Abstract
Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome.
Highlights
Chitin is an homopolymer of b-1,4-linked N-acetylglucosamine (N-acetyl-D-glucose-2-amine, NAG) with a critical biological role in both terrestrial and aquatic ecosystems as a major constituent of fungi and plant cell walls, as well as insect, krill and shellfish exoskeletons [1]
Efficient bacterial chitin degraders were isolated through culture, including representatives from Actinobacteria (e.g. Streptomyces sp.) [11], b-proteobacteria (e.g. Burkholderia sp.) [12] and c-proteobacteria (e.g. Xanthomonas sp.) [13]
After removal of the soil background activity 06, this represents 0.169 and 1.335 mM of chitin degraded over the enrichment, respectively
Summary
Chitin is an homopolymer of b-1,4-linked N-acetylglucosamine (N-acetyl-D-glucose-2-amine, NAG) with a critical biological role in both terrestrial and aquatic ecosystems as a major constituent of fungi and plant cell walls, as well as insect, krill and shellfish exoskeletons [1]. Uncultured and unknown bacteria might be involved in the degradation process as active key players (e.g. cooperating degraders), or passive players (e.g. opportunist cheaters), through establishment of local biofilm structures on chitin fibers [14], [15]. Apart from their fundamental role in ecosystems functioning, chitin degraders and their enzymes received a particular attention during the last decade for numerous applications. Chitin degraders are candidates for in situ application as biocontrol agents of soil born plant-pathogenic fungi [11], while shellfish wastes can be treated in the frame of enzymatic industrial processes, involving new and efficient chitinases characterized from environmental microbial communities [16], [17]
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