Legume–microbiome interactions unlock mineral nutrients in regrowing tropical forests

Legume trees form an abundant and functionally important component of tropical forests worldwide with N₂-fixing symbioses linked to enhanced growth and recruitment in early secondary succession. However, it remains unclear how N₂-fixers meet the high demands for inorganic nutrients imposed by rapid biomass accumulation on nutrient-poor tropical soils. Here, we show that N₂-fixing trees in secondary Neotropical forests triggered twofold higher in situ weathering of fresh primary silicates compared to non-N₂–fixing trees and induced locally enhanced nutrient cycling by the soil microbiome community. Shotgun metagenomic data from weathered minerals support the role of enhanced nitrogen and carbon cycling in increasing acidity and weathering. Metagenomic and marker gene analyses further revealed increased microbial potential beneath N₂-fixers for anaerobic iron reduction, a process regulating the pool of phosphorus bound to iron-bearing soil minerals. We find that the Fe(III)-reducing gene pool in soil is dominated by acidophilic Acidobacteria, including a highly abundant genus of previously undescribed bacteria, Candidatus Acidoferrum, genus novus. The resulting dependence of the Fe-cycling gene pool to pH determines the high iron-reducing potential encoded in the metagenome of the more acidic soils of N₂-fixers and their nonfixing neighbors. We infer that by promoting the activities of a specialized local microbiome through changes in soil pH and C:N ratios, N₂-fixing trees can influence the wider biogeochemical functioning of tropical forest ecosystems in a manner that enhances their ability to assimilate and store atmospheric carbon.

The legume family is the most diverse angiosperm family in the Neotropics (1–3), with dinitrogen (N₂)-fixing legume trees growing fast and supplying tropical forests with substantial quantities of nitrogen (N) during succession (4). This N₂-fixing strategy requires that trees can access scarce sources of inorganic nutrients, including bioavailable forms of phosphorus (P) for metabolites and growth and molybdenum (Mo) for nitrogenase functioning (5–7) (the enzyme that catalyzes conversion of atmospheric N₂ to bioavailable N).However, in highly weathered tropical soils, in addition to their pools in organic matter (8, 9), large amounts of P and Mo are often occluded in an inorganic form in insoluble iron (Fe) and aluminum (Al)-bearing minerals (10, 11) and thus not available for immediate biological uptake. For example, both P and Mo are scarce in the oxisols and inceptisols that have developed from Mo-poor basalt bedrock in Panamanian tropical forests (7, 12) (SI Appendix, Table S1) and that contain P-adsorbing kaolinite, goethite, and hematite secondary minerals (SI Appendix, Fig. S1). Our own observations from these Panamanian forests show significant differences in the chemistry of soils beneath N₂ fixing versus nonfixing trees, with significantly lower concentrations of nitric acid–extractable P, Fe, and Al and lower pH below N₂-fixing trees (SI Appendix, Table S2). Moreover, a strong association between extracted P and Fe plus Al, but not between P and soil organic carbon, implies that soil P is significantly influenced by mineral dynamics within these tropical soils (SI Appendix, Fig. S2, P < 0.001 for Fe and Al and P > 0.10 for carbon, Pearson test).These patterns raise the biogeochemical hypothesis that N₂-fixing legume trees may strategically employ specific mechanisms to enhance mineral weathering (5, 13, 14), resulting in improved access to occluded inorganic mineral nutrients, enhanced N₂-fixation, and enhanced carbon sequestration by forest biomass during succession. Here, we address this hypothesis by investigating 1) whether N₂-fixing trees induce locally elevated rates of silicate mineral (olivine) weathering (compared to nonfixing trees), causing the depletion of elements critical to N₂-fixation; 2) whether the altered soil beneath N₂-fixing trees is linked to compositional and functional differences in the microbiomes and metagenomes associated with soil minerals; and 3) whether the presence of N₂-fixers affects biogeochemical nutrient cycling in rooting zone soils beneath neighboring non-N₂–fixing forest trees.