Genome-centric view of metagenomes from methanogenic wastewater treatment sludge: a new opportunity to understand microbial ecology of engineered systems

Despite the biotechnological significance of industrial-scale anaerobic wastewater treatment processes, our understanding of the microbial ecology that underpins these processes is still rudimentary because most microorganisms cannot be cultured. An example of such uncultured microbial populations is the filament belonging to candidate bacterial phylum KSB3, which occasionally triggers bulking of methanogenic sludge in high-rate wastewater treatment processes. The study of these uncultured bacteria will contribute to our understanding of and ability to engineer anaerobic wastewater treatment systems, but has often been hampered by an inability to obtain a pure culture despite repeated and long term isolation efforts. However, emerging culture-independent molecular techniques such as differential coverage binning of metagenomic data, which allows genome-centric metagenomics involving even low abundance population genomes, are providing new opportunities to understand such systems. In our study, draft population genomes from the majority of microbial community members in a full-scale methanogenic wastewater treatment reactor were obtained via differential coverage binning of metagenomic data. From the sludge metagenomes, 14 archaeal and 49 bacterial population genome bins were obtained with >65% completeness and <10% contamination, representing approx. 60% of the total metagenomic reads. Most of the archaeal genomes belong to methanogenic lineages, such as Methanolinea and Methanosaeta, with a few genomes from uncultured lineages. The bacterial genome bins obtained were distributed amongst a variety of phyla, including a wide range of candidate (uncultured) phyla such as KSB3, AC1, OD1, and TM6. These genomic data provide a basis for a comprehensive genome-centric view of this engineered ecosystem.