Analysis of the population dynamics of methanogens and sulfate-reducers in aquatic sediments by nucleic acid probes

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We improved the hydroxyapatite spin column method to extract nucleic acids from aquatic sediments with low biological activities. On the rRNA extracted by this method from sediments of Lakes Kizaki and Biwa, and Tokyo Bay quantitative dot-blot hybridization was carried out using several oligonucleotide probes and the results were compared with metabolic activities such as methane production and sulfate reduction. The relative abundance of rRNA of Desulfobulbus was high compared with other sulfate-reducing bacteria (SRB) and correlated with the rate of sulfate reduction in sediment of L. Kizaki. Therefore, Desulfobulbus appears to be dominant in the active SRB population there. In Tokyo Bay Desulfobacter was a dominant SRB genus at a dredged site where the bottom water tended to be stagnant, while the generic composition of SRB was complex at a natural sea bed. At the former site the rate of sulfate reduction did not correlate with the relative abundance of Desulfobocter rRNA, but did with its ATP amount which calculated from the product of total ATP content in sediment and its relative RNA abundance. In the sediment of L. Biwa, the relative RNA abundances of Desulfobulbus and Desulfobacterium increased in winter when sulfate reduction rate was relatively high. The relative RNA abundance of archaea containing methanogens increased with depth of the sediment, but was low from 1.3 to 3.0%. The hybridization signals with probes targeting genera of methanogens were too week to be detected.