The Phylogeny, Metabolic Potentials, and Environmental Adaptation of an Anaerobe, Abyssisolibacter sp. M8S5, Isolated from Cold Seep Sediments of the South China Sea

• Published in: Microorganisms (Basel) 2023-08, Vol.11 (9), p.2156
• Main Authors: Liu, Ying, Chen, Songze, Wang, Jiahua, Shao, Baoying, Fang, Jiasong, Cao, Junwei
• Format: Article
• Language: English
• Subjects: Abyssisolibacter sp. M8S5; Adaptation; adaption genomic analysis; Amino acids; Annotations; Bacillota; Biodegradation; Biogeochemical cycles; Biosynthesis; Carbohydrates; Carbon sources; Cellulose; Chitin; Cold; cold seep; Ecological function; Ecosystems; Ethanolamine; Genes; Genomes; Glycine; Glycine betaine; Glycine reductase; Histidine; Hydrocarbons; Low temperature; Marine ecosystems; metabolic potentials; Metabolism; Microorganisms; Nitrogen sources; Organic matter; Osmoprotectants; PCB; Phylogenetics; Phylogeny; Polychlorinated biphenyls; Proline; Proteins; Putrescine; Reactive oxygen species; Reductases; Scavenging; Sediments; Spermidine; Taxonomy; Trehalose
• ISSN: 2076-2607; 2076-2607
• DOI: 10.3390/microorganisms11092156

are widely distributed in various environments, owing to their versatile metabolic capabilities and remarkable adaptation strategies. Recent studies reported that species were highly enriched in cold seep sediments, but their metabolic capabilities, ecological functions, and adaption mechanisms in the cold seep habitats remained obscure. In this study, we conducted a systematic analysis of the complete genome of a novel bacterium strain M8S5, which we isolated from cold seep sediments of the South China Sea at a depth of 1151 m. Phylogenetically, strain M8S5 was affiliated with the genus within the phylum . Metabolically, M8S5 is predicted to utilize various carbon and nitrogen sources, including chitin, cellulose, peptide/oligopeptide, amino acids, ethanolamine, and spermidine/putrescine. The pathways of histidine and proline biosynthesis were largely incomplete in strain M8S5, implying that its survival strictly depends on histidine- and proline-related organic matter enriched in the cold seep ecosystems. On the other hand, strain M8S5 contained the genes encoding a variety of extracellular peptidases, e.g., the S8, S11, and C25 families, suggesting its capabilities for extracellular protein degradation. Moreover, we identified a series of anaerobic respiratory genes, such as glycine reductase genes, in strain M8S5, which may allow it to survive in the anaerobic sediments of cold seep environments. Many genes associated with osmoprotectants (e.g., glycine betaine, proline, and trehalose), transporters, molecular chaperones, and reactive oxygen species-scavenging proteins as well as spore formation may contribute to its high-pressure and low-temperature adaptations. These findings regarding the versatile metabolic potentials and multiple adaptation strategies of strain M8S5 will expand our understanding of the species in cold seep sediments and their potential roles in the biogeochemical cycling of deep marine ecosystems.