title: Contemporary molecular tools in microbial ecology and their application to advancing biotechnology.
abstract: Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70-80% of microbial diversity - recently called the "microbial dark matter" - remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology.
authors.affiliation: Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. Electronic address: rashidmamoon@gmail.com.
authors.forename: Mamoon
authors.initials: M
authors.lastname: Rashid
authors.affiliation: Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. Electronic address: Uli.Stingl@kaust.edu.sa.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Stingl
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D001709:Biotechnology; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D054892:Metagenome; D059010:Single-Cell Analysis
keywords: Biotechnology; Ecology; Enzymes; Metagenomics; Natural products; Single-cell genomics