Metagenome-assembled genomes of non-axenic cyanobacteria: taxonomy, functional potential, and selection of promising strains for agrobiotechnologies

Abstract

The search for novel highly effective microbial strains and the engineering of polyfunctional microbial inoculants based on them represents a key vector in the development of modern agrobiotechnologies. In this study, a comprehensive taxonomic and functional characterization of nine non-axenic strains of soil filamentous cyanobacteria belonging to the order Nostocales was conducted using metagenomic whole-genome sequencing. The assembly of metagenome-assembled genomes (MAGs) allowed for the reconstruction of high-quality genomic sequences of the target taxon, bypassing the labor-intensive step of strain axenization. According to the phylogenomic analysis, the studied cultures occupy a distinct position on the phylogenetic tree and can be considered candidates for novel taxa; however, this requires further verification as the current shortage of reference genomes for soil cyanobacteria is overcome. Based on ribosomal marker genes, the composition of the accompanying satellite microbiota localized within the exopolysaccharide sheaths of the hosts was characterized. The presence of beneficial heterotrophic bacteria from the genera Devosia, Lysobacter, Brevundimonas, Variovorax, Bosea, Achromobacter, and Pseudoflavitalea, which possess pronounced plant growth-promoting and biocontrol potential, was verified. Functional genome annotation revealed that all strains harbor a complete nitrogen fixation gene cluster and well-developed phosphorus mobilization systems. The strain Nostoc sp. VKM Al-56 was distinguished by a unique iron metabolism apparatus, whereas Nostoc edaphicum VKM Al-156 stood out for its aromatic compound degradation pathways. An integrated analysis considering taxonomic and biogeographic diversity, as well as the presence of key agronomically valuable traits (the capacity for phytohormone synthesis, nitrogen fixation, phosphate mobilization, pathogen defense, and abiotic stress tolerance), allowed for the selection of three candidate strains for further applied research on the development of biological formulations for crop production: Nostoc sp. VKM Al-115, Hassallia pseudoramosissima VKM Al-158, and Anabaena pirinica VKM Al-153.