DOI: 10.5061/dryad.70rxwdccp
title: Elevation, soil pH, and calcium availability shape regional and local scale spatial patterns of PhoD gene abundance in tropical and subtropical forests

description: Organic phosphorus mineralization is a critical process in the phosphorus
 cycle, governing phosphorus bioavailability for plants. The PhoD gene,
 which encodes the key enzyme alkaline phosphatase, serves as a valuable
 biomarker for this process. Soil microbes harboring the PhoD gene mediate
 this process by secreting extracellular alkaline phosphatases. This gene
 is widespread across diverse bacterial phyla, and its significance has
 been extensively reported in agroecosystems, particularly in response to
 fertilizer inputs. However, the spatial distribution of the PhoD gene in
 natural ecosystems along environmental gradients and its consequent
 effects on phosphorus dynamics remain unclear. We investigated the spatial
 distribution of the PhoD gene abundance across 20-ha study areas in
 tropical (Nabanhe, Bubeng) and subtropical (Ailaoshan) forests spanning
 broad elevation gradients but narrow latitudinal ranges. Our objectives
 were to: (a) characterize its spatial patterns, (b) identify the key
 drivers of its variation across local and regional scales, and (c)
 determine the influence of soil chemical properties. PhoD gene abundance
 and detectability differed sharply among forests. Abundance was highest
 and most ubiquitous in mid-elevation Nabanhe (1015.86-1235.64 m),
 intermediate in low-elevation Bubeng (712.05-860.05 m), and lowest in
 high-elevation Ailaoshan (2443.78-2586.13 m), where the gene was
 frequently undetectable. The most striking contrast was the high
 prevalence of non-detection in Ailaoshan compared to the other sites. The
 results identified elevation, soil pH, and calcium as the top three
 predictors of PhoD gene abundance and distribution at the regional scale.
 Soil pH was a consistent driver at both regional and local scales.
 Regionally, the effect of elevation was mediated by changes in soil pH and
 macronutrients (TC, TN, TP). However, at local scales, the spatial pattern
 was associated with variations in soil parent material, which influenced
 both soil pH and calcium. In summary, PhoD gene abundance varied
 significantly across the forest ecosystems. Our investigation demonstrates
 how elevation-driven environmental changes shape the genetic potential for
 phosphorus mineralization, underscoring the need for broader-scale studies
 to project the responses of this key microbial process to global change.
description: # Elevation, soil pH, and calcium availability shape regional and local
 scale spatial patterns of PhoD gene abundance in tropical and subtropical
 forests Dataset DOI:
 [10.5061/dryad.70rxwdccp](https://doi.org/10.5061/dryad.70rxwdccp) ##
 Description of the data and file structure The attached file contains the
 data used in the paper "Elevation, soil pH and calcium availability
 shape regional and local scale spatial patterns of PhoD gene abundance in
 tropical and subtropical forests" by Sandhya Mishra*, Shangwen Xia,
 Wenting Wang, Xiaodong Yang* - Functional Ecology ### Files and variables
 #### File name: Dataset.csv **Description:**  Variables of data Datasheet
 1 contains data from three forest sites in Yunnan, China: Nabanhe, Bubeng,
 and Ailaoshan. Each site comprises 260 spatially referenced sampling
 points collected across a 20‑hectare study area. Samples are named with
 site-specific prefixes: NB1–NB260 (Nabanhe), BB1–BB260 (Bubeng), and
 AL1–AL260 (Ailaoshan). Sheet 1. Named as Dataset. We put data of
 geographical locations (Latitude and Longitude), topography (Elevation,
 Slope, Aspect), soil physicochemical properties, litter biomass, and PhoD
 gene abundance in their original raw forms. Abbreviations in Sheet 1. TC,
 total carbon; TN, total nitrogen; TP, total phosphorus; Ca, available
 calcium; Fe, available iron; K, available potassium; Mg, available
 magnesium; Mn, available manganese; AP, available phosphorus; S, available
 sulfur; Moisture, soil moisture. #### Variables with units  * Elevation
 (m) * Latitude (°) * Longitude (°) * Slope, Aspect, pH (unitless) * TC:
 Total carbon (g/kg) * TN: Total nitrogen (g/kg) * TP: Total phosphorus
 (g/kg) * Ca: Available calcium (mg/kg) * Fe: Available iron (mg/kg) * K:
 Available potassium (mg/kg) * Mg: Available magnesium (mg/kg) * Mn:
 Available manganese (mg/kg) * AP: Available phosphorus (mg/kg) * S:
 Available sulfur (mg/kg) * Moisture: Soil moisture (%) * Litter biomass
 (g) * PhoD gene abundance (copies/µL) ## Code/software All statistical
 analyses were performed in the R environment (version 4.4.2) using the
 following R packages: gstat package ([Pebesma,
 200](https://www.sciencedirect.com/science/article/pii/S0048969722039602?via%3Dihub#bb0255)4; Goldman et al., 2020) , FactoMineR and factoextra packages ([Husson et al., 2017](https://www.sciencedirect.com/science/article/pii/S0925857423000241#bb0185); Kassambara & Mundt, 2017; Bayranvand et al., 2021), glmmTMB package (Brooks et al., 2017; Yang et al., 2025), randomForest package ([Liaw & Wiener, 2002](https://www.sciencedirect.com/science/article/pii/S0160412020309922#b0145); Li et al., 2025), rfPermute package (Archer, 2018; Wang et al., 2023c), pdp R package (v.0.8) (Greenwell, 2017; Knight et al., 2024), and plspm package (Sanchez et al., 2015; Zhou et al., 2024). R codes supporting this dataset are available from the authors upon request.