Review
Metagenomic analysis of uncultured microorganisms and their enzymatic attributes

https://doi.org/10.1016/j.mimet.2018.11.014Get rights and content

Abstract

Although second generation biofuel technology is a sustainable route for bioethanol production it is not currently a robust technology because of certain hindrances viz., unavailability of potential enzyme resources, low efficiency of enzymes and restricted availability of potent enzymes that work under harsh conditions in industrial processes. Therefore, bioprospecting of extremophilic microorganisms using metagenomics is a promising alternative to discover novel microbes and enzymes with efficient tolerance to unfavourable conditions and thus could revolutionize the energy sector. Metagenomics a recent field in “omics” technology enables the genomic study of uncultured microorganisms with the goal of better understanding microbial dynamics. Metagenomics in conjunction with NextGen Sequencing technology facilitates the sequencing of microbial DNA directly from environmental samples and has expanded, and transformed our knowledge of the microbial world. However, filtering the meaningful information from the millions of genomic sequences offers a serious challenge to bioinformaticians. The current review holds the opinion tool ‘know- how’ to unravel the secrets of nature while expediting the bio-industrial world. We also discuss the novel biocatalytic agents discovered through metagenomics and how bioengineering plays a pivotal role to enhance their efficiency.

Introduction

Microbes adapted themselves to reside within harsh environmental conditions or in extremophilic sites (viz. high/low temperature, salinity, low atmospheric pressure at high altitudes, and pH) by secreting enzymes (extremozymes) or by employing mechanisms that tamper the intracellular milieu from the extrinsic environment (Escuder-Rodríguez et al., 2018). In the current scenario, the study of such microbial populations is strictly restricted by accessible techniques, which have limited reference genomes for the comparison. The advent of next-generation sequencing (NGS) permits us to explore vast sequences of an individual genome that revolutionizing sequencing technology and changing the landscape of metagenomics. These unexplored microbial niches are still in a quest where metagenomics tools are being exploited to disclose the mysterious potential of such precious microbiomes. Currently, the metagenomic approach has led to the discovery of efficient and novel cellulases and other enzymes from extremophilic sites that play a pivotal role in the biofuel sector thus making the technology cost-effective (Mori et al., 2014; Montella et al., 2015; Yang et al., 2016; Lewin et al., 2017; Dadheech et al., 2018). Schroder et al. (2014) led to the discovery of thermophilic β-glucosidase from hot spring via metagenomic analysis that has the capability to retain 40% activity at extreme temperature (105 °C). Similarly, Khalili Ghadikolaei et al. (2018) carried out the metagenomic analysis of camel rumen and found a novel cold tolerant endoglucanase (CelCM3) that showed a significant activity at 4 °C and also exhibited resistance to detergents, metal ions and other organic solvents. These discoveries of novel cell-wall degrading enzymes using the metagenomic approach has revolutionized second-generation biofuel production by cutting down the costs on pre-treatment processes and thus helping to commercialize the technology.

Section snippets

Metagenomics: novel route in “omics” technology

Currently, large-scale sequencing projects employ NGS technologies to identify the genetic composition and specific function of microbial populations leading to the discovery of novel microbes with an understanding of their physiological/biochemical interactions as well as population dynamics (Morales and Holben, 2011). The functional genomic studies (ability to clone and express metagenomic DNA fragments in vitro) have helped in overcoming the limitation of culture-based techniques (Xing et

Metagenomics - an important tool in the biofuel sector

Cell-wall degrading enzymes are considered as key players in converting lignocellulosic biomass into bio-alcohol. It has been estimated that the commercial enzyme market during 2010 was about $3.3 billion and is predicted to reach approximately $6.3 billion by 2021 (Tiwari et al., 2018). In this direction, the bioprospecting of microbes from extremophilic conditions is required to identify novel cellulolytic microbes with high biomass to biofuel conversion efficiency for commercializing

Metagenomics - a key technology for the development of novel biotechnological products

Nature in itself has engineered microorganisms to be sustainable in harsh climatic conditions by modifying enzymes. The thermophilic fungal endogluconases (Talaromyces emersonii) does not exhibit activity on microcrystalline cellulose (Avicel) or carboxymethyl cellulose (CMC) (Murray et al., 2001). These enzymes can be bioengineered for efficiently degrading the cell wall in accordance with industrial parameters e.g. three fungal cellulases were shuffled by means of homologous protein shuffling

Conclusion

With the escalation in oil prices, depletion of non-renewable energy resources and environmental issues, the production of second generation biofuel has rapidly gained momentum in the energy sector. Advanced metagenomics technology provides a promising route for mining novel cell-wall degrading enzymes with high potency to breakdown the lignocellulosic biomass into fermentable sugars for bioethanol production. Technical questions that have not been raised in this review but should eventually be

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