Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat

Zhaobin Huang; Meiqin Li; Aharon Oren; Qiliang Lai

doi:10.3389/fmicb.2024.1376777

Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat

Front Microbiol. 2024 Apr 30:15:1376777. doi: 10.3389/fmicb.2024.1376777. eCollection 2024.

Authors

Zhaobin Huang^{1

2}, Meiqin Li¹, Aharon Oren³, Qiliang Lai^{4

5}

Affiliations

¹ College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China.
² Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, Quanzhou Normal University, Quanzhou, China.
³ The Hebrew University of Jerusalem, Edmond J. Safra Campus, The Institute of Life Sciences, Jerusalem, Israel.
⁴ Department of Marine Biology, Xiamen Ocean Vocational College, Xiamen, China.
⁵ Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.

Abstract

Two bacterial strains, designated FR2A1^T and MT2-5-38, were isolated from the surface sediments of an oyster farm on a tidal flat in Quanzhou Bay, China. Both strains were Gram-stain-negative, rod-shaped, aerobic, catalase-positive, and oxidase-positive. The 16S rRNA gene sequences of the two strains were 100% identical and had the highest similarity (97.1%) with Phaeovulum vinaykumarii JA123^T. The average nucleotide identity (ANI) value and digital DNA-DNA hybridization (DDH) value indicated that the two strains belonged to a single species. Gene annotation revealed that the two strains contained a gene cluster for nitrate reduction and a gene cluster for sulfur oxidation, indicating a possible role in N and S cycling in the tidal flat sediment. The phylogeny inferred from the 16S rRNA gene and 120 conserved proteins indicated that the two strains formed a distinct monophyletic clade within the family Paracoccaceae. The respiratory quinone was Q-10. The major fatty acids consisted of summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) and C_18:0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and several unidentified phospholipids. Based on the above characteristics, strains FR2A1^T and MT2-5-38 represent a novel genus and a novel species, for which we propose the name Ostreiculturibacter nitratireducens gen. nov., sp. nov. The type strain is FR2A1^T (=MCCC 1K08809^T = KCTC 8317^T). Phylogenomic analysis of 1,606 high-quality genomes of the family Paracoccaceae, including type strains, non-type strains, and uncultivated bacteria, was performed using the Genome Taxonomic Database Toolkit (GTDB-Tk), and the average amino acid identity (AAI) value of the phylogenetic clade was estimated. We found that 35 species of the family Paracoccaceae needed re-classification, and an AAI value of 70% was chosen as the genus boundary within the family Paracoccaceae.

Keywords: Ostreiculturibacter; Paracoccaceae; phylogenomic tree; polyphasic taxonomy; “Rhodobacteraceae”.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This study was supported by the Quanzhou City Science and Technology Program of China (2022C018R) and the National Science and Technology Fundamental Resources Investigation Program of China (2021FY100900).