Comparative Metagenomics for Monitoring the Hidden Dynamics of the Algal-Bacterial Wastewater Community under the Influence of Drugs

Modern methods of metagenomics, including those based on long reads of nanopore sequencing, are especially relevant for environmental-monitoring tasks, in particular, for assessing the anthropogenic impact on natural communities of microorganisms. These include algal-bacterial communities that live in water-treatment plants and participate in the biological treatment of wastewater from excess organic waste and nutrients (phosphorus and nitrogen). Metagenomic analysis shows changes in the taxonomic composition and functional profile of the algal-bacterial community when simulating the release of drugs into wastewater: broad-spectrum antibiotics (for example, ceftriaxone) and nonsteroidal anti-inflammatory drugs (for example, diclofenac). The results of metagenomic analysis based on long reads of nanopore sequencing and classical methods of environmental monitoring, including metabarcoding based on short reads on a second-generation sequencing platform, are compared. Nanopore sequencing of the entire metagenome shows a greater biodiversity of samples compared to the DNA metabarcoding of short reads, makes it possible to determine the taxonomic affiliation of particular organisms more accurately, identify groups of eukaryotic oxygenic phototrophs, and also reveal the presence of antibiotic-resistance genes in the community. It is shown that under the influence of medicinal substances, the algal-bacterial community is enriched with antibiotic-resistant bacteria. At the same time, despite maintaining the rate of phosphorus removal, the community’s potential for the removal of nutrients is reduced, which is expressed in a two-order reduction in the relative representation of inorganic-nutrient metabolism genes. Simultaneous exposure to ceftriaxone and excess nutrients in the wastewater leads to the maximum enrichment of antibiotic-resistant organisms, as well as the replacement of cyanobacteria originally present in the community with eukaryotic microalga.