A communal catalogue reveals Earth’s multiscale microbial diversity
Luke Thompson(National Oceanic and Atmospheric Administration), Jon G. Sanders(University of California San Diego), Daniel McDonald(University of California San Diego), Amnon Amir(University of California San Diego), Joshua Ladau(Gladstone Institutes), Kenneth J. Locey(Indiana University Bloomington), Robert J. Prill(IBM Research - Almaden), Anupriya Tripathi(University of California San Diego), Sean M. Gibbons(Broad Institute), Gail Ackermann(University of California San Diego), José A. Navas-Molina(University of California San Diego), Stefan Janssen(University of California San Diego), Evguenia Kopylova(University of California San Diego), Yoshiki Vázquez‐Baeza(University of California San Diego), Antonio González(University of California San Diego), James T. Morton(University of California San Diego), Siavash Mirarab(University of California San Diego), Zhenjiang Zech Xu(University of California San Diego), Lingjing Jiang(University of California San Diego), Mohamed Fauzi Haroon(Harvard University), Jad Kanbar(University of California San Diego), Qiyun Zhu(University of California San Diego), Se Jin Song(University of California San Diego), Tomasz Kościółek(University of California San Diego), Nicholas A. Bokulich(Northern Arizona University), Joshua Lefler(University of California San Diego), Colin Brislawn(Pacific Northwest National Laboratory), Gregory Humphrey(University of California San Diego), Sarah M. Owens(Argonne National Laboratory), Jarrad Hampton‐Marcell(Argonne National Laboratory), Donna Berg-Lyons(University of Colorado Boulder), Valerie J. McKenzie(University of Colorado Boulder), Noah Fierer(Cooperative Institute for Research in Environmental Sciences), Jed A. Fuhrman(University of Southern California), Aaron Clauset(University of Colorado Boulder), Rick Stevens(Argonne National Laboratory), Ashley Shade(Michigan State University), Katherine S. Pollard(Gladstone Institutes), Kelly D. Goodwin(National Oceanic and Atmospheric Administration), Janet Jansson(Pacific Northwest National Laboratory), Jack A. Gilbert(Argonne National Laboratory), Rob Knight(University of California San Diego), Jose L. Agosto Rivera(University of Puerto Rico System), Lisa Al-Moosawi(Plymouth Marine Laboratory), John C. Alverdy(University of Chicago), Katherine R. Amato(Northwestern University), Jason Andras(Mount Holyoke College), Largus T. Angenent(Cornell University), Dionysios A. Antonopoulos(Argonne National Laboratory), Amy Apprill(Woods Hole Oceanographic Institution), David Armitage(University of Notre Dame), Kate A. Ballantine(Mount Holyoke College), Jiří Bárta(University of South Bohemia in České Budějovice), Julia K. Baum(University of Victoria), Allison Berry(University of California, Davis), Ashish Bhatnagar(Maharshi Dayanand Saraswati University), Monica Bhatnagar(Maharshi Dayanand Saraswati University), Jennifer F. Biddle(University of Delaware), Lucie Bittner(Sorbonne Université), Bazartseren Boldgiv(National University of Mongolia), Eric Bottos(Pacific Northwest National Laboratory), Donal M. Boyer(Wildlife Conservation Society), Josephine Braun(San Diego Zoo Institute for Conservation Research), William J. Brazelton(University of Utah), Francis Q. Brearley(Manchester Metropolitan University), Alexandra H. Campbell(UNSW Sydney), J. Gregory Caporaso(Northern Arizona University), César Cardona(University of Chicago), JoLynn Carroll(UiT The Arctic University of Norway), S. Craig Cary(University of Waikato), Brenda B. Casper(University of Pennsylvania), Trevor C. Charles(University of Waterloo), Haiyan Chu(Chinese Academy of Sciences), Danielle C. Claar(University of Victoria), Robert G. Clark(Environment and Climate Change Canada), Jonathan B. Clayton(University of Minnesota), José C. Clemente(Icahn School of Medicine at Mount Sinai), Alyssa T. Cochran(Colorado State University), Maureen L. Coleman(University of Chicago), Gavin Collins(Ollscoil na Gaillimhe – University of Galway), Rita R. Colwell(University of Maryland, College Park), Mónica Contreras(Instituto Venezolano de Investigaciones Científicas), Benjamin B. Crary(University of Wisconsin–Madison), Simon Creer(Bangor University), Daniel A. Cristol(William & Mary), Byron C. Crump(Oregon State University), Duoying Cui, Sarah E. Daly(Purdue University West Lafayette), Liliana M. Dávalos(Stony Brook University), Russell D. Dawson(University of Northern British Columbia), Jennifer R. DeFazio(University of Chicago), Frédéric Delsuc(Centre National de la Recherche Scientifique), Hebe M. Dionisi(Centro Científico Tecnológico Patagónico), Maria Gloria Domínguez-Bello(New York University), Robin D. Dowell(University of Colorado Boulder), Eric A. Dubinsky(Lawrence Berkeley National Laboratory), Peter O. Dunn(University of Wisconsin–Milwaukee), Danilo Ercolini(University of Naples Federico II), Robert E. Espinoza(California State University, Northridge), Vanessa O. Ezenwa(University of Georgia), Nathalie Fenner(Bangor University), Helen S. Findlay(Plymouth Marine Laboratory), Irma D Fleming(Vanderbilt University), Vincenzo Fogliano(University of Naples Federico II), Anna Forsman(University of Central Florida), Chris Freeman(Bangor University), Elliot S. Friedman(Cornell University), Giancarlo Galindo(Lawrence Berkeley National Laboratory), Liza Garcia(University of Puerto Rico System), María Alexandra García-Amado(Instituto Venezolano de Investigaciones Científicas), David L. Garshelis(Minnesota Department of Natural Resources), Robin B. Gasser(The University of Melbourne), Gunnar Gerdts(Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung), Molly K. Gibson(Washington University in St. Louis), Isaac Gifford(University of California, Davis), Ryan T. Gill(University of Colorado Boulder), Tuğrul Giray(University of Puerto Rico System), Antje Gittel(Aarhus University), Peter N. Golyshin(Bangor University), Donglai Gong, Hans‐Peter Grossart(University of Potsdam), Kristina Guyton(University of Chicago), Sarah–Jane Haig(University of Michigan), Vanessa L. Hale(The Ohio State University), Ross S. Hall(The University of Melbourne), Steven Hallam(University of British Columbia), Kim M. Handley(University of Auckland), Nur A. Hasan(University of Maryland, College Park), Shane R. Haydon(Melbourne Water), Jonathan E. Hickman(Columbia University), Glida Hidalgo, Kirsten Hofmockel(Pacific Northwest National Laboratory), Jeff Hooker(Chief Dull Knife College), Stefan Hulth(University of Gothenburg), Jenni Hultman(University of Helsinki), Embriette R. Hyde(University of California San Diego), Juan Diego Ibáñez‐Álamo(University of Groningen), Julie Jastrow(Argonne National Laboratory), Aaron R. Jex(The University of Melbourne), L. Scott Johnson(Towson University), Eric R. Johnston(Georgia Institute of Technology), Stephen Joseph(UNSW Sydney), Stephanie D. Jurburg(Wageningen University & Research), Diogo Jurelevicius(Universidade Federal do Rio de Janeiro), Anders Karlsson, Roger Karlsson, Seth N. Kauppinen(University of California, Berkeley), Colleen T. E. Kellogg(University of British Columbia), Suzanne Kennedy, Lee J. Kerkhof(Rutgers, The State University of New Jersey), Gary M. King(Louisiana State University), George W. Kling(University of Michigan), Anson V. Koehler(The University of Melbourne), Monika A. Krezalek(University of Chicago), Jordan G. Kueneman(Smithsonian Tropical Research Institute), Regina Lamendella(Juniata College), Emily Landon(University of Chicago), K. E. Lane-deGraaf(Fontbonne University), Julie LaRoche(Dalhousie University), Peter A. Larsen(Argonne National Laboratory), Bonnie Laverock(University of Technology Sydney), Simon Lax(University of Chicago), Miguel Lentino(Colección Ornitológica Phelps), Iris I. Levin(University of Colorado Boulder), Pierre Liancourt(Institute of Botany of the Slovak Academy of Sciences), Wenju Liang(Chinese Academy of Sciences), Alexandra M. Linz(University of Wisconsin–Madison), David A. Lipson(San Diego State University), Yongqin Liu(Chinese Academy of Sciences), Manuel E. Lladser(University of Colorado Boulder), Mariana Lozada(Centro Científico Tecnológico Patagónico), Catherine M. Spirito(Cornell University), Walter P. Mac Cormack(Universidad de Buenos Aires), Aurora MacRae-Crerar(University of Pennsylvania), Magda Magris, Antonio M. Martín‐Platero(Universidad de Granada), Manuel Martín‐Vivaldi(Universidad de Granada), L. Margarita Martínez(Colección Ornitológica Phelps), Manuel Martínez‐Bueno(Universidad de Granada), Ezequiel M. Marzinelli(UNSW Sydney), Olivia U. Mason(Florida State University), Gregory D. Mayer(Texas Tech University), Jamie M. McDevitt‐Irwin(University of Victoria), James E. McDonald(Bangor University), Krista L. McGuire(University of Oregon), Katherine D. McMahon(University of Wisconsin–Madison), Ryan McMinds(Oregon State University), Mónica Medina(Pennsylvania State University), Joseph R. Mendelson(Georgia Institute of Technology), Jessica L. Metcalf(Colorado State University), Folker Meyer(Argonne National Laboratory), Fabián A. Michelangeli(Instituto Venezolano de Investigaciones Científicas), Kimberley E. Miller(Ohio University), David A. Mills(University of California, Davis), Jeremiah J. Minich(University of California San Diego), Stéfano Mocali(Centro Agricoltura Ambiente (Italy)), Lucas Moitinho‐Silva(UNSW Sydney), A. W. Moore(Morningside College), Rachael M. Morgan‐Kiss(Miami University), Paul Munroe(UNSW Sydney), David D. Myrold(Oregon State University), Josh D. Neufeld(University of Waterloo), Yingying Ni(Chinese Academy of Sciences), Graeme W. Nicol(Université Claude Bernard Lyon 1), Shaun Nielsen(UNSW Sydney), Jozef I. Nissimov(Rutgers, The State University of New Jersey), Kefeng Niu(Fanjingshan National Nature Reserve), Matthew J. Nolan(The University of Melbourne), Karen V. Noyce(Minnesota Department of Natural Resources), S. L. O'Brien(Argonne National Laboratory), Noriko Okamoto(University of British Columbia), Ludovic Orlando(Université Toulouse III - Paul Sabatier), Yadira Ortiz Castellano(University of Puerto Rico System), Olayinka Osuolale(Elizade University), Wyatt Oswald(Emerson College), Jacob Parnell(Novozymes (United States)), Juan Manuel Peralta‐Sánchez(Universidad de Granada), Peter S. Petraitis(University of Pennsylvania), Catherine A. Pfister(University of Chicago), Elizabeth A. H. Pilon‐Smits(Colorado State University), Paola Piombino(University of Naples Federico II), Stephen B. Pointing(Auckland University of Technology), F. Joseph Pollock(Pennsylvania State University), Caitlin Potter(Bangor University), Bharath Prithiviraj(City University of New York), Christopher Quince(University of Warwick), Asha Rani(University of Illinois Chicago), Ravi Ranjan(University of Illinois Chicago), Subramanya Rao(Hong Kong Polytechnic University), Andrew P. Rees(Plymouth Marine Laboratory), Miles Richardson(University of Chicago), Ulf Riebesell(GEOMAR Helmholtz Centre for Ocean Research Kiel), Carol Robinson(University of East Anglia), Karl J. Rockne(University of Illinois Chicago), Selena Marie Rodriguezl, Forest Rohwer(San Diego State University), Wayne Roundstone, Rebecca J. Safran(University of Colorado Boulder), Naseer Sangwan(University of Chicago), Virginia Sanz(Instituto Venezolano de Investigaciones Científicas), Matthew O. Schrenk(Michigan State University), Mark D. Schrenzel(Valley Hospital), Nicole M. Scott(Biota Pharmaceuticals (United States)), Rita L. Seger(University of Maine), Andaine Seguin‐Orlando(University of Copenhagen), Lucy Seldin(Universidade Federal do Rio de Janeiro), Lauren Seyler(Michigan State University), Baddr A. Shakhsheer(Washington University in St. Louis), Gabriela M. Sheets(Emory University), Congcong Shen(Chinese Academy of Sciences), Yu Shi(Chinese Academy of Sciences), Hakdong Shin(Sejong University), Benjamin D. Shogan(University of Chicago), Dave Shutler(Acadia University), Jeffrey A. Siegel(University of Toronto), Steve Simmons, Sara Sjöling(Södertörn University), Daniel P. Smith(Baylor College of Medicine), Juan José Soler(Estacion Experimental de Zonas Aridas), Martin Sperling(GEOMAR Helmholtz Centre for Ocean Research Kiel), Peter D. Steinberg(UNSW Sydney), Brent Stephens(Illinois Institute of Technology), Melita Stevens(Melbourne Water), Safiyh Taghavi, Vera Tai(Western University), Karen Tait(Plymouth Marine Laboratory), Chia L. Tan, Neslihan Taş(Lawrence Berkeley National Laboratory), D. Lee Taylor(University of New Mexico), Torsten Thomas(UNSW Sydney), Ina Timling(University of Alaska Fairbanks), Benjamin L. Turner(Smithsonian Tropical Research Institute), Tim Urich(University of Vienna), Luke K. Ursell(Biota Pharmaceuticals (United States)), Daniël van der Lelie, William Van Treuren(University of Colorado Boulder), Lukas Van Zwieten(UNSW Sydney), Daniela Vargas-Robles(University of Puerto Rico System), Rebecca Vega Thurber(Oregon State University), Paola Vitaglione(University of Naples Federico II), Donald A. Walker(University of Alaska Fairbanks), William A. Walters(Max Planck Institute for Developmental Biology), Shi Wang(Lawrence Berkeley National Laboratory), Tao Wang(The University of Melbourne), Tom Weaver(University of Colorado Boulder), Nicole S. Webster(Australian Institute of Marine Science), Beck A. Wehrle(University of California, Irvine), Pamela Weisenhorn(Argonne National Laboratory), Sophie Weiss(University of Colorado Boulder), Jeffrey J. Werner(Cornell University), Kristin West(Research Triangle Park Foundation), Andrew Whitehead(University of California, Davis), Susan R. Whitehead(Virginia Tech), Linda A. Whittingham(University of Wisconsin–Milwaukee), Eske Willerslev(University of Copenhagen), Allison E. Williams(University of Georgia), Stephen A. Wood(Yale University), Douglas C. Woodhams(University of Massachusetts Boston), Yeqin Yang(Tongren University), Jesse Zaneveld(University of Washington Bothell), Iratxe Zarraonaindia(University of the Basque Country), Qikun Zhang(Institute of Microbiology), Hongxia Zhao(Institute of Microbiology)
Cited by 2,877Open Access
Abstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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