Monitoring Microbial Diversity of Bioreactors Using Metagenomic Approaches
With the rapid development of molecular techniques, particularly ‘omics’ technologies, the field of microbial ecology is growing rapidly. The applications of next generation sequencing have allowed researchers to produce massive amounts of genetic data on
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Monitoring Microbial Diversity of Bioreactors Using Metagenomic Approaches Joshua T. Ellis, Ronald C. Sims, and Charles D. Miller
Abstract With the rapid development of molecular techniques, particularly ‘omics’ technologies, the field of microbial ecology is growing rapidly. The applications of next generation sequencing have allowed researchers to produce massive amounts of genetic data on individual microbes, providing information about microbial communities and their interactions through in situ and in vitro measurements. The ability to identify novel microbes, functions, and enzymes, along with developing an understanding of microbial interactions and functions, is necessary for efficient production of useful and high value products in bioreactors. The ability to optimize bioreactors fully and understand microbial interactions and functions within these systems will establish highly efficient industrial processes for the production of bioproducts. This chapter will provide an overview of bioreactors and metagenomic technologies to help the reader understand microbial communities, interactions, and functions in bioreactors. Keywords Bioproducts • Bioreactors • Metagenomics • Microbial diversity
Abbreviations BLAST COG IMG JGI mcrA NCBI
basic local alignment search tool clusters of orthologous groups integrated microbial genomes joint genome institute methyl coenzyme-M reductase national center for biotechnology information
J.T. Ellis • R.C. Sims • C.D. Miller (*) Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105, USA e-mail: [email protected] X. Wang et al. (eds.), Reprogramming Microbial Metabolic Pathways, Subcellular Biochemistry 64, DOI 10.1007/978-94-007-5055-5_4, © Springer Science+Business Media Dordrecht 2012
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RDP10 SAMS Y Y p/N Y p/O2 Y p/s
4.1
ribosomal database project sequence analysis and management system yield mass of bioproduct per mass of nitrogen utilized mass of bioproduct per mass of oxygen utilized mass of bioproduct produced per mass of carbon substrate utilized
Introduction
Bioreactors are typically considered vessels that produce products in a controlled manner via biological conversion. These systems convert materials (substrates) by influencing metabolic pathways to transform materials into products of interest (Williams 2002). Microbial bioreactors have been used for many years to produce products such as cheese, wine, beer, and bread through traditional fermentation, a process that was studied in depth by the famous microbiologist Louis Pasteur. Current technologies not only produce these products, but also a variety of other products such as industrial solvents (biofuels), biogas, acids, sugars, vitamins, antibiotics, and enzymes for bioconversion processes, as well as other primary and secondary metabolites (Williams 2002; Ullmann 2007). Several bioreactor designs are used to produce bioproducts, and include, but are not limited to: batch reactors, fed-batch reactors, continuous cultivation
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