Structure, fluctuation and magnitude of a natural grassland soil metagenome View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-09

AUTHORS

Tom O Delmont, Emmanuel Prestat, Kevin P Keegan, Michael Faubladier, Patrick Robe, Ian M Clark, Eric Pelletier, Penny R Hirsch, Folker Meyer, Jack A Gilbert, Denis Le Paslier, Pascal Simonet, Timothy M Vogel

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 × 10(9) 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. More... »

PAGES

1677

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ismej.2011.197

DOI

http://dx.doi.org/10.1038/ismej.2011.197

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1052772799

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22297556


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