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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Journal ArticleDOI
Response of microbial communities to pesticide residues in soil restored with Azolla imbricata.
Xiao-Ming Lu,Peng-Zhen Lu +1 more
TL;DR: Under conditions of Azolla imbricata restoration, the high-throughput sequencing technology was employed to determine change trends of microbial community structures in the soil that had undergone long-term application of pesticides and indicated that the microbial diversity was strongly negatively correlated with the contents of pesticide residues in the soils.
Journal ArticleDOI
Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils
TL;DR: Evidence is provided that long-term nickel pollution shifted the soil bacterial communities, resulting in the decrease of microbial biomass although the bacterial diversity was not significantly changed.
Posted ContentDOI
Rootstocks shape the rhizobiome: Rhizosphere and endosphere bacterial communities in the grafted tomato system
Ravin Poudel,Ari Jumpponen,Megan M. Kennelly,Cary L. Rivard,L. Gomez-Montano,Karen A. Garrett +5 more
TL;DR: The potential for using plant genotype to indirectly select bacterial taxa in endosphere and rhizosphere microbiomes is identified and taxa responsive to each rootstock treatments are identified, which may represent candidate taxa useful for biocontrol and in biofertilizers.
Journal ArticleDOI
Contrasting patterns of plant and microbial diversity during long‐term ecosystem development
Benjamin L. Turner,Benjamin L. Turner,Graham Zemunik,Graham Zemunik,Etienne Laliberté,Etienne Laliberté,Jeremy J. Drake,F. Andrew Jones,F. Andrew Jones,Kristin Saltonstall +9 more
Journal ArticleDOI
Functional properties of bacterial communities in water and sediment of the eutrophic river-lake system of Poyang Lake, China.
TL;DR: The results suggested thatacterial communities in this eutrophic river-lake system of Poyang Lake were vulnerable to nutrient perturbations, especially the bacterial communities in water column, which had a lower functional redundancy than in sediment.
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.
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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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