Three novel diazotrophic species, Paenibacillus oryziterrae sp. nov., Paenibacillus paludis sp. nov. and Paenibacillus diazotrophicus sp. nov., isolated from red paddy soil with potential for consortium-based rice growth promotion

Biological nitrogen fixation is central to sustainable rice cultivation, yet diazotrophic Paenibacillus species from red paddy soils remain poorly characterized. Here, three novel Paenibacillus strains, sgz500958^T, sgz500992^T and sgz5001063^T, were isolated from red paddy soils in China. Phylogenetic and phylogenomic analyses based on 16S rRNA and whole-genome data revealed that the three strains formed distinct lineages within Paenibacillus, with average nucleotide identity values below 95% relative to their closest reference strains. All strains possessed a complete nif gene cluster and exhibited nitrogenase activity, and strain sgz5001063^T maintained high activity at low concentrations (0–3 mM), was inhibited at intermediate concentrations (4–30 mM) and recovered at very high ammonium concentrations (30–300 mM). Utilizing complementary plant growth-promoting traits and co-culture compatibility, two nitrogen-fixing synthetic communities (NFSCs) were assembled. In rice assays, NFSC2 markedly enhanced germination (100%), shoot height (+72.5%) and root growth relative to sgz5001063^T alone and NFSC1. The isolates are proposed as Paenibacillus oryziterrae sp. nov. (sgz500958^T=MCCC 1K09377^T=KCTC 43740^T), Paenibacillus paludis sp. nov. (sgz500992^T=MCCC 1K09376^T=KCTC 43729^T) and Paenibacillus diazotrophicus sp. nov. (sgz5001063^T=MCCC 1K09391^T=KCTC 43741^T).