Cyanobacteria-based seed coatings differentially modulate rhizosphere bacterial community and predicted functional...

Direct-seeded (DSR) and transplanted (TPR) rice impose contrasting ecological filters on rhizosphere bacterial communities, yet the influence of cyanobacteria in these systems remain poorly resolved. 16S  rRNA amplicon sequencing was used to explore how a cyanobacterial consortium (BF1-4) and a multispecies biofilm (An-Tr-PW5), applied as seed coatings in DSR and TPR, reshape the taxonomic composition of rhizosphere microbiome, to facilitate correlation with soil metabolic and crop-associated traits. Cultivation mode was predicted as the dominant driver of community structure, accounting for 69.5 and 62.4% of phylum-level of genus-level variance respectively. Coatings superimposed distinct secondary shifts, associated with enriched copiotrophic phyla (Actinomycetota, Pseudomonadota, Bacteroidota, Cyanobacteriota) and diminished oligotrophic groups (Acidobacteriota, Chloroflexota). Seed coatings were associated with increased abundance of Sphingomonas, Lysobacter, Flavisolibacter and Gemmatiomonas linked to strong positive correlations (|ρ| ≥ 0.4, p_adj ≤ 0.05) with soil organic carbon, available N, nitrogen-fixation (ARA), urease and dehydrogenase activities, biomass, grain micronutrient content and harvest indices. Network analysis predicted these genera as central hubs positively associated with nutrient-cycling and plant performance, whereas control-associated taxa (Gaiella, Nitrospira, Microvirga) were negatively associated. Predictive functional analysis suggested system-dependent responses: in DSR, with coatings associated with enrichment of KEGG orthologs for carbohydrate metabolism, nitrogen assimilation, lipid activation and energy-generation pathway. TPR was affiliated with modulation of signal-transduction and chemotaxis-related functions. Both cyanobacteria-based interventions were associated with rewiring of dominance indices (higher Simpson, reduced Fisher's α), favouring enrichment of putatively competitive taxa. Overall, the cyanobacteria-based seed coatings were associated with shifts towards beneficial bacterial communities involved in effective nutrient-cycling.