Mechanism driving efficient organic acid synthesis by agricultural waste epiphytic microbiota in anaerobic co-fermentation

Anaerobic co-fermentation is a microbially driven technology for the valorization of agricultural waste using multiple feedstocks. However, the coexistence of epiphytic microbes from different substrates complicates the assessment of their individual contributions to organic acid production. Here, we investigated the roles of epiphytic microbiota from cabbage waste (C-EMs) and epiphytic microbiota from wheat bran (W-EMs) by selectively reducing one microbiota via γ-irradiation during co-fermentation. C-EMs produced 255.10 g/kg DM of lactic acid and 11.45 g/kg DM of acetic acid on day 30, representing increases of 26.32% and 49.87%, respectively, compared with W-EMs. Microbiologically, C-EMs were associated with a faster succession from acid-sensitive to acid-tolerant bacteria and a higher relative abundance of genes related to the Embden-Meyerhof-Parnas and pentose phosphate pathways, which may be associated with differences in metabolic potential relevant to organic acid production. Metabolic reconstruction based on genome-resolved metagenomic data analysis indicated that Enterobacter ludwigii may act as a potential contributor within C-EMs, with genomic features suggesting a capacity for utilizing diverse substrates. It may also be associated with interactions with Weissella cibaria , Lactiplantibacillus plantarum , and Levilactobacillus brevis , which could be relevant to organic acid production. This study provides a framework for examining substrate-specific epiphytic microbiome contributions and offers insights into factors associated with organic acid production, which may inform future strategies for optimizing anaerobic co-fermentation.