Multi-omics deciphers details of chitin decomposition in soil by a model bacterial consortium.

Soil microorganisms carry out decomposition of complex organic carbon molecules, such as chitin. High diversity of the soil microbiome and complexity of the soil habitat has posed a challenge to elucidate specific interactions between soil microorganisms. Here, we overcame this challenge by studying a model soil consortium (MSC-2) that is composed of 8 species. The MSC-2 isolates were originally obtained from the same soil that was enriched with chitin as a substrate. Our aim was to elucidate specific roles of the 8 member species during chitin metabolism in soil. The 8 species were added to sterile soil with chitin and incubated for 3 months. Multi-omics was used to understand how the community composition, transcript and protein expression and chitin-related metabolites shifted during the incubation period. The data clearly and consistently revealed a temporal shift during chitin decomposition and defined contributions by individual species. A Streptomyces species was a key player in early steps of chitin decomposition, followed by other members of MSC-2. These results illustrate how multi-omics applied to a defined consortium untangles complex interactions between soil microorganisms. Overall design: MSC-2 species were inoculated into sterile soil and incubated at KSC. A set of tubes was inoculated for each dilution and timepoint (five replicates). At each timepoint (0, 4, 8 and 12 weeks) that set of tubes (both dilutions) was stored at -80C. At the final 12 week timepoint all tubes were processed for RNA extraction and sequencing using Illumina technology. RNA was aligned to reference genomes for each of the eight species using the Burrows Wheeler Aligner and counted using HTSeq. Raw counts were normalized using DESeq2 and comparisons were made between timepoints to identify differentially expressed genes