Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.

中文翻译：

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基于培养和基因组学的方法揭示了海洋亚硝酸盐氧化细菌的多样性和代谢多功能性。


亚硝酸盐氧化细菌（NOB）是普遍存在且丰富的微生物，在全球氮和碳生物地球化学循环中发挥着关键作用。尽管最近在理解 NOB 生理学和分类学方面取得了进展，但目前存在很少的培养 NOB 或来自海洋环境的代表性 NOB 基因组序列。在这项研究中，我们采用富集培养和基因组方法来阐明海洋 NOB 的系统发育和代谢能力。我们成功富集了两个海洋 NOB（指定为 MSP 和 DJ），并从每个生物体中获得了高质量的宏基因组组装基因组（MAG）。 MSP 和 DJ 富集培养物的最大亚硝酸盐氧化速率分别为每天 13.8 和 30.0 μM 亚硝酸盐，这些最佳速率分别发生在 0.1 mM 和 0.3 mM 亚硝酸盐时。每种富集培养物对不同的亚硝酸盐和盐浓度表现出不同的耐受性。基于系统发育位置和整体基因组相关性指数，两种 NOB MAG 都被提议为 Nitrospinota 和 Nitrospirota 门内的新分类群。功能预测表明，两种 NOB MAG 与其他 NOB 具有许多高度保守的代谢特征。两种 NOB MAG 都编码用于氢和有机化合物代谢的蛋白质以及氧化应激的防御机制。此外，这些生物可能具有产生钴胺素（一种在许多环境中受到限制的必需酶辅因子）的遗传潜力，因此可能在海洋沉积物中回收钴胺素方面发挥重要作用。总体而言，这项研究显着扩展了我们对 Nitrospinota 和 Nitrospirota 门的理解，并表明这些 NOB 在海洋生境中发挥着重要的生物地球化学作用。