Contributions
PGP Gene Distribution Across Environments & Pangenomes surveyed 13 plant-growth-promoting (PGP) gene markers across the KBase Data Lakehouse pangenome and found that 11,272 of 27,702 species carried at least one marker, drawing on 32,736 PGP gene clusters, 27,690 species with GapMind tryptophan-completeness scores, and 291,279 genomes with isolation-source metadata 1. The project tested co-occurrence among five focal genes and found that eight of 10 pairs were significantly associated after Benjamini–Hochberg false-discovery-rate (BH-FDR) correction, where the false discovery rate (FDR) is the expected share of false positives among significant calls; five pairs were positive and three negative 1. The strongest positive pair was pqqC × acdS (odds ratio (OR) = 7.24, n = 286 co-occurring species, q = 1.2e-83), although the summary notes that the report’s wording that the two are “nearly always found together” overstates the data, since 286 is far fewer than the 3,028 pqqC-bearing species 1. nifH was negatively associated with hcnC (OR = 0.23, q = 5.8e-29) and pqqC (OR = 0.57, q = 2.9e-19) and showed no significant association with ipdC (OR = 1.13, q = 0.54), which the project read as ecological separation between diazotrophs and pqqC/acdS-bearing rhizobacteria 1. Only 157 species (1.4%) carried at least three focal traits, and the report’s trait-combination counts are internally inconsistent: it ranks pqqC + acdS (n = 153) above nifH + pqqC (n = 225), and its pqqC + acdS count of 153 differs from the co-occurrence count of 286, with neither discrepancy resolved 1.
The project compared 1,039 soil/rhizosphere species with 10,233 other species and found significant soil enrichment of acdS (15.8% vs 2.6%, OR = 7.02, q = 5.1e-62), pqqC (43.8% vs 21.2%, OR = 2.90, q = 2.8e-53), and hcnC (11.3% vs 6.4%, OR = 1.85, q = 6.1e-08) 1. nifH was depleted in soil (12.9% vs 19.7%, OR = 0.60, q = 5.5e-08), and ipdC was not significantly enriched in the raw comparison (1.5% vs 1.9%, OR = 0.79, q = 0.47) 1. acdS enrichment held under phylum-level fixed effects (OR = 6.98, p = 4.8e-61) and in a strict rhizosphere-only sensitivity analysis (OR = 10.6, q = 7.6e-38), while Bacillota_A was an exception showing nifH soil enrichment (OR = ∞, q = 2.5e-4) 1. The report attributed overall nifH soil depletion partly to database composition, which the summary flags as an interpretation rather than a separately tested result 1.
The project tested whether PGP genes are predominantly horizontally transferred accessory genes and rejected that hypothesis (H3): all 13 genes had significantly higher core fractions than the genome-wide baseline of 46.8% core (BH-FDR q < 0.05), for example pqqC at 81.5% core and nifH at 63.8% core 1. The mean accessory fraction across PGP genes was 29.7%, compared with 53.2% genome-wide, and the report states that this rejects predominance of transfer but does not rule out every horizontal gene transfer event 1. Singleton fraction correlated negatively with PGP gene richness (Spearman ρ = −0.195, p = 2.0e-97, n = 11,272 species with ≥2 genomes), consistent with PGP-rich species having more closed pangenomes 1. pqqD was an outlier at 55.5% core with the highest singleton fraction (27.5%), which the report takes to suggest occasional standalone horizontal spread, but it documents no specific transfer event 1. The report also found that the nifH gene-cluster count was 2,756 rather than the approximately 1,913 estimated in the research plan, a discrepancy it states did not affect the analyses 1.
Using GapMind (a computational pathway-completeness predictor), the project found that tryptophan-pathway completeness predicted ipdC presence (2.5% vs 0.9%, Fisher OR = 2.81, p = 6.3e-10; logistic OR = 2.81, 95% CI 1.97–4.01, p = 1.4e-08, n = 11,272) 1. The tyrosine-pathway negative control also predicted ipdC (OR = 3.62, p = 2.3e-11), so the result does not support a tryptophan-specific mechanism 1. The association reversed within soil/rhizosphere species (OR = 0.30, p = 0.02, n = 1,039) while remaining positive in non-soil species (OR = 3.56, p = 7.7e-13, n = 10,233), a result the report treats as hypothesis-generating 1. A phylum-plus-soil model failed from quasi-complete separation because ipdC occurred in only 214 species (1.9%) 1. The project’s caveats include noisy environment classification, with only 1,637 species (5.9% of labelled species) classed as soil/rhizosphere dominant and NCBI sampling biased toward clinical and host-associated isolates 1. Further caveats are that PGP detection relied on exact Bakta gene-name matches, and that gene clusters were not functionally validated for truncations, frameshifts, or pseudogenization 1.