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Investigation of the microbial retting community of kenaf (Hibiscus cannabinus) under differing conditions using next-generation semiconductor sequencing

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The use of the natural fibers requires the development of cost-efficient processing of fibers with consistent, uniform properties. The microbial communities associated with kenaf (Hibiscus cannabinus) plant fibers during retting were determined in an effort to identify possible means of accelerating this process for industrial scale-up. Microbial communities were identified by semiconductor sequencing of 16S rRNA gene amplicons from DNA harvested from plant-surface associated samples and analyzed using an Ion Torrent PGM. The communities were sampled after 96 hours from each of three different conditions, including amendments with pond water, sterilized pond water, or with a mixture of pectinolytic bacterial isolates. Additionally, plants from two different sources having different pretreatment conditions were compared. We report that the best retting communities are dominated by members of the order Clostridiales. These bacteria appear to be naturally associated with the plant material, although slight variations between source materials were found. Additionally, heavy inoculations of pectinolytic bacteria failed to establish themselves on the plant material surface, but their presence facilitated the rapid dominance of the original plant-associated Clostridiales. These data suggest that members of the order Clostridiales dominate the community and are most closely associated with efficient and effective retting. The results further suggest that establishment of the community structure is first driven by the switch to anaerobic conditions, and subsequently by possible competition for nitrogen. These findings reveal important bacterial groups involved in fiber retting, and suggest mechanisms for the manipulation of the community and retting efficiency by modifying nutrient availability.
David K. Visi , Nandika D'Souza , Brian G. Ayre , Charles L. Webber III , Michael S. Allen
USDA Scientist Submission
Journal of Industrial microbiology & Biotechnology 2013 5 v.40 no.5
Journal Articles, USDA Authors, Peer-Reviewed
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