Versantvoort Wouter, Guerrero-Cruz Simon, Speth Daan R, Frank Jeroen, Gambelli Lavinia, Cremers Geert, van Alen Theo, Jetten Mike S M, Kartal Boran, Op den Camp Huub J M, Reimann Joachim
Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands.
Department of Biotechnology, Delft University of Technology, Delft, Netherlands.
Front Microbiol. 2018 Jul 24;9:1672. doi: 10.3389/fmicb.2018.01672. eCollection 2018.
Methane is a potent greenhouse gas, which can be converted by microorganism at the expense of oxygen, nitrate, nitrite, metal-oxides or sulfate. The bacterium ' Methylomirabilis oxyfera,' a member of the NC10 phylum, is capable of nitrite-dependent anaerobic methane oxidation. Prolonged enrichment of ' M. oxyfera' with cerium added as trace element and without nitrate resulted in the shift of the dominant species. Here, we present a high quality draft genome of the new species ' Methylomirabilis lanthanidiphila' and use comparative genomics to analyze its metabolic potential in both nitrogen and carbon cycling. To distinguish between gene content specific for the '. Methylomirabilis' genus and the NC10 phylum, the genome of a distantly related NC10 phylum member, CSP1-5, an aerobic methylotroph, is included in the analysis. All genes for the conversion of nitrite to N identified in ' M. oxyfera' are conserved in ' M. lanthanidiphila,' including the two putative genes for NO dismutase. In addition both species have several heme-copper oxidases potentially involved in NO and O respiration. For the oxidation of methane ' Methylomirabilis' species encode a membrane bound methane monooxygenase. CSP1-5 can act as a methylotroph, but lacks the ability to activate methane. In contrast to ' M. oxyfera,' which harbors three methanol dehydrogenases (MDH), both CSP1-5 and ' M. lanthanidiphila' only encode a lanthanide-dependent XoxF-type MDH, once more underlining the importance of rare earth elements for methylotrophic bacteria. The pathways for the subsequent oxidation of formaldehyde to carbon dioxide and for the Calvin-Benson-Bassham cycle are conserved in all species. Furthermore, CSP1-5 can only interconvert nitrate and nitrite, but lacks subsequent nitrite or NO reductases. Thus, it appears that although the conversion of methanol to carbon dioxide is present in several NC10 phylum bacteria, the coupling of nitrite reduction to the oxidation of methane is a trait so far unique to the genus ' Methylomirabilis.'
甲烷是一种强效温室气体，可被微生物利用氧气、硝酸盐、亚硝酸盐、金属氧化物或硫酸盐作为代价进行转化。“嗜氧甲基奇异菌”（Methylomirabilis oxyfera）这种细菌属于NC10门，能够进行依赖亚硝酸盐的厌氧甲烷氧化。在添加铈作为微量元素且无硝酸盐的条件下，对“嗜氧甲基奇异菌”进行长时间富集培养导致了优势菌种的转变。在此，我们展示了新物种“嗜镧甲基奇异菌”（Methylomirabilis lanthanidiphila）的高质量基因组草图，并利用比较基因组学分析其在氮循环和碳循环中的代谢潜力。为了区分“甲基奇异菌”属和NC10门特有的基因内容，分析中纳入了一个亲缘关系较远的NC10门成员、需氧甲基营养菌CSP1-5的基因组。在“嗜氧甲基奇异菌”中鉴定出的将亚硝酸盐转化为氮气的所有基因在“嗜镧甲基奇异菌”中都是保守的，包括两个推测的一氧化氮歧化酶基因。此外，这两个物种都有几个可能参与一氧化氮和氧气呼吸的血红素-铜氧化酶。对于甲烷氧化，“甲基奇异菌”物种编码一种膜结合甲烷单加氧酶。CSP1-5可以作为甲基营养菌，但缺乏激活甲烷的能力。与含有三种甲醇脱氢酶（MDH）的“嗜氧甲基奇异菌”不同，CSP1-5和“嗜镧甲基奇异菌”都只编码一种依赖镧系元素的XoxF型MDH，这再次强调了稀土元素对甲基营养菌的重要性。甲醛随后氧化为二氧化碳以及卡尔文-本森-巴斯姆循环的途径在所有物种中都是保守的。此外，CSP1-5只能相互转化硝酸盐和亚硝酸盐，但缺乏后续的亚硝酸盐或一氧化氮还原酶。因此，似乎虽然甲醇转化为二氧化碳存在于几种NC10门细菌中，但亚硝酸盐还原与甲烷氧化的耦合是迄今为止“甲基奇异菌”属独有的特征。
