Bacterial Communities in Various Conditions of the Composting Reactor Revealed by 16S rDNA Clone Analysis and DGGE - Sustainable Biotechnology: Sources of Renewable Energy - page 167

1 Introduction
Composting is one of the efficient and cost-effective biological processes to treat
organic waste. However, some trouble may occur in a composting reactor, for exam-
ple, aggregation of contents, decreasing pH and decreasing rate of decomposition. In
composting processes, thermophilic and mesophilic microorganisms have important
respective functions in terms of nutrient recycling and decomposition of complex
organic substrates [1]. Therefore, an understanding of the microbial community and
its succession is important to effectively manage the composting process. Thus, in
this chapter, bacterial communities in the various composting reactors are revealed
by using molecular biological methods, as a case study. These methods are simi-
larly applicable to environmental samples, anaerobic digestion treatment reactors,
and industrial reactors.
2 Background Research
Culture-based approaches have previously been used for this purpose, and vari-
ous species of bacteria, e.g. members of the family Bacillaceae , Clostridiaceae ,
Flavobacteriaceae , Neisseriaceae , Nocardiopsaceae , Staphylococcaceae , etc.,
were isolated from composting reactors [2-7]. During the 1970s, a method which
involved community DNA extraction from samples without cultivation of microor-
ganisms was developed. Results of this type of analysis showed that the abundance
of microorganisms which is able to be cultivated in the laboratory is less than
1%, and the remaining 99% are viable but non-culturable (VBNC) microorganisms
[8, 9]. Dees and Ghiorse revealed microbial communities in compost by combining
the cultivation method and 16S rDNA clone analysis. Furthermore, they detected
some species which had not previously been detected from compost, and showed
that the results of both methods were inconsistent, except for Bacillus coagulans
[10]. Therefore, the cultivation method is not useful to reveal the “true (real)”
microbial community.
All prokaryotes have 16S rDNA whose average length is about 1,500 bp. There
are both conserved and variable regions (the V1-V9 regions), and sufficient infor-
mation has been compiled with which to conduct for reliable phylogenetic analyses
[8, 11]. Almost all the known sequences are registered on a DNA database, and it
is possible to estimate the species on this basis. Mixed DNA extracted from envi-
ronmental samples directly (without the cultivation of microorganisms) is called
community DNA or environmental DNA. As mentioned above, by using 16S
rDNA in this community DNA for analysis, it is possible to reveal the microbial
community.
2.1 16S rRNA Gene (rDNA) Clone Analysis
Clone analysis is a method which uses recombinant DNA. PCR amplified-16S
rDNA is cloned into a plasmid vector and a plasmid library is constructed. The
microbial community can be estimated by analyzing this library. This method is