Bacterial diversity in an agricultural soil Metagenome

In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work we used barcoded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyse bacterial diversity in a profile (depths: 10 cm, 25 cm, and 45 cm) of a well-characterized field of winter wheat. To ensure that the results obtained closely reflect real-life conditions, taxonomic assignment with the RDP classifier program was carried out with three bootstrap scores: 0, 0.80, and 0.99. We found biomass and bacterial quantity and diversity to decrease greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81% of the most represented OTUs (relative abundance =1%), notably the OTUs Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 cm and 25 cm) and subsoil (45 cm) than between levels in the topsoil. The subsoil also contained more unknown bacteria, 53.96% on the average, than did the topsoil, with 42.06% at 10 cm and 45.59% at 25 cm. Most of these unknown bacteria seem to belong to the taxa Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.