A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments

Abstract

Although representatives with spiral-shaped cells are described for many functional groups of bacteria, this cell morphotype has never been observed among methanotrophs. Here, we show that spiral-shaped methanotrophic bacteria do exist in nature but elude isolation by conventional approaches due to the preference for growth under micro-oxic conditions. The helical cell shape may enable rapid motility of these bacteria in water-saturated, heterogeneous environments with high microbial biofilm content, therefore offering an advantage of fast cell positioning under desired high methane/low oxygen conditions. The pmoA genes encoding a subunit of particulate methane monooxygenase from these methanotrophs form a new genus-level lineage within the family Methylococcaceae, type Ib methanotrophs. Application of a pmoA-based microarray detected these bacteria in a variety of high-latitude freshwater environments including wetlands and lake sediments. As revealed by the environmental pmoA distribution analysis, type Ib methanotrophs tend to live very near the methane source, where oxygen is scarce. The former perception of type Ib methanotrophs as being typical for thermal habitats appears to be incorrect because only a minor proportion of pmoA sequences from these bacteria originated from environments with elevated temperatures.

Metagenomic Binning Recovers a Transcriptionally Active Gammaproteobacterium Linking Methanotrophy to Partial Denitrification in an Anoxic Oxygen Minimum Zone

“…Genes for fatty acid metabolism were also among the most abundant transcripts recruiting to GD_7, as were those mediating flagellar biosynthesis and regulation. The high transcription of flagellar genes is consistent with prior reports of the importance of motility in type 1 methanotrophs from low oxygen environments (Danilova et al, 2016), suggesting a need to traverse redox gradients to access zones of optimal substrate (e.g., methane) or oxygen conditions, potentially including those at the micron scale on suspended or sinking particles. Enzymes involved in amino acid metabolism were also abundant in the GD_7 transcript pool (Supplementary Table 5, Supplementary Figure 5), with proline dehydrogenase being among the most highly transcribed GD_7-specific protein at 90 m. This enzyme is involved in proline catabolism, producing reductant in the form of reduced co-enzyme Q10 (i.e., ubiquinol).…”

“…Bacterial groups canonically associated with aerobic methanotrophy may also play a role in nitrogen loss by directly using nitrate or nitrite as terminal oxidants in AOM. Evidence for these groups, predominantly of the gammaproteobacterial order Methylococcales, has been found in both culture-dependent and -independent studies of diverse low oxygen environments (Kalyuzhnaya et al, 2013;Chistoserdova, 2015;Kits et al, 2015a,b;Danilova et al, 2016), including meromictic lakes (Biderre-Petit et al, 2011;Blees et al, 2014) and marine water columns (Hayashi et al, 2007;Tavormina et al, 2013). Studies with isolates of two methanotrophic Methylococcales genera (Methylomonas and Methylomicrobium) show that hypoxic conditions stimulate denitrification to produce N 2 O accompanied by increased cellular ATP yields (Kits et al, 2015a,b).…”

Thriving in Wetlands: Ecophysiology of the Spiral-Shaped Methanotroph Methylospira mobilis as Revealed by the Complete Genome Sequence

“…The culture of Candidatus Methylospira mobilis described by Danilova et al [11] was grown in the modified liquid DSMZ medium 1181 (DNMS, [23]) containing (in gram per litre) MgSO 4 , 0.2; KNO 3 , 0.2; CaCl 2 , 0.04; KH 2 PO 4 , 0.054; Na 2 HPO 4 × 12H 2 O, 0.143 with the addition of 0.1% (v/v) of a trace elements stock solution. Final pH of the medium was 5.8.…”

“…Methanotrophic bacteria display an impressive range of phenotypes and habitat-specific adaptations. One of the most surprising, recently described phenotypes of proteobacterial methanotrophs is represented by Candidatus Methylospira mobilis, a spiral-shaped, micro-aerophilic methanotroph, which is capable of rapid motility in water-saturated, heterogeneous habitats with high microbial biofilm content [11]. As suggested by culture-independent studies, Methylospira-like methanotrophs are widely distributed in various northern environments, such as wetlands, organic soils, and lake sediments.…”

“…They displayed CH 4 -tactic responses, thereby being capable of fast moving through semisolid agar medium under methane and oxygen concentration gradients. Despite all purification efforts, this methanotroph could not be obtained in pure culture and, therefore, was assigned the status Candidatus [11]. We, however, continued our purification work, which finally resulted in obtaining the first axenic culture of this unique methanotroph, strain Shm1.…”