Fig. 3: Functional enrichment and pathway map of C metabolism gene expression in R. aquatilis.

Enrichment of functional categories (P < 0.05) among differentially expressed genes in R. aquatilis in the RI⁺ RA⁺ treatment vs RI⁻ RA⁺ treatment under a low (35 μM KH₂PO₄) and b high (700 μM KH₂PO₄) P availabilities. Each section of the circle plot represents an enrichment pathway. Inner bar plot indicates the log₁₀ of the adjusted P-value for each enrichment pathway and the color shows the z-score value, indicating global upregulation (the value > 0) of genes within each pathway. Detailed log₂ fold-change (log₂FC) value of each gene within each pathway is plotted as a dot plot in the outer circle (upregulated in red and downregulated in blue). c Transcriptional responses of key genes in R. aquatilis pathways including sugar transport and metabolism, TCA cycle, chemotaxis, two-component system, and flagellar synthesis and regulation under low and high P availabilities. The heat map shows the log₂ of transcripts per kilobase million (TPM) calculated based on the initial reads count. The dashed lines represent simplified pathways. The asterisks are used to indicate a significant difference in gene expression level between (2) P^Low RI⁺ RA⁺ and (1) P^Low RI⁻ RA⁺ treatments; between (4) P^High RI⁺ RA⁺ and (3) P^High RI⁻ RA⁺ treatments; and between (2) P^Low RI⁺ RA⁺ and (4) P^High RI⁺ RA⁺ treatments (DESeq2 test, *p < 0.05; **p < 0.01; ***p < 0.001, n = 4 biologically independent sample). Abbreviations: RI^- RA⁺ only R. aquatilis cells present in the HC, RI⁺ RA⁻ only R. irregularis hyphae present in the HC, RI⁺ RA⁺ both R. irregularis hyphae and R. aquatilis cells present in the HC.