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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Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes.
TL;DR: It is reported that almost all anthropogenic environmental changes that took place in a grassland ecosystem affected soil bacterial community assembly primarily through promoting or restraining stochastic processes, challenging the traditional determinism-dominated view.
Journal ArticleDOI
Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils
Haitao Wang,Christopher W. Marshall,Minying Cheng,Huijuan Xu,Hu Li,Xiao-Ru Yang,Tianling Zheng +6 more
TL;DR: Results indicate a more pivotal role of AOA in nitrification, especially in urban soils, and could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.
Journal ArticleDOI
Assessment of microbial communities in PM1 and PM10 of Urumqi during winter.
TL;DR: Investigation of the microbial composition of Urumqi's PM1 and PM10 pollutants in winter showed that the bacterial community is mainly composed of Proteob bacteria, Firmicutes and Actinobacteria, and some fungal genera may cause several plant diseases.
Journal ArticleDOI
Managing soil carbon stocks to enhance the resilience of urban ecosystems
Klaus Lorenz,Rattan Lal +1 more
TL;DR: In this article, the authors proposed a C-friendly soil and land-use management practices to enhance soil-derived ecosystem services in urban areas, and the resilience of urban ecosy...
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Mammal diversity influences the carbon cycle through trophic interactions in the Amazon.
Mar Sobral,Mar Sobral,Mar Sobral,Kirsten M. Silvius,Han Overman,Luiz Flamarion B. Oliveira,Theodore K. Raab,José M. V. Fragoso +7 more
TL;DR: An extensive dataset collected in a high-diversity Amazonian system is used to parse out the relationship between animal and plant species richness, feeding interactions, tree biomass and carbon concentrations in soil, supporting the view that whole community complexity—including vertebrate richness and trophic interactions—drives ecosystem function in tropical systems.
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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