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

Abstract

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.

Bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting with Bacillus cereus HDYM-02

“…In the BA samples, Bacillaceae almost totally replaced Enterobacteriaceae within 24 h, which almost completely disappeared throughout the whole retting period. The competition for oxygen and nutrients resulted in the replacement of Enterobacteriaceae by Bacillaceae, in accordance with the replacement of the inherent Entrerobacteriales by Bacillales after inoculating Bacillus and Paenibacillus strains during kenaf retting16. In this study, the competition among aerobes following inoculation with B. cereus HDYM-02 also led to the decrease of Chryseobacterium , Flavobacteriaceae, and Acinetobacter , Moraxellaceae (Fig.…”

“…2). Pseudomonas is the dominant genus involved in the microbial retting of flax1214 and kenaf16. Nevertheless, in this study, the average abundance of Pseudomonas was less than 2.0% across all of the retting samples.…”

“…Recently, one high-throughput sequencing platform, semiconductor sequencing, has been applied in investigations of the bacterial retting community of kenaf under different retting conditions at the order level16. In this study, high-throughput sequencing was first used to reveal the bacterial succession from phylum to species during the entire retting period for flax straw.…”

“…1), indicating their naturally association with the flax straw, similar to kenaf16. Short-length sequencing always loses accuracy as it moves lower in the taxonomic arrangement (i.e., more sequences start to be unclassified), which resulted in the assignment of several Clostridium sensu stricto rather than specific species (Fig.…”

“…Recently, several researchers have identified the bacterial community in the retting ecosystem using modern molecular techniques, such as 16S gene library13 and denatured gradient gel electrophoresis (DGGE)121415, and have shown that the common dominant groups present during retting are Clostridiaceae, Pseudomonadaceae and Bacillaceae. Visi et al used next-generation semiconductor sequencing to conclude that the community structure during kenaf retting the was first driven by the switch to anaerobic conditions and subsequently by possible competition for nitrogen16. Retting is a substantially complicated ecosystem that involves interaction between biotic and abiotic factors, i.e., microbes and metabolites.…”