A metagenomic study on the effect of aboveground plant cover on soil bacterial diversity.

To study the effect of cropping and plant cover on soil microbial diversity, three adjacent sites characterized by the same soil, but differing for land use and cover, were sampled at Carovigno (Brindisi). The soil bacterial communities from replicated samples of a traditional greenhouse horticultural crop, a close olive grove and an adjacent Mediterranean (Quercus ilex) forest spot were identified with a metagenomic NGS approach. Total RNAs were extracted from 2 g soil subsamples and the V3-V4 hypervariable regions of the 16S rRNAs were sequenced with the Illumina MiSeq technology. A total of 2.46 ? 106 reads was produced from 13 samples, of which 85% passed the quality threshold, yielding an average of 97 - 239 x 103 reads per sample. Almost all (99%) sequences belonged to the Kingdom Bacteria, and 30% were informative up to the species level. Using the Greengenes classification system, the average number of species per sample was around 103. Most represented phyla in all samples were Proteobacteria, Actinobacteria, Firmicutes, Planctomycetes and Verrucomicrobia, with Proteobacteria as most represented classes. NGS data showed that samples from cultivated soils (olive and vegetables) had higher frequencies (5-10%) of Bacillales, under-represented in the Mediterranean forest. Data at the species level identified changes in the bacterial composition at deeper taxonomic levels, related to agricultural practices.