Environmental factors-driven microbial succession and indigo marker accumulation during fermentation

This study investigated how environmental conditions and microbial community dynamics drive marker compound transformation during indigo paste fermentation. Fermentation broths were collected at multiple time points from an open-air natural fermenter and analyzed via physicochemical methods combined with Illumina metagenomic sequencing, enabling simultaneous quantification of indicator levels, environmental variations, and microbial structure changes, along with their contributions to marker synthesis and accumulation. Proteobacteria and Firmicutes dominated bacterial communities before and after indigo extraction, respectively; Ascomycota prevailed in early fermentation and post-extraction stages, dynamically alternating with Basidiomycota. Redundancy (RDA) and canonical correlation analyses (CCA) identified oxidation-reduction potential (ORP) and pH as critical drivers of microbial composition (P < 0.05). Microbial diversity correlated positively with ORP and temperature early, shifting to pH association later. Markers (e.g., tryptanthrin, indigo, indirubin) showed significant negative correlations with ORP and pH. Functional genus analysis revealed 7 bacterial (e.g., Clostridium sensu stricto 1, unclassified_f_Enterobacteriaceae) and 4 fungal (e.g., Carlosrosaea) genera positively linked to marker content (P < 0.05), suggesting roles in promoting synthesis; Chryseobacterium was negatively correlated, indicating inhibition. These results demonstrate that optimizing pH and ORP enhances microbial structure by suppressing unfavorable microbes and enriching functional populations that facilitate indigo reduction, significantly improving target marker synthesis efficiency in indigo paste.