Metagenomics-metabolomics analysis of microbial function and metabolism in petroleum-contaminated soil

• Published in: Brazilian journal of microbiology Vol. 54; no. 2; pp. 935 - 947
• Main Authors: Li, Yong-Quan, Xin, Ying, Li, Caili, Liu, Jin, Huang, Tao
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01.06.2023; Springer Nature B.V
• Subjects: Acidic soils; Biodegradation; Biomedical and Life Sciences; Bioremediation; Degradation; Dihydroxybenzoic acid; Dioxygenase; Environmental Microbiology - Research Paper; Food Microbiology; Genomes; Gentisic acid; Hydrocarbon-degrading bacteria; Hydrocarbons; Hydroxylation; Life Sciences; Medical Microbiology; Metabolism; Metabolites; Metabolomics; Metagenomics; Microbial contamination; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microbiomes; Microorganisms; Mycology; Naphthalene; Oil pollution; Petroleum; Polycyclic aromatic hydrocarbons; Relative abundance; Ring opening; Salicylic acid; Soil contamination; Soil degradation; Soil microorganisms; Soil pollution; Toluene; Xenobiotics; Xylene; Soil; Pollution; Microorganism; Metabolism; Petroleum
• ISSN: 1517-8382; 1678-4405
• DOI: 10.1007/s42770-023-01000-7

Contamination of soil by petroleum is becoming increasingly serious in the world today. However, the research on gene functional characteristics, metabolites and distribution of microbial genomes in oil-contaminated soil is limited. Considering that, metagenomic and metabonomic were used to detect microbes and metabolites in oil-contaminated soil, and the changes of functional pathways were analyzed. We found that oil pollution significantly changed the composition of soil microorganisms and metabolites, and promoted the relative abundance of Pseudoxanthomonas , Pseudomonas , Mycobacterium , Immundisolibacter, etc. The degradation of toluene, xylene, polycyclic aromatic hydrocarbon and fluorobenzoate increased in Xenobiotics biodegradation and metabolism. Key monooxygenases and dioxygenase systems were regulated to promote ring opening and degradation of aromatic hydrocarbons. Metabolite contents of polycyclic aromatic hydrocarbons (PAHs) such as 9-fluoronone and gentisic acid increased significantly. The soil microbiome degraded petroleum pollutants into small molecular substances and promoted the bioremediation of petroleum-contaminated soil. Besides, we discovered the complete degradation pathway of petroleum-contaminated soil microorganisms to generate gentisic acid from the hydroxylation of naphthalene in PAHs by salicylic acid. This study offers important insights into bioremediation of oil-contaminated soil from the aspect of molecular regulation mechanism and provides a theoretical basis for the screening of new oil degrading bacteria.