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Analysis of communities of ammonia oxidizers, methanotrophs, and methanogens associated with microcrustaceans in the floodwater of a rice field microcosm

Abstract Ammonia-oxidizing bacteria (AOB), methanotrophs (MOB), and methanogens that were associated with Moina sp., Mesocyclops sp., Heterocypris sp. in the floodwater of a rice field microcosm were studied by using DGGE and sequence analysis with amoA / pmoA and methanogen-specific primer sets. Only one AOB and two MOB DGGE bands with the same mobility were detected, irrespective of the microcrustaceans. Effect of the incubation period was observed only in the AOB community associated with Moina sp., and an additional AOB clone appeared in the late period of incubation. Sequence analysis of the bands revealed that both of the closest relatives of the AOB clones belonged to uncultured ammonium monooxygenase genes of α-Proteobacteria, while those of the MOB clones to Methylomicrobium buryatense, an uncultured methanotroph bacterium, and Methylococcus capsulatus within type I methanotrophs belonging to γ-Proteobacteria. In contrast, no amplification products of 16S rDNA of the methanogenic archaea were obtained from any of the microcrustacean samples, indicating the absence or very small populations of methanogens.