Decoding Complex Soil Microbial Communities through New Age "Omics"

Nair, Girish R; Raja, Suresh SS

doi:10.4172/1948-5948.1000382

Cited by 5 publications

(4 citation statements)

References 91 publications

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“…A greater read length and read number would increase sequencing depth, thereby generating more information from the sample. This depends, to a great extent, on the sequencing methodology used and the MinION sequencer from Oxford Nanopore produces longer read length, which allows detailed bacterial community characterization, down to the family or even genus level at low sequencing cost [54]. However, the accuracy and sequencing output is limited compared to reads obtained using a shorter-read platform like Illumina [92,93].…”

Section: Discussionmentioning

confidence: 99%

“…Next-generation sequencing (NGS) is possibly the best effective approach for evaluating and characterizing soil microbial community pro le and has undergone constant upgradation in the past years with improvements in sequence quality, depth with lesser cost and time [52][53][54]. Oxford Nanopore sequencer is among the newest third-generation sequencers with promising deep sequencing strategy coupled with robust characterization e ciency and has become choice of many research labs for indepth metagenomic studies [55][56][57].…”

Section: Introductionmentioning

confidence: 99%

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Insights Into the Diversity of Terrestrial Soil Bacterial Communities Associated With Four Contrasting Köppen Climatic Zones.

Nair¹,

Raja²

2021

Preprint

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Background: The multidirectional relationship between soil, its microbiota, and climate is crucial in modulating the bacterial community diversity and its survival in the terrestrial ecosystem. Therefore, it is imperative to understand the dynamics of soil bacterial communities thriving in geographical areas of varied climatic exposure. Results: The diversity of terrestrial soil bacterial communities thriving in four contrasting Köppen climatic zones of India was investigated for the first time using high-throughput sequencing. The results revealed that the bacterial species diversity, evenness and richness were highest in HSCZ (humid subtropical climatic zone). Firmicutes was the most abundant phylum in TWCZ (tropical wet climatic zone), ACZ (arid climatic zone), and HSCZ (humid subtropical climatic zone) while Proteobacteria in MCZ (Mountain climatic zone). The predominance of class Alphaproteobacteria, Actinobacteria with genera Bradyrhizobium, Chthoniobacter, and Mycobacterium, was observed in MCZ in contrast to class Bacilli with genera Bacillus and Paenibacillus in the rest of the zones. Correlation analysis showed that H’ (Shannon diversity) index, S (species richness), OTU abundance were positively correlated with moisture, TOC, K, MAP (mean annual precipitation) and negatively correlated with pH, Ca, N, B. Fe, P, Mg and MAT (mean annual temperature). Conclusion: This work mapped the occurrence and distribution of terrestrial soil bacterial communities in contrasting climatic zones that enabled us to assess the effect of climate in mentioned Köppen climatic zones on a taxonomic scale.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Insights Into the Diversity of Terrestrial Soil Bacterial Communities Associated With Four Contrasting Köppen Climatic Zones.

Nair¹,

Raja²

2021

Preprint

Self Cite

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“…In this direction, the field of metagenomics continues to be a ground-breaking technology, which has made it possible to explore microbial diversity with its full potential [16]. Besides the soil ecosystem, microbes could quickly react to anthropogenic pressures, making it feasible to be an indication of soil quality as well as wellness [17,18]. Lately, efforts have been attempted to determine genes from environmental samples via culture-independent techniques [19,20].…”

Section: Introductionmentioning

confidence: 99%

“…However, they had been amplified or perhaps recognized due to their similarity to the earlier identified genes, that invalidates for exploiting novel elements of metal resistance [21,22]. As the development of culture-independent metagenomic methods, it has been employed to evaluate the soil microbial community as well as enhances our awareness of the soil ecosystem [17,20]. Furthermore, the soil microbial communities are primarily made up of some dominant species and numerous other rare taxa [23].…”

Section: Introductionmentioning

confidence: 99%

Soil Metagenomics: Prospects and Challenges

Kaushik¹,

Sandhu²,

Brar³

et al. 2021

Mycorrhizal Fungi - Utilization in Agriculture and Industry

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The better strategies to examine RNA or DNA from soil allow us to understand the microbial diversity and features in the soil, which are challenging to identify by typical culture techniques. In this direction, the literature on soil metagenomics and its usefulness is ever-increasing and so as its implementation experiences. Omics techniques are going to assist the metagenomics in achieving agricultural sustainability. In doing so, essential understanding on the reference soil would serve to help upcoming soil survey initiatives, lessening bias and raising objectivity. Although the interpretation of limited details has influenced microbial ecologists, the scope of methodological bias remains unfamiliar. A detailed catalog of functional genes and soil microorganisms does not yet exist for any soil. Overall, this chapter provides thoughts related to the soil metagenomics, its importance, and conventional methods of analysis, along with prospects and challenges of soil metagenomics.

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