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

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• 作者：Dedysh ; Svetlana N. ; Dunfield ; Peter F. ; Derakshani ; Manigee ; Stubner ; Stephan ; Heyer ; Jü ; rgen ; et. al.
• 关键词：Fluorescent in situ hybridisation (FISH) ; Oligonucleotide probe ; Type II methanotroph ; Methylocystis sp. ; Acidic peatlands ; Methylocapsa acidiphila ; Methylocella palustris
• 刊名：FEMS Microbiology Ecology
• 出版年：2003
• 期刊代码：33_01686496
• 类别：imm
• 出版时间：April 1, 2003
• 卷：43
• 期：3
• 页码：299-308
• 文件大小：376 K

摘要

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±0.1×10⁶ cells g^−1 (wet weight) of peat from Siberia and 5.5±0.5×10⁶ 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.