Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
Int J Syst Evol Microbiol. 2014 Mar;64(Pt 3):989-999. doi: 10.1099/ijs.0.058172-0. Epub 2013 Dec 18.
A novel methane-oxidizing bacterium, strain IT-9(T), was isolated from a shallow submarine hydrothermal system occurring in a coral reef in Japan. Strain IT-9(T) was a Gram-negative, aerobic, motile, coccoid or oval-shaped bacterium with the distinctive intracytoplasmic membrane arrangement of a type I methanotroph. Strain IT-9(T) was a moderately thermophilic, obligate methanotroph that grew on methane and methanol at 30-55 °C (optimum 45-50 °C). The strain possessed the particulate methane monooxygenase (pMMO). The ribulose monophosphate pathway was operative for carbon assimilation. NaCl was required for growth within a concentration range of 1-5 % (optimum 3 %). The hao gene encoding hydroxylamine oxidoreductase (HAO) involved in nitrification was detected by a PCR experiment. The major phospholipid fatty acids were C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The DNA G+C content was 66.0 mol%. The 16S rRNA gene sequence of strain IT-9(T) was only moderately related to the sequences of members of the closest genera Methylohalobius (94.1 % similarity) and Methylothermus (91.7-91.9 % similarity); however, those sequences formed a deeply branching monophyletic group within the order Methylococcales. Phylogenies based on 16S rRNA gene sequences, deduced partial PmoA sequences and deduced partial Hao sequences and physiological and chemotaxonomic characteristics revealed that strain IT-9(T) represents a novel species of a new genus, for which the name Methylomarinovum caldicuralii gen. nov., sp. nov. is proposed. The type strain of Methylomarinovum caldicuralii is IT-9(T) ( = JCM 13666(T) = DSM 19749(T)). In addition, we propose a new family, Methylothermaceae fam. nov., in the order Methylococcales, to accommodate the genera Methylothermus, Methylohalobius and Methylomarinovum. The genera Methylothermus and Methylohalobius have been recognized as being distinct from other genera in the methane-oxidizing order Methylococcales in the class Gammaproteobacteria. These genera form a distinctive monophyletic lineage within the order on the basis of 16S rRNA gene sequence phylogeny. This seems consistent with their distinctive physiological traits; the genus Methylothermus includes the most thermophilic species, and the genus Methylohalobius includes the most halophilic species, within the order. Although these two genera include only three species at the time of writing, similar sequences of 16S rRNA genes and pmoA genes encoding pMMO have been detected in a geothermal area or deep-sea hydrothermal vent fields by studies using culture-independent techniques. This suggests that unknown methanotrophs of this lineage inhabit various extreme environments.
一株新型甲烷氧化细菌，菌株 IT-9(T)，从日本珊瑚礁浅海海底热液系统中分离得到。菌株 IT-9(T) 是革兰氏阴性、需氧、运动、球形或椭圆形细菌，具有 I 型甲烷氧化菌特有的细胞内内膜排列。菌株 IT-9(T) 是一种中度嗜热的专性甲烷氧化菌，可在 30-55°C（最佳温度为 45-50°C）下利用甲烷和甲醇生长。该菌株具有颗粒状甲烷单加氧酶（pMMO）。核酮糖单磷酸途径是用于碳同化的途径。在 1-5%（最佳 3%）的范围内需要 NaCl 才能生长。通过 PCR 实验检测到参与硝化作用的羟胺氧化还原酶（HAO）的 hao 基因。主要磷脂脂肪酸为 C16:0 和 C18:1ω7c。主要异戊二烯醌为 Q-8。DNA G+C 含量为 66.0 mol%。菌株 IT-9(T) 的 16S rRNA 基因序列与最接近的属 Methylohalobius（94.1%相似度）和 Methylothermus（91.7-91.9%相似度）的成员序列仅中度相关；然而，这些序列在甲基球菌目中形成了一个分支很深的单系群。基于 16S rRNA 基因序列、部分 PmoA 序列和部分 Hao 序列以及生理和化学分类特征的系统发育分析表明，菌株 IT-9(T) 代表了一个新属的新型物种，建议将其命名为 Marinevum caldicuralii 属 nov.，sp. nov.。 Marinevum caldicuralii 的模式菌株是 IT-9(T)（=JCM 13666(T)=DSM 19749(T)）。此外，我们在甲基球菌目中提出了一个新的科，即 Methylohalobius 科 nov.，以容纳 Methylohalobius、Methylothermus 和 Marinevum caldicuralii 属。Methylothermus 和 Methylohalobius 属在 γ-变形菌纲的甲烷氧化菌目中已被认为与其他属不同。这些属在 16S rRNA 基因序列系统发育树上形成了一个独特的单系谱系。这似乎与它们独特的生理特征一致；属内最嗜热的物种属于 Methylohalobius 属，最嗜盐的物种属于 Methylothermus 属。尽管这两个属在撰写本文时仅包含三个物种，但通过使用非培养技术的研究，在热区或深海热液喷口场中已检测到类似的 16S rRNA 基因和编码 pMMO 的 pmoA 基因序列。这表明该谱系中的未知甲烷氧化菌栖息在各种极端环境中。
