Research Projects

Logos GenomEnviron and Ampere
Laboratoire Ampere
Ecole Centrale de Lyon . France
(33) 472 18 65 14



Metagenomic discovery and exploitation of the soil microbial community



Timothy M. Vogel
Funding Source:

French National Research Agency (ANR) Projet ANR-08-GENM-025




Libragen SA, Genoscope, UCBL, INRA (Dijon, Nancy, ParisAgroTech)


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 4.88109 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 o50% of reads were assigned at an E value cutoff of 105. 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 o105, thus, considerable genomic reconstructions efforts still have to be performed.


To create a metagenomic and genetic resource of an internationally unique, well characterised soil

To identify and contrast the diversity of the active bacteria and their key functional genes, establishing a baseline of a “healthy” soil

To correlate variation in genetic diversity of soil microbial ecosystems to soil management and environmental perturbations (climate change, pollution) over the last 100 years.

of the work:

Mutliple samples from Rothamsted's Park Grass were sampled and the soil DNA extracted by a range of different extraction methods. DNA pools (subsamples of the entire metagenome) were sequenced by 454 pyrosequencing. In addition, a 2 million 40kb insert clone library was created and is available to interested parties depending on the request and budget.


Publications & Communications:

Delmont, T.O., Simonet, P., Vogel, T.M. 2012. Describing microbial communities and performing global comparisons in the ‘omic era. ISME Journal 6: 1625-1628.

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., Vogel, T.M. 2012. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME Journal 6: 1677-1687.

Delmont, T.O. Cedric Malandain, C., Prestat, E. Catherine Larose, C. Monier, J-M., Simonet, P. Vogel, T.M. 2011. Metagenomic mining for microbiologists. ISME Journal 5: 1837-1843.

Monier J-M, Demanèche S, Delmont TO, Mathieu A, Vogel, T.M. and Simonet P. 2011. Metagenomic exploration of antibiotic resistance in soil. Current Opinion in Microbiology. 14: 236-243.

Delmont TO, Robe P, Clark I, Simonet P and Vogel TM. 2011. Metagenomic comparison of direct and indirect soil DNA extraction approaches. J. Microbiol. Methods. 86: 397-400.

Delmont T.O., Robe P, Cecillon S, Clark I.M., Constancias F, Simonet P, Hirsch P.R., Vogel TM. 2011. Accessing Microbial Diversity for Soil Metagenomic Studies. Appl Environ Microbiol. 77:1315–1324

Vogel T.M., Simonet P, Jansson J, Hirsch PR, Tiedje JM, Van Elsas JD, Bailey MJ, Nalin R and Philippot L. 2009. TerraGenome: a consortium for the sequencing of a soil metagenome. Nat. Rev. Microbiol. 7: 252.

Demanèche, S., Philippot, L., David, M.M., Navarro, E., Vogel, T.M., Simonet, P. 2009. Characterization  of Denitrification Gene Clusters of Soil Bacteria via a Metagenomic Approach. Appl. Environ. Microbiol.75: 534-537

Demanèche, S., Philippot, L., David, M.M., Navarro, E., Simonet, P., Vogel, T.M. 2009. Evaluation of functional gene enrichment in a soil metagenomic clone library. J. Microbiol. Methods 76: 105-107