Description of the first cultured representative of "Candidatus Synoicihabitans" genus, isolated from deep-sea sediment of South China Sea

Tariq Ahmad; Sidra Erum Ishaq; Lewen Liang; Jialin Hou; Ruize Xie; Yijing Dong; Tiantian Yu; Fengping Wang

doi:10.1016/j.syapm.2024.126490

Description of the first cultured representative of "Candidatus Synoicihabitans" genus, isolated from deep-sea sediment of South China Sea

Syst Appl Microbiol. 2024 May;47(2-3):126490. doi: 10.1016/j.syapm.2024.126490. Epub 2024 Feb 5.

Authors

Tariq Ahmad¹, Sidra Erum Ishaq¹, Lewen Liang², Jialin Hou², Ruize Xie², Yijing Dong³, Tiantian Yu², Fengping Wang⁴

Affiliations

¹ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
² Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China.
³ School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, PR China.
⁴ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China; Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China. Electronic address: fengpingw@sjtu.edu.cn.

PMID: 38330528
DOI: 10.1016/j.syapm.2024.126490

Abstract

In this study we describe the first cultured representative of Candidatus Synoicihabitans genus, a novel strain designated as LMO-M01^T, isolated from deep-sea sediment of South China Sea. This bacterium is a facultative aerobe, Gram-negative, non-motile, and has a globular-shaped morphology, with light greenish, small, and circular colonies. Analysis of the 16S rRNA gene sequences of strain LMO-M01^T showed less than 93% similarity to its closest cultured members. Furthermore, employing advanced phylogenomic methods such as comparative genome analysis, average nucleotide identity (ANI), average amino acids identity (AAI), and digital DNA-DNA hybridization (dDDH), placed this novel species within the candidatus genus Synoicihabitans of the family Opitutaceae, Phylum Verrucomicrobiota. The genomic analysis of strain LMO-M01^T revealed 175 genes, encoding putative carbohydrate-active enzymes. This suggests its metabolic potential to degrade and utilize complex polysaccharides, indicating a significant role in carbon cycling and nutrient turnover in deep-sea sediment. In addition, the strain's physiological capacity to utilize diverse biopolymers such as lignin, xylan, starch, and agar as sole carbon source opens up possibilities for sustainable energy production and environmental remediation. Moreover, the genome sequence of this newly isolated strain has been identified across diverse ecosystems, including marine sediment, fresh water, coral, soil, plants, and activated sludge highlighting its ecological significance and adaptability to various environments. The recovery of strain LMO-M01^T holds promise for taxonomical, ecological and biotechnological applications. Based on the polyphasic data, we propose that this ecologically important strain LMO-M01^T represents a novel genus (previously Candidatus) within the family Opitutaceae of phylum Verrucomicrobiota, for which the name Synoicihabitans lomoniglobus gen. nov., sp. nov. was proposed. The type of strain is LMO-M01^T (= CGMCC 1.61593^T = KCTC 92913^T).

Keywords: Candidatus; Deep-sea sediment; Opitutaceae; Synoicihabitans lomoniglobus; Verrucomicrobiota.

MeSH terms

Bacterial Typing Techniques
Base Composition
China
DNA, Bacterial* / genetics
Fatty Acids / analysis
Genome, Bacterial / genetics
Geologic Sediments* / microbiology
Nucleic Acid Hybridization
Phylogeny*
RNA, Ribosomal, 16S* / genetics
Seawater / microbiology
Sequence Analysis, DNA*

Substances

RNA, Ribosomal, 16S
DNA, Bacterial
Fatty Acids