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

• Main Authors: Neshat, Soheil Asgarineshat, Krithika Arumugam, Uma Shankari Chandra Segaran, Prabu Sekar, Purbojati, Rikky, Nguyen, T. Q. N., Cokro, Angel Anika, Santillan, Ezequeil, Ng, T. C. A., Williams, Rohan B. H., Wuertz, Stefan
• Other Authors: School of Civil and Environmental Engineering
• Format: Conference or Workshop Item
• Language: English
• Published: 2022
• Subjects: Engineering::Bioengineering; Science::Biological sciences::Molecular biology; Anaerobic Digestion; Metagenomics; Genome-centric; Microbiome
• Online Access: https://hdl.handle.net/10356/156928; https://www.siww.com.sg/qql/slot/u143/SIWW%202022/Programme/Water%20Convention/22_0022%20SIWW%20Water%20Convention%20Advanced%20Programme%20Booklet%202022_V13.pdf
• Institution: Nanyang Technological University

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 <10%), putative high-quality (Completeness > 90% and contamination <5%), and high-quality criteria (Completeness > 90% and contamination <5% and presence of rRNA and tRNA genes), respectively. Taxonomical classification of the MAGs with at least medium quality (n =7666) revealed that 12.9%, 37.4%, and 77.1% of them belong to a novel family, genus, and species, respectively. A co-occurrence network analysis of the community structures in three replicate digesters revealed a highly interconnected network of microorganisms, suggesting the presence of a backbone in a functional AD microbial community. Functional analysis of the recovered MAGs showed the presence of three methanogenesis pathway modules, namely, methanogenesis via CO2, acetate, and trimethylamine. In addition, a specialization was observed in the hydrolytic bacterial community using CAZy annotation. In conclusion, we have obtained a catalogue of 166 MIMAG high-quality MAGs from a time-series metagenome survey of three full-scale anaerobic digesters situated in a tropical wastewater treatment plant, leading to novel ecological insights into the AD microbial community.