Methanobacterium arcticum sp. nov., a methanogenic archaeon from Holocene Arctic permafrost

Abstract

A mesophilic, non-motile, hydrogenotrophic, rod-shaped methanogen, designated M2 T , was isolated from Holocene permafrost sediments of the Kolyma lowland in the Russian Arctic. Cells were 3-6 mm long and 0.45-0.5 mm wide. Strain M2 T grew on H 2 /CO 2 and formate. Optimum conditions for growth were 37 6C, pH 6.8-7.2 and 0.1 M NaCl. The DNA G+C content was 38.1 mol%. On the basis of 16S rRNA gene sequence comparison with known methanogens, strain M2 T was affiliated with the genus Methanobacterium and was most closely related to Methanobacterium veterum MK4 T and Methanobacterium bryantii DSM 863 T (both 99 % 16S rRNA gene sequence similarity). However, no significant DNA-DNA relatedness was observed between strain M2 T and these type strains. We propose that strain M2 T represents a novel species, with the name Methanobacterium arcticum sp. nov., with type strain M2 T (5DSM 19844 T 5VKM B-2371 T ).At the time of writing, the genus Methanobacterium comprises 24 species with validly published names, although a number of them have been reclassified (http://www. bacterio.cict.fr/m/methanobacterium.html). The remaining members of the genus are hydrogenotrophic mesophiles, and only Methanobacterium subterraneum (Kotelnikova et al., 1998) and Methanobacterium aarhusense (Shlimon et al., 2004) were isolated from permanently cold habitats.One of the reasons for the presence of methane in permafrost is methane formation in sediments at above-zero temperatures followed by its conservation during freezing. At the same time, one cannot exclude the possibility of methane formation in permafrost at sub-zero temperatures. Previously, we isolated three strains of methanogenic archaea from samples of Pliocene and Holocene permafrost from Eastern Siberia (Rivkina et al., 2007). Strains M2 T , MK3 and MK4 T were non-motile hydrogenotrophic rods. Strain MK4 T has been assigned to a novel species, Methanobacterium veterum (Krivushin et al., 2010). In the present study, we report the characterization of strain M2 T .Strain M2 T was isolated from a sample of deep (2.0 m) Holocene permafrost sediments of the Kolyma lowland, Russia (70 u 069 N 154 u 049 E), by long-term enrichment (Rivkina et al., 2007). The protocols for drilling and subsequent handling of cores ensured that the retrieved material remained uncontaminated (Shi et al., 1997). Purity of the culture of strain M2 T was confirmed using the chromosomal DNA restriction pattern. The polyphasic characterization used the minimal standards detailed by Boone & Whitman (1988). M. veterum MK4 T and Methanobacterium bryantii VKM B-1629 T were used as reference strains.Gram-staining was performed following standard protocols (Smibert & Krieg, 1994) and cells of strain M2 T stained Gram-negative. Cell morphology was examined using phase-contrast microscopy (I-2; Lumam) at 61350 magnification and electron microscopy (JEM-100; JEOL) with ultrathin sections as described previously (Shcherbakova et al., 2005). Cells of strain M2 T were non-motile, slightly curved rods (Fig. 1a), 0.45-0.50...

Permafrost-affected soils and their carbon pools with a focus on the Russian Arctic

“…Wüthrich et al, 1999;Rivkina et al, 2007;Knoblauch et al, 2008Knoblauch et al, , 2013Liebner et al, 2011;Shcherbakova et al, 2011). The emissions of greenhouse gases were initially captured in the northern Siberian Lena River Delta starting in 2000 via small- Figure 10.…”

“…The properties and the spatial distribution of the permafrost-affected soils within the various countries were collected by Tarnocai (2004) and Smith and Veldhuis (2004) for Canada; by Ping et al (2004a) for Alaska; by Ignatenko (2004), Naumov (2004), Karavaeva (2004), Sokolov et al (2004) and Gracheva (2004) for the diverse and extensive areas of Russia; by Maximovich (2004) for Mongolia; and by Ping et al (2004b) . The book contains a comprehensive description of the research into permafrost-affected soils and their history, as well as the spatial distribution of these soils along with their properties.…”

Methanobacterium lacus sp. nov., isolated from the profundal sediment of a freshwater meromictic lake

“…The cultivated, recognized species that appeared most closely related to strain 17A1 T , with a 16S rRNA gene sequence similarity of 96.3 %, was Methanobacterium beijingense 8-2 T (Ma et al, 2005). Since its 16S rRNA gene sequence showed ,97 % similarity with the corresponding sequences of recognized species of the genus Methanobacterium, strain 17A1 T should be considered to represent a novel species (Stackebrandt & Goebel, 1994).At the time of writing, the genus Methanobacterium comprised 19 species with validly published names (Bonin & Boone, 2006;Kitamura et al, 2011;Krivushin et al, 2010;Ma et al, 2005;Mori & Harayama, 2011;Shcherbakova et al, 2011;Shlimon et al, 2004;Zhu et al, 2011). These species usually grow by reducing CO 2 with H 2 .…”

“…At the time of writing, the genus Methanobacterium comprised 19 species with validly published names (Bonin & Boone, 2006;Kitamura et al, 2011;Krivushin et al, 2010;Ma et al, 2005;Mori & Harayama, 2011;Shcherbakova et al, 2011;Shlimon et al, 2004;Zhu et al, 2011). These species usually grow by reducing CO 2 with H 2 .…”

Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium lacus isolated from northern peatlands

“…The high sequence similarity (99 %) between strain AL-21 and Methanobacterium lacus 17A1 T (Borrel et al, 2012) suggests the two strains are members of the same species. However, note that recent reports on Methanobacterium species taxonomy have found that even strains sharing 99 % 16S rRNA gene sequence similarity can be considered to represent different species in conjunction with other genomic assessments including DNA G+C content and DNA-DNA hybridization (Shcherbakova et al, 2011). Differences in DNA G+C content between strain AL-21 (35.8 mol%) and Methanobacterium lacus 17A1 T (37 mol%) are within limits previously found between different species of the genus Methanobacterium with 99 % 16S rRNA gene sequence similarity (Shcherbakova et al, 2011).…”