Gammaproteobacterial Methanotrophs Dominate Cold Methane Seeps in Floodplains of West Siberian Rivers

Abstract

A complex system of muddy fluid-discharging and methane (CH 4 )-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH 4 flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH 4 h ؊1 , while some seeps emitted up to 5.54 g CH 4 h ؊1 . The ␦ 13 C value of methane released from these seeps varied between ؊71.1 and ؊71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low in situ temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH 4 ml ؊1 day ؊1 ) were measured in mud samples. Fluorescence in situ hybridization detected 10 7 methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of methanotrophs in this habitat was further assessed by pyrosequencing of pmoA genes, encoding particulate methane monooxygenase. A total of 53,828 pmoA gene sequences of seep-inhabiting methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the Methylobacter-Methylovulum-Methylosoma group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH 4 sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant methanotrophs, thereby providing a challenge for future isolation studies.

Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog

“…The Methylovulum 16S rRNA gene sequences detected in our experiments were not closely related to those of M. miyakonense, suggesting the existence of as yet uncultivated members of this genus that may be acidotolerant or acidophilic. Methylovulum populations from other environments have also been identified as potentially psychrotolerant and capable of oxidizing methane at low concentrations, suggesting adaptability of Methylovulum to the changing environmental conditions at the surface of boreal peatlands (52). This would not be the first example of an organism seemingly suited to one particular environment playing a role in a wholly different environmental system.…”

Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum

“…The seeps were characterized by low in situ temperatures (3.5 to 5 o C), high concentrations of emitted methane (70-99 % of gases released from these bubbling pools) and near-neutral pH of 6.8 to 6.9 (Oshkin et al, 2014). Aliquots (0.5 ml) of mud suspensions were placed in 120 ml serum bottles containing 20 ml of liquid diluted nitrate mineral salts medium (DNMS; Dunfield et al, 2003) with the addition of 0. and Na 2 MoO 4 , 0.03.…”

“…These methanotrophs were also found in water discharged during summer seasons from Russell Glacier, a land-terminating outlet glacier at the western margin of the Greenland Ice Sheet (Dieser et al, 2014). In our recent study of cold methane seeps in floodplains of West Siberian rivers, Methyluvulum-related bacteria were also identified among the dominant methanotroph groups (Oshkin et al, 2014). Our further efforts, therefore, were focused on obtaining cold-tolerant representatives of this genus in pure culture.…”

Methanotroph‐derived bacteriohopanepolyol signatures as a function of temperature related growth, survival, cell death and preservation in the geological record

“…Crenothrix spp. have been previously identified in low temperature environments, for instance, cold methane seeps in West Siberian river flood plains (Oshkin et al ., ). Conversely, type II methanotrophs ( Alphaproteobacterial, Rhizobiales ) were absent in the CH 4 amended incubations (Supporting Information Table S2).…”