Unravelling the Genetic and Function Diversity of Dominant Bacterial Communities Involved in Co-Composting Bioremediation of Complex Crude Oil Waste Sludge

Abstract

The present study aimed at using metagenomic analysis for profiling the dominant endogenous bacterial diversity in a compost matrix throughout co-composting of crude oil waste sludge and animal manures using a static co-composting technique. A total of 280,666 good and filtered reads were obtained which was distributed into 17 phyla, 42 classes, 83 orders, 162 families and 359 genera. The dominant 4 phyla include Proteobacteria, Actinobacteria, Firmicutes, and Acidobacteria. At genus level both classified and unclassified, the top 12 genera’s OTUs were Sphingomonas, Pseudomonas, Burkholderia-Paraburkholderia, Microbacterium Rhodococcus, Bradyrhizobiaceae_unclassified, Sphingomonadaceae_unclassified Afipia, Methylobacterium, Bacillus, Phenylobacterium and Achromobacter. These genera have been found to be PAH-degraders because of their unique and distinct capabilities as well as vital roles they play in ex-situ and in-situ bioremediation as shown by GC/MS analysis results indicating reduction in the selected PAHs ranging from 36.52 to 99.98% over a period of 10 months of incubation and by different microbial diversity of each individual sample. With the help of metagenomics analysis, essential detailed information on the dominant bacterial diversity directly from the co-composted samples have been revealed extensively via a high-throughput Illumina sequencing application. The results indicated that the composition of the dominant bacteria community must have influenced PAH degradation. Interestingly, estimated community diversity and richness of dominant OTUs showed that co-composting of crude oil refinery waste sludge generated and harbours higher bacterial diversity as well as very important rich species for in-situ or ex-situ bioremediation. Furthermore, most OTUs for the class; Proteobacteria_unclassified, Bacteria_unclassified, Bacteroidetes_unclassified, Firmicutes_unclassified, phyla Bacteria_unclassified and genus; Bradyrhizobiaceae_unclassified, Sphingomonadaceae_unclassified, Corynebacteriales_unclassified, Enterobacteriaceae_unclassified, Rhizobiales_unclassified, Unclassified_bacteria that were identified in most of the samples have not been classified from class to genus level and this suggests that they may stand out for novel bacterial species which needs more research as well as exploration on them with regards to their capabilities in bioremediation technology.