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Contemporary Molecular Tools in Microbial Ecology and Their Application to Advancing Biotechnology

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Contemporary Molecular Tools in Microbial Ecology and Their Application to Advancing Biotechnology Contemporary molecular tools in microbial ecology and their application to advancing biotechnology Item Type Article Authors Rashid, Mamoon; Stingl, Ulrich Citation Contemporary molecular tools in microbial ecology and their application to advancing biotechnology 2015 Biotechnology Advances Eprint version Post-print DOI 10.1016/j.biotechadv.2015.09.005 Publisher Elsevier BV Journal Biotechnology Advances Rights NOTICE: this is the author’s version of a work that was accepted for publication in Biotechnology Advances. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Biotechnology Advances, 25 September 2015. DOI: 10.1016/ j.biotechadv.2015.09.005 Download date 27/09/2021 10:28:52 Link to Item http://hdl.handle.net/10754/578848 ÔØ ÅÒÙ×Ö ÔØ Contemporary molecular tools in microbial ecology and their application to advancing biotechnology Mamoon Rashid, Ulrich Stingl PII: S0734-9750(15)30038-0 DOI: doi: 10.1016/j.biotechadv.2015.09.005 Reference: JBA 6973 To appear in: Biotechnology Advances Received date: 30 May 2015 Revised date: 19 September 2015 Accepted date: 20 September 2015 Please cite this article as: Rashid Mamoon, Stingl Ulrich, Contemporary molecular tools in microbial ecology and their application to advancing biotechnology, Biotechnology Ad- vances (2015), doi: 10.1016/j.biotechadv.2015.09.005 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ACCEPTED MANUSCRIPT THIS VERSION WAS CAREFULLY EDITED FROM THE PREVIOUS REVISED MANUSCRIPT Contemporary molecular tools in microbial ecology and their application to advancing biotechnology Mamoon Rashid and Ulrich Stingl Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia Correspondence to: [email protected] or [email protected] ACCEPTED MANUSCRIPT 1 ACCEPTED MANUSCRIPT Table of Contents ABSTRACT .................................................................................................................................................. 4 1 INTRODUCTION .................................................................................................................................... 5 1.1 MICROBIAL ECOLOGY: HISTORICAL PERSPECTIVE ....................................................................................... 5 1.2 MOLECULAR METHODS AND TOOLS IN MICROBIAL ECOLOGY .................................................................... 5 1.3 APPLICATION OF MICROBIAL ECOLOGICAL TOOLS TO ADVANCING BIOTECHNOLOGY ............................ 7 1.4 WHY IS THIS REVIEW TIMELY? ....................................................................................................................... 8 2 MOLECULAR REVOLUTION IN MICROBIAL ECOLOGY.............................................................. 9 3 METAGENOMICS: TAPPING INTO THE UNKNOWNS FOR BIOTECHNOLOGY ................ 13 3.1 SEQUENCE-BASED SCREENING OF METAGENOMES FOR NOVEL ENZYMES ............................................ 14 3.1.1 Methods of sequence-based screening ............................................................................................. 14 3.1.2 Examples of novel enzymes identified by sequence-based metagenomics ..................... 16 3.2 FUNCTION-BASED SCREENING FOR DETECTION OF NOVEL ENZYMES .................................................... 16 3.2.1 Functional complementation .............................................................................................................. 17 3.2.2 High-Performance Thin Layer Chromatography (HPTLC) ................................................... 17 3.2.3 Phenotypic MicroArray (PM) ............................................................................................................... 17 3.2.4 Community Isotope Array (CIArray) ................................................................................................ 17 3.2.5 In vitro Compartmentalization-Fluorescence Activated Cell Sorting (IVC-FACS) ...... 18 3.2.6 Substrate-Induced Gene Expression (SIGEX) ............................................................................... 18 3.2.7 Product-InducedACCEPTED Gene Expression (PIGEX)MANUSCRIPT ................................................................................... 19 3.2.8 Examples of function-based screening of metagenomes for novel enzymes ................. 19 3.3 COMBINED SEQUENCE- AND FUNCTION-BASED SCREENINGS OF METAGENOMES FOR THE DETECTION OF NOVEL ENZYMES ......................................................................................................................... 19 3.4 NATURAL PRODUCTS THROUGH METAGENOMICS ..................................................................................... 21 3.4.1 Natural products from free-living bacteria .................................................................................. 22 3.4.2 Natural products from symbiotic bacteria ................................................................................... 22 3.4.3 Examples of natural product discoveries through metagenomics ..................................... 23 3.4.4 Drug discovery through metagenomics .......................................................................................... 24 3.5 METAGENOMIC ENRICHMENT TECHNOLOGIES .......................................................................................... 25 3.6 BOTTLENECKS IN THE METAGENOMICS DISCOVERY PIPELINE ............................................................... 26 2 ACCEPTED MANUSCRIPT 3.6.1 Sampling metagenomes: random or intuitive ............................................................................. 26 3.6.2 DNA extraction ........................................................................................................................................... 27 3.6.3 Choice of vectors ........................................................................................................................................ 28 3.6.4 Choice of hosts ............................................................................................................................................ 29 4 SINGLE-CELL GENOMICS: TAPPING THE UNTAPPED FOR APPLICATION IN BIOTECHNOLOGY.................................................................................................................................. 31 4.1 ANALYSES OF SINGLE-CELL GENOMES FOR BIOTECHNOLOGY ................................................................. 32 5 PROPOSITION: FUNCTIONAL SINGLE-CELL GENOMICS ....................................................... 33 6 CONCLUSION ....................................................................................................................................... 34 FIGURE LEGENDS .................................................................................................................................. 59 TABLES ..................................................................................................................................................... 62 ACCEPTED MANUSCRIPT 3 ACCEPTED MANUSCRIPT 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. Keywords: Ecology, Biotechnology, Metagenomics, Single-cell genomics, Natural products, EnzymesACCEPTED MANUSCRIPT 4 ACCEPTED MANUSCRIPT 1 Introduction 1.1 Microbial ecology: historical perspective The word ecology was coined in the late nineteenth century from the two Greek words oikos (household) and logos (law) to suggest that the study of the relations between organisms comes from “law of the household”. Ernst Haeckel (Haeckel 1866), a German biologist, identified ecology as a separate branch of science that deals with
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