Agriculture Reference
In-Depth Information
known as fatty acid methyl ester (FAME) analysis. This method has been used to
monitor the microbial community succession in a number of thermophilic compost-
ing processes. The process is limited by the fact that it does not identify the spe-
cies; rather it provides a description of microbial communities based on functional
groups (Eiland et al.
2001
).
6.3.4
Molecular Methods
The last decade has seen an upsurge in the use of molecular phylogenetic techniques
for analysis of microbial diversity, community structure analysis and community
succession monitoring.
6.3.4.1
Mole Percentage Guanine + Cytosine (mol% G + C)
Mol% G + C is determined by the thermal denaturation of DNA, within bacteria this
value ranges from 25 % up to 75 %, although it remains constant for a certain spe-
cies. The method is not influenced by the anomalies associated with PCR and has
been used to uncover rare members in microbial populations (Tiedje et al.
1999
).
6.3.4.2
Nucleic Acid Hybridization
Nucleic acid hybridization provides a powerful tool for the qualitative and quantita-
tive assessment of bacterial ecology and community structure. The method uses oli-
gonucleotide or polynucleotide's probes obtained from sequences available in the
library specific to a community or species and can be tagged with markers at the 5′
end (Goris et al.
2007
). Dot-blot hybridization and cellular level hybridization have
been successfully used to provide valuable information regarding the distribution
of microbial communities in a natural environment. Fluorescent In-situ hybridiza-
tion (FISH) is a very popular method to study bacterial diversity and community
structure (Fakruddin and Mannann
2013
).
6.3.4.3
DNA Re-association
The diversity of the microbial communities of an environment can be studied based
upon the kinetics of DNA re-association, which reflects the variety of sequences
present in the environment and thus provides a measurement that reflects the genetic
complexity of the microbial community (Torsvik et al.
1996
). The rate of annealing
or re-association of the total DNA will depend upon the diversity of the microbial
community and a decrease in the rate of association will indicate the complexity of
the microbial community in a given environment (Theron and Cloete
2000
).
