An artificial selection procedure enriches for known and suspected chitin degraders from the prokaryotic rare biosphere of multiple marine biotopes

TL;DR

Researchers enriched for bacteria that can break down chitin from different marine environments, discovering new and known species involved in this process.

Contribution

A novel artificial selection method successfully enriched low-abundance chitin-degrading bacteria from the rare biosphere of multiple marine biotopes.

Findings

Distinct chitin-degrading bacterial consortia were enriched from each marine biotope.

Low-abundance bacteria from the rare biosphere were recruited in enrichment cultures.

Novel taxa like Aureivirga and Halodesulfovibrio were identified as potential chitin degraders.

Abstract

Biological chitin degradation is a major process in the ocean, governed primarily by the action of microorganisms. It is known that the structure and taxonomic profile of chitin-degrading microbial communities change across marine biotopes, but efforts to isolate chitin degraders within these communities in the laboratory have seldom been attempted. We characterized the prokaryotic communities associated with the marine sponge Sarcotragus spinosulus, the octocoral Eunicella labiata, and their surrounding sediment and seawater and applied an artificial selection procedure to enrich bacterial consortia capable of degrading chitin from the abovementioned biotopes. Throughout the procedure, chitin degradation was monitored, and the taxonomic composition was studied along four successive enrichment cultures from each biotope.

The naturally occurring prokaryotic communities of the two host species (Sarcotragus spinosulus and Eunicella labiata) were distinct from each other and from those of seawater and sediments, even though they were co-inhabiting the same geographic area. We found that low-abundance bacteria from the rare biosphere were recruited in the enrichment cultures from all biotopes, while dominant bacterial symbionts likely to play a role in chitin degradation within marine sponges and octocorals remained “unculturable” under our experimental conditions. Well-known chitin degraders such as Vibrio, Pseudoalteromonas and Aquimarina, as well as other taxa not known or poorly known for their role(s) in chitin degradation such as Aureivirga, Halodesulfovibrio, Motilimonas, Muricauda, Psychromonas, Poseidonibacter, Reichenbachiella, and Thalassotalea, among others, were enriched using our artificial selection approach. Distinct chitin-degrading consortia were enriched from each marine biotope, highlighting the feasibility of this approach in fostering the discovery of novel microorganisms and enzymes involved in chitin degradation pathways of relevance in applied biotechnology.

This study unveils distinct bacterial consortia possessing moderate to high efficiency at degrading chitin. They were composed of a mix of known chitin degraders, known chitin utilizers and many taxa poorly or not yet known for their role(s) in chitin degradation such as Aureivirga, Psychromonas, Motilimonas, Reichenbachiella, or Halodesulfovibrio. The latter taxa are potential key players in marine chitin degradation whose study could lead to the discovery of novel enzyme variants able to degrade chitin and its derivatives.

The online version contains supplementary material available at 10.1186/s12866-025-04218-7.

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