Table_7_Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis.xlsx

Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the “H. desiderata group.” To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the “H. desiderata group,” in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the “H. desiderata group,” while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.

盐单胞菌属（Halomonas）细菌广泛分布于各类生境，在营养循环中发挥着重要作用。本研究从不同生境中分离得到14株兼具好氧反硝化与异养硫氧化能力的菌株。通过表型、基因型及化学分类学分析，确认这些菌株隶属于盐单胞菌属的6个新物种，分别命名为漳州盐单胞菌（Halomonas zhangzhouensis sp. nov.），模式菌株CXT3-11^T（= MCCC 1A11036^T = KCTC 72087^T）；反硝化盐单胞菌（Halomonas aerodenitrificans sp. nov.），模式菌株CYD-9^T（= MCCC 1A11058^T = KCTC 72088^T）；硫化物氧化盐单胞菌（Halomonas sulfidoxydans sp. nov.），模式菌株CYN-1-2^T（= MCCC 1A11059^T = KCTC 72089^T）；乙醇盐单胞菌（Halomonas ethanolica sp. nov.），模式菌株CYT3-1-1^T（= MCCC 1A11081^T = KCTC 72090^T）；噬硫化物盐单胞菌（Halomonas sulfidivorans sp. nov.），模式菌株NLG_F1E^T（= MCCC 1A13718^T = KCTC 72091^T）；以及天休盐单胞菌（Halomonas tianxiuensis sp. nov.），模式菌株BC-M4-5^T（= MCCC 1A14433^T = KCTC 72092^T）。值得注意的是，该类群与另外11个物种共同构成了一个独特的进化簇，即"H. desiderata group"（希氏盐单胞菌群）。为深入解析其特征性代谢机制，本研究对参与反硝化与硫氧化过程的基因，以及该属已公开的193个完整基因组进行了分析。结果一致表明，"H. desiderata group"（希氏盐单胞菌群）具备完整的反硝化通路，其基因组中同时存在napA、narG、nirS、norB及nosZ基因。该类群的亚硝酸还原酶NirS形成了一个独特的进化支系，与盐单胞菌属内其他反硝化菌株显著区分。此外，盐单胞菌属不同系统发育分支中的反硝化基因呈现出多样的分布模式。在硫氧化方面，参与硫化物氧化的fccAB基因在"H. desiderata group"（希氏盐单胞菌群）中普遍存在，而sqr基因分布更为广泛，可在更多物种中被检测到；本研究的8株菌株同时携带sqr与fccAB基因，这赋予其更强的硫化物氧化活性。此外，编码硫代硫酸盐氧化为连四硫酸盐酶的tsdA基因在盐单胞菌属中广泛分布。sqr/fccAB、pdo以及tsdA基因在盐单胞菌属中的广泛存在，表明多数盐单胞菌可作为异养硫氧化菌。本研究结果全面揭示了盐单胞菌属整体的反硝化与硫氧化潜力。针对盐单胞菌属的全球分布特征，本研究暗示了其在生物地球化学循环中不可忽视的重要作用。