The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
Open accessAbstract
For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.
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Cites
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Self-citationGlobal patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., Fierer, N., & Knight, R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,711
Self-citationUltra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839
Self-citationOrigins and evolution of antibiotic resistance
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The diversity and biogeography of soil bacterial communities
Fierer, N., & Jackson, R. B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507535103 · Cited by 5,711
Self-citationTOWARD AN ECOLOGICAL CLASSIFICATION OF SOIL BACTERIA
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Self-citationSoil bacterial and fungal communities across a pH gradient in an arable soil
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Vive la différence: plant functional diversity matters to ecosystem processes
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Cited by
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116
Self-citationSchubert, M., Ermini, L., Sarkissian, C. D., Jónsson, H., Ginolhac, A., Schaefer, R., Martin, M. D., Fernández, R., Kircher, M., McCue, M., et al. (2014) · Nature Protocols · doi:10.1038/nprot.2014.063 · Cited by 562
Zhou, J., He, Z., Yang, Y., Deng, Y., Tringe, S. G., & Alvarez-Cohen, L. (2015) · mBio · doi:10.1128/mbio.02288-14 · Cited by 474
Nayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research · doi:10.1101/gr.201863.115 · Cited by 470
Ramirez, K. S., Leff, J. W., Barberán, A., Bates, S. T., Betley, J., Crowther, T. W., Kelly, E. F., Oldfield, E. E., Shaw, E. A., Steenbock, C., et al. (2014) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2014.1988 · Cited by 423
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Metadata
- Authors
- Fierer, N., Leff, J. W., Adams, B. J., Nielsen, U. N., Bates, S. T., Lauber, C. L., Owens, S., Gilbert, J. A., Wall, D. H., & Caporaso, J. G.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2012-12-10
- Volume
- 109
- Issue
- 52
- Pages
- 21390-21395
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2009906332
- Cited by
- 1,643
- References
- 58
- FWCI
- 52.87
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Fierer, N., Leff, J. W., Adams, B. J., Nielsen, U. N., Bates, S. T., Lauber, C. L., Owens, S., Gilbert, J. A., Wall, D. H., & Caporaso, J. G. (2012). Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1215210110
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