Soil microbial functional genes and the enzymes they encode drive nutrient cycling and underpin soil biogeochemical processes. However, how well these gene–enzyme systems can maintain ecological functions as environmental conditions change remains poorly understood. Understanding their functional plasticity (i.e. their ability to maintain function under changing conditions) is important for sustaining microbial activity and enzyme-mediated ecological functions under climate change.

In a study published in Soil Biology and Biotechnology, researchers from Xishuangbanna Tropical Botanical Garden (XTBG) of the Chinese Academy of Sciences and their collaborators suggest that the PhoD gene and the alkaline phosphatase (ALP) it encodes may help sustain organic phosphorus (P) mineralization even in acidic soils.

The researchers analyzed the relationships among PhoD gene distribution, alkaline phosphatase activity and soil pH, and examined the mechanisms that sustain ALP activity and organic phosphorus mineralization.

Using global data on PhoD gene abundance, ALP activity and soil pH, the researchers found that although ALP activity clearly has an alkaline pH optimum, the PhoD gene encoding this enzyme was widely detected in acidic, neutral and alkaline soils. It was distributed across a broad pH range (pH 3–9) and in multiple ecosystem types. In acidic soils, PhoD abundance, ALP activity and pH were positively correlated, suggesting that PhoD-mediated organic phosphorus mineralization may continue under non-optimal pH conditions.

Molecular modeling showed that organic phosphorus substrates accumulate and remain stably bound at the PhoD catalytic site under acidic conditions, although binding energies were lower than under alkaline conditions. At the community level, taxonomic turnover functions as another plausible mechanism.

Acid-tolerant PhoD-harboring taxa such as Pseudomonas, Amycolatopsis, and Ralstonia have been reported in acidic soils and linked positively with ALP activity. The researchers argue that replacement of pH-sensitive taxa by acid-tolerant counterparts may provide functional compensation, helping maintain organic phosphorus mineralization as soil pH shifts.

The researchers further explored horizontal gene transfer (HGT) as a possible genetic mechanism for pH plasticity, though direct evidence linking HGT to acid adaptation in PhoD-harboring communities is currently lacking.

“Our study synthesizes existing evidence and proposes that pH plasticity operates through three interacting mechanisms: community-level taxonomic turnover, molecular substrate binding and residual catalysis, and potentially HGT-mediated acquisition of divergent PhoD variants,” said YANG Xiaodong of XTBG.

The researchers call for future research to empirically validate pH plasticity across diverse ecosystems, quantify the roles of taxonomic turnover, HGT, and enzyme-level adaptation, and integrate PhoD-pH plasticity into ecosystem models.

Available online: 5 October 2026