A novel denitrifying methanotroph of the NC10 phylum and its microcolony

Abstract

The NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich, and our knowledge regarding this phylum is largely limited to the first species ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it ‘Candidatus Methylomirabilis sinica’ (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7–1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25–0.5 × 0.8–1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies.

Bloom of a denitrifying methanotroph, ‘Candidatus Methylomirabilis limnetica’, in a deep stratified lake

“…Comparative analysis of the 16S rRNA gene sequence showed 95.1% identity to ‘ Ca . M. sinica’ (He et al ., ) and 96.3% identity to ‘ Ca . M. oxyfera’ (Raghoebarsing et al ., ; Ettwig et al ., ).…”

“…The first described representative of this clade, 'Candidatus Methylomirabilis oxyfera' has been proposed to have a unique capacity to disproportionate nitric oxide intracellularly and produce molecular oxygen, which is used for methane oxidation (Ettwig et al, 2010;Ettwig et al, 2012). This unique pathway allows NC10 to thrive in oxygen-depleted habitats, despite the obligate need for oxygen to activate and oxidize methane (Raghoebarsing et al, 2006;López-Archilla et al, 2007;Zhu et al, 2012;He et al, 2016;Padilla et al, 2016;Shen et al, 2016). Recent studies have demonstrated that NC10-related methanotrophs are present in the anoxic water column of a freshwater reservoir and sediments of deep freshwater lakes such as Lake Constance (Deutzmann and Schink, 2011;Deutzmann et al, 2014) and Lake Biwa (Kojima et al, 2012).…”

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species

“…Interestingly rare taxa <1% belong to Armatimonadetes, AC1, NC10, NKB19, OP8 and GN04 (Table S1) were detected in both the enrichments. Presence of NC10 group in both the samples suggests their involvement in methane oxidation coupled with nitrification process 44,45 (Fig. S3).…”

Response of microbial community function to fluctuating geochemical conditions within a legacy radioactive waste trench environment

“…This interpretation is supported by the lack of measurable sulfides in the trench water (see Chemical analyses of trench waters), along with previous reports showing sulfate reduction based on isotopic fractionation and severe (10 to 100-fold) depletion in sulfate concentrations in trench waters relative to surrounding wells (11). The potential contribution of sulfate- and nitrite-dependent anaerobic methane oxidation (S-DAMO and N-DAMO respectively) was discounted due to the near complete absence of ANME taxa ( Archaea ) aside from ANME-2d, and NC10 ( Bacteria ) (see Nitrogen cycling) (44, 59, 64, 65).…”