10  Elemental cycling

In ecosystems, nutrients are recycled continuously through biogeochemical cycles, where all chemical elements undergo circulation between living organisms and the environment.

Microorganisms play a crucial role in mediating various redox reactions in anaerobic environments. Research on the metabolism of essential elements such as nitrogen, carbon, sulfur, and iron, as well as their impacts on the environment, has greatly advanced through the continuous refinement of specific enzyme functions involved in the cycling of substances like \(NO^{3-}\), \(Fe^{3+}\), and \(SO_4^{2-}\). This progress has significantly promoted our understanding of biogeochemical cycling processes. Analyzing functional proteins and their encoding genes involved in different metabolic pathways, and enhancing the diversity of environmental functional genes in microorganisms, further drives research in environmental microbial ecology, a vital aspect of studying biogeochemical cycles.

The pctax package includes built-in pathways for the cycling of five elements: nitrogen (N), carbon (C), sulfur (S), phosphorus (P), and iron (Fe). It enables users to conveniently visualize all genes or KO (KEGG Orthology) identifiers involved in these cycling pathways. Additionally, the package offers annotation capabilities to provide further insights into the functions and roles of the genes or KO identifiers within these elemental cycling pathways.

plot_element_cycle(cycle = "Nitrogen cycle")
Figure 10.1: N-cycle in microbial metabolism

Click these pictures to see clearly.

for (i in c("Carbon cycle", "Sulfur cycle", "Phosphorus cycle", "Iron cycle")) {
  plot_element_cycle(cycle = i) %>% print()
Figure 10.2: C-cycle in microbial metabolism
Figure 10.3: S-cycle in microbial metabolism
Figure 10.4: P-cycle in microbial metabolism
Figure 10.5: Fe-cycle in microbial metabolism