The dot blotting technique frequently has been used in metabolic study of a
microbial community by investigation of the changes in the gene expression level.
By the use of DGGE/TGGE, complex communities of bacteria and fungi can be
analyzed after PCR amplification with the use of primers designed to specifically
bind to conserved regions of bacterial 16S rRNA genes or fungal 18S rRNA. By the
usage of group-particular primers, it is likewise possible to investigate bacterial
communities, together with actinomycetes or Archaea. Although the 16S and 18S
rRNA genes are most often used, other genes along with the β-subunit of bacterial
RNA polymerase (rpoB) also can be used to analyze the microbial range and
survival of inoculated microorganisms in soil (Dahllof et al. 2000). DGGE has
been proven to be useful in monitoring the bioremediation of freshly and aged
PAH-infected soils (Cunliffe and Kertesz 2006), allowing monitoring of the survival
of inoculated Sphingobium yanoikuyae in addition to tracking adjustments within the
local bacterial communities over time. In some studies (Zhou et al. 2009; Wang and
Tam 2011; HuiJie et al. 2011), DGGE has also been used to observe microbial
community dynamics and biodegradation throughout PAH biodegradation in soils
and sediments.
DGGE/TGGE is a preferred method although the desired information is no longer
as phylogenetically exhaustive as that furnished by 16S rRNA gene clone libraries;
however, these methods can determine the dominant participants of microbial
communities with average phylogenetic definition (Sanz and Kochling 2007). For
environmental or contaminated supply samples wherein microbial diversity is basically unknown, the DGGE/TGGE method may provide identification of the microbial population through the excision of selected bands followed through their
reamplification, cloning, and sequencing, which can indicate the phylogenetic affiliation of the ribotypes (Evans et al. 2004; Forney et al. 2004; Van Elsas et al. 2007).
DGGE specifically has been widely used for the evaluation of microbial community
shape in infected soil and water (Chang et al. 2000; Ralebitso et al. 2000; Watanabe
et al. 2000; Kleikemper et al. 2002; Cummings et al. 2003; El-Latif Hesham et al.
2006; Mahmoud et al. 2009). Apart from microbial network profiling, the DGGE
technique has been used to study gene clusters such as dissimilar sulfite reductase
β-subunit (dsrB) genes in sulfate-decreasing bacterial communities (Geets et al.
2006) and benzene, toluene, ethylbenzene, and xylene (BTEX) monooxygenase
genes from bacterial traces obtained from hydrocarbon-polluted aquifers (Hendrickx
et al. 2006). Coulon et al. (2012) used DGGE evaluation of opposite-transcribed
bacterial 16S rRNA from the upper 1.5 cm of a hydrocarbon-polluted sediment in
coastal mudflats to examine the essential function of dynamic tidal biofilms by using
aerobic hydrocarbonoclastic bacteria and diatoms in the biodegradation of hydrocarbons. Their research found phylotypes related to straight chain and polycyclic
hydrocarbon degradation including Cycloclasticus, Alcanivorax, Oleibacter, and
Oceanospirillales strain ME113.
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S. K. Shekhar et al.
microbial community by investigation of the changes in the gene expression level.
By the use of DGGE/TGGE, complex communities of bacteria and fungi can be
analyzed after PCR amplification with the use of primers designed to specifically
bind to conserved regions of bacterial 16S rRNA genes or fungal 18S rRNA. By the
usage of group-particular primers, it is likewise possible to investigate bacterial
communities, together with actinomycetes or Archaea. Although the 16S and 18S
rRNA genes are most often used, other genes along with the β-subunit of bacterial
RNA polymerase (rpoB) also can be used to analyze the microbial range and
survival of inoculated microorganisms in soil (Dahllof et al. 2000). DGGE has
been proven to be useful in monitoring the bioremediation of freshly and aged
PAH-infected soils (Cunliffe and Kertesz 2006), allowing monitoring of the survival
of inoculated Sphingobium yanoikuyae in addition to tracking adjustments within the
local bacterial communities over time. In some studies (Zhou et al. 2009; Wang and
Tam 2011; HuiJie et al. 2011), DGGE has also been used to observe microbial
community dynamics and biodegradation throughout PAH biodegradation in soils
and sediments.
DGGE/TGGE is a preferred method although the desired information is no longer
as phylogenetically exhaustive as that furnished by 16S rRNA gene clone libraries;
however, these methods can determine the dominant participants of microbial
communities with average phylogenetic definition (Sanz and Kochling 2007). For
environmental or contaminated supply samples wherein microbial diversity is basically unknown, the DGGE/TGGE method may provide identification of the microbial population through the excision of selected bands followed through their
reamplification, cloning, and sequencing, which can indicate the phylogenetic affiliation of the ribotypes (Evans et al. 2004; Forney et al. 2004; Van Elsas et al. 2007).
DGGE specifically has been widely used for the evaluation of microbial community
shape in infected soil and water (Chang et al. 2000; Ralebitso et al. 2000; Watanabe
et al. 2000; Kleikemper et al. 2002; Cummings et al. 2003; El-Latif Hesham et al.
2006; Mahmoud et al. 2009). Apart from microbial network profiling, the DGGE
technique has been used to study gene clusters such as dissimilar sulfite reductase
β-subunit (dsrB) genes in sulfate-decreasing bacterial communities (Geets et al.
2006) and benzene, toluene, ethylbenzene, and xylene (BTEX) monooxygenase
genes from bacterial traces obtained from hydrocarbon-polluted aquifers (Hendrickx
et al. 2006). Coulon et al. (2012) used DGGE evaluation of opposite-transcribed
bacterial 16S rRNA from the upper 1.5 cm of a hydrocarbon-polluted sediment in
coastal mudflats to examine the essential function of dynamic tidal biofilms by using
aerobic hydrocarbonoclastic bacteria and diatoms in the biodegradation of hydrocarbons. Their research found phylotypes related to straight chain and polycyclic
hydrocarbon degradation including Cycloclasticus, Alcanivorax, Oleibacter, and
Oceanospirillales strain ME113.
450
S. K. Shekhar et al.