Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog

Abstract

Two dense and highly enriched (up to 10(9) cells ml(-1), <10% of bacterial satellites) acido-tolerant (pH 4.0-6.5) methanogenic consortia, '26' and 'K', were isolated from the peat beneath a Sphagnum-Eriophorum-Carex community in West Siberia. Both consortia produced methane from CO2:H2 on chemically defined, diluted N-free media containing Ti(III)citrate as reducing agent. The phylogenetic analysis of 16S ribosomal DNA revealed three archaeal and nine bacterial sequence types. Consortium '26' contained single archaea Methanobacterium sp., represented by rods of 1.5-10x0.5-1.0 microm. In consortium 'K', there were two archaeal phylotypes, the respective methanogens were further differentiated morphologically with the fluorescence in situ hybridization technique: one less abundant (<2%) population of the long-curved rods (50-100x0.3-0.4 microm) fell into the order of Methanomicrobiales, while the dominant organism ( approximately 98%), represented by straight rods with abrupt rectangular ends (3-9x0.5 microm), was affiliated with earlier uncultured 'Rice cluster I'. The main bacterial satellite used citrate as a single carbon and energy source; it was similar in both consortia, and after isolation in pure culture, it was identified as a new member of the alpha-subclass of Proteobacteria. The other bacterial satellites were distributed among four taxonomic groups: the delta-subclass of Proteobacteria, the Flavobacterium-Bacteroides-Cytophaga line of descent, the Acidobacterium-Fibrobacter line of descent and the Green non-sulfur bacteria line of descent. At least 11 out of 12 components of acido-tolerant consortia are new to science at the species, genus and order levels; their existence until now was evident only from environmental gene retrievals. The Sphagnum wetlands, attracting attention only recently because of their global environmental role, are shown to be an especially valuable source of novel prokaryotic organisms.

Biodiversity, Distributions and Adaptations of Arctic Species in the Context of Environmental Change

“…It was found that most of the boreal and sub-Arctic wetlands contain a wide diversity of methanogens (40,41) and methanotrophs (42,43), most of them being distantly related to known species. Only recently, some of these obscure microbes were obtained in pure culture or stable consortia (44,45). The novel microbes of methane cycles are extreme oligotrophic species that evolved to function in media with very low concentrations of mineral nutrients.…”

“…The novel microbes of methane cycles are extreme oligotrophic species that evolved to function in media with very low concentrations of mineral nutrients. Taxonomically, the novel oligotrophic methanogens form new species, genera and even families within the Archaea domain (45). The acidophilic methanotrophs form two new groups: Methylocapsa and Methylocella (44,46), the last one affiliating with heterotrophic Beijerinckia indica.…”

Occurrence and distribution of tetraether membrane lipids in soils: Implications for the use of the TEX86 proxy and the BIT index

“…DeLong et al, 1994;MacGregor et al, 1997;Schleper et al, 1997;Vetriani et al, 1999;Jurgens et al, 2000;Karner et al, 2001;Keough et al, 2003), peat bogs, wetlands and soils (e.g. Buckley et al, 1998;Ochsenreiter et al, 2003;Sizova et al, 2003;Kotsyurbenko et al, 2004) and the deep subsurface (Takai et al, 2001). Despite being ubiquitous, only a limited number of archaeal cultures is available, mostly thermophiles and methanogens, one 'symbiont culture' of a mesophilic Crenarchaeota: Cenarchaeum symbiosum, an archaeon living in symbiosis with the marine sponge Axinella mexicana (Preston et al, 1996) and a nitrifying crenarchaeote isolated from a sea aquarium (Kö nneke et al, 2005).…”

Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov.

“…Previous culture-dependent and -independent investigations have provided evidence that members of the RC-I lineage utilize H 2 (Lueders et al, 2001;Sizova et al, 2003;Erkel et al, 2005Erkel et al, , 2006Lehmann-Richter et al, 1999). Erkel et al (2006) constructed a complete genome sequence of an RC-I methanogen from an enrichment culture growing on H 2 and revealed that the RC-I methanogen had a full set of genes involved in methanogenesis from H 2 /CO 2 .…”

“…Erkel et al (2006) constructed a complete genome sequence of an RC-I methanogen from an enrichment culture growing on H 2 and revealed that the RC-I methanogen had a full set of genes involved in methanogenesis from H 2 /CO 2 . Abundant populations of RC-I Archaea were detected in an acidophilic methanogenic consortium supplemented with H 2 as sole energy source (Sizova et al, 2003). The 16S rRNA gene sequences from those RC-I enrichments were determined and are available from the Genbank/EMBL/ DDBJ databases as AM114193 for the metagenome (the genome contained three rrn operons) and AF524853 for the acidophilic consortium.…”