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Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes

Author:
Dedysh, S.N., Dunfield, P.F., Derakshani, M., Stubner, S., Heyer, J., Liesack, W.
Source:
FEMS microbiology ecology 2003 v.43 no.3 pp. 299-308
ISSN:
0168-6496
Subject:
Methylocella palustris, Methylocystis, Methylosinus sporium, Methylosinus trichosporium, Sphagnum, bacteria, databases, fluorescence, fluorescence in situ hybridization, methanotrophs, nucleotide sequences, oligonucleotide probes, oligonucleotides, peat, peatlands, phylogeny, population size, ribosomal RNA, Germany, Siberia
Abstract:
Based on an extensive 16S rRNA sequence database for type II methanotrophic bacteria, a set of 16S rRNA-targeted oligonucleotide probes was developed for differential detection of specific phylogenetic groups of these bacteria by fluorescence in situ hybridisation (FISH). This set of oligonucleotides included a genus-specific probe for Methylocystis (Mcyst-1432) and three species-specific probes for Methylosinus sporium (Msins-647), Methylosinus trichosporium (Msint-1268) and the recently described acidophilic methanotroph Methylocapsa acidiphila (Mcaps-1032). These novel probes were applied to further characterise the type II methanotroph community that was detected in an acidic Sphagnum peat from West Siberia in a previous study (Dedysh et al. (2001) Appl. Environ. Microbiol. 67, 4850-4857). The largest detectable population of indigenous methanotrophs simultaneously hybridised with a group-specific probe targeting all currently known Methylosinus/Methylocystis spp. (M-450), with a genus-specific probe for Methylocystis spp. (Mcyst-1432), and with an additional probe (Mcyst-1261) that had been designed to target a defined phylogenetic subgroup of Methylocystis spp. The same subgroup of Methylocystis was also detected in acidic peat sampled from Sphagnum-dominated wetland in northern Germany. The population size of this peat-inhabiting Methylocystis subgroup was 2.0 +/- 0.1 x 10(6) cells g-1 (wet weight) of peat from Siberia and 5.5 +/- 0.5 x 10(6) cells g-1 of peat from northern Germany. This represented 60 and 95%, respectively, of the total number of methanotroph cells detected by FISH in these two wetland sites. Other major methanotroph populations were M. acidiphila and Methylocella palustris. Type I methanotrophs accounted for not more than 1% of total methanotroph cells. Neither M. trichosporium nor M. sporium were detected in acidic Sphagnum peat.
Agid:
2979062