Abstract
Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.
Highlights
Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry
We present the benefits of HQ metagenome-assembled genomes (MAGs), by linking genomic functional potential to the comprehensive MiDAS3 16S rRNA gene database, with >13 years of amplicon data, used to cost-effectively monitor wastewater treatment plants (WWTPs) microbial communities in Denmark[13,18] (Fig. 1)
A streamlined single contig genome was recently recovered for a Proteobacteria[7] and our recovery of closed MAGs (CMAGs) for a novel Micavibrionales (2 Mbp) and Burkholderiales (0.9 Mbp) provides additional evidence of genome reduction in some members of this phylum
Summary
Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. We present the benefits of HQ MAGs, by linking genomic functional potential to the comprehensive MiDAS3 16S rRNA gene database, with >13 years of amplicon data, used to cost-effectively monitor WWTP microbial communities in Denmark[13,18] (Fig. 1). This approach enabled us to target, visualize, and experimentally confirm the metabolic potential of an abundant, yet uncharacterized, genus widespread in Danish WWTPs (Fig. 1)
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