Differential restructuring of a complex compost microbiome by metabolically distinct Streptomyces through community-dependent microbial interactions

Abstract

Microbial interactions are key determinants of soil and compost ecosystem function, yet remain difficult to dissect in complex, heterogeneous environments. This study introduces a reproducible, biologically active compost microcosm that enables controlled investigation of interactions between defined microbial species and established compost microbial communities while retaining an ecologically relevant environmental context.

Using two metabolically distinct Streptomyces species, Streptomyces venezuelae and Streptomyces rimosus, we combined amplicon sequencing, untargeted metabolomics and transcriptomics to characterise community responses within this experimental system. Introduction of either Streptomyces caused significant but distinct restructuring of the prokaryotic community, characterised by reduced alpha-diversity and increased dominance of selected taxa, while fungal diversity was reshaped through redistribution of previously dominant taxa.

Metabolomic and transcriptomic analyses revealed extensive changes in specialised metabolite production and biosynthetic gene cluster expression in response to the surrounding community, including specific induction of desferrioxamine E biosynthesis in S. venezuelae but not S. rimosus. However, exogenous addition of desferrioxamine E did not reproduce the observed community shifts, suggesting that these ecological responses arise from complex metabolite-mediated interactions rather than the activity of a single metabolite alone.

Together, our results demonstrate that the two Streptomyces tested exert distinct ecological effects on compost microbiomes through complex, community-dependent metabolic interactions. More broadly, this work establishes a versatile experimental framework for investigating microbial interactions within biologically active soil-derived communities while highlighting the importance of resolving ecological interactions at fine taxonomic and functional scales.