Monitoring the Microbiomes of Agricultural and Food Waste Treating Biogas Plants over a One-Year Period

The knowledge of the microbiome in the anaerobic digestion (AD) is critical for stabilizing the process and optimizing the biogas yield. This work investigates the microbial ecology in four full-scale biogas plants with different feedstocks and process parameters. The three agricultural plants sharing similar feedstocks’ composition (mostly rich in proteins, cellulose and hemicellulose), have several hydrolytic and methanogenic species in common, suggesting that their substrates specifically shape the microbiomes. Particularly, the hydrolytic and likely syntrophic Defluviitoga tunisiensis was detected as the most abundant species in one reactor, representing 21.2% of the community. On the other hand, the biogas plant treating the organic fraction of municipal solid waste (OFMSW), whose composition was much higher in hash and lower in proteins, displayed a quite different microbiome with a much lower abundance of Bacteroidales sp. much higher of Clostridiaceae. Moreover, this AD was clearly influenced by COVID-19 restrictions as both substrate availability and composition suddenly changed causing the wash-out of most bacterial and methanogenic species and leading to a deep modification of the microbial structure. The abundance of Methanosarcina flavescens greatly increased up to 36.5% of the total operational taxonomic units (OTUs), suggesting a switch from the hydrogenotrophic to the acetoclastic methanogenic pathway. This is the first report on the COVID-19 impact on the AD microbiome of a full-scale anaerobic digestor. Moreover, this paper demonstrated that the feedstock composition can differentially shape both bacterial and archaeal strains of the AD process.