Investigation of Bacterial and Methanogen Community Composition and Diversity in full-scale Anaerobic Manure Digesters

Abstract

Anaerobic digestion of biopolymers into methane is accomplished by complex microbial communities that remain poorly characterized. Their composition tends to vary, likely as a result of many factors such as substrate composition, operating parameters, and microbial succession. In order to gain further insight, we performed a comparative analysis of microbial community composition amongst four mesophilic full scale anaerobic digesters, using a combined total of 133,789 high quality, non-chimeric bacterial and methanogen sequence reads from PCR-generated amplicons of the 16S rRNA gene. In three digesters that used manure as their main substrate, methanogen populations were composed predominantly of a common Methanosarcina-related Operational Taxonomic Unit (OTU). The composition of bacterial populations in these digesters was more diverse, with the most highly represented OTUs consisting of different combinations of Bacteroidetes-Chloroflexi or Bacteroidetes-Firmicutes-unclassified bacteria. In contrast, the dominant methanogen OTU in the remaining digester, whose substrate consisted of manure and offfarm lipid waste, was related to species of the genus Methanoculleus, and two bacterial OTUs (Chloroflexi and unclassified) together represented 83.7% of bacterial sequence reads. Our results suggest that while methanogen composition in anaerobic dairy manure digesters appeared to be limited to two main profiles, there was very limited convergence in bacterial phylogenetic composition. Since the major bacterial OTUs identified corresponded to uncultured species belonging to uncharacterized genera, future investigations will be required to determine their biochemical roles and assess the level of functional redundancy among them.