Linking geographic flavor signatures to microbial origin in high-temperature Daqu: An integrated metaproteomics and metabolomics approach

Elucidating the molecular architecture of microbial terroir is vital for precision fermentation, yet functional decoupling between taxonomic abundance and in situ expression remains a fundamental challenge. To resolve this "abundance-activity paradox," we integrated metaproteomics, metabolomics, and metagenomics across the Chishui River gradient. We identified distinct chemosensory fingerprints: upstream thermotolerant consortia (<i>Bacillus</i> and <i>Oceanibacillus</i>) specialize in 2,3,5,6-tetramethylpyrazine biosynthesis mediated by bacterial acetolactate decarboxylase, while downstream microbiota (<i>Weissella</i> and <i>Debaryomyces</i>) prioritize alcohol and ester formation. Crucially, metaproteomic profiling unmasked the "rare biosphere" as a primary driver of core metabolic fluxes. While <i>Bacillus</i> was genomically dominant, keystone functional taxa-specifically low-abundance fungi like <i>Hyphopichia</i> and <i>Paecilomyces</i>-were the actual executors of rate-limiting starch hydrolysis. Furthermore, functional resilience was uniquely maintained through robust fungal co-occurrence networks despite geographic constraints. This study challenges abundance-centric paradigms, providing an activity-based framework for the rational design of synthetic microbial consortia to standardize flavor while preserving regional identity.