Monitoring co-cultures of Clostridium carboxidivorans and Clostridium kluyveri by fluorescence in situ hybridization with specific 23S rRNA oligonucleotide probes |
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| Affiliation: | 1. Chair of Microbiology, Technical University of Munich, TUM School of Life Science, Freising, Germany;2. Department of Mechanical Engineering, Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany;3. Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden;4. Research Infrastructure Fluorescence in Situ Hybridization (FISH), Chemical Biological Centre, Umeå University, Umeå, Sweden;1. Department of Chemical and Biomolecular Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA;2. Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA;1. Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing 100084, PR China;2. Department of Environmental Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark;1. School of Bioengineering, Dalian University of Technology, Dalian 116024, China;2. William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 Woodruff Ave., Columbus, OH 43210, USA;3. Bioprocessing Innovative Company, 4734 Bridle Path Ct., Dublin, OH 43017, USA;4. School of Environment, Harbin Institute of Technology, Harbin 150090, China |
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| Abstract: | The development of co-cultures of clostridial strains which combine different physiological traits represents a promising strategy to achieve the environmentally friendly production of biofuels and chemicals. For the optimization of such co-cultures it is essential to monitor their composition and stability throughout fermentation. FISH is a quick and sensitive method for the specific labeling and quantification of cells within microbial communities. This technique is neither limited by the anaerobic fermenter environment nor by the need of prior genetic modification of strains. In this study, two specific 23S rRNA oligonucleotide probes, ClosKluy and ClosCarb, were designed for the monitoring of C. kluyveri and C. carboxidivorans, respectively. After the optimization of hybridization conditions for both probes, which was achieved at 30% (v/v) formamide, a high specificity was observed with epifluorescence microscopy using cells from different pure reference strains. The discriminating properties of the ClosKluy and ClosCarb probes was verified with samples from heterotrophic co-cultures in anaerobic flasks as well as autotrophic stirred-tank bioreactor co-cultures of C. kluyveri and C. carboxidivorans. Besides being suited to monitor defined co-cultures of these two species, the new specific FISH oligonucleotide probes for C. kluyveri and C. carboxidivorans additionally have potential to be applied in environmental studies. |
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| Keywords: | 23S rRNA Specific oligonucleotide probe Co-cultivation |
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