Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor

Methane-arrested anaerobic digestion (AAD) is a waste management strategy that produces carboxylic acid precursors to industrial products (fuels, bio-based polymers, and pharmaceuticals) from organic wastes. A major challenge preventing application of AAD is highly variable product profiles resulting from an inability to control the microbial communities underlying waste decomposition and product biosynthesis. Over time, lactic acid bacteria (LAB) often dominate AAD bioreactors and overproduce shorter chain acids causing acidosis. Here an AAD bioreactor where caproic acid production increased from an average of 3.9 g/L to an average of 12.3 g/L when the feedstock was switched from manure and paperboard to food waste. Time series shotgun metagenomics is used to investigate how microbial dynamics drive performance shifts. The dominant LAB shifted from Lactobacillus amylovorus spp. to Lactiplantibacillus pentosus spp. following the feedstock switch, corresponding with increased diversity and relative abundance (26.2%) of Caproicibacter spp. (putative chain elongator). Additionally, L. amylovorus MAGs encoded biosynthesis genes to produce the bacteriocin helveticin often produced by LAB to target closely related species. L. pentosus MAG.84 encodes bacteriocin-degrading enzymes and helveticin resistance genes, suggesting putitive mechanisms for bacteriocin resistance. These results suggest that bacteriocins may be an underappreciated mechanism for shaping microbial community dynamics in AAD.