Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil, Yao 2018

In this study, long-term phosphorus fertilization limited the extent to which the genes and proteins of microbial communities were allocated to degrading recalcitrant soil phytate to acquire phosphorus. In phosphorus-deficient soil, on the other hand, the genes responsible for breaking down recalcitrant substrate to acquire phosphorus were more prevalent in microbial communities. In other words, microbial communities can adapt genetically to different levels of nutrients in the soil in order to continue meeting their nutritional requirements. This adds to the body of evidence that fertilizer use impairs the inherent qualities of a living soil to nourish the plants growing there.

A greater than fourfold increase in the gene abundance of 3-phytase was the strongest response of soil communities to phosphorus deficiency. Phytase catalyses the release of phosphate from phytate, the most recalcitrant phosphorus-containing compound in soil organic matter. Genes and proteins for the degradation of phosphorus-containing nucleic acids and phospholipids, as well as the decomposition of labile carbon and nitrogen, were also enhanced in the phosphorus-deficient soils. In contrast, microbial communities in the phosphorus-rich soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, transformation of nitrogenous compounds and assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in soil microbial communities in response to shifting nutrient constraints [Yao 2018: 499].

In conclusion, our proteogenomics results provide systems biology insights into the adaptation of soil microbial communities to different levels of phosphorus availability in a humid tropical forest environment. Phosphorus deficiency significantly enhanced the genetic capabilities of microbial communities to extract phosphorus from phytate and, to a lesser extent, from nucleic acids and phospholipids. Long-term phosphorus fertilization altered the allocation of genes and proteins by microbial communities to acquire carbon, nitrogen and sulfur from a variety of substrates. The results suggest that the selective degradation of recalcitrant substrates, including phytate in phosphorus-deficient soils and aromatic compounds in phosphorus-rich soils, is an important means for microbial communities to balance their elemental requirements. The adaptive allocation of genes and proteins for acquisition of these nutrients in different soils can be explained as an optimal foraging strategy by which microbial communities maintain efficient growth under resource limitation [Yao 2018: 505].