Genomic Screening of Nitrogen-Fixing Nostocales Cyanobacteria Reveals Predicted Traits for Soil Fertility and Plant Growth Promotion
TL;DR
This genome-based bioprospecting serves as a cost-effective pre-selection filter, providing a strong scientific rationale for downstream experimental validation of these strains, suggesting that these strains possess strong predictive potential for future development as safe biological resources for sustainable agriculture.
Abstract
Background: The urgent need for sustainable agricultural drives the search for effective microbial biostimulants. Cyanobacteria of the order Nostocales are promising candidates due to their nitrogen-fixing capabilities and bioactive secondary metabolites. However, the genomic potential of many soil strains from microorganism collection remains largely unexplored. Methods: We performed a targeted genomic screening of five cyanobacterial strains from the All-Russian Collection of Microorganisms (VKM): Nostoc commune VKM Al-35, Nostoc punctiforme VKM Al-37, Nostoc minutum VKM Al-168, Anabaena pirinica VKM Al-153, and Hassallia pseudoramosissima VKM Al-158. The workflow involved WGS, de novo assembly, and comparative metabolic profiling using KEGG, SEED, PLaBAse, antiSMASH, and RhizoSMASH to identify predicted plant growth-promoting (PGP) traits, biosynthetic gene clusters (BGCs), and rhizosphere competence mechanisms. Biosafety was evaluated via Comprehensive Antibiotic Resistance Database (CARD) and in silico toxomics screening. Results: High-quality genome assemblies were obtained for all strains (completeness > 99%). Functional annotation uncovered complete genetic machinery for nitrogen fixation, predicted phosphate mobilization, and phytohormone biosynthesis pathways. Comparative analysis revealed two distinct genomic strategies: a versatile support profile in Nostoc strains (expanded genomes and diverse accessory pathways) and a specialized stimulation profile in Anabaena and Hassallia strains (focused phytohormone pathways). Comprehensive CARD and antiSMASH screenings demonstrated an excellent biosafety profile, confirming the complete absence of regulated cyanotoxin clusters or acquired antibiotic resistance genes of clinical concern. Conclusions: This genome-based bioprospecting serves as a cost-effective pre-selection filter, providing a strong scientific rationale for downstream experimental validation of these strains. The presence of predicted gibberellin biosynthesis pathways and T6SS/T4SS secretion systems in H. pseudoramosissima VKM Al-158 represents a notable genomic feature among soil cyanobacteria. The identified genomic prerequisites suggest that these strains possess strong predictive potential for future development as safe biological resources for sustainable agriculture.