Journal ArticleDOI
Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.
Noah Fierer,Noah Fierer,Joshua Ladau,Jose C. Clemente,Jonathan W. Leff,Jonathan W. Leff,Sarah M. Owens,Sarah M. Owens,Katherine S. Pollard,Rob Knight,Rob Knight,Jack A. Gilbert,Jack A. Gilbert,Rebecca L. McCulley +13 more
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TLDR
The soil microbial diversity that once existed in this biome was reconstructed by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairies.Abstract:
Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Shotgun metagenomic data suggested that these spatial patterns were associated with strong shifts in carbon dynamics. We show that metagenomic approaches can be used to reconstruct below-ground biogeochemical and diversity gradients in endangered ecosystems; such information could be used to improve restoration efforts, given that even small changes in below-ground microbial diversity can have important impacts on ecosystem processes.read more
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Restoration age and re-introduced bison may shape soil bacterial communities in restored tallgrass prairies.
TL;DR: The authors studied soil bacterial communities in a restored tallgrass prairie chronosequence over six years to document how diversity and composition changed with age, management through fire and grazing by re-introduced bison, and in comparison to pre-restoration agricultural fields and remnant prairies.
Journal ArticleDOI
Contrasting effect of irrigation practices on the cotton rhizosphere microbiota and soil functionality in fields
TL;DR: In this paper , the authors investigated how changes in rhizosphere bacterial diversity alter soil nutrient cycling and found that drip irrigation under plastic film mulch significantly decreased the richness of the core module and reduced the functional potential of soil.
Journal ArticleDOI
Soil pqqC-harboring bacterial community response to increasing aridity in semi-arid grassland ecosystems: Diversity, co-occurrence network, and assembly process
TL;DR: Zhang et al. as discussed by the authors investigated the response patterns of the diversity, co-occurrence networks, and assembly mechanisms of the soil pqqC communities along a natural aridity gradient in adjacent pairs of natural and disturbed grasslands in Inner Mongolia, China.
Strain-resolved metagenomic analysis of the premature infant microbiome and other natural microbial communities
TL;DR: Banfield et al. as discussed by the authors developed a custom genome-resolved metagenomic method to determine the structure of microbial communities, monitor the activities of bacteria in situ, and track their evolution.
Journal ArticleDOI
Biogenic factors explain soil carbon in paired urban and natural ecosystems worldwide
Manuel Delgado-Baquerizo,Pablo García-Palacios,Mark A. Bradford,David J. Eldridge,Miguel Berdugo,Tadeo Sáez-Sandino,Yu-Rong Liu,Fernando D. Alfaro,Sebastián Abades,Adebola Bamigboye,Felipe Bastida,José Luis Blanco-Pastor,Jorge Durán,Juan José Gaitán,Javier Gutiérrez Illán,Tine Grebenc,Thulani P. Makhalanyane,Durgesh Kumar Jaiswal,T. U. Nahberger,Gabriel Felipe Peñaloza-Bojacá,Ana Maria Rey,Alexandra Aparicio Rodríguez,Christina Siebe,Alberto L. Teixido,Wei Sun,Pankaj Trivedi,Jay Prakash Verma,Ling Wang,Jianyong Wang,Tianxue Yang,Eli Zaady,Xiaobin Zhou,Xin-Quan Zhou,César Plaza +33 more
References
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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
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
Journal ArticleDOI
BLAT—The BLAST-Like Alignment Tool
TL;DR: How BLAT was optimized is described, which is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
Journal ArticleDOI
The diversity and biogeography of soil bacterial communities
Noah Fierer,Robert B. Jackson +1 more
TL;DR: Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in this study.
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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