Potential and trade-offs of native versus sludge-derived microbiota in dark fermentation of agro-industrial effluents

Dark fermentation offers a scalable route to low-carbon hydrogen, yet performance depends on inoculum origin and feedstock. This study contrasts native microbiota with pretreated granular sludge for hydrogen and metabolite production from agro-industrial residues, agave bagasse enzymatic hydrolysates (EH1, EH2), cheese whey (CW), and winery wastewater (WW). Sludge inoculum consistently enhanced H 2 , reaching 842 mL H 2 /L in EH1. Native microbiota, while producing lower H 2 (e.g., 536 mL H 2 /L in EH1), showed metabolic flexibility: rapid carbohydrate/lactate use, activation of formate hydrogenase, and frequent electron diversion to propionate/lactate. Community profiling showed sludge-derived consortia converged to specialized structures, whereas native microbiota remained substrate-specific and diverse. Despite taxonomic divergence, functional predictions indicated redundant core hydrogenogenic pathways and complementary strengths: sludge maximized H 2 efficiency, while native microbiota minimized inputs by avoiding inoculum supply/pretreatment. These trade-offs support selective pretreatment, co-inoculation, or target microbial management to optimize dark fermentation in integrated biorefineries. • Native microbiota degrades complex substrates with high metabolic flexibility. • Distinct inocula activate different hydrogenogenic routes. • Pretreated sludge boosts H 2 yield by enriching hydrogenogenic Clostridium . • Trade-offs highlight that native microbiota reduce external inputs.