Data_Sheet_8_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.PDF

Two bacterial strains, designated FR2A1T 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 JA123T. 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 (C18:1ω7c and/or C18:1ω6c) and C18:0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and several unidentified phospholipids. Based on the above characteristics, strains FR2A1T 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 FR2A1T (=MCCC 1K08809T = KCTC 8317T). 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.

从中国泉州湾潮滩的牡蛎养殖场表层沉积物中分离出两种细菌菌株，分别命名为FR2A1T和MT2-5-38。这两种菌株均为革兰氏染色阴性、杆状、需氧、过氧化氢酶阳性以及氧化酶阳性。其16S rRNA基因序列完全一致，与Phaeovulum vinaykumarii JA123T的相似度最高（97.1%）。平均核苷酸同源性（ANI）值和数字DNA-DNA杂交（DDH）值表明，这两个菌株属于同一物种。基因注释显示，这两种菌株含有硝酸盐还原基因簇和硫氧化基因簇，暗示它们可能在潮滩沉积物中的氮和硫循环中发挥重要作用。基于16S rRNA基因和120个保守蛋白推断的进化树表明，这两种菌株在Paracoccaceae科内形成一个独特的单系群。呼吸醌为Q-10。主要脂肪酸由特征8（C18:1ω7c和/或C18:1ω6c）和C18:0组成。极性脂类包括磷脂酰乙醇胺、磷脂酰甘油以及数种未确定的磷脂。根据上述特征，菌株FR2A1T和MT2-5-38代表一种新属和一种新种，我们提议命名为Ostreiculturibacter nitratireducens gen. nov., sp. nov.。模式菌株为FR2A1T（=MCCC 1K08809T=KCTC 8317T）。使用基因组分类数据库工具包（GTDB-Tk）对Paracoccaceae科的1606个高质量基因组进行了系统发育基因组分析，包括模式菌株、非模式菌株和未培养细菌，并估算出系统发育群的平均氨基酸同源性（AAI）值。我们发现该科中有35个物种需要重新分类，并在Paracoccaceae科内选择70%的AAI值作为属的界限。