Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3–12.8 g salt/l), highly alkaline (pH 8.9–10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, “Candidatus Nitrospira alkalitolerans”, revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. “Ca. Nitrospira alkalitolerans” also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

Nitrospira属的亚硝酸盐氧化细菌是生物地球化学氮循环的关键参与者。然而，人们对它们在极端 pH 环境中的发生和生存策略知之甚少。在此，我们报告了生理上多功能、耐卤碱的Nitrospira的发现，该 Nitrospira 在极高 pH 下可驱动亚硝酸盐氧化。通过扩增子测序、宏基因组学和基于培养的方法，在低盐度和亚盐度（1.3-12.8 g 盐/升）、高碱性（pH 8.9-10.3）湖泊中研究了硝化螺菌的分布、多样性和生态生理学。令人惊讶的是，不仅检测到了Nitrospira种群，而且它们也相当多样化，存在来自Nitrospira谱系 I、II 和 IV 的成员。此外，还证明了Nitrospira富集培养物在中性至高碱性 pH 值 10.5 下氧化亚硝酸盐的能力。对新富集的Nitrospira谱系 IV 物种“ Candidatus Nitrospira 耐碱”的宏基因组分析揭示了该生物体对其极端环境的许多适应性特征。其中包括钠依赖性 N 型 ATP 酶和 NADH：醌氧化还原酶，以及通常在Nitrospira中发现的质子驱动形式。其他功能有助于 pH 值和阳离子稳态以及渗透应激防御。 “ Ca. Nitrospira 耐碱菌”还拥有 2a 组和 3b 组 [NiFe] 氢化酶，表明它可以使用氢作为替代能源。这些结果揭示了Nitrospira如何应对剧烈波动的 pH 和盐度条件，并扩展了我们对极端栖息地氮循环的了解。