Methanogenic communities in permafrost-affected soils of the Laptev Sea coast, Siberian Arctic, characterized by 16S rRNA gene fingerprints

Abstract

Permafrost environments in the Arctic are characterized by extreme environmental conditions that demand a specific resistance from microorganisms to enable them to survive. In order to understand the carbon dynamics in the climate-sensitive Arctic permafrost environments, the activity and diversity of methanogenic communities were studied in three different permafrost soils of the Siberian Laptev Sea coast. The effect of temperature and the availability of methanogenic substrates on CH4 production was analysed. In addition, the diversity of methanogens was analysed by PCR with specific methanogenic primers and by denaturing gradient gel electrophoresis (DGGE) followed by sequencing of DGGE bands reamplified from the gel. Our results demonstrated methanogenesis with a distinct vertical profile in each investigated permafrost soil. The soils on Samoylov Island showed at least two optima of CH4 production activity, which indicated a shift in the methanogenic community from mesophilic to psychrotolerant methanogens with increasing soil depth. Furthermore, it was shown that CH4 production in permafrost soils is substrate-limited, although these soils are characterized by the accumulation of organic matter. Sequence analyses revealed a distinct diversity of methanogenic archaea affiliated to Methanomicrobiaceae, Methanosarcinaceae and Methanosaetaceae. However, a relationship between the activity and diversity of methanogens in permafrost soils could not be shown.

Methanogenic activity and biomass in Holocene permafrost deposits of the Lena Delta, Siberian Arctic and its implication for the global methane budget

“…This indicates a tolerance of permafrost methanogens to their cold environment. This assumption is also supported by the finding of Ganzert et al (2007) who reported increasing methane production activity close to the permafrost table at low in situ temperature conditions. The zone of high methane concentrations in the permafrost deposits was characterized by in situ temperatures between approximately À2 and À9 1C.…”

“…Although, only a few psychrophilic strains of methanogenic archaea have been isolated so far (Simankova et al, 2003;Cavicchioli, 2006), there are some indications of methanogenic activity in cold permafrost environments (Kotsyurbenko et al, 1993;Wagner et al, 2003a, b; Ganzert et al, 2007). However, this study actually revealed methane production under in situ permafrost temperature conditions of down to À6 1C.…”

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

“…More than 60% of all OTUs and more than 70% of all sequences detected belong to these clusters. Specific clusters for Siberian permafrost-affected soils based on the 16S rRNA gene could already be detected for other groups of microorganisms such as methanogenic archaea [19], which was interpreted as clusters formed by methanogens characterized by a specific adaptation to the Figure 4 Phylogenetic tree showing the relation of representative amino acid sequences (translated pmoA gene sequences) from active layer samples of Samoylov Island, Lena Delta, to most closely branching pmoA gene sequences of cultured and uncultured aerobic methanotrophic bacteria and to Crenothrix polyspora (outgroup sequence). The tree represents a maximum likelihood tree calculated according to the PhyML algorithm [20] using a 30% filter (amino acid position 63-201).…”

“…Members of the Methylococcaceae are termed type I MOB and belong to the γ-subdivision of the Proteobacteria phylum. Members of the Methylocystaceae and Beijerinckiaceae are termed type II MOB and belong to the α-subdivision of the Proteobacteria phylum [10][11][12][13][14][15][16][17][18][19][20][21]. The diversity and composition of MOB have been investigated in several environments such as freshwater sediments [8,42], landfill soils [59], rice field soils [22,24], habitats with only atmospheric methane concentrations [29,33,35], and peat bogs with very low pH values [39,40].…”

Methanogenic System of a Small Lowland Stream Sitka, Czech Republic

“…Methanogenic archaea are ubiquitous in anoxic environments and require an extremely low redox potential to grow. They can be found both in moderate habitats such as rice paddies (Grosskopf et al 1998a,b), lakes (Jürgens et al 2000, Keough et al 2003) and lake sediments (Chan et al 2005), as well as in the gastrointestinal tract of animals (Lin et al 1997) and in extreme habitats such as hydrothermal vents (Jeanthon et al 1999), hypersaline habitats (Mathrani & Boone 1995) and permafrost soils (Kobabe et al 2004, Ganzert et al 2006. Rates of methane production and consumption in sediments are controlled by the relative availability of substrates for methanogenesis (especially acetate or hydrogen and carbon dioxide).…”