microbial systems Louca, Stilianos; Polz, Martin F.; Mazel, Florent Nature Ecology & Evolution, Vol. 2, Issue 6 https://doi.org/10.1038/s41559-018-0519-1	journal	April 2018
A trait-based approach for modelling microbial litter decomposition Allison, S. D. Ecology Letters, Vol. 15, Issue 9 https://doi.org/10.1111/j.1461-0248.2012.01807.x	journal	May 2012
VAMPS: a website for visualization and analysis of microbial population structures Huse, Susan M.; Mark Welch, David B.; Voorhis, Andy BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2105-15-41	journal	February 2014
Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology Prosser, James I. Nature Reviews Microbiology, Vol. 13, Issue 7 https://doi.org/10.1038/nrmicro3468	journal	June 2015
Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes Iwai, Shoko; Weinmaier, Thomas; Schmidt, Brian L. PLOS ONE, Vol. 11, Issue 11 https://doi.org/10.1371/journal.pone.0166104	journal	November 2016
Application of metatranscriptomics to soil environments Carvalhais, Lilia C.; Dennis, Paul G.; Tyson, Gene W. Journal of Microbiological Methods, Vol. 91, Issue 2 https://doi.org/10.1016/j.mimet.2012.08.011	journal	November 2012
Linking microbial community structure and microbial processes: an empirical and conceptual overview Bier, Raven L.; Bernhardt, Emily S.; Boot, Claudia M. FEMS Microbiology Ecology, Vol. 91, Issue 10 https://doi.org/10.1093/femsec/fiv113	journal	September 2015
Binning metagenomic contigs by coverage and composition Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino Nature Methods, Vol. 11, Issue 11 https://doi.org/10.1038/nmeth.3103	journal	September 2014
Trait-based approaches for understanding microbial biodiversity and ecosystem functioning Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00251	journal	May 2014
Bacterial community assembly based on functional genes rather than species Burke, C.; Steinberg, P.; Rusch, D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 34 https://doi.org/10.1073/pnas.1101591108	journal	August 2011
Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes Polz, Martin F.; Hunt, Dana E.; Preheim, Sarah P. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1475 https://doi.org/10.1098/rstb.2006.1928	journal	October 2006
Emergent simplicity in microbial community assembly Goldford, Joshua E.; Lu, Nanxi; Bajić, Djordje Science, Vol. 361, Issue 6401 https://doi.org/10.1126/science.aat1168	journal	August 2018
Bacteria Are Smartphones and Mobile Genes Are Apps Young, J. Peter W. Trends in Microbiology, Vol. 24, Issue 12 https://doi.org/10.1016/j.tim.2016.09.002	journal	December 2016
GroopM: an automated tool for the recovery of population genomes from related metagenomes Imelfort, Michael; Parks, Donovan; Woodcroft, Ben J. PeerJ, Vol. 2 https://doi.org/10.7717/peerj.603	journal	January 2014
Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota Raguideau, Sébastien; Plancade, Sandra; Pons, Nicolas PLOS Computational Biology, Vol. 12, Issue 12 https://doi.org/10.1371/journal.pcbi.1005252	journal	December 2016
A functional evenness index for microbial ecology Troussellier, Marc; Legendre, Pierre Microbial Ecology, Vol. 7, Issue 4 https://doi.org/10.1007/BF02341423	journal	December 1981
Defining and measuring ecological specialization Devictor, Vincent; Clavel, Joanne; Julliard, Romain Journal of Applied Ecology, Vol. 47, Issue 1 https://doi.org/10.1111/j.1365-2664.2009.01744.x	journal	February 2010
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis Callahan, Benjamin J.; McMurdie, Paul J.; Holmes, Susan P. The ISME Journal, Vol. 11, Issue 12 https://doi.org/10.1038/ismej.2017.119	journal	July 2017
Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria Barberán, Albert; Ramirez, Kelly S.; Leff, Jonathan W. Ecology Letters, Vol. 17, Issue 7 https://doi.org/10.1111/ele.12282	journal	April 2014
Biodiversity as spatial insurance in heterogeneous landscapes Loreau, M.; Mouquet, N.; Gonzalez, A. Proceedings of the National Academy of Sciences, Vol. 100, Issue 22 https://doi.org/10.1073/pnas.2235465100	journal	October 2003
Reinforcing loose foundation stones in trait-based plant ecology Shipley, Bill; De Bello, Francesco; Cornelissen, J. Hans C. Oecologia, Vol. 180, Issue 4 https://doi.org/10.1007/s00442-016-3549-x	journal	January 2016
Microbial services: challenges for microbial ecologists in a changing world Ducklow, H. Aquatic Microbial Ecology, Vol. 53 https://doi.org/10.3354/ame01220	journal	September 2008
Not all traits are ‘functional’: insights from taxonomy and biodiversity-ecosystem functioning research Mlambo, Musa C. Biodiversity and Conservation, Vol. 23, Issue 3 https://doi.org/10.1007/s10531-014-0618-5	journal	January 2014
Bergey's Manual of Determinative Bacteriology S., F. A.; Buchanan, R. E. T.; Gibbons, N. E. Taxon, Vol. 24, Issue 2/3 https://doi.org/10.2307/1218353	journal	May 1975
Biodiversity in a complex world: consolidation and progress in functional biodiversity research: Consolidation and progress in BDEF research Hillebrand, Helmut; Matthiessen, Birte Ecology Letters, Vol. 12, Issue 12 https://doi.org/10.1111/j.1461-0248.2009.01388.x	journal	October 2009
Toward Understanding, Managing, and Protecting Microbial Ecosystems Bodelier, Paul L. E. Frontiers in Microbiology, Vol. 2 https://doi.org/10.3389/fmicb.2011.00080	journal	January 2011
What is microbial community ecology? Konopka, Allan The ISME Journal, Vol. 3, Issue 11 https://doi.org/10.1038/ismej.2009.88	journal	August 2009
Microdiversity shapes the traits, niche space, and biogeography of microbial taxa: The ecological function of microdiversity Larkin, Alyse A.; Martiny, Adam C. Environmental Microbiology Reports, Vol. 9, Issue 2 https://doi.org/10.1111/1758-2229.12523	journal	March 2017
Plant trait-based models identify direct and indirect effects of climate change on bundles of grassland ecosystem services Lamarque, P.; Lavorel, S.; Mouchet, M. Proceedings of the National Academy of Sciences, Vol. 111, Issue 38 https://doi.org/10.1073/pnas.1216051111	journal	September 2014
Benefits of plant diversity to ecosystems: immediate, filter and founder effects Grime, J. P. Journal of Ecology, Vol. 86, Issue 6 https://doi.org/10.1046/j.1365-2745.1998.00306.x	journal	December 1998
Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes Souza, Renata Carolini; Hungria, Mariangela; Cantão, Maurício Egídio Applied Soil Ecology, Vol. 86 https://doi.org/10.1016/j.apsoil.2014.10.010	journal	February 2015
GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater Bayer, Kristina; Moitinho-Silva, Lucas; Brümmer, Franz FEMS Microbiology Ecology, Vol. 90, Issue 3 https://doi.org/10.1111/1574-6941.12441	journal	November 2014
The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands Yue, Haowei; Wang, Mengmeng; Wang, Shiping The ISME Journal, Vol. 9, Issue 9 https://doi.org/10.1038/ismej.2015.19	journal	February 2015
Resistance, resilience, and redundancy in microbial communities Allison, S. D.; Martiny, J. B. H. Proceedings of the National Academy of Sciences, Vol. 105, Issue Supplement 1 https://doi.org/10.1073/pnas.0801925105	journal	August 2008
Measuring the biodiversity of microbial communities by flow cytometry Props, Ruben; Monsieurs, Pieter; Mysara, Mohamed Methods in Ecology and Evolution, Vol. 7, Issue 11 https://doi.org/10.1111/2041-210X.12607	journal	July 2016
The generation and maintenance of diversity in microbial communities Fierer, Noah; Lennon, Jay T. American Journal of Botany, Vol. 98, Issue 3 https://doi.org/10.3732/ajb.1000498	journal	March 2011
Let the concept of trait be functional! Violle, Cyrille; Navas, Marie-Laure; Vile, Denis Oikos, Vol. 116, Issue 5 https://doi.org/10.1111/j.0030-1299.2007.15559.x	journal	May 2007
Giving microbes their due - animal life in a microbially dominant world McFall-Ngai, M. J. Journal of Experimental Biology, Vol. 218, Issue 12 https://doi.org/10.1242/jeb.115121	journal	June 2015
Mapping the niche space of soil microorganisms using taxonomy and traits Lennon, Jay T.; Aanderud, Zachary T.; Lehmkuhl, B. K. Ecology, Vol. 93, Issue 8 https://doi.org/10.1890/11-1745.1	journal	August 2012
Topographic diversity of fungal and bacterial communities in human skin Findley, Keisha; Oh, Julia; Yang, Joy Nature, Vol. 498, Issue 7454 https://doi.org/10.1038/nature12171	journal	May 2013
Microbial Biogeography: From Taxonomy to Traits Green, J. L.; Bohannan, B. J. M.; Whitaker, R. J. Science, Vol. 320, Issue 5879 https://doi.org/10.1126/science.1153475	journal	May 2008
Theoretical microbial ecology without species Tikhonov, Mikhail Physical Review E, Vol. 96, Issue 3 https://doi.org/10.1103/PhysRevE.96.032410	journal	September 2017
Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities Carrara, Francesco; Giometto, Andrea; Seymour, Mathew Ecology, Vol. 96, Issue 5 https://doi.org/10.1890/14-1324.1	journal	May 2015
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1. Aßhauer, Kathrin P.; Wemheuer, Bernd; Daniel, Rolf Bioinformatics, Vol. 31, Issue 17 https://doi.org/10.1093/bioinformatics/btv287	journal	May 2015
Functional metagenomic profiling of nine biomes Dinsdale, Elizabeth A.; Edwards, Robert A.; Hall, Dana Nature, Vol. 452, Issue 7187 https://doi.org/10.1038/nature06810	journal	March 2008
Exploration of community traits as ecological markers in microbial metagenomes: METAGENOMIC COMMUNITY TRAITS BarberÁN, Albert; FernÁNdez-Guerra, Antoni; Bohannan, Brendan J. M. Molecular Ecology, Vol. 21, Issue 8 https://doi.org/10.1111/j.1365-294X.2011.05383.x	journal	November 2011
Decoupling function and taxonomy in the global ocean microbiome Louca, S.; Parfrey, L. W.; Doebeli, M. Science, Vol. 353, Issue 6305 https://doi.org/10.1126/science.aaf4507	journal	September 2016
A Common Toolbox to Understand, Monitor or Manage Rarity? A Response to Carmona et al. Violle, Cyrille; Thuiller, Wilfried; Mouquet, Nicolas Trends in Ecology & Evolution, Vol. 32, Issue 12 https://doi.org/10.1016/j.tree.2017.10.001	journal	December 2017
The Niche-Relationships of the California Thrasher Grinnell, Joseph The Auk, Vol. 34, Issue 4 https://doi.org/10.2307/4072271	journal	October 1917
Response diversity determines the resilience of ecosystems to environmental change: Response diversity and ecosystem resilience Mori, Akira S.; Furukawa, Takuya; Sasaki, Takehiro Biological Reviews, Vol. 88, Issue 2 https://doi.org/10.1111/brv.12004	journal	December 2012
Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis Schloss, Patrick D.; Westcott, Sarah L. Applied and Environmental Microbiology, Vol. 77, Issue 10 https://doi.org/10.1128/AEM.02810-10	journal	March 2011
Predicting microbial traits with phylogenies Goberna, Marta; Verdú, Miguel The ISME Journal, Vol. 10, Issue 4 https://doi.org/10.1038/ismej.2015.171	journal	September 2015
Traits Without Borders: Integrating Functional Diversity Across Scales Carmona, Carlos P.; de Bello, Francesco; Mason, Norman W. H. Trends in Ecology & Evolution, Vol. 31, Issue 5 https://doi.org/10.1016/j.tree.2016.02.003	journal	May 2016
Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities Fierer, Noah; BarberÃ¡n, Albert; Laughlin, Daniel C. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00614	journal	November 2014
Consequences of changing biodiversity Chapin III, F. Stuart; Zavaleta, Erika S.; Eviner, Valerie T. Nature, Vol. 405, Issue 6783 https://doi.org/10.1038/35012241	journal	May 2000
Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient Cheaib, Bachar; Le Boulch, Malo; Mercier, Pierre-Luc Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00869	journal	May 2018
The emergence and promise of functional biogeography Violle, C.; Reich, P. B.; Pacala, S. W. Proceedings of the National Academy of Sciences, Vol. 111, Issue 38 https://doi.org/10.1073/pnas.1415442111	journal	September 2014
Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties Powell, Jeff R.; Welsh, Allana; Hallin, Sara Ecology, Vol. 96, Issue 7 https://doi.org/10.1890/14-1127.1	journal	July 2015
Functional Structure of Biological Communities Predicts Ecosystem Multifunctionality Mouillot, David; Villéger, Sébastien; Scherer-Lorenzen, Michael PLoS ONE, Vol. 6, Issue 3 https://doi.org/10.1371/journal.pone.0017476	journal	March 2011
Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units Glassman, Sydney I.; Martiny, Jennifer B. H. mSphere, Vol. 3, Issue 4 https://doi.org/10.1128/mSphere.00148-18	journal	July 2018
Community niche predicts the functioning of denitrifying bacterial assemblages Salles, Joana F.; Poly, Franck; Schmid, Bernhard Ecology, Vol. 90, Issue 12 https://doi.org/10.1890/09-0188.1	journal	December 2009
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13219	journal	October 2016
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes Meyer, F.; Paarmann, D.; D'Souza, M. BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-386	journal	September 2008
Biodiversity and Ecosystem Functioning: Current Knowledge and Future Challenges Loreau, M. Science, Vol. 294, Issue 5543 https://doi.org/10.1126/science.1064088	journal	October 2001
A unified initiative to harness Earth's microbiomes Alivisatos, A. P.; Blaser, M. J.; Brodie, E. L. Science, Vol. 350, Issue 6260 https://doi.org/10.1126/science.aac8480	journal	October 2015
The microbiome beyond the horizon of ecological and evolutionary theory Koskella, Britt; Hall, Lindsay J.; Metcalf, C. Jessica E. Nature Ecology & Evolution, Vol. 1, Issue 11 https://doi.org/10.1038/s41559-017-0340-2	journal	October 2017
New Multidimensional Functional Diversity Indices for a Multifaceted Framework in Functional Ecology Villéger, Sébastien; Mason, Norman W. H.; Mouillot, David Ecology, Vol. 89, Issue 8 https://doi.org/10.1890/07-1206.1	journal	August 2008
Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease Mourkas, Evangelos; Florez‐Cuadrado, Diego; Pascoe, Ben Environmental Microbiology, Vol. 21, Issue 12 https://doi.org/10.1111/1462-2920.14760	journal	August 2019
Microbial genotype–phenotype mapping by class association rule mining Tamura, Makio; D'haeseleer, Patrik Bioinformatics, Vol. 24, Issue 13 https://doi.org/10.1093/bioinformatics/btn210	journal	May 2008
The Microbial Engines That Drive Earth's Biogeochemical Cycles Falkowski, P. G.; Fenchel, T.; Delong, E. F. Science, Vol. 320, Issue 5879 https://doi.org/10.1126/science.1153213	journal	May 2008
Sizing up metatranscriptomics Moran, Mary Ann; Satinsky, Brandon; Gifford, Scott M. The ISME Journal, Vol. 7, Issue 2 https://doi.org/10.1038/ismej.2012.94	journal	August 2012
Integrating microbial ecology into ecosystem models: challenges and priorities Treseder, Kathleen K.; Balser, Teri C.; Bradford, Mark A. Biogeochemistry, Vol. 109, Issue 1-3 https://doi.org/10.1007/s10533-011-9636-5	journal	September 2011
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies Schnoes, Alexandra M.; Brown, Shoshana D.; Dodevski, Igor PLoS Computational Biology, Vol. 5, Issue 12 https://doi.org/10.1371/journal.pcbi.1000605	journal	December 2009
Functional trait space and the latitudinal diversity gradient J., McGill, B.; B., Blonder,; K., Wiser, S. The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/6ywd-y194	text	January 2014
Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities Carrara, Francesco; Giometto, Andrea; Seymour, Mathew Ecological Society of America https://doi.org/10.5167/uzh-119075	text	January 2015
Community niche predicts the functioning of denitrifying bacterial assemblages Salles, J. F.; Poly, F.; Schmid, B. Ecological Society of America https://doi.org/10.5167/uzh-26837	text	January 2009
Functional diversity: back to basics and looking forward Petchey, Owen L.; Gaston, Kevin J. Wiley-Blackwell https://doi.org/10.5167/uzh-61815	text	January 2006
Bergey's Manual of Determinative Bacteriology Ravenel, Mazÿck P. American Journal of Public Health and the Nations Health, Vol. 24, Issue 7 https://doi.org/10.2105/ajph.24.7.770-b	journal	July 1934
Trait-based approaches for understanding microbial biodiversity and ecosystem functioning Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A. Frontiers Research Foundation https://doi.org/10.5167/uzh-107535	text	January 2014
Bergey's Manual of Determinative Bacteriology Young, C. C. American Journal of Public Health, Vol. 16, Issue 5 https://doi.org/10.2105/ajph.16.5.520	journal	May 1926
Data from: Microbial functional diversity: from concepts to applications Escalas, Arthur; Hale, Lauren; Voordeckers, James Dryad https://doi.org/10.5061/dryad.m3r1r2t	dataset	January 2019
Data from: Microbial functional diversity: from concepts to applications Escalas, Arthur; Hale, Lauren; Voordeckers, James Dryad https://doi.org/10.5061/dryad.m3r1r2t	dataset	January 2019
Defining Disturbance for Microbial Ecology Plante, Craig J. Microbial Ecology, Vol. 74, Issue 2 https://doi.org/10.1007/s00248-017-0956-4	journal	March 2017
Reinforcing loose foundation stones in trait-based plant ecology Shipley, Bill; De Bello, Francesco; Cornelissen, J. Hans C. Oecologia, Vol. 180, Issue 4 https://doi.org/10.1007/s00442-016-3549-x	journal	January 2016
Not all traits are ‘functional’: insights from taxonomy and biodiversity-ecosystem functioning research Mlambo, Musa C. Biodiversity and Conservation, Vol. 23, Issue 3 https://doi.org/10.1007/s10531-014-0618-5	journal	January 2014
Integrating microbial ecology into ecosystem models: challenges and priorities Treseder, Kathleen K.; Balser, Teri C.; Bradford, Mark A. Biogeochemistry, Vol. 109, Issue 1-3 https://doi.org/10.1007/s10533-011-9636-5	journal	September 2011
A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning Wallenstein, Matthew D.; Hall, Edward K. Biogeochemistry, Vol. 109, Issue 1-3 https://doi.org/10.1007/s10533-011-9641-8	journal	September 2011
Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes Souza, Renata Carolini; Hungria, Mariangela; Cantão, Maurício Egídio Applied Soil Ecology, Vol. 86 https://doi.org/10.1016/j.apsoil.2014.10.010	journal	February 2015
High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved Turaev, Dmitrij; Rattei, Thomas Current Opinion in Biotechnology, Vol. 39 https://doi.org/10.1016/j.copbio.2016.04.011	journal	June 2016
Application of metatranscriptomics to soil environments Carvalhais, Lilia C.; Dennis, Paul G.; Tyson, Gene W. Journal of Microbiological Methods, Vol. 91, Issue 2 https://doi.org/10.1016/j.mimet.2012.08.011	journal	November 2012
Cultivation of unculturable soil bacteria Pham, Van H. T.; Kim, Jaisoo Trends in Biotechnology, Vol. 30, Issue 9 https://doi.org/10.1016/j.tibtech.2012.05.007	journal	September 2012
Bacteria Are Smartphones and Mobile Genes Are Apps Young, J. Peter W. Trends in Microbiology, Vol. 24, Issue 12 https://doi.org/10.1016/j.tim.2016.09.002	journal	December 2016
Consequences of changing biodiversity Chapin III, F. Stuart; Zavaleta, Erika S.; Eviner, Valerie T. Nature, Vol. 405, Issue 6783 https://doi.org/10.1038/35012241	journal	May 2000
What is microbial community ecology? Konopka, Allan The ISME Journal, Vol. 3, Issue 11 https://doi.org/10.1038/ismej.2009.88	journal	August 2009
Which is more important for classifying microbial communities: who’s there or what they can do? Xu, Zhenjiang; Malmer, Daniel; Langille, Morgan G. I. The ISME Journal, Vol. 8, Issue 12 https://doi.org/10.1038/ismej.2014.157	journal	August 2014
Predicting microbial traits with phylogenies Goberna, Marta; Verdú, Miguel The ISME Journal, Vol. 10, Issue 4 https://doi.org/10.1038/ismej.2015.171	journal	September 2015
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis Callahan, Benjamin J.; McMurdie, Paul J.; Holmes, Susan P. The ISME Journal, Vol. 11, Issue 12 https://doi.org/10.1038/ismej.2017.119	journal	July 2017
Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling Wu, Linwei; Yang, Yunfeng; Wang, Shiping The ISME Journal, Vol. 11, Issue 9 https://doi.org/10.1038/ismej.2017.75	journal	May 2017
Effects of biodiversity on the functioning of trophic groups and ecosystems Cardinale, Bradley J.; Srivastava, Diane S.; Emmett Duffy, J. Nature, Vol. 443, Issue 7114 https://doi.org/10.1038/nature05202	journal	October 2006
Functional metagenomic profiling of nine biomes Dinsdale, Elizabeth A.; Edwards, Robert A.; Hall, Dana Nature, Vol. 452, Issue 7187 https://doi.org/10.1038/nature06810	journal	March 2008
Belowground biodiversity and ecosystem functioning Bardgett, Richard D.; van der Putten, Wim H. Nature, Vol. 515, Issue 7528 https://doi.org/10.1038/nature13855	journal	November 2014
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13219	journal	October 2016
Binning metagenomic contigs by coverage and composition Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino Nature Methods, Vol. 11, Issue 11 https://doi.org/10.1038/nmeth.3103	journal	September 2014
Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology Prosser, James I. Nature Reviews Microbiology, Vol. 13, Issue 7 https://doi.org/10.1038/nrmicro3468	journal	June 2015
Probing the active fraction of soil microbiomes using BONCAT-FACS Couradeau, Estelle; Sasse, Joelle; Goudeau, Danielle Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10542-0	journal	June 2019
The microbiome beyond the horizon of ecological and evolutionary theory Koskella, Britt; Hall, Lindsay J.; Metcalf, C. Jessica E. Nature Ecology & Evolution, Vol. 1, Issue 11 https://doi.org/10.1038/s41559-017-0340-2	journal	October 2017
Function and functional redundancy in microbial systems Louca, Stilianos; Polz, Martin F.; Mazel, Florent Nature Ecology & Evolution, Vol. 2, Issue 6 https://doi.org/10.1038/s41559-018-0519-1	journal	April 2018
Environmental factors shape the epiphytic bacterial communities of Gracilariopsis lemaneiformis Pei, Pengbing; Aslam, Muhammad; Du, Hong Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-87977-3	journal	April 2021
Disentangling biodiversity effects on ecosystem functioning: deriving solutions to a seemingly insurmountable problem Naeem, Shahid; Wright, Justin P. Ecology Letters, Vol. 6, Issue 6 https://doi.org/10.1046/j.1461-0248.2003.00471.x	journal	June 2003
Bacterial community assembly based on functional genes rather than species Burke, C.; Steinberg, P.; Rusch, D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 34 https://doi.org/10.1073/pnas.1101591108	journal	August 2011
Plant trait-based models identify direct and indirect effects of climate change on bundles of grassland ecosystem services Lamarque, P.; Lavorel, S.; Mouchet, M. Proceedings of the National Academy of Sciences, Vol. 111, Issue 38 https://doi.org/10.1073/pnas.1216051111	journal	September 2014
The emergence and promise of functional biogeography Violle, C.; Reich, P. B.; Pacala, S. W. Proceedings of the National Academy of Sciences, Vol. 111, Issue 38 https://doi.org/10.1073/pnas.1415442111	journal	September 2014
Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis Yachi, S.; Loreau, M. Proceedings of the National Academy of Sciences, Vol. 96, Issue 4 https://doi.org/10.1073/pnas.96.4.1463	journal	February 1999
Explaining microbial phenotypes on a genomic scale: GWAS for microbes Dutilh, B. E.; Backus, L.; Edwards, R. A. Briefings in Functional Genomics, Vol. 12, Issue 4 https://doi.org/10.1093/bfgp/elt008	journal	April 2013
Microbial genotype–phenotype mapping by class association rule mining Tamura, Makio; D'haeseleer, Patrik Bioinformatics, Vol. 24, Issue 13 https://doi.org/10.1093/bioinformatics/btn210	journal	May 2008
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1. Aßhauer, Kathrin P.; Wemheuer, Bernd; Daniel, Rolf Bioinformatics, Vol. 31, Issue 17 https://doi.org/10.1093/bioinformatics/btv287	journal	May 2015
Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy Miki, Takeshi; Yokokawa, Taichi; Matsui, Kazuaki Proceedings of the Royal Society B: Biological Sciences, Vol. 281, Issue 1776 https://doi.org/10.1098/rspb.2013.2498	journal	February 2014
Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes Polz, Martin F.; Hunt, Dana E.; Preheim, Sarah P. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1475 https://doi.org/10.1098/rstb.2006.1928	journal	October 2006
Partitioning of functional and taxonomic diversity in surface-associated microbial communities: Partitioning of microbial diversity Roth-Schulze, Alexandra J.; Zozaya-Valdés, Enrique; Steinberg, Peter D. Environmental Microbiology, Vol. 18, Issue 12 https://doi.org/10.1111/1462-2920.13325	journal	May 2016
In situabundance and carbon fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica Pjevac, Petra; Dyksma, Stefan; Goldhammer, Tobias Environmental Microbiology, Vol. 21, Issue 10 https://doi.org/10.1111/1462-2920.14739	journal	July 2019
Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease Mourkas, Evangelos; Florez‐Cuadrado, Diego; Pascoe, Ben Environmental Microbiology, Vol. 21, Issue 12 https://doi.org/10.1111/1462-2920.14760	journal	August 2019
GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater Bayer, Kristina; Moitinho-Silva, Lucas; Brümmer, Franz FEMS Microbiology Ecology, Vol. 90, Issue 3 https://doi.org/10.1111/1574-6941.12441	journal	November 2014
Interactions in the microbiome: communities of organisms and communities of genes Boon, Eva; Meehan, Conor J.; Whidden, Chris FEMS Microbiology Reviews, Vol. 38, Issue 1 https://doi.org/10.1111/1574-6976.12035	journal	January 2014
Microdiversity shapes the traits, niche space, and biogeography of microbial taxa: The ecological function of microdiversity Larkin, Alyse A.; Martiny, Adam C. Environmental Microbiology Reports, Vol. 9, Issue 2 https://doi.org/10.1111/1758-2229.12523	journal	March 2017
Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria Barberán, Albert; Ramirez, Kelly S.; Leff, Jonathan W. Ecology Letters, Vol. 17, Issue 7 https://doi.org/10.1111/ele.12282	journal	April 2014
Defining and measuring ecological specialization Devictor, Vincent; Clavel, Joanne; Julliard, Romain Journal of Applied Ecology, Vol. 47, Issue 1 https://doi.org/10.1111/j.1365-2664.2009.01744.x	journal	February 2010
Functional diversity: back to basics and looking forward Petchey, Owen L.; Gaston, Kevin J. Ecology Letters, Vol. 9, Issue 6 https://doi.org/10.1111/j.1461-0248.2006.00924.x	journal	June 2006
A trait-based approach for modelling microbial litter decomposition Allison, S. D. Ecology Letters, Vol. 15, Issue 9 https://doi.org/10.1111/j.1461-0248.2012.01807.x	journal	May 2012
Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints Mouchet, Maud A.; Bouvier, Corinne; Bouvier, Thierry FEMS Microbiology Ecology, Vol. 79, Issue 3 https://doi.org/10.1111/j.1574-6941.2011.01241.x	journal	December 2011
The Microbial Engines That Drive Earth's Biogeochemical Cycles Falkowski, P. G.; Fenchel, T.; Delong, E. F. Science, Vol. 320, Issue 5879 https://doi.org/10.1126/science.1153213	journal	May 2008
A unified initiative to harness Earth's microbiomes Alivisatos, A. P.; Blaser, M. J.; Brodie, E. L. Science, Vol. 350, Issue 6260 https://doi.org/10.1126/science.aac8480	journal	October 2015
Microbiomes in light of traits: A phylogenetic perspective Martiny, J. B. H.; Jones, S. E.; Lennon, J. T. Science, Vol. 350, Issue 6261 https://doi.org/10.1126/science.aac9323	journal	November 2015
Decoupling function and taxonomy in the global ocean microbiome Louca, S.; Parfrey, L. W.; Doebeli, M. Science, Vol. 353, Issue 6305 https://doi.org/10.1126/science.aaf4507	journal	September 2016
Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers Chao, Anne; Chiu, Chun-Huo; Jost, Lou Annual Review of Ecology, Evolution, and Systematics, Vol. 45, Issue 1 https://doi.org/10.1146/annurev-ecolsys-120213-091540	journal	November 2014
VAMPS: a website for visualization and analysis of microbial population structures Huse, Susan M.; Mark Welch, David B.; Voorhis, Andy BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2105-15-41	journal	February 2014
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes Meyer, F.; Paarmann, D.; D'Souza, M. BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-386	journal	September 2008
Biodiversity Loss Threatens Human Well-Being Díaz, Sandra; Fargione, Joseph; Chapin, F. Stuart PLoS Biology, Vol. 4, Issue 8 https://doi.org/10.1371/journal.pbio.0040277	journal	August 2006
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies Schnoes, Alexandra M.; Brown, Shoshana D.; Dodevski, Igor PLoS Computational Biology, Vol. 5, Issue 12 https://doi.org/10.1371/journal.pcbi.1000605	journal	December 2009
Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota Raguideau, Sébastien; Plancade, Sandra; Pons, Nicolas PLOS Computational Biology, Vol. 12, Issue 12 https://doi.org/10.1371/journal.pcbi.1005252	journal	December 2016
Functional Structure of Biological Communities Predicts Ecosystem Multifunctionality Mouillot, David; Villéger, Sébastien; Scherer-Lorenzen, Michael PLoS ONE, Vol. 6, Issue 3 https://doi.org/10.1371/journal.pone.0017476	journal	March 2011
Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets Nagpal, Sunil; Haque, Mohammed Monzoorul; Mande, Sharmila S. PLOS ONE, Vol. 11, Issue 2 https://doi.org/10.1371/journal.pone.0148347	journal	February 2016
Functional trait space and the latitudinal diversity gradient J., McGill, B.; B., Blonder,; K., Wiser, S. The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/6ywd-y194	text	January 2014
Community niche predicts the functioning of denitrifying bacterial assemblages Salles, Joana F.; Poly, Franck; Schmid, Bernhard Ecology, Vol. 90, Issue 12 https://doi.org/10.1890/09-0188.1	journal	December 2009
Mapping the niche space of soil microorganisms using taxonomy and traits Lennon, Jay T.; Aanderud, Zachary T.; Lehmkuhl, B. K. Ecology, Vol. 93, Issue 8 https://doi.org/10.1890/11-1745.1	journal	August 2012
Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities Carrara, Francesco; Giometto, Andrea; Seymour, Mathew Ecology, Vol. 96, Issue 5 https://doi.org/10.1890/14-1324.1	journal	May 2015
Phytoplankton traits predict ecosystem function in a global set of lakes Zwart, Jacob A.; Solomon, Christopher T.; Jones, Stuart E. Ecology, Vol. 96, Issue 8 https://doi.org/10.1890/14-2102.1	journal	August 2015
Bergey's Manual of Determinative Bacteriology S., F. A.; Buchanan, R. E. T.; Gibbons, N. E. Taxon, Vol. 24, Issue 2/3 https://doi.org/10.2307/1218353	journal	May 1975
The Niche-Relationships of the California Thrasher Grinnell, Joseph The Auk, Vol. 34, Issue 4 https://doi.org/10.2307/4072271	journal	October 1917
Microbial services: challenges for microbial ecologists in a changing world Ducklow, H. Aquatic Microbial Ecology, Vol. 53 https://doi.org/10.3354/ame01220	journal	September 2008
Toward Understanding, Managing, and Protecting Microbial Ecosystems Bodelier, Paul L. E. Frontiers in Microbiology, Vol. 2 https://doi.org/10.3389/fmicb.2011.00080	journal	January 2011
Fundamentals of Microbial Community Resistance and Resilience Shade, Ashley; Peter, Hannes; Allison, Steven D. Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00417	journal	January 2012
Trait-based approaches for understanding microbial biodiversity and ecosystem functioning Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00251	journal	May 2014
Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities Fierer, Noah; BarberÃ¡n, Albert; Laughlin, Daniel C. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00614	journal	November 2014
Microbial resource utilization traits and trade-offs: implications for community structure, functioning, and biogeochemical impacts at present and in the future Litchman, Elena; Edwards, Kyle F.; Klausmeier, Christopher A. Frontiers in Microbiology, Vol. 06 https://doi.org/10.3389/fmicb.2015.00254	journal	April 2015
Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient Cheaib, Bachar; Le Boulch, Malo; Mercier, Pierre-Luc Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00869	journal	May 2018
The generation and maintenance of diversity in microbial communities Fierer, Noah; Lennon, Jay T. American Journal of Botany, Vol. 98, Issue 3 https://doi.org/10.3732/ajb.1000498	journal	March 2011

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