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Archaeal community dynamics and detection of ammonia-oxidizing archaea during composting of cattle manure using culture-independent DNA analysis

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Abstract

The composting process is carried out under aerobic conditions involving bacteria, archaea, and fungi. Little is known about the diversity of archaeal community in compost, although they may play an important role in methane production and ammonia oxidation. In the present study, archaeal community dynamics during cattle manure composting were analyzed using a clone library of the archaeal 16S rRNA gene. The results indicated that methane-producing archaea (methanogen) and ammonia-oxidizing archaea (AOA) may be the dominant microbes throughout the composting. The community consisted primarily of Methanocorpusculum-like and Methanosarcina-like sequences until day 2, while the number of Candidatus Nitrososphaera-like sequences increased from day 6 to day 30. Methanosarcina thermophila-like sequences were dominant from day 2, suggesting that M. thermophila-like species can adapt to increasing temperature or nutrient loss. A denaturant gradient gel electrophoresis analysis of the archaeal amoA genes revealed that the dominant amoA gene sequence with 99% homology to that of Candidatus Nitrososphaera gargensis was identical to those obtained from a different composting facility. These data suggested that AOA may play a role in ammonia oxidation in several composting practices. Our results provide fundamental information regarding archaeal community dynamics that will help in understanding the collective microbial community in compost.

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Acknowledgements

This work was partially supported by the Foundation of the Ministry of Education, Culture, Sports, Science, and Technology, Japan, as a “Project of Integrated Compost Science” and by a grant from the Livestock Technology Association, Japan. We would like to thank M. Tannai for making and managing compost.

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  1. Laboratory of Sustainable Environmental Biology, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan

    Nozomi Yamamoto, Ryoki Asano, Hiroki Yoshii, Kenichi Otawa & Yutaka Nakai

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  1. Nozomi Yamamoto
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Correspondence to Yutaka Nakai.

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Fig. S1

Phylogenetic tree of the archaeal 16S rRNA gene sequences obtained from composting materials. Boot-strap values (>60%) are indicated at the branch points. All sequences obtained from the present study are indicated in bold letters. The scale bar represents 5% sequence divergence. Accession numbers are indicated in parentheses. (TIFF 9039 kb)

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Yamamoto, N., Asano, R., Yoshii, H. et al. Archaeal community dynamics and detection of ammonia-oxidizing archaea during composting of cattle manure using culture-independent DNA analysis. Appl Microbiol Biotechnol 90, 1501–1510 (2011). https://doi.org/10.1007/s00253-011-3153-2

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