Other studies used those fingerprinting techniques when monitoring the effects of
different remediation techniques such as amending mine tailings with a mixture of
organic carbon sources to treat pore water and drainage (Lindsay et al. 2011),
incorporating compost into a heavy metal-contaminated acidic soil (Farrell et al.
2010), or testing the effects of phytoremediation approaches (Martinez Inigo et al.
2009) or land-farming on oil refinery sludge (Ros et al. 2010).
In laboratory-based studies, fingerprinting techniques have been used when
testing the effect of different contaminants/elements on microbial communities.
Jakobs-Schonwandt et al. (2010) investigated the shift of soil microbial communities
when subjected to a biocide frequently found in wood preservatives. Brandt et al.
(2010) compared a Cu-adapted and a corresponding nonadapted soil microbial
community for the ability to resist experimental Cu pollution. Other studies investigated the abilities of indigenous bacteria on arsenic mobilization (Corsini et al.
2011) or the ability of specialized mixed communities to selectively precipitate
transition metals from acidic mine waters (Nancucheo and Johnson 2011), or the
acid tolerance response of a bioremediation system based on sulfate reduction
(Lu et al. 2011a, b).
Fingerprinting techniques are extremely useful when starting to investigate an
unknown microbial community; however, as mentioned previously, they have their
limitations and can be time and labor extensive. On their own, both techniques can
either quantify or identify fragments but not both.
5 Molecular Techniques for In Situ Monitoring
of Microbial Communities, Bioremediation Processes,
and Environmental Pollution
Traditional methods for characterizing microbial communities have been based on
analysis of those bacteria that can be cultured. The overall structure of the community has been difficult to interpret as most of the bacteria are not culturable (Dokic
et al. 2010). Modern methods focus towards molecular techniques, which do not
require culturing the microorganisms but provide measures based on genetic diversity. The molecular-phylogenetic perspective is a reference framework within which
microbial diversity is described; the sequences of genes can be used to identify
organisms. A variety of approaches (Table 18.3) that have been developed to study
molecular microbial diversity include DNA–DNA and mRNA–DNA hybridization,
DNA re-association, DNA cloning and sequencing, and other PCR-based methods
such as denaturing gradient gel electrophoresis (DGGE), temperature gradient gel
electrophoresis (TGGE), and ribosomal intergenic spacer analysis (RISA). Other
advanced techniques, such as DNA microarrays, have also improved specificity to a
great extent.
446
S. K. Shekhar et al.
different remediation techniques such as amending mine tailings with a mixture of
organic carbon sources to treat pore water and drainage (Lindsay et al. 2011),
incorporating compost into a heavy metal-contaminated acidic soil (Farrell et al.
2010), or testing the effects of phytoremediation approaches (Martinez Inigo et al.
2009) or land-farming on oil refinery sludge (Ros et al. 2010).
In laboratory-based studies, fingerprinting techniques have been used when
testing the effect of different contaminants/elements on microbial communities.
Jakobs-Schonwandt et al. (2010) investigated the shift of soil microbial communities
when subjected to a biocide frequently found in wood preservatives. Brandt et al.
(2010) compared a Cu-adapted and a corresponding nonadapted soil microbial
community for the ability to resist experimental Cu pollution. Other studies investigated the abilities of indigenous bacteria on arsenic mobilization (Corsini et al.
2011) or the ability of specialized mixed communities to selectively precipitate
transition metals from acidic mine waters (Nancucheo and Johnson 2011), or the
acid tolerance response of a bioremediation system based on sulfate reduction
(Lu et al. 2011a, b).
Fingerprinting techniques are extremely useful when starting to investigate an
unknown microbial community; however, as mentioned previously, they have their
limitations and can be time and labor extensive. On their own, both techniques can
either quantify or identify fragments but not both.
5 Molecular Techniques for In Situ Monitoring
of Microbial Communities, Bioremediation Processes,
and Environmental Pollution
Traditional methods for characterizing microbial communities have been based on
analysis of those bacteria that can be cultured. The overall structure of the community has been difficult to interpret as most of the bacteria are not culturable (Dokic
et al. 2010). Modern methods focus towards molecular techniques, which do not
require culturing the microorganisms but provide measures based on genetic diversity. The molecular-phylogenetic perspective is a reference framework within which
microbial diversity is described; the sequences of genes can be used to identify
organisms. A variety of approaches (Table 18.3) that have been developed to study
molecular microbial diversity include DNA–DNA and mRNA–DNA hybridization,
DNA re-association, DNA cloning and sequencing, and other PCR-based methods
such as denaturing gradient gel electrophoresis (DGGE), temperature gradient gel
electrophoresis (TGGE), and ribosomal intergenic spacer analysis (RISA). Other
advanced techniques, such as DNA microarrays, have also improved specificity to a
great extent.
446
S. K. Shekhar et al.