Global biogeography of highly diverse protistan communities in soil
Scott T. Bates,Jose C. Clemente,Gilberto E. Flores,William A. Walters,Laura Wegener Parfrey,Rob Knight,Rob Knight,Noah Fierer,Noah Fierer +8 more
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TLDR
Soil protistan communities were highly diverse, approaching the extreme diversity of their bacterial counterparts across the same sites, and like bacterial taxa, protistan taxa were not globally distributed, and the composition of these communities diverged considerably across large geographic distances.Abstract:
Protists are ubiquitous members of soil microbial communities, but the structure of these communities, and the factors that influence their diversity, are poorly understood. We used barcoded pyrosequencing to survey comprehensively the diversity of soil protists from 40 sites across a broad geographic range that represent a variety of biome types, from tropical forests to deserts. In addition to taxa known to be dominant in soil, including Cercozoa and Ciliophora, we found high relative abundances of groups such as Apicomplexa and Dinophyceae that have not previously been recognized as being important components of soil microbial communities. Soil protistan communities were highly diverse, approaching the extreme diversity of their bacterial counterparts across the same sites. Like bacterial taxa, protistan taxa were not globally distributed, and the composition of these communities diverged considerably across large geographic distances. However, soil protistan and bacterial communities exhibit very different global-scale biogeographical patterns, with protistan communities strongly structured by climatic conditions that regulate annual soil moisture availability.read more
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Global diversity and geography of soil fungi
Leho Tedersoo,Mohammad Bahram,Sergei Põlme,Urmas Kõljalg,Nourou S. Yorou,Ravi L. C. Wijesundera,Luis Villarreal Ruiz,Aída M. Vasco-Palacios,Pham Q uang Thu,Ave Suija,Matthew E. Smith,Cathy Sharp,Erki Saluveer,Alessandro Saitta,Miguel Rosas,Taavi Riit,David A. Ratkowsky,Karin Pritsch,Kadri Põldmaa,Meike Piepenbring,Cherdchai Phosri,Marko Peterson,Kaarin Parts,Kadri Pärtel,Eveli Otsing,Eduardo Nouhra,André Ledoux Njouonkou,R. Henrik Nilsson,Luis N. Morgado,Jordan R. Mayor,Tom W. May,Luiza Majuakim,D. Jean Lodge,Su S ee Lee,Karl-Henrik Larsson,Petr Kohout,Kentaro Hosaka,Indrek Hiiesalu,Terry W. Henkel,Helery Harend,Liang-Dong Guo,Alina Greslebin,Gwen Grelet,József Geml,Genevieve Gates,W. Dunstan,Chris W. Dunk,Rein Drenkhan,John Dearnaley,André De Kesel,Tan Dang,Xin Chen,Franz Buegger,Francis Q. Brearley,Gregory Bonito,Sten Anslan,Sandra E. Abell,Kessy Abarenkov +57 more
TL;DR: Diversity of most fungal groups peaked in tropical ecosystems, but ectomycorrhizal fungi and several fungal classes were most diverse in temperate or boreal ecosystems, and manyfungal groups exhibited distinct preferences for specific edaphic conditions (such as pH, calcium, or phosphorus).
Journal ArticleDOI
FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild
Nhu H. Nguyen,Zewei Song,Scott T. Bates,Sara Branco,Leho Tedersoo,Jon Menke,Jonathan S. Schilling,Peter G. Kennedy +7 more
TL;DR: Fungi typically live in highly diverse communities composed of multiple ecological guilds, and FUNGuild is a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline.
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Belowground biodiversity and ecosystem functioning
TL;DR: Recent progress in understanding belowground biodiversity and its role in determining the ecological and evolutionary responses of terrestrial ecosystems to current and future environmental change are reviewed.
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The global soil community and its influence on biogeochemistry
Thomas W. Crowther,J. van den Hoogen,Joe Wan,Melanie A. Mayes,Melanie A. Mayes,Ashley D. Keiser,Ashley D. Keiser,Lidong Mo,Colin Averill,Colin Averill,Daniel S. Maynard +10 more
TL;DR: The state of science relating soil organisms to biogeochemical processes is reviewed, focusing particularly on the importance of microbial community variation on decomposition and turnover of soil organic matter.
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Soil biodiversity and human health.
TL;DR: Current research indicates that soil biodiversity can be maintained and partially restored if managed sustainably, and promotes the ecological complexity and robustness of soil biodiversity through improved management practices.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
UCHIME improves sensitivity and speed of chimera detection
TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
Journal ArticleDOI
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
J. Gregory Caporaso,Christian L. Lauber,William A. Walters,Donna Berg-Lyons,Catherine A. Lozupone,Peter J. Turnbaugh,Noah Fierer,Rob Knight +7 more
TL;DR: This work sequences a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample to demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature.
Journal ArticleDOI
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Catherine A. Lozupone,Rob Knight +1 more
TL;DR: The results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.
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