Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.
Research Organization for Nano and Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.
Environ Microbiol. 2020 Jun;22(6):2365-2382. doi: 10.1111/1462-2920.15015. Epub 2020 Apr 28.
Oxidation of nitrite to nitrate is an important process in the global nitrogen cycle. Recent molecular biology-based studies have revealed that the widespread nitrite-oxidizing bacteria (NOB) belonging to the genus 'Candidatus Nitrotoga' may be highly important for the environment. However, the insufficient availability of pure Nitrotoga cultures has limited our understanding of their physiological and genomic characteristics. Here, we isolated the 'Ca. Nitrotoga' sp. strain AM1P, from a previously enriched Nitrotoga culture, using an improved isolation strategy. Although 'Ca. Nitrotoga' have been recognized as cold-adapted NOB, the strain AM1P had a slightly higher optimum growth temperature at 23°C. Strain AM1P showed a pH optimum of 8.3 and was not inhibited even at high nitrite concentrations (20 mM). We obtained the complete genome of the strain and compared the genome profile to five previously sequenced 'Ca. Nitrotoga' strains. Comparative genomics suggested that lactate dehydrogenase may be only encoded in the strain AM1P and closely related genomes. While the growth yield of AM1P did not change, we observed faster growth in the presence of lactate in comparison to purely chemolithoautotrophic growth. The characterization of the new strain AM1P sheds light on the physiological adaptation of this environmentally important, but understudied genus 'Ca. Nitrotoga'.
亚硝酸盐氧化为硝酸盐是全球氮循环中的一个重要过程。最近基于分子生物学的研究表明，广泛存在的亚硝酸盐氧化细菌（NOB）属于“候选硝化螺旋菌属”（Ca. Nitrotoga），可能对环境非常重要。然而，由于纯 Nitrotoga 培养物的供应不足，限制了我们对其生理和基因组特征的理解。在这里，我们使用改进的分离策略，从先前富集的 Nitrotoga 培养物中分离出“候选硝化螺旋菌属”（Ca. Nitrotoga）sp. 菌株 AM1P。尽管“候选硝化螺旋菌属”（Ca. Nitrotoga）被认为是耐冷的 NOB，但 AM1P 菌株的最适生长温度略高，为 23°C。菌株 AM1P 的 pH 最适值为 8.3，即使在高亚硝酸盐浓度（20 mM）下也不会受到抑制。我们获得了该菌株的完整基因组，并将基因组图谱与之前测序的五个“候选硝化螺旋菌属”（Ca. Nitrotoga）菌株进行了比较。比较基因组学表明，只有 AM1P 菌株及其密切相关的基因组中编码了乳酸脱氢酶。虽然 AM1P 的生长产量没有变化，但与纯化能自养生长相比，我们观察到在存在乳酸的情况下生长更快。新菌株 AM1P 的特性揭示了这个对环境重要但研究不足的“候选硝化螺旋菌属”（Ca. Nitrotoga）的生理适应机制。
