Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions.
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions.
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亚硝酸盐氧化细菌 Nitrospira marina 的代谢多样性及其对限氧条件的蛋白质组反应。
DOI：
10.1038/s41396-020-00828-3
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发表时间：
2021-04
期刊：
影响因子：
--
通讯作者：
Santoro AE
中科院分区：
文献类型：
--
作者：
Bayer B;Saito MA;McIlvin MR;Lücker S;Moran DM;Lankiewicz TS;Dupont CL;Santoro AE
硝化螺旋菌属是分布最广的亚硝酸盐氧化细菌群，在各种自然和工程生态系统中茁壮成长。硝酸螺旋菌Nb-295T是30多年前从海洋中分离出来的；然而，它的基因组尚未被分析。在此，我们基于N. marina的全基因组序列研究了其代谢潜力，并进行了生理实验来验证基因组衍生的假设。我们的数据证实，N. marina受益于添加未定义的有机碳基质，具有抵抗氧化、渗透和紫外线诱导的应激和低溶解二氧化碳分压的适应性，并且需要外源性维生素B12。此外，N. marina能够在甲酸盐上进行化学有机营养生长，因此不是专性的化学无机自养生物。我们进一步研究了N. marina对低（~ 5.6µM） O2浓度的蛋白质组学响应。在氧气限制下，可能更有效的固定二氧化碳的丙酮酸：铁氧还蛋白氧化还原酶（POR）复合物和高亲和力的cbb3型末端氧化酶的丰度增加，表明它们在维持亚硝酸盐氧化驱动的自养中起作用。这种对O2更敏感的POR复合物可能受到Cu/ zn结合超氧化物歧化酶的保护，在低氧条件下，这种酶的丰度也会增加。此外，参与替代能量代谢的蛋白质，包括3b组[NiFe]氢化酶和甲酸脱氢酶的上调，表明具有高代谢多功能性，可以在不利于有氧亚硝酸盐氧化的条件下生存。综上所述，第一个海洋硝化螺旋菌分离物的基因组和蛋白质组学鉴定了对缺氧海洋生活的适应，并为海洋环境中NOB的代谢多样性和生态位分化提供了见解。
The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO2, and requires exogenous vitamin B12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.
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