Accessing the soil metagenome for studies of microbial diversity


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.


Tom O. Delmont1, Patrick Robe2, Sébastien Cecillon1, Ian M. Clark3, Florentin Constancias1, Pascal Simonet1, Penny R. Hirsch3 and Timothy M. Vogel1

  • 1. Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Central de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
  • 2. LibraGen, 3 Rue de Satellites, 31400 Toulouse, France
  • 3. Rothamsted Research, Harpenden, Hertfordshie AL5 2JQ, United Kingdom


Parc d'activités Activestre
31390 Carbonne - FRANCE


Tél. +33 561 971 974
Fax +33 561 971 975