Advances of high-throughput sequencing for unraveling biotechnological potential of microalgal-bacterial communities

Although established biotechnological applications of microalgae e.g., the production of high-value metabolites is based on axenic cultures, exploitation of the mutualistic consortia of microalgae and bacteria quickly comes to foreground, especially in bioremediation and wastewater treatment. This trend shifts the focus from genomic research of certain microalgal species to metagenomic studies of interactions between microalgae and bacteria in natural communities and in artificial consortia. Dissection of the genetic determinants of the robustness and productivity of the consortia become a hot research direction, too. Admirable contribution to this topic had been made by high-throughput sequencing (HTS), while recent breakthrough in this field was entailed by the advent and rapid development of the 3rd generation nanopore sequencing which becomes increasingly accurate while providing unprecedented sequencing performance. Recent progress of the Oxford Nanopore Technologies (ONT) enabled both classical metagenomic analysis of microalgal-bacterial communities based on whole metagenome sequencing as well as taxonomic and genetic profiling based on the amplicon sequencing. The parallel emergence of novel bioinformatic algorithms for processing the metagenomic datasets opened new opportunities for the analysis of structure and physiology of microalgal-bacterial communities. From the practical perspective, the new HTS techniques became a time- and labor-savers in discovery of new microalgae with a high potential for the accumulation of valuable metabolites, biodegradation of hazardous micropollutants, and biosequestration of nutrients from waste streams. Search for prokaryotic species boosting the biotechnological potential of eukaryotic microalgae via mutualistic interactions with them is another important goal. The insights from the both short-read and long-read metagenomics will form a solid foundation for the rational design of microalgal-bacterial consortia for biotechnology. In this review, we briefly outline the benefits of the long-read sequencing for structural and functional investigation of algal-bacterial consortia and summarize recent reports on using this approach for achieving the biotechnology-related goals.