Bacterial Diversity and Population Structure of PCP Degrading Soil Bacteria.

Degradation of pesticides in soil is highly influenced by microbial composition in that soil. At the end, due to the degradation processes, specific microbial species may be enriched. In this study, we used PCR-DGGE and massively parallel 454 pyrosequencing of hypervariable regions in rRNA genes to profile microbial communities in untreated and treated soils with and without grass to assess the degradation of PCP.  PCR-DGGE bands were cloned and sequenced for species identifications and diversity indices were determined. All pyrosequencing data were analyzed using MOTHUR, for rarefaction curves, diversity indices (Shannon, Simpson, Chao, ACE, etc.), Venn diagrams, heat maps, whole sample dendrograms, Parsimony analysis, and Unifrac analysis using 81793 sequence tags. A total of over 15000 sequence tags with over 8000 OTUs were identified in soil without PCP compared to about 12000 sequences and about 6000 OTUs in soils with PCP at the end of the study. Using the Venn diagram at 3% similarity level, the percentage of species that shared in control groups with and without grass were about 17.2% with a total richness of 28113.9 compared to percentage of species that shared in PCP soils with and without grass that were at about 10.7% with a total richness of 16588.5. High-abundance groups within Proteobacteria (39%), Actinobacteria (26.3%), Firmicutes (18.3%), Chloroflexi (6.25%), Gemmatimonadetes (2.74%), Bacteroides (1.52%), Cyanobacteria (1.49%), Planctomycetes (1.15%), and others that were less than 1% dominated the major sequence tags at the end of the study. The high abundance of Proteobacteria suggest that members of this phylum may be involved in PCP degradation.