Microbial Community Dynamics During the Composting Process of Animal Manure as Analyzed by Molecular Biological Methods

  • Nozomi YamamotoEmail author
  • Yutaka Nakai
Part of the Advances in Environmental Microbiology book series (AEM, volume 6)


Composting is a useful technique that transforms livestock manure into stable organic fertilizer. In composting, the biodegradation of substrates is conducted by microbial communities of bacteria, archaea, and fungi. Bacteria are assumed to play an important role in the decomposition of organic substances. However, only a few studies have tracked bacterial communities throughout the composting process. Furthermore, the role of archaea in composting remains to be fully elucidated. To uncover the dynamics of these bacterial and archaeal communities, a variety of molecular biological methods like PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and clone library were utilized. A clone library constructed from bacterial 16S rRNA genes showed that the structure of the bacterial community changed dynamically with compost processing time. At first, phyla Firmicutes and Bacteroidetes were dominant. Phylum Firmicutes maintained abundance for 20 days, indicating that these bacteria may be active under high temperatures. In the final compost, the library consisted of sequences belonging to the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria.

A clone library constructed from archaeal 16S rRNA genes showed that the archaeal community was mainly comprised of methane-producing archaea (methanogen) and ammonia-oxidizing archaea (AOA). During first 2 days, it was revealed that fecal methanogens could survive the early stage of composting. Thermophilic Methanosarcina spp. were present throughout the process, indicating that they may adapt to environmental changes such as high temperatures. Detecting AOA-like sequences showed that AOA could be actively involved in the nitrification of composting systems. Furthermore, the abundance of AOA varies markedly with the raw materials and composting technique used.


16S rRNA gene Animal manure Archaea Bacteria Compost 



This work was supported, in part, 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.

Compliance with Ethical Standards


This study was funded 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.

Conflict of Interest

Nozomi Yamamoto declares that she has no conflict of interest. Yutaka Nakai declares that he has no conflict of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.


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Authors and Affiliations

  1. 1.Department of Life Science and TechnologyTokyo Institute of TechnologyTokyoJapan
  2. 2.Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan

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