Influence of feedstock and operational parameters on the composition, temporal dynamics, and sensitivity of microbiomes from nineteen full-scale anaerobic municipal sludge digesters and anaerobic fat, oil, and grease co-digesters.

Anaerobic co-digestion is a key microbial-based technology in the bioeconomy. However, the effects of lipidic co-substrates on full-scale anaerobic digester microbiomes, including composition, structure and sensitivity to organic overload shocks, have yet to be fully explored. This study sequenced 12 wastewater solids mono-digesters and 7 high-strength lipidic waste co-digesters monthly for 14  months. The presence of co-substrates enriched hydrolytic bacteria, fermentative bacteria, and acetoclastic methanogens, resulting in a novel co-digester core microbiome. It also decreased microbiome richness, alpha diversity, structural fluidity (i.e., mean rank shifts - MRS), and the relative abundance of sub-dominant bacterial taxa (from 45 % to 37 %). The less rich and more compositionally stable microbiomes of anaerobic co-digesters resulted in higher methane yields at lower organic shock loads (i.e., 1  mL of canola oil) compared with anaerobic mono-digesters (239.9 ± 54.6  mL CH4/mL canola oil and 87.5 ± 22.3  mL CH4/mL canola oil, respectively). However, anaerobic co-digesters had greater sensitivity to higher organic shock loads (5-20  mL of canola oil), quantified by percent reduction of methane yields, compared to anaerobic mono-digesters. A multivariate linear regression model predicting a full-scale anaerobic digester's sensitivity to organic overload shocks (Significance F = 1.99 × 10-12) revealed that higher operational temperature (p < 0.00) and lower bacterial richness (p < 0.00), archaeal richness (p < 0.00), bacterial MRS (p = 0.02) and archaeal MRS (p < 0.00) increased the sensitivity of anaerobic digesters to organic overloads. Thus, several co-digestion adaptations that contributed to higher methane yields at lower organic shock loads (e.g., lower bacterial richness and greater microbiome compositional stability), also led to greater sensitivity to higher organic shock loads.