Novel Analysis using Pyrosequencing for Characterization of Soil Bacterial Diversity.

The impacts of management and land uses on the soil bacterial diversity have not been well documented.  Here we present the use of a novel bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) diversity method, which will promote studies in soil microbiomes.  Using this modified FLX pyrosequencing approach we evaluated bacterial diversity of a soil (Fine, mixed, thermic Torrertic Paleustolls) with 38% clay and 34% sand (0-5 cm) under four systems.  We evaluated two non-disturbed grass systems such as pasture (Bothriochloa bladhii (Retz) S.T. Blake) [P] and Conservation Reserve Program under a diverse mixture of grasses [CRP], and two agricultural systems such as a cotton (Gossypium hirsutum L.) -winter wheat (Triticum aestivum L.)-corn (Zea mays L.) rotation [Ct-W-Cr] and the typical practice of the region, which is continuous monoculture cotton.  Differences due to the land use and management were observed in the soil microbial biomass C (CRP>P=Ct-W-Cr>Ct-Ct).  Using 3 estimators of diversity, the maximum number of unique sequences operational taxonomic units (OTU; roughly corresponding to the species level) never exceeded 4,500 in these soils at the 3% dissimilarity level.  The following trend was found using the most common estimators of bacterial diversity: Ct-W-Cr>P=CRP>Ct-Ct.  Predominant phyla in this soil were Actinobacteria, Bacteriodetes and Fermicutes.  Bacteroidetes were more predominant in soil under agricultural systems (Ct-W-Cr and Ct-Ct) compared to the same soil under non-disturbed grass systems (P and CRP).  The opposite trend was found for the Actinobacteria, which were more predominant under non-disturbed grass systems (P and CRP).  Higher G- bacteria and lower G+ bacteria were found under Ct-W-Cr rotation and highest abundance of actinomycetes under CRP.  The bTEFAP technique proved to be a powerful method to characterize the bacterial diversity of the soil studied under different management and land use in terms not only on the presence or absence, but also in terms of distribution.