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Title: Phylogenetic analysis of the kenaf fiber microbial retting community by semiconductor sequencing of 16S rDNA amplicons

Author
item VISI, DAVID - University Of North Texas
item SOUZA, NANDIKA - University Of North Texas
item AYRE, BRIAN - University Of North Texas
item Webber Iii, Charles
item ALLEN, MICHAEL - University Of North Texas

Submitted to: American Society for Microbiology
Publication Type: Abstract Only
Publication Acceptance Date: 3/10/2012
Publication Date: 3/27/2012
Citation: Visi, D.K., Souza, N.A., Ayre, B.G., Webber III, C.L., Allen, M.S. 2012. Phylogenetic analysis of the kenaf fiber microbial retting community by semiconductor sequencing of 16S rDNA amplicons [abstract]. American Society for Microbiology. p. 1921.

Interpretive Summary:

Technical Abstract: Kenaf, hemp, and jute have been used for cordage and fiber production since prehistory. To obtain the fibers, harvested plants are soaked in ponds where indigenous microflora digests pectins and other heteropolysaccharides, releasing fibers in a process called retting. Renewed interest in “green” substitutes for inorganic fibers (e.g. fiberglass) and desire for biodegradable composites has led to the re-evaluation of the retting process. Numerous studies have identified cultivable bacteria from retting solutions, but to date, there has been no investigation of the microbial community using next-generation sequencing methods. The main microbial community members in the retting process (C1) of the fibrous plant Hibiscus cannabinus (kenaf) was identified. The system was tested after inoculation with a defined consortium of bacteria (C2) previously isolated from the environment using pectin enrichment, and ascertained the extent to which the introduced species could establish themselves in the community. C1 consisted of Millipore water (750 mL) and fresh pond water (250 mL), and represented a “traditional” retting environment. C2 was similar but with autoclaved pond water (250 mL) and addition of three bacterial isolates: Bacillus DP1, Paenibacillus DP2, and Bacillus K1. Following a 4-day incubations, DNA was extracted and subjected to two-stage nested PCR before sequencing the difference130bp amplicons on an Ion Torrent PGM. Firmicutes dominated C2 at 87.9%. In C2, with the addition of pectinase-degrading isolates, Bacillus DP1 and DP2 failed to establish themselves in the surface-attached community at day 4; whereas Paenibacillus DP2 grew to make up approximately 17.1% of the flora. By comparison, C1 had 28.6% Firmicutes and 54.8% Bacteroidetes at the phylum level. In addition, Clostridia were found to be a major constituent in the microbial retting community as indicated by their presence in both retting environments. Large numbers of Prevotellacae in C1 indicate these organisms should be targeted in future enrichments. Understanding the microbial interactions during the retting process will be essential to optimizing fiber quality and process efficiency.