Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems

Abstract

Summary Marine ecosystems are home to bacteria which are exposed to a wide variety of environmental conditions, such as extremes in temperature, salinity, nutrient availability and pressure. Survival under these conditions must have necessitated the adaptation and the development of unique cellular biochemistry and metabolism by these microbes. Thus, enzymes isolated from these microbes have the potential to possess quite unique physiological and biochemical properties. This review outlines a number of function‐based metagenomic approaches which are available to screen metagenomic libraries constructed from marine ecosystems to facilitate the exploitation of some of these potentially novel biocatalysts. Functional screens to isolate novel cellulases, lipases and esterases, proteases, laccases, oxidoreductases and biosurfactants are described, together with approaches which can be employed to help overcome some of the typical problems encountered with functional metagenomic‐based screens.

A Novel Cold Active Esterase from a Deep Sea Sponge Stelletta normani Metagenomic Library

“…One approach which has been successfully employed to this end is metagenomics which helps facilitate access to genetic resources from uncultured microorganism (Kennedy et al, 2011;Baweja et al, 2016;Parages et al, 2016). Lipolytic enzymes such as esterases and lipases which catalyze the hydrolysis and synthesis of ester substrates are widely used in the agrochemical, cosmetics, dairy, detergent, food, paper processing, and pharmaceutical industries amongst others (Jaeger and Eggert, 2002).…”

“…Metagenomic based approaches have proven extremely useful as a means of discovering microbial enzymes with entirely new biochemical properties, thereby exploiting the microbial diversity of a variety of different environmental ecosystems (Kennedy et al, 2011). These approaches are typically employed to help overcome the problem of cultivating bacteria from different environments, where typically only 0.001 to 1% of bacterial isolates can be recovered and grown under standard laboratory conditions (Bernard et al, 2000).…”

Screening concepts, characterization and structural analysis of microbial-derived bioactive lipopeptides: a review

“…Thus, it is likely that the distribution of BS producers in different environments is underestimated. [33] According to our current knowledge, no metagenomic approach has been widely used for the screening of BS-producing strains [35][36][37][38]. Such an approach could be designed for LP-producers due to the following: the high homology of NRPS operons in different species, the number of already designed primers in the literature and the possibility of utilizing different databases and platforms, like BLAST, NRPS predictor or AntiSMASH as examples.…”

Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa

“…Microbes play critical functional roles in diverse environments ranging from soil and oceans to the human gut. The emergence of culture-independent techniques has provided insights into microbial ecology by revealing genetic signatures of uncultured microbial taxa (1)(2)(3)(4)(5). It also suggests that certain microbes may impact host phenotypes such as obesity, inflammation, and gastrointestinal integrity (6,7).…”