Fig. 3: Mining and validating key microbial functional genes for citrulline degradation.
From: Enhancing soil citrulline degrading function to mitigate soil-borne Fusarium wilt
a Candidate functional genes were linked to taxa via meta-linking analysis using Healthy plant field soil-1 and Diseased plant field soil-1 (Supplementary Table 3). b Relative abundances (%) of major bacterial genera in citrulline-incubated soils compared to the control. c Genus-level bacterial networks highlighting hub modules and Pseudomonas in control and citrulline-incubated soils. d Circular genome map of P. putida YDTA3. A detailed description of the figure elements is provided in the Methods section under Whole genome sequencing and ANI analysis. e Schematic of arc and arg gene clusters in P. putida YDTA3 showing homologous recombination of arcB and argH with a gentamicin resistance cassette (GmR). Dashed lines indicate omitted unrelated genes. f Citrulline degradation kinetics (bars, left y-axis) and growth dynamics (points with Boltzmann model94 fit, right y-axis) of P. putida YDTA3 (WT) at initial citrulline concentrations of 0–5,000 μM as the sole C/N source. g Degradation capacity (bars, left y-axis) and growth kinetics (blue points with Boltzmann fit, right y-axis) of ΔarcB (P = 8.99×10-13) and ΔargH (P = 5.33×10-18) mutant strains with 5,000 μM citrulline as the sole C/N source. Different letters indicate significant differences (one-way ANOVA with Duncan’s test). ΔarcB growth was not fitted due to non-convergence. For f–g, degradation data are shown as mean ± s.e.m. with individual data points overlaid (n = 6 biologically independent cultures), and growth curves show the mean of n = 6 biologically independent cultures. h Metabolic profiles of the converted compounds (arginine and ornithine) during citrulline degradation by wild-type, ΔarcB, and ΔargH strains over 120 h. Data are presented as individual data points (n = 6 biologically independent replicates). Pairwise comparisons at the final time point (120 h) were performed using two-sided Student’s t-tests (WT: citrulline vs arginine (P = 5.66 × 10-13) and citrulline vs ornithine (P = 2.56 × 10-13); ΔarcB: arginine vs ornithine (P = 2.66 × 10-7); ΔargH: arginine vs ornithine (P = 3.21 × 10-9)). WT: wild-type. Source data are provided as a Source Data file.
