Degradation, altered microbial community composition, and protein expression in bacterial consortium/fungus inoculated crude oil contaminated loamy soil

Accidental discharge of crude oil due to rupturing of old oil pipelines and blasts in oil refineries leads to contamination of agricultural land/adjacent areas and changes in microbial community and protein expression in the contaminated soil. Our previous study identified a bacterial consortium (Bacillus amyloliquefaciens MW532755+ Pseudomonas sp. MW444887) and a fungus (Aspergillus sydowii KY614299) with crude oil degrading ability. These microorganisms were used in the present investigation to degrade total petroleum hydrocarbon in naturally contaminated loamy soil (25% w/w) collected from the Assam region of India. The half-life of crude oil in uninoculated (T1), bacterial consortium (T2), and fungus-inoculated (T3) soils were 135.9, 47.5, and 58.2 days, respectively. The bacterial consortium and the fungus treatments altered the soil bacterial community and metabolic pathways, evidently from the analyses using metagenomics and predicted functional proteomics. The sequencing analysis using Ion Torrent showed the presence of 287 genera in the oil-polluted and treated soil samples. At the Genus level, abundances of Pseudomonas and Bacilli were observed, and the reads representing those of the Domain Bacteria for uninoculated (T1), bacterial consortium (T2), and fungus (T3) treated soils were 214525, 584054 and 489423, respectively. The predicted functional proteomics analysis for the protein-regulating genes, functional pathways, and protein families showed the presence of diversified pathways responsible for higher metabolic activities (q < 0.05). The quantitative polymerase chain reaction (qPCR) analysis showed that, compared to fungus treatment, bacterial consortium increased the abundance of 16S rRNA gene copies of Archaea, Alphaproteobacteria, and Bacteroidetes and also the gene copies of nitrogen cycling such as nifH (10(6) to 10(8)) were highest, followed by nirK (10(4) to 10(8)), amoA (10(4) to 10(5)), and nirS (10(4) to 10(6))The present study suggested that the bacterial consortium as the hydrocarbon degraders was better than fungus and can be used in the future for oil remediation purposes.

Automated summary

A bacterial consortium and a fungus with crude oil degrading ability were used to degrade petroleum hydrocarbon in contaminated soil. The bacterial consortium showed better degradation performance and altered the soil bacterial community and metabolic pathways compared to the fungus treatment.