Consequences of crude oil contamination on the structure and function of autochthonous microbial community of a tropical agricultural soil

Abstract

Crude oil contamination of soil matrices is a persistent problem with deleterious consequences due to the recalcitrant, toxic and mutagenic properties of its constituents. To decipher the effects of crude oil contamination on the microbial community structure and function of an agricultural soil, field moist soil microcosms 2S (agricultural soil) and AB6 (agricultural soil polluted with crude oil) were set up. Taxonomic profiling of the two microcosms using next generation shotgun sequencing revealed massive decline in the number of recovered sequences from 3,267,616 (2S) to 250,241 (AB6). It also revealed the dominance of the phyla Actinobacteria (46.86%), and Firmicutes (51.20%) in 2S and AB6 with preponderance of Conexibacter (11.40%), and Singulisphaera (4.43%) in 2S, and Bacillus (38.52%), Sphingobium (10.51%), and Clostridium (7.06%) in AB6, respectively. Gas chromatographic fingerprints of residual crude oil in AB6 revealed complete disappearance of 50% of the hydrocarbon fractions at the end of 42 days while the others were degraded to < 6% of their initial concentrations. Functional annotation of the predicted ORFs in the two metagenomes revealed diverse metabolic features of the autochthonous microbial community. It also revealed the exclusive detection of diverse genes in AB6 metagenome responsible for degradation of various classes of hydrocarbons and the detoxification, transport and resistance to heavy metals. This study has established the deleterious effects of crude oil contamination on the microbial community structure of a tropical agricultural soil and revealed the adaptive features of the microbial community to various environmental stressors.