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. 2023 Mar 21;11(3):798.
doi: 10.3390/microorganisms11030798.

Genomic Analysis of the Deep-Sea Bacterium Shewanella sp. MTB7 Reveals Backgrounds Related to Its Deep-Sea Environment Adaptation

Sicong Li  1 , Jiahua Wang  1 , Jie Liu  1 , Hongcai Zhang  1 , Tianqiang Bao  1 , Chengwen Sun  1 , Jiasong Fang  1   2 , Junwei Cao  1
Affiliations

Genomic Analysis of the Deep-Sea Bacterium Shewanella sp. MTB7 Reveals Backgrounds Related to Its Deep-Sea Environment Adaptation

Sicong Li et al. Microorganisms. .

Abstract

Shewanella species are widely distributed in various environments, especially deep-sea sediments, due to their remarkable ability to utilize multiple electron receptors and versatile metabolic capabilities. In this study, a novel facultatively anaerobic, psychrophilic, and piezotolerant bacterium, Shewanella sp. MTB7, was isolated from the Mariana Trench at a depth of 5900 m. Here, we report its complete genome sequence and adaptation strategies for survival in deep-sea environments. MTB7 contains what is currently the third-largest genome among all isolated Shewanella strains and shows higher coding density than neighboring strains. Metabolically, MTB7 is predicted to utilize various carbon and nitrogen sources. D-amino acid utilization and HGT-derived purine-degrading genes could contribute to its oligotrophic adaptation. For respiration, the cytochrome o ubiquinol oxidase genes cyoABCDE, typically expressed at high oxygen concentrations, are missing. Conversely, a series of anaerobic respiratory genes are employed, including fumarate reductase, polysulfide reductase, trimethylamine-N-oxide reductase, crotonobetaine reductase, and Mtr subunits. The glycine reductase genes and the triplication of dimethyl sulfoxide reductase genes absent in neighboring strains could also help MTB7 survive in low-oxygen environments. Many genes encoding cold-shock proteins, glycine betaine transporters and biosynthetic enzymes, and reactive oxygen species-scavenging proteins could contribute to its low-temperature adaptation. The genomic analysis of MTB7 will deepen our understanding of microbial adaptation strategies in deep-sea environments.

Keywords: Shewanella; complete genome; deep sea; psychrophilic.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The phylogenetic tree of genus Shewanella based on 120 concentration proteins. This tree was constructed with all 117 genomes of Shewanella in the NCBI RefSeq database, and only the strain MTB7-related branch is shown. The bootstrap values were also shown in number.
Figure 2
Figure 2
Graphical representation of the Shewanella sp. MTB7 (A) and Shewanella woodyi ATCC 51908 (B) genomes (window, 5000 bp; step, 2500 bp). 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); RNA genes are highlighted with different colors (tRNAs blue and rRNAs red); gene islands are shown in green; genes of transposases, recombinases, and integrases are shown in orange; proviruses are show in different colors (red for high qualified, pink for medium qualified, and blue for low qualified); GC content is shown in yellow/blue; and GC skew is shown in orange/purple.
Figure 3
Figure 3
Gene clusters of type TMAO reductase (A,B), glycine reductase (C), and crotonobetaine reductase (D) in Shewanella sp. MTB7 genome.
See this image and copyright information in PMC

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