Agriculture Reference
In-Depth Information
6.3
Methods for Analysing Microbial Diversity
and Community Structure during Composting
Compost bears a rich microbial diversity and community structure during process.
Several methods including advantageous molecular method though employed in
analysis of microbial community dynamics in composting processes, among few
are discussed-
6.3.1
Enrichment Methods
Enrichment is a culture dependent approach and has been traditionally used for
cultivation of selective microbial communities. The compost provides a complex
nutritional source that can support different types of microbes with unique growth
requirements. Thus, the enrichment process uses different incubation and cultiva-
tion conditions that can support the group of multiple communities with specific
growth requirements. Enrichment methods have been successfully used for the enu-
meration and observation of microbial community dynamics during composting
of animal manures (Tiquia et al.
2002
), municipal solid (Hassen et al.
2001
), food
waste (Ryckeboer et al.
2003
) etc. These types of methods can only account for
0.1-10.0 % fraction of the total microbial diversity and thus have been replaced
with a number of cultivation independent approaches.
6.3.2
Biochemical Methods
The analysis of community structure using biochemical identification systems such
as API and Biolog were introduced by Garland and Mills (
1991
). It is termed as
the Sole-Carbon-Source Utilization (SCSU) and also known as Community Level
Physiological Profiling (CLPP). The method is based on the metabolic machin-
ery of the microbes and their ability to utilize different carbon sources. However,
this method is limited by the availability of kits that can be used to decipher the
physiological and metabolic diversity (Derry et al.
1998
). Optimization of substrate
combinations for the study of environmental isolates is limited that often results in
problems leading to invalid identification of microbial species.
6.3.3
Phospholipid Fatty Acid (PLFA) Analysis
Microbial characterization based on fatty acid composition has been extensively
used. The method is quantitative, robust, and reproducible. The method analyses the
differences in the fatty acid composition of the microbes, especially in the range of
C2 to C24, and is independent of plasmids, mutations, or damaged cells. It is also
