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. 2023 Aug 25;11(9):2156.
doi: 10.3390/microorganisms11092156.

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

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

Ying Liu et al. Microorganisms. .

Abstract

Bacillota are widely distributed in various environments, owing to their versatile metabolic capabilities and remarkable adaptation strategies. Recent studies reported that Bacillota 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 Bacillota 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 Abyssisolibacter within the phylum Bacillota. 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 Bacillota species in cold seep sediments and their potential roles in the biogeochemical cycling of deep marine ecosystems.

Keywords: Abyssisolibacter sp. M8S5; Bacillota; adaption genomic analysis; cold seep; metabolic potentials.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Graphical representation of M8S5 genome. Genes on the forward (shown in the outer circle) and reverse (shown in the inner circle) strands are colored according to their cluster of orthologous gene (COG) categories (except those colored in black for no hits); tRNA and rRNA genes are highlighted with blue and red colors, respectively; gene islands are shown in green; genes encoding D-amino acids and peptidases are shown in green and orange, respectively; genes encoding polysaccharides are shown in blue color; GC content is shown in yellow and blue; and GC skew is shown in orange and purple (window, 5000 bp; step, 2500 bp).
Figure 2
Figure 2
The phylogenetic tree of strain M8S5 was constructed based on 120 concentration proteins. Strains M8S5 and MCWD3 are highlighted in red and blue color, respectively. The black nodes represent the bootstrap values ≥ 80.
Figure 3
Figure 3
Environmental distribution of the strain M8S5. The sampling site F in this study is highlighted in red color.
Figure 4
Figure 4
Reconstructed metabolic pathways of strain M8S5. X marks in the red color represent the genes absent in M8S5.
Figure 5
Figure 5
Two gene clusters of type glycine reductase in the genome of strain M8S5. (A) glycine reductase I, (B) glycine reductase II.

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References

    1. Wang X., Guan H., Qiu J.-W., Xu T., Peckmann J., Chen D., Feng D. Macro-ecology of cold seeps in the South China Sea. Geosyst. Geoenviron. 2022;1:100081. doi: 10.1016/j.geogeo.2022.100081. - DOI
    1. Feng D., Qiu J.-W., Hu Y., Peckmann J., Guan H., Tong H., Chen C., Chen J., Gong S., Li N., et al. Cold seep systems in the South China Sea: An overview. J. Asian Earth Sci. 2018;168:3–16. doi: 10.1016/j.jseaes.2018.09.021. - DOI
    1. Dong X., Rattray J.E., Campbell D.C., Webb J., Chakraborty A., Adebayo O., Matthews S., Li C., Fowler M., Morrison N.M., et al. Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nat. Commun. 2020;11:5825. doi: 10.1038/s41467-020-19648-2. - DOI - PMC - PubMed
    1. Niu M., Fan X., Zhuang G., Liang Q., Wang F. Methane-metabolizing microbial communities in sediments of the Haima cold seep area, northwest slope of the South China Sea. FEMS Microbiol. Ecol. 2017;93:fix101. doi: 10.1093/femsec/fix101. - DOI - PubMed
    1. Cui H., Su X., Chen F., Holland M., Yang S., Liang J., Su P., Dong H., Hou W. Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea. Mar. Environ. Res. 2019;144:230–239. doi: 10.1016/j.marenvres.2019.01.009. - DOI - PubMed

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