22
(Nadeem et al. 2014). We do have knowledge of the in vitro requirements of the
microorganisms, but we still lack information about differential utilization of the
nutrients by these microbes in the rhizosphere, phyllosphere, and endophytic compartments. Such information would be useful in enhancing the performance of particular microorganisms in their niches. The cost-effectiveness of the microbe-based
products, response time, and their shelf life reduces the popularity of these products
among users in comparison to synthetic chemicals. Still, successful utilization of
plant–microbe interactions has great potential to protect plants, enhance soil fertility, and increase crop production, offering an alternative environment-friendly strategy for increasing crop production with reduced chemical inputs. We need a
systematic strategy to increase our knowledge about the plant–microbe partnership
with metabolomic, genomic, and transcriptomic approaches to utilize their potential
effectively. The soil is being contaminated with various hazardous chemicals as it
acts as a primary sink for pollutants. Because of such anthropogenic practices, agricultural lands are being degraded and are losing their productivity. Restoration of
such contaminated, degraded lands becomes imperative to feed the burgeoning
population. The changing climate could also alter tree speciation, root exudation,
resource allocation in plants, and the fate of the soil pollutants (Abhilash et al.
2013b, 2015). Some microbes present in the soil have the capability to degrade the
xenobiotic compounds, promote plant growth, and restore the degraded lands. It is
important to decipher the vast diversity of microbial taxa present in the soil for the
development of better soil management practices and to understand the shift in the
microbial community under the changing climate regime (Abhilash et al. 2013b). A
better understanding of microbial community structure will be helpful in determining the deleterious environmental impacts of climate change. Despite the importance of studying soil microbial ecology, very few populations of the soil microbial
diversity have been captured to date and more than 99% of them are not culturable
in existing laboratory setups (Singh et al. 2009). To overcome the problem of nonculturable microbiota, culture-independent approaches such as metagenomics can
be used to explain the unknown microbial diversity from direct environmental
DNA. Nowadays, myriads of methods are available to study the spatiotemporal
structure of soil microorganism diversity. In the past decade, application of nucleic
acid-based molecular technologies has completely revolutionized and added multidimensional orientation to studying soil microbial diversity. Now it is possible to
capture the diversity of nonculturable communities in the soil by sequencing soil
DNA using next-generation sequencing technologies. Acquisition of metagenomic
data requires the organisation of short overlapping sequences into the full reading
sequence and further analysing it as an expressible gene. Sequencing technologies
that have helped to exploit metagenomics for structural and functional community
analysis include 454-pyrosequencing, Illumina, and single-cell resolution. The
single- cell resolution technique can provide a better idea about the sequence of
microbial community inhabiting with low abundance in comparison to metagenomics whereas the advantage of meta-transcriptomics lies in the RNA-level knowledge
ultimately covering gene expression and proteome-level activity about the soil
microbiome (Segata et al. 2013).
2 Belowground Microbial Communities: Key Players for Soil and Environmental…
(Nadeem et al. 2014). We do have knowledge of the in vitro requirements of the
microorganisms, but we still lack information about differential utilization of the
nutrients by these microbes in the rhizosphere, phyllosphere, and endophytic compartments. Such information would be useful in enhancing the performance of particular microorganisms in their niches. The cost-effectiveness of the microbe-based
products, response time, and their shelf life reduces the popularity of these products
among users in comparison to synthetic chemicals. Still, successful utilization of
plant–microbe interactions has great potential to protect plants, enhance soil fertility, and increase crop production, offering an alternative environment-friendly strategy for increasing crop production with reduced chemical inputs. We need a
systematic strategy to increase our knowledge about the plant–microbe partnership
with metabolomic, genomic, and transcriptomic approaches to utilize their potential
effectively. The soil is being contaminated with various hazardous chemicals as it
acts as a primary sink for pollutants. Because of such anthropogenic practices, agricultural lands are being degraded and are losing their productivity. Restoration of
such contaminated, degraded lands becomes imperative to feed the burgeoning
population. The changing climate could also alter tree speciation, root exudation,
resource allocation in plants, and the fate of the soil pollutants (Abhilash et al.
2013b, 2015). Some microbes present in the soil have the capability to degrade the
xenobiotic compounds, promote plant growth, and restore the degraded lands. It is
important to decipher the vast diversity of microbial taxa present in the soil for the
development of better soil management practices and to understand the shift in the
microbial community under the changing climate regime (Abhilash et al. 2013b). A
better understanding of microbial community structure will be helpful in determining the deleterious environmental impacts of climate change. Despite the importance of studying soil microbial ecology, very few populations of the soil microbial
diversity have been captured to date and more than 99% of them are not culturable
in existing laboratory setups (Singh et al. 2009). To overcome the problem of nonculturable microbiota, culture-independent approaches such as metagenomics can
be used to explain the unknown microbial diversity from direct environmental
DNA. Nowadays, myriads of methods are available to study the spatiotemporal
structure of soil microorganism diversity. In the past decade, application of nucleic
acid-based molecular technologies has completely revolutionized and added multidimensional orientation to studying soil microbial diversity. Now it is possible to
capture the diversity of nonculturable communities in the soil by sequencing soil
DNA using next-generation sequencing technologies. Acquisition of metagenomic
data requires the organisation of short overlapping sequences into the full reading
sequence and further analysing it as an expressible gene. Sequencing technologies
that have helped to exploit metagenomics for structural and functional community
analysis include 454-pyrosequencing, Illumina, and single-cell resolution. The
single- cell resolution technique can provide a better idea about the sequence of
microbial community inhabiting with low abundance in comparison to metagenomics whereas the advantage of meta-transcriptomics lies in the RNA-level knowledge
ultimately covering gene expression and proteome-level activity about the soil
microbiome (Segata et al. 2013).
2 Belowground Microbial Communities: Key Players for Soil and Environmental…