Structure, fluctuation and magnitude of a natural grassland soil metagenome

A - Papers appearing in refereed journals

Delmont, T. O., Prestat, E., Keegan, K. P., Faubladier, M., Robe, P., Clark, I. M., Pelletier, E., Hirsch, P. R., Meyer, F., Gilbert, J. A., Le Paslier, D., Simonet, P. and Vogel, T. M. 2012. Structure, fluctuation and magnitude of a natural grassland soil metagenome. The ISME Journal. 6, pp. 1677-1687.

AuthorsDelmont, T. O., Prestat, E., Keegan, K. P., Faubladier, M., Robe, P., Clark, I. M., Pelletier, E., Hirsch, P. R., Meyer, F., Gilbert, J. A., Le Paslier, D., Simonet, P. and Vogel, T. M.
Abstract

The soil ecosystem is critical for human health, affecting aspects of the environment from key agricultural and edaphic parameters to critical influence on climate change. Soil has more unknown biodiversity than any other ecosystem. We have applied diverse DNA extraction methods coupled with high throughput pyrosequencing to explore 4.88 × 109 bp of metagenomic sequence data from the longest continually studied soil environment (Park Grass experiment at Rothamsted Research in the UK). Results emphasize important DNA extraction biases and unexpectedly low seasonal and vertical soil metagenomic functional class variations. Clustering-based subsystems and carbohydrate metabolism had the largest quantity of annotated reads assigned although <50% of reads were assigned at an E value cutoff of 10−5. In addition, with the more detailed subsystems, cAMP signaling in bacteria (3.24±0.27% of the annotated reads) and the Ton and Tol transport systems (1.69±0.11%) were relatively highly represented. The most highly represented genome from the database was that for a Bradyrhizobium species. The metagenomic variance created by integrating natural and methodological fluctuations represents a global picture of the Rothamsted soil metagenome that can be used for specific questions and future inter-environmental metagenomic comparisons. However, only 1% of annotated sequences correspond to already sequenced genomes at 96% similarity and E values of <10−5, thus, considerable genomic reconstructions efforts still have to be performed.

Year of Publication2012
JournalThe ISME Journal
Journal citation6, pp. 1677-1687
Digital Object Identifier (DOI)doi:10.1038/ismej.2011.197
Open accessPublished as bronze (free) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeThe Rothamsted Long-Term Experiments including Sample Archive and e-RA database [2012-2017]
Publisher's version
Output statusPublished
Publication dates
Online02 Feb 2012
Publication process dates
Accepted24 Nov 2011
Copyright licensePublisher copyright
ISSN1751-7362
PublisherNature Publishing Group

Permalink - https://repository.rothamsted.ac.uk/item/8qw7x/structure-fluctuation-and-magnitude-of-a-natural-grassland-soil-metagenome

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