Phosphorus Addition Reshapes Soil Bacterial Networks in Pine Plantations

The study, published in Frontiers in Forests and Global Change, used metagenomic sequencing to follow three functional genes that serve as proxies for microbial phosphorus cycling: gcd, which mediates inorganic phosphorus solubilization; phoD, which mediates organic phosphorus mineralization; and phoR, which governs the phosphorus-starvation response that allows microorganisms to sense and use external phosphorus sources.

Fertilizer was broadcast in four quarterly splits beginning in July 2024 and ending in April 2025. One year after the first application, the team sampled rhizosphere soil from five healthy trees per plot, following a five-point scheme at the corners and center of each plot. The soil was separated into subsamples for physicochemical analysis, phosphorus fractionation using the modified Hedley sequential extraction method, and DNA extraction for metagenomic sequencing on an Illumina NovaSeq 6000 platform.

Against this baseline, the researchers asked whether a year of phosphorus addition would shift the communities of bacteria carrying the three target genes. The answer, at the level of overall gene abundance and diversity, was no. Phosphorus addition had no significant effect on the alpha-diversity or the relative abundance, measured in RPKM, of the gcd, phoD and phoR genes. Principal coordinate analysis coupled with PERMANOVA indicated only slight differences in community structure among treatments, with an R-squared of 0.3 and p-values above 0.05, meaning none of the structural shifts reached statistical significance.

Yet the story was not one of complete indifference. At the genus level, phosphorus addition significantly increased the relative abundance of two taxa, Terracidiphilus and Rhodopila, across all three gene-harboring communities. It also raised the abundance of Puia in the gcd- and phoR-harboring communities and Edaphobacter in the phoD-harboring community. These shifts mattered because correlation analysis revealed that the increased abundance of Terracidiphilus significantly enhanced carbon metabolism, ABC transporters and microbial metabolism in diverse environments within the three functional communities.

This interpretation addresses an apparent paradox in the data: phosphorus addition did not significantly alter the relative abundance of the target genes, yet it enhanced carbon metabolism. The authors propose that phosphorus addition may have stimulated plant growth and belowground carbon allocation, increasing labile carbon substrates for heterotrophic microorganisms such as Terracidiphilus, so the enhanced carbon metabolic activity may reflect elevated microbial carbon demand rather than a relaxation of phosphorus limitation. They note that in phosphorus-limited soils, organic matter addition can initially intensify plant phosphorus limitation because microorganisms immobilize phosphorus to build biomass, creating a temporary phosphorus sink, and that plants may incur a carbon cost through root exudates or symbionts to recruit microbial partners, gaining a net phosphorus benefit only when microbes release or transfer a portion of the acquired phosphorus.

The study also examined how phosphorus fractions and general soil properties relate to these bacterial communities. Redundancy analysis revealed that soil phosphorus fractions and physicochemical properties collectively explained between 17 and 35 percent of the variation in community composition, with microbial biomass phosphorus, nitrate nitrogen, concentrated hydrochloric acid-extractable organic phosphorus and residual phosphorus identified as major environmental variables. Soil phosphorus fractions strongly explained variation in community diversity, whereas general physicochemical properties showed no significant explanatory power. Dilute hydrochloric acid-extractable inorganic phosphorus and residual phosphorus were both significantly positively correlated with the alpha-diversity of the target communities.

Available phosphorus was significantly and positively correlated with Granulicella, Edaphobacter, Acidisarcina and Paracidobacterium, and the authors concluded that it significantly affected the gcd-, phoD- and phoR-harboring bacterial communities. Edaphobacter, a member of the phylum Acidobacteriota, can utilize organic compounds such as glucose and cellobiose as carbon sources and participates in organic matter decomposition. Acidisarcina secretes extracellular enzymes including chitinases and cellulases, playing a role in litter degradation.

To probe the architecture of relationships between bacteria and phosphorus pools, the team constructed two-way co-occurrence networks linking the top 200 most abundant taxa in each community to soil phosphorus fractions using Spearman rank correlations. Phosphorus addition increased network complexity, producing more nodes, edges, average path length and modules across the gcd, phoD and phoR communities. It also reduced the proportion of positive correlations while increasing negative ones. Available phosphorus and sodium bicarbonate-extractable organic phosphorus became central nodes, with the degree of available phosphorus in the two-way network increasing by 6.06 to 233.33 percent and that of sodium bicarbonate-extractable organic phosphorus increasing by 57.69 to 330.77 percent compared with the unfertilized control.

The network shifts carried functional hints. In the gcd-harboring community, phosphorus addition increased positive correlations between available phosphorus and bacterial genera, suggesting that available phosphorus availability may structure that community. Rhizomicrobium was positively associated with available phosphorus, while taxa including Phenylobacterium, Pseudomonas, Dokdonella and Caballeronia were negatively associated with sodium bicarbonate-extractable organic phosphorus, consistent with a potential role in organic phosphorus mineralization, though the authors caution that whether these taxa actively convert organic phosphorus to inorganic phosphorus requires functional validation. Phosphorus addition also disrupted positive associations between water-extractable inorganic phosphorus and Chloroflexota and strengthened associations between Planctomycetota and phosphorus fractions, a phylum linked to anaerobic ammonium oxidation.

The authors frame their findings as new insight into how microbial consortia mediating phosphorus solubilization, mineralization and starvation respond to phosphorus addition in subtropical plantation ecosystems. The correlational nature of the network and redundancy analyses means the underlying causal mechanisms remain open to experimental verification, and the authors note that future research should prioritize carbon metabolism to elucidate the coupled biogeochemical processes linking phosphorus addition, microbial communities and soil carbon turnover.

Subject of Research: Responses of phosphorus-cycling bacterial communities carrying the gcd, phoD and phoR genes to phosphorus addition in a subtropical pine plantation

Article Title: Differential responses of gcd‑, phoD‑ and phoR‑harboring bacterial communities to P addition in the soil of Pinus massoniana plantations

Article References: Huang, Z., Peng, J., Huang, C., Wu, J., Xiang, Y., Lan, X., Wu, J., Hou, G., Fan, C., & Li, X. (2026). Differential responses of gcd‑, phoD‑ and phoR‑harboring bacterial communities to P addition in the soil of Pinus massoniana plantations. Frontiers in Forests and Global Change, 9, Article 1985000. https://doi.org/10.3389/ffgc.2026.1985000

Image Credits: AI Generated

DOI: 10.3389/ffgc.2026.1985000

Keywords: phosphorus addition, soil bacteria, Pinus massoniana, gcd gene, phoD gene, phoR gene, metagenomics, phosphorus fractions, co-occurrence network, subtropical plantation, rhizosphere soil, soil acidification