Labile substrate availability shapes interactions in a synthetic chitin-degrading soil bacterial community

Chitin decomposition involves different extracellular enzymes and intermediate products, giving rise to complex social dynamics within chitin-degrading communities. These communities are therefore an ideal model system to investigate how complex organic matter is decomposed in soil, and what effect microbial interactions have on the decomposition process. We used a synthetic consortium consisting of three unrelated, potentially chitin-degrading soil bacterial strains (Paenibacillus alginolyticus, Paraburkholderia xenovorans and Solirubrobacter soli) to investigate how their interactions affect the decomposition of chitin, and how the availability of labile carbon influences these interactions.

The strains were grown in monoculture and in all possible combinations on three different substrates (2% chitin, 2% n-acetylglucosamine (NAG, the monomer of chitin) and a mixture of 1% chitin and 1% NAG). Cumulative respiration as a community performance metric was measured over the course of two weeks using the MicroResp^tm system. We measured the concentration of chitin oligomers (chitobiose and chitotriose) at the endpoint using PMP-derivatisation and UPLC-Orbitrap MS. The final microbial community composition was assessed via 16s Amplicon sequencing and the 16s gene copy number was measured with droplet-digital PCR.

Depending on the substrate, each strain showed distinct respiration patterns in monoculture, indicating different functionalities. We found both competitive and synergistic interactions in the strain combinations, depending on the involved species and available substrate. P. xenovorans dominated the other strains whenever the labile substrate (NAG) was added. The relative abundance of the less competitive strains (P. alginolyticus and S. soli) was however increased in the treatment containing only chitin compared to the NAG-treatments. Chitin was degraded a lot more when all three strains were included, as shown by both the maximum respiration and chitobiose concentration. All three strains were still detectable in this treatment, which was not the case when NAG was present from the beginning.

Based on these results we assume that energy limitation forces synergistic interactions in this model community, increasing the chitin decomposition efficiency. Adding labile substrate alters these interactions, leading to the exclusion of less competitive strains. Our results emphasize how interacting bacteria of different functional groups can result in increased decomposition of complex soil organic matter and how the relationships between different species in a microbial community at a soil microsite might change based on the available substrate.