Data_Sheet_7_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.

两种细菌菌株，分别命名为FR2A1T和MT2-5-38，系从中国泉州湾一潮间带贝类养殖场的表层沉积物中分离得到。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的相似度高达97.1%。平均核苷酸身份（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，这两个菌株含有一个硝酸盐还原基因簇和一个硫氧化基因簇，暗示其在潮间带沉积物中的氮和硫循环中可能发挥作用。根据16S rRNA基因和120个保守蛋白推断的进化树表明，这两个菌株在Paracoccaceae科内形成一个独特的单系群。呼吸醌为Q-10。主要脂肪酸由总特征8（C18:1ω7c和/或C18:1ω6c）和C18:0组成。极性脂类包括磷脂酰乙醇胺、磷脂酰甘油以及若干未鉴定磷脂。基于上述特征，菌株FR2A1T和MT2-5-38代表一个新属和一个新种，我们建议命名为Ostreiculturibacter nitratireducens gen. nov., sp. nov. 其中，FR2A1T（=MCCC 1K08809T=KCTC 8317T）为模式菌株。利用基因组分类数据库工具包（GTDB-Tk）对Paracoccaceae科1,606个高质量基因组进行了系统发育分析，包括模式菌株、非模式菌株以及未培养细菌，并估算出系统发育群的平均氨基酸身份（AAI）值。我们发现Paracoccaceae科中35个物种需要重新分类，并在该科内选取了AAI值70%作为属的界限。