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

  • David K. Visi
  • Nandika D’Souza
  • Brian G. Ayre
  • Charles L. Webber III
  • Michael S. Allen
Environmental Microbiology


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 h 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 and 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 established themselves and in addition 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.


Microbial diversity Retting Semiconductor Sequencing Bioproducts 



This work was supported by a grant from the National Science Foundation’s Partnerships for Innovation award #IIP-1114389 to NAD and MSA. We would also like to thank Dr. Sheldon Shi for providing us with kenaf from Mississippi.

Supplementary material

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Copyright information

© Society for Industrial Microbiology and Biotechnology 2013

Authors and Affiliations

  • David K. Visi
    • 1
    • 4
  • Nandika D’Souza
    • 2
  • Brian G. Ayre
    • 4
  • Charles L. Webber III
    • 3
  • Michael S. Allen
    • 1
    • 4
  1. 1.Department of Forensics and Investigative GeneticsUniversity of North Texas Health Science CenterFt. WorthUSA
  2. 2.Department of Mechanical and Energy EngineeringUniversity of North TexasDentonUSA
  3. 3.Sugarcane Research UnitUSDA, ARSHoumaUSA
  4. 4.Department of Biological SciencesUniversity of North TexasDentonUSA

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