The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Accessing the Soil Metagenome for Studies of Microbial Diversity
Open accessAbstract
Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.
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Cites
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Pyrosequencing enumerates and contrasts soil microbial diversity
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Comparative Metagenomics of Microbial Communities
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Cited by
Xiang, L., Harindintwali, J. D., Wang, F., Redmile-Gordon, M., Chang, S. X., Fu, Y., He, C., Muhoza, B., Brahushi, F., Bolan, N., et al. (2022) · Environmental Science & Technology · doi:10.1021/acs.est.2c02976 · Cited by 450
Measuring the effects of pesticides on bacterial communities in soil: A critical review
Imfeld, G., & Vuilleumier, S. (2012) · European Journal of Soil Biology · doi:10.1016/j.ejsobi.2011.11.010 · Cited by 323
Nesme, J., & Simonet, P. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.12631 · Cited by 303
Self-citationEcotoxicological assessment of antibiotics: A call for improved consideration of microorganisms
Brandt, K. K., Amézquita, A., Backhaus, T., Boxall, A., Coors, A., Heberer, T., Lawrence, J. R., Lazorchak, J., Schönfeld, J., Snape, J. R., et al. (2015) · Environment International · doi:10.1016/j.envint.2015.09.013 · Cited by 303
Green Infrastructure Design Influences Communities of Urban Soil Bacteria
Joyner, J. L., Kerwin, J., Deeb, M., Lozefski, G., Prithiviraj, B., Paltseva, A., McLaughlin, J., Groffman, P., Cheng, Z., & Muth, T. R. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00982 · Cited by 59
Metadata
- Authors
- Delmont, T. O., Robe, P., Cecillon, S., Clark, I. M., Constancias, F., Simonet, P., Hirsch, P. R., & Vogel, T. M.
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2011-02-15
- Volume
- 77
- Issue
- 4
- Pages
- 1315-1324
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- OpenAlex
- W1985479482
- Cited by
- 332
- References
- 39
- FWCI
- 19.04
- Type
- journal article
- Language
- en
- Open access
- green
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