Ho Jia Yee, Koh Xiu Qi, Kang Deborah Yebon, Low Adrian, Hu Dalong, Haryono Mindia A S, Williams Rohan B H, Case Rebecca J, Boucher Yann Felix
Saw Swee Hock School of Public Health, National University of Singapore and National University Health System and National University Hospital System, Singapore, Singapore.
Singapore Centre for Environmental Life Sciences Engineering (SCELSE), National University of Singapore, Singapore, Singapore.
Front Microbiol. 2025 Mar 28;16:1437936. doi: 10.3389/fmicb.2025.1437936. eCollection 2025.
Marine heterotrophic bacteria in coastal waters respond to the influx of carbon from natural and anthropogenic sources. We identified two nearly identical, (99.9% average nucleotide identity; 100% amino acid identity; same DNA G + C content of 52.3 mol%) high-quality (≥99% CheckM completeness and ≤ 1.3% contamination) draft metagenome-assembled genomes (MAGs; SJ0813 and SJ0972) from seawater microbiomes of a southern island of Singapore that is in a protected marine park. The MAGs were only assigned to the family according to Genome Taxonomy Database. Overall genome related indices to KU41G as the closest phylogenetic relative revealed no more than 70.45% average nucleotide identity (ANI < 95%), below the 50% percentage of conserved proteins (POCP = 43.54%) for genera cutoff and low digital DNA-DNA hybridization values (DDH = 20.6 and 20.8%). The major respiratory quinone is predicted to be ubiquinone-9 from the annotation of 3-demethylubiquinone-9 3-methyltransferase (, K00568) involved in the last step of the ubiquinone biosynthesis pathway (M00117), which differed from the ubiquinone-8 utilized by known members of . Both MAGs contained a complete pathway for dissimilatory nitrate reduction to ammonia, which increases bioavailability of nitrogen in seawater. An identical choline dehydrogenase found in both MAGs have a low amino-acid identity (≤64.47%) compared to existing GMC family oxidoreductases, expanding on the diversity of this family of enzymes. The MAGs meet nearly all the minimum requirements but lack a 16S rRNA gene of sufficient length required for the proposed novel genus and species under SeqCode. Nevertheless, phylogenetic trees based on core-genome and RpoB as an alternative phylogenetic marker are congruent with the taxon standing as a monophyletic clade to other taxa of the order Cellvibrionales. Taken together, the MAGs (SJ0813 and SJ0972) represent an uncultured, undescribed genus and species in which we tentatively propose the name Pelagadaptatus aseana gen. nov., sp. nov. and strain SJ0813 (=BAABNI000000000.1) as type sequence. Phylogenetic inference from core-genome and RpoB phylogenetic trees placed KMM 3891 outside . We, therefore, propose the transfer of the genus from the family to a new family according to the International Code of Nomenclature of Prokaryotes.
沿海水域中的海洋异养细菌会对来自自然和人为来源的碳流入做出反应。我们从新加坡一个位于受保护海洋公园的南部岛屿的海水微生物群落中鉴定出了两个几乎相同的（平均核苷酸同一性为99.9%；氨基酸同一性为100%；DNA G+C含量均为52.3 mol%）高质量（≥99% CheckM完整性且≤1.3%污染率）的宏基因组组装基因组（MAGs；SJ0813和SJ0972）。根据基因组分类数据库，这些MAGs仅被归类到科。与最接近的系统发育亲缘种KU41G相比，整体基因组相关指数显示平均核苷酸同一性不超过70.45%（ANI<95%），低于属的保守蛋白百分比截断值50%（POCP=43.54%），且数字DNA-DNA杂交值较低（DDH=20.6和20.8%）。从参与泛醌生物合成途径最后一步的3-去甲基泛醌-9 3-甲基转移酶（K00568，M00117）的注释预测，主要呼吸醌为泛醌-9，这与已知成员所利用的泛醌-8不同。两个MAGs都包含一条将异化硝酸盐还原为氨的完整途径，这增加了海水中氮的生物可利用性。与现有的GMC家族氧化还原酶相比，两个MAGs中发现的一种相同的胆碱脱氢酶氨基酸同一性较低（≤64.47%），这扩展了该酶家族的多样性。这些MAGs几乎满足了所有最低要求，但缺乏SeqCode提议的新属和新物种所需的足够长度的16S rRNA基因。然而，基于核心基因组和作为替代系统发育标记的RpoB构建的系统发育树与该分类单元作为Cellvibrionales目其他分类单元的单系分支的分类地位一致。综上所述，MAGs（SJ0813和SJ0972）代表了一个未培养、未描述的属和种，我们暂定将其命名为Pelagadaptatus aseana gen. nov., sp. nov.，并将菌株SJ0813（=BAABNI000000000.1）作为模式序列。基于核心基因组和RpoB系统发育树的系统发育推断将KMM 3891置于……之外。因此，我们根据《原核生物命名国际准则》提议将……属从……科转移到一个新的科。
