Additional file 1 of Exploration of genes encoding KEGG pathway enzymes in rhizospheric microbiome of the wild plant Abutilon fruticosum
Creators: name: Abulfaraj, Aala A.
name: Shami, Ashwag Y.
name: Alotaibi, Nahaa M.
name: Alomran, Maryam M.
name: Aloufi, Abeer S.
name: Al-Andal, Abeer
name: AlHamdan, Nawwaf R.
name: Alshehrei, Fatimah M.
name: Sefrji, Fatmah O.
name: Alsaadi, Khloud H.
name: Abuauf, Haneen W.
name: Alshareef, Sahar A.
name: Jalal, Rewaa S.
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Plant Biology

description: Additional file 1: Figure S1. Number of genes encoding enzymes of the different functional categories and sub-categories of KEGG database across microbiomes of rhizosphere and surrounding bulk soils of A. fruticosum. Red arrows refer to subcategories investigated further. Figure S2. Heatmap referring to KEGG categories in terms of gene abundance in microbiomes of rhizosphere (R) and surrounding bulk (S) soils of A. fruticosum. Red arrows refer to categories investigated further. Figure S3. Heatmap referring to KEGG sub-categories in terms of gene abundance in microbiomes of rhizosphere (R) and surrounding bulk (S) soils of A. fruticosum. Red arrows refer to sub-categories investigated further. Figure S4. Heatmap referring to KEGG pathways in terms of gene abundance in microbiomes of rhizosphere (R) and surrounding bulk (S) soils of A. fruticosum. Red arrows refer to pathways investigated further. Figure S5. Heatmap referring to enriched enzymes of microbiomes of rhizosphere (R) and surrounding bulk (S) soils of A. fruticosum. Red arrows refer to the most enriched enzymes that were investigated further. Detailed information for the different enzymes are shown in Table S15. Figure S6. KEGG pathway “Quorum sensing” of sub-category “Cellular community - prokaryotes” (category “Cellular Processes”) referring to the enriched steps at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the enriched enzyme, e.g., long-chain acyl-CoA synthetase (EC 6.2.1.3), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S7. KEGG pathway “ABC transporters” of sub-category “Membrane transport” (category “Environmental Information Processing”) referring to the enriched steps at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the most enriched enzyme, e.g., ribose transport system ATP-binding protein (EC 3.6.3.17/7.5.2.7), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S8. KEGG pathway “Two-component system” of sub-category “Signal transduction” (category “Environmental Information Processing”) referring to the enriched steps at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the most enriched enzyme, e.g., phosphate regulon sensor histidine kinase PhoR (EC 2.7.13.3), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S9. KEGG pathway “Aminoacyl-tRNA biosynthesis” of sub-category “Translation” (category “Genetic Information Processing”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the most enriched enzyme, e.g., aspartyl-tRNA(Asn)/glutamyltRNA( Gln) amidotransferase subunit B (EC 6.3.5.6/6.3.5.7), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S10. KEGG pathway “Valine, leucine and isoleucine biosynthesis” of sub-category “Amino acids metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the most enriched enzyme, e.g., acetolactate synthase I/II/III large subunit (EC 2.2.1.6), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S11. KEGG pathway “Valine, leucine and isoleucine degradation” of sub-category “Amino acids metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the most enriched enzyme, e.g., acetyl-CoA C-acetyltransferase (EC 2.3.1.9), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S12. KEGG pathway “Glycolysis / Gluconeogenesis” of sub-category “Carbohydrate metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the most enriched enzyme, e.g., pyruvate dehydrogenase E1 component beta subunit (EC 1.2.4.1), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S13. KEGG pathway “Citrate cycle (TCA cycle)” of sub-category “Carbohydrate metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the most enriched enzyme, e.g., pyruvate dehydrogenase E1 component beta subunit (EC 1.2.4.1), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S14. KEGG pathway “Pyruvate metabolism” of sub-category “Carbohydrate metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrows refer to the steps with the most enriched enzymes, e.g., acetyl-CoA C-acetyltransferase (EC 2.3.1.9) and pyruvate dehydrogenase E1 component beta subunit (EC 1.2.4.1), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S15. KEGG pathway “Glyoxylate and dicarboxylate metabolism” of sub-category “Carbohydrate metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the most enriched enzyme, e.g., acetyl-CoA Cacetyltransferase (EC 2.3.1.9), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S16. KEGG pathway “Oxidative phosphorylation” of sub-category “Energy metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrows refer to the steps with the most enriched enzymes, e.g., NADH-quinone oxidoreductase subunit J (EC 1.6.5.3/7.1.1.2), cytochrome c oxidase subunit III (EC 1.9.3.1/7.1.1.9) and F-type H+-transporting ATPase subunit beta (EC 3.6.3.14/7.1.2.2), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S17. KEGG pathway “Carbon fixation pathways in prokaryotes” of sub-category “Energy metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrow refers to the step with the most enriched enzyme, e.g., acetyl-CoA C-acetyltransferase (EC 2.3.1.9), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S18. KEGG pathway “Purine metabolism” of sub-category “Nucleotide metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrows refer to the steps with the most enriched enzymes, e.g., DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6), DNA polymerase III subunit delta (EC 2.7.7.7) and nucleoside-diphosphate kinase (EC 2.7.4.6), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the highest and blue refers to the lowest. See scale in the figure for intermediate enrichment levels. Figure S19. KEGG pathway “Pyrimidine metabolism” of sub-category “Nucleotide metabolism” (category “Metabolism”) referring to ECs of the enriched enzymes at varying levels in rhizospheric microbiome of A. fruticosum. Blue arrows refer to the steps with the most enriched enzymes, e.g., DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6), DNA polymerase III subunit delta (EC 2.7.7.7), nucleoside-diphosphate kinase (EC 2.7.4.6), carbamoyl-phosphate synthase large subunit (EC 6.3.5.5) and CMP/dCMP kinase (EC 2.7.4.25), in the pathway. Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil. See scale in the figure for intermediate enrichment levels. Figure S20. The less enriched KEGG pathway “Fatty acid biosynthesis” of sub-category “Lipid metabolism” (category “Metabolism”) that refers to the highly enriched enzyme, e.g., long-chain acyl-CoA synthetase (EC 6.2.1.3). Colored boxes around enzyme EC or metabolite refer to the enrichment level, where red refers to the high level compared with that of the bulk soil, while blue refers to the low level compared with that of the bulk soil.