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Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures. 2021

Junhui Li, and Chongjian Jia, and Qihong Lu, and Bruce A Hungate, and Paul Dijkstra, and Shanquan Wang, and Cuiyu Wu, and Shaohua Chen, and Deqiang Li, and Hojae Shim
Vanderbilt Microbiome Initiative, Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA. Electronic address: tim.junhuili@gmail.com.

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.

UI MeSH Term Description Entries
D001673 Biodegradation, Environmental Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers. Bioremediation,Phytoremediation,Natural Attenuation, Pollution,Environmental Biodegradation,Pollution Natural Attenuation
D015262 Xenobiotics Chemical substances that are foreign to the biological system. They include naturally occurring compounds, drugs, environmental agents, carcinogens, insecticides, etc. Xenobiotic
D054892 Metagenome A collective genome representative of the many organisms, primarily microorganisms, existing in a community. Metagenomes
D056186 Metagenomics The systematic study of the GENOMES of assemblages of organisms. Community Genomics,Environmental Genomics,Population Genomics,Genomics, Community,Genomics, Environmental,Genomics, Population
D064307 Microbiota The full collection of microbes (bacteria, fungi, virus, etc.) that naturally exist within a particular biological niche such as an organism, soil, a body of water, etc. Human Microbiome,Microbiome,Microbiome, Human,Microbial Community,Microbial Community Composition,Microbial Community Structure,Community Composition, Microbial,Community Structure, Microbial,Community, Microbial,Composition, Microbial Community,Human Microbiomes,Microbial Communities,Microbial Community Compositions,Microbial Community Structures,Microbiomes,Microbiotas

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