Converge or Diverge? Exploring the Fate of Taxonomically Different Anaerobic Digestion Communities Under Uniform Growth Conditions

Biogas inocula with distinct taxonomic compositions often converge to similar communities when fed the same substrate, indicating strong substrate-driven deterministic assembly. Nevertheless, stochastic processes have also been suggested as a critical element for microbial assembly in biogas systems. To date, assembly processes have mainly been investigated with undefined, non-sterile substrates, making it difficult to exclude the influence of external microorganisms. The aim of the present study was to investigate whether three taxonomically distinct anaerobic digestion (AD) communities would converge when exposed to uniform growth conditions during semi-continuous operation with a sterilised defined medium. The inocula originated from mesophilic processes using different substrates (food waste, sludge, and manure) and total ammonia levels (0.5–7.2 g/L). The medium was formulated to support all four main metabolic steps of AD: hydrolysis, fermentation, anaerobic oxidation, and methanogenesis. Taxonomic, phylogenetic, and functional analyses conducted via 16S and metagenomic sequencing showed that the substrate had no deterministic effect on microbial community taxonomic composition. Instead, the final community structure was dictated primarily by the initial inoculum, regardless of changes in substrate composition or ammonia levels. Despite taxonomic divergence, broad-level functionality and operational performance remained similar between communities.