Bacterial Communities in Various Conditions of the Composting Reactor Revealed by 16S rDNA Clone Analysis and DGGE - Sustainable Biotechnology: Sources of Renewable Energy - page 168

more cumbersome and expensive than other methods, i.e. DGGE analysis. However,
it is suitable to detect minor species and to estimate species abundance. In addition,
cell counting is helpful for clone analysis to estimate species abundance.
2.2 Denaturing Gradient Gel Electrophoresis (DGGE)
Denaturing gradient gel electrophoresis (DGGE) is a gel electrophoresis method
used to separate DNA fragments of the same length, but containing different base-
pair sequences; it is used to determine the presence and abundance of different
microbial species in a mixed population [12]. It is based on the principle that
increasing the denaturant concentration will melt double-stranded DNA in distinct
domains. When the melting temperature (T m ) of the lowest domain is reached, the
DNA will partially melt, creating branched molecules with reduced mobility in a
polyacrylamide gel [13]. DGGE analysis is able to compare many samples at the
same time and to analyze them more easily than clone analysis and is thus suitable
to reveal microbial community succession.
2.3 Case Study
2.3.1 Different Conditions of the Reactor
There are many types of fed-batch composting (FBC) reactors. However, FBC reac-
tors cannot function continuously because the contents, which usually include waste
and biomass-carriers such as wood chips, often aggregate after prolonged opera-
tion. Therefore, it is necessary to remove excess contents from the reactor regularly
because of decreasing decomposition rate, and this requires secondary treatment of
the aggregated contents. Since considerable amounts of partially degraded materials
remain during the FBC process, secondary treatment of the products is necessary
to obtain matured compost or complete degradation of waste to organic mat-
ter. Although the mechanism of aggregation in reactors is unknown, this process
decreases the decomposition rate [14], and probably changes the microbial commu-
nity. Therefore, this study was conducted to compare the optimal and aggregated
conditions of a bacterial community in a FBC reactor using 16S rDNA clone
analysis.
2.3.2 Types of Bulking Agent - Wood Chips or Polyethylene Terephthalate
In a long-term FBC reactor, a problem that is likely to occur and which needs to be
monitored is the significant abrasion of the bulking agents. Nagao et al. noted that
both plastic bottle flakes and wood chips were capable of maintaining a high rate of
decomposition. In addition, the bacterial community was examined by 16S rDNA
clone analysis and the difference in the community between the two bulking agents
was compared [15].