A genome-centric metagenomics approach to explain microbial community structure in anaerobic digesters

A functioning anaerobic digestion (AD) microbiome is integral for sludge management to be successful. Comprehensive ecological insights, and a full accounting of important microbial species, can help to improve and validate operational strategies. We analysed a time-series of metagenome samples obtained from full-scale anaerobic digesters and performed genome-resolved analysis to gain insight into the microbial community structure and potential functions of the AD microbiome. Ninety samples from three full-scale digesters were collected over a period of nine months and their nucleic acids extracted and subjected to shotgun sequencing (Illumina HiSeq2500; average 70M PE reads/sample). The raw reads were quality controlled, trimmed, assembled, binned, and dereplicated to obtain metagenome-assembled genomes (MAGs). Genome quality was assessed using the MIMAG criteria. The taxonomic assignment of the recovered MAGs was conducted using GTDB-Tk, and gene-level functional annotations were obtained using the KEGG, and CAZy databases. From ninety metagenome assemblies, 14,236 MAGs were recovered, of which 37%, 16%, and 1% satisfied medium-quality (Completeness > 50% and contamination 90% and contamination 90% and contamination