## 3 Results
### Functional Analysis of DEGs, GSEA and KEGG Pathways Analysis
Similarly, within the categories of \"organophosphate metabolic process\" (GO:0019637), \"phosphorylation process\" (GO:0016310) and \"phospholipid metabolic process\" (GO:0006644), all of which fall under the broader \"phosphorus metabolic process\", a notable trend emerged with a significant predominance of downregulated DEGs, which was particularly evident in the S1-S3 comparison. In \"phosphorus metabolic process\", \"phosphate-containing compound metabolic process\" and \"phosphorylation\", a progressive decrease was observed in the total number of downregulated DEGs from P0 to P2, while in \"organophosphate metabolic process\" and \"phospholipid metabolic process\" a fluctuation was observed and the most DEGs were found in the P1 treatment. GO enrichment analysis was implemented to further investigate the biological processes, molecular functions and metabolic pathways associated with the genes found within the highlighted regions (Elements 1-5) in Figure 5's heatmap. The results of GO enrichment analysis unveiled significant gene associations across various areas of the heatmap. In the biological process domain, predominant gene categories encompassed \"macromolecule metabolic process\" (GO:0043170), \"nitrogen compound metabolic process\" (GO:0006807) and \"biological regulation\" (GO:0065007). Additionally, \"localization\" (GO:0051179) featured prominently across all heatmap areas except Element 3, while \"phosphorylation\" (GO:0016310) was detected specifically in Elements 1 and 5. Within the molecular function domain, genes were primarily classified into \"nucleotide binding\" (GO:0000166), \"hydroxy-like activity\" (GO:0016787) and \"protein binding\" (GO:0005515). Noteworthy categories included \"transferase activity\" (GO:0016740) in Elements 1, 3 and 4, \"oxidoreductase activity\" (GO:0016491) in Elements 1, 4 and 5, \"transporter activity\" (GO:0005215) in Elements 2 and 5, and \"ion binding\" (GO:0043167) across all Elements except Element 2. While delving into more specific GOs, several intriguing terms emerged. \"Methyltransferase activity\" (GO:0008168) was evident in Elements 1, 3 and 4, while \"heat shock protein binding\" (GO:0031072) was selectively identified in Elements 1 and 3. \"GTP binding\" (GO:0005525) exhibited widespread representation across Elements 1, 2, 3 and 5, while \"pyrophosphate activity\" (GO:0016462) spanned Elements 2, 3, 4 and 5. Elements 2 and 3 prominently featured \"cellular response to stress\" (GO:0033554), Elements 1 and 5 displayed \"signal transduction\" (GO:0007165) and \"pigment biosynthesis process\" (GO:0046148) was notably associated with Element 1. These findings hold significance for potential inclusion in further research. The KEGG pathway analysis showed the top 30 pathways under the different P treatments (Figure 7). Among the upregulated DEGs, the pathways that demonstrated the highest number of enriched DEGs were the spliceosome pathway in the P0 treatment, protein processing in the endoplasmic reticulum pathway in the P1 treatment, and the ribosome pathway in the P2 treatment. The pathways with the highest enrichment factor were the ribosome biogenesis in the eukaryotic pathway for the P0 treatment, and the alpha linolenic acid metabolism in the P1 and P2 treatments. Among downregulated DEGs, the ribosome pathway consistently exhibited the highest number of DEGs. The pathways with the highest enrichment factor were the photosynthesis pathway in the P0 treatment, the DNA replication pathway in the P1 treatment, and the photosynthesis-antenna protein pathway in the P2 treatment. Figure 7: The bubble plots represent the KEGG pathways in each P treatment ((**A**) P0, (**B**) P1 and (**C**) P2) where the upregulated and downregulated DEGs were found. The X-axis represents the enrichment factor (DEGs enriched in a pathway/genes of all genes in the background gene set).