25
should be cautiously analysed when handling such soil samples (Lester et al. 2007).
PLFA analysis is applied to study the vertical distribution of microbe communities
and identify the environmental factors that contribute to the soil depth gradient (Li
et al. 2017). The technique is also used to set biomarkers that show the beneficial
response of soil microbial communities to soil management through crop rotations
(Lupwayi et al. 2017). The difference in PLFA content provides an immense amount
of information on the microbial community during sludge composting with an inorganic bulking agent (Wu et al. 2016). These data help in the structural-functional
characterization of the microbe communities in contaminated soils such as semiarid mine soil for assessing the mycorrhizal-amended phyto-management practices
(Kohler et al. 2016). Various management practices are adopted in agricultural fields
to improve soil organic matter (SOM), microbial functions, crop productivity, and
agricultural sustainability. The structure of the microbial communities is specifically altered with each management strategy and these alterations can be easily
indentified through PLFA analysis. For example, under rice field biochar amendment, soil type, cover crops, irrigation practices, and land use pattern affect the
SOM quality and microbial community structure, crop rotation, and conservation
(Calderon et al. 2016; Li et al. 2017). PLFA has been used in studying microbial
community structure under soils contaminated by hydrocarbons, polyaromatic
hydrocarbons, and heavy metals and acidic soils from mining (Markowicz et al.
2016; Zornoza et al. 2016).
3.2 Fluorescence In Situ Hybridization (FISH)
Microbial cells can be studied through applying the fluorescence in situ hybridization (FISH) technique without cultivating the microbes under in vitro conditions.
FISH is used to detect small deletions as well as duplications that are not visible in
microscopic analysis. The technique can be used to detect chromosome types and
their rearrangements in microbial cells. FISH uses certain chemicals that fluoresce
and are detected in the specific region on a chromosome (Teira et al. 2004). Through
FISH, the microbial world in environmental samples (soil, water, contaminated
land) can be characterized taxonomically by means of rRNA-mediated oligonucleotide probes and subsequently analysed for signal amplification through catalysed
reporter deposition (CARD) (Ishii et al. 2004).
Microorganism cells are subjected to adhesion with chemical fixatives and
hybridized with oligonucleotide probes on a glass slide or in a solution. The probes
are generally 15 to 25 nucleotides in length and covalently labelled with fluorescent
dye at the 5′-C end. These probes are also linked with horseradish peroxidase (HRP)
enzyme. As soon as the hybridization and the following deposition of fluorescent
tryamides occurs, the signal on the target cells is intensified in comparison to the
directly fluorochrome-labelled FISH probes. The FISH method has been used for
analysing changes in bacterial populations of agricultural soils subjected to various
pesticides and herbicides (Caracciolo et al. 2010). After proper washing, the
3.2 Fluorescence In Situ Hybridization (FISH)
should be cautiously analysed when handling such soil samples (Lester et al. 2007).
PLFA analysis is applied to study the vertical distribution of microbe communities
and identify the environmental factors that contribute to the soil depth gradient (Li
et al. 2017). The technique is also used to set biomarkers that show the beneficial
response of soil microbial communities to soil management through crop rotations
(Lupwayi et al. 2017). The difference in PLFA content provides an immense amount
of information on the microbial community during sludge composting with an inorganic bulking agent (Wu et al. 2016). These data help in the structural-functional
characterization of the microbe communities in contaminated soils such as semiarid mine soil for assessing the mycorrhizal-amended phyto-management practices
(Kohler et al. 2016). Various management practices are adopted in agricultural fields
to improve soil organic matter (SOM), microbial functions, crop productivity, and
agricultural sustainability. The structure of the microbial communities is specifically altered with each management strategy and these alterations can be easily
indentified through PLFA analysis. For example, under rice field biochar amendment, soil type, cover crops, irrigation practices, and land use pattern affect the
SOM quality and microbial community structure, crop rotation, and conservation
(Calderon et al. 2016; Li et al. 2017). PLFA has been used in studying microbial
community structure under soils contaminated by hydrocarbons, polyaromatic
hydrocarbons, and heavy metals and acidic soils from mining (Markowicz et al.
2016; Zornoza et al. 2016).
3.2 Fluorescence In Situ Hybridization (FISH)
Microbial cells can be studied through applying the fluorescence in situ hybridization (FISH) technique without cultivating the microbes under in vitro conditions.
FISH is used to detect small deletions as well as duplications that are not visible in
microscopic analysis. The technique can be used to detect chromosome types and
their rearrangements in microbial cells. FISH uses certain chemicals that fluoresce
and are detected in the specific region on a chromosome (Teira et al. 2004). Through
FISH, the microbial world in environmental samples (soil, water, contaminated
land) can be characterized taxonomically by means of rRNA-mediated oligonucleotide probes and subsequently analysed for signal amplification through catalysed
reporter deposition (CARD) (Ishii et al. 2004).
Microorganism cells are subjected to adhesion with chemical fixatives and
hybridized with oligonucleotide probes on a glass slide or in a solution. The probes
are generally 15 to 25 nucleotides in length and covalently labelled with fluorescent
dye at the 5′-C end. These probes are also linked with horseradish peroxidase (HRP)
enzyme. As soon as the hybridization and the following deposition of fluorescent
tryamides occurs, the signal on the target cells is intensified in comparison to the
directly fluorochrome-labelled FISH probes. The FISH method has been used for
analysing changes in bacterial populations of agricultural soils subjected to various
pesticides and herbicides (Caracciolo et al. 2010). After proper washing, the
3.2 Fluorescence In Situ Hybridization (FISH)