Data and code from: Plant invasion in mountain ecosystems reduces soil micro-food web complexity at higher elevations
Data files
Sep 28, 2026 version files 202.10 KB
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Data_on_Margalef_diversity_index_of_native_plant_communities_at_different_altitudes.xlsx
10.24 KB
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Data_on_plant_diversity__soil_nutrient_cycling_capacity__soil_nutrient_status__multitrophic_diversity__soil_microfood_w.xlsx
12.72 KB
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Data_on_Shannon_diversity_index_of_native_plant_communities_at_different_altitudes.xlsx
10.22 KB
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Data_on_soil_available_nitrogen_of_native_and_invasive_plant_communities_at_different_elevations.xlsx
10.56 KB
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Data_on_soil_soluble_organic_carbon_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
10.53 KB
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Data_on_soil_total_organic_carbon_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
10.28 KB
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Data_on_the_average_degree_of_soil_micro-food_webs_in_native_and_invasive_plant_communities_at_different_elevations.xlsx
10.66 KB
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Data_on_the_average_path_length_of_soil_micro-food_webs_in_native_and_invasive_plant_communities_at_different_elevation.xlsx
10.63 KB
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Edge_data_of_soil_micro-food_webs_in_native_and_invasive_plant_communities_at_different_elevations.xlsx
10.45 KB
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Multiple_linear_regression_analysis.R
2.26 KB
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README.md
13.08 KB
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Soil_BG_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
10.52 KB
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Soil_carbon-acquiring_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
10.57 KB
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Soil_CBH_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
10.53 KB
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Soil_LAP_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
10.51 KB
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Soil_micro-food_web_analysis.R
5.49 KB
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Soil_microbial_food_web_node_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
10.42 KB
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Soil_NAG_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
10.54 KB
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Soil_nitrogen-acquiring_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_elevations.xlsx
10.68 KB
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Soil_total_nitrogen_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
10.34 KB
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Structural_Equation_Model_Analysis.R
875 B
Abstract
Anthropogenic activities have accelerated plant invasions in mountain ecosystems, impacting the structure and functions of native plant communities. Changes in aboveground vegetation can drive shifts in belowground biota, yet the effects of plant invasions on soil micro-food web structure and complexity along elevational gradients and the underlying mechanisms remain poorly understood. This study examined the differences between the communities of native herbaceous plants invading Ageratina adenophora along an elevational gradient in the Gaoligong Mountains. We surveyed the composition of the plant community, measured the physicochemical properties of the soil and the enzyme activities of carbon and nitrogen acquisition. The complexity of the soil micro-food web complexity index (including bacteria, fungi, nematodes, and protists) using high-throughput sequencing and network analysis. Structural equation modeling and two-way ANOVA were used to analyze the effects of elevation, invasion, and their interaction on the micro-food web. We found that native plant diversity, soil micro-food web complexity, and soil carbon- and nitrogen-acquiring enzyme activities all increased significantly with elevation. However, invasion by A. adenophora invasion both reduced native plant diversity and altered the original elevation pattern of the soil micro-food web. At the highest elevation (2300 m), the complexity index of the soil micro-food web in native communities was approximately 4.8 units higher than in invaded communities, while the activities of the C-acquiring enzymes of the soil were 135% higher and the activities of the N-acquiring enzymes 119% higher. The complexity of the soil micro-food web was directly influenced by plant diversity, soil nutrient cycling capacity, and multitrophic diversity, whereas environmental factors such as mean temperature and soil moisture exerted indirect effects through soil nutrient status and cycling processes. Our findings demonstrate that the invasion of A. adenophora invasion primarily affects high-elevation ecosystems by reducing native herbaceous plant diversity, thus reducing the complexity of the micro-food web of the soil and altering the carbon and nitrogen cycling of the soil. This study advances the mechanistic understanding of how plant invasions impact soil food webs and associated mountain ecosystem processes, providing insights into invasion management and control strategies.
Dataset DOI: 10.5061/dryad.ns1rn8q8s
Description of the data and file structure
The data and R code that supports the findings of this study.
Files and variables
File: Data_on_Margalef_diversity_index_of_native_plant_communities_at_different_altitudes.xlsx
Description: Margalef diversity index of native herbaceous plant communities at different altitudes. Each elevation row contains six replicate values.
Variables
Elevation: altitude in metres (1400, 2000, 2300).Margalef index: native plant community Margalef diversity index; six replicate columns per elevation.
File: Data_on_plant_diversity__soil_nutrient_cycling_capacity__soil_nutrient_status__multitrophic_diversity__soil_microfood_w.xlsx
Description: Sample-level dataset used for multiple linear regression and structural equation modeling. It contains plant diversity, soil micro-food web complexity, soil moisture, multitrophic diversity, soil nutrient status, soil nutrient cycling capacity, and mean temperature across elevations. The dataset contains 36 observations. Rows with Plant diversity = 0 correspond to invaded communities where native plant diversity was not recorded or was set to zero; see the manuscript for details.
Variables
Elevation: altitude in metres (1400, 2000, 2350/2300).Plant diversity: plant diversity index, normalised/averaged as described in the manuscript.soil micro-food web complexity: composite complexity index of the soil micro-food web, derived from network topological properties.Soil moisture: soil moisture content (proportion/gravimetric water content).Multitrophic diversity: multitrophic diversity index, based on Shannon diversity of bacteria, fungi, protists, and nematodes, Z-score normalised and averaged.Soil nutrient status: composite soil nutrient status index.Soil nutrient cycle: composite soil nutrient cycling capacity index.Mean temperature: mean temperature at the site (°C).
File: Data_on_Shannon_diversity_index_of_native_plant_communities_at_different_altitudes.xlsx
Description: Shannon diversity index of native herbaceous plant communities at different altitudes. Each elevation row contains six replicate values.
Variables
Elevation: altitude in metres (1400, 2000, 2300).Shannon index: native plant community Shannon diversity index; six replicate columns per elevation.
File: Data_on_soil_available_nitrogen_of_native_and_invasive_plant_communities_at_different_elevations.xlsx
Description: Soil available nitrogen (AN = NH₄⁺-N + NO₃⁻-N) in native and invasive plant communities at different elevations.
Variables
Elevation: altitude in metres (1400, 2000, 2300).AN(Native): available nitrogen in native plots; six replicate columns.AN(Invasive): available nitrogen in invaded plots; six replicate columns.
File: Data_on_soil_total_organic_carbon_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
Description: Soil total organic carbon (SOC) in native and invasive plant communities at different altitudes.
Variables
Elevation: altitude in metres (1400, 2000, 2300).SOC(Native): soil organic carbon in native plots; six replicate columns.SOC(Invasive): soil organic carbon in invaded plots; four replicate columns as provided.
File: Data_on_soil_soluble_organic_carbon_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
Description: Soil soluble/dissolved organic carbon (DOC) in native and invasive plant communities at different altitudes.
Variables
Elevation: altitude in metres (1400, 2000, 2300).DOC(Native): dissolved organic carbon in native plots; six replicate columns.DOC(Invasive): dissolved organic carbon in invaded plots; six replicate columns.
File: Data_on_the_average_degree_of_soil_micro-food_webs_in_native_and_invasive_plant_communities_at_different_elevations.xlsx
Description: Average degree of soil micro-food webs in native and invasive plant communities at different elevations.
Variables
Elevation: altitude in metres (1400, 2000, 2350).Native: average degree of the soil micro-food web in native plots; six replicates per elevation.Invasive: average degree of the soil micro-food web in invaded plots; six replicates per elevation.
File: Edge_data_of_soil_micro-food_webs_in_native_and_invasive_plant_communities_at_different_elevations.xlsx
Description: Edge counts of soil micro-food webs in native and invasive plant communities at different elevations.
Variables
Elevation: altitude in metres (1400, 2000, 2350).Native: number of edges in native plots; six replicates per elevation.Invasive: number of edges in invaded plots; six replicates per elevation.
File: Data_on_the_average_path_length_of_soil_micro-food_webs_in_native_and_invasive_plant_communities_at_different_elevation.xlsx
Description: Average path length of soil micro-food webs in native and invasive plant communities at different elevations.
Variables
Elevation: altitude in metres (1400, 2000, 2350).Native: average path length in native plots; six replicates per elevation.Invasive: average path length in invaded plots; six replicates per elevation.
File: Soil_BG_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
Description: Soil β-1,4-glucosidase (BG) activity in native and invasive plant communities at different altitudes.
Variables
Elevation: altitude in metres (1400, 2000, 2300).BG(Native): BG activity in native plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.BG(Invasive): BG activity in invaded plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.
File: Soil_carbon-acquiring_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
Description: Soil carbon-acquiring enzyme activities (BG + CBH) in native and invasive plant communities at different altitudes.
Variables
- Elevation: altitude in metres (1400, 2000, 2300).
- C-acquiring enzyme activities (Native): combined BG + CBH activity in native plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.
- C-acquiring enzyme activities (Invasive): combined BG + CBH activity in invaded plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.
File: Multiple_linear_regression_analysis.R
Description: R script for multiple linear regression and hierarchical partitioning. It reads sem2026.csv, fits a linear model for soil micro-food web complexity as a function of plant diversity, multitrophic diversity, soil nutrient status, and soil nutrient cycling capacity, then extracts model summary, ANOVA results, and hierarchical partitioning percentages. The script prepares a sorted data frame for plotting variable importance.
Main variables:
- Response:
soil micro-food web complexity. - Predictors:
Plant diversity,Multitrophic diversity,Soil nutrient status,Soil nutrient cycle. - Output columns:
variable,percentage,p_value,significance,Sig.
File: Soil_CBH_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
Description: Soil β-D-cellobiosidase (CBH) activity in native and invasive plant communities at different altitudes.
Variables
Elevation: altitude in metres (1400, 2000, 2300).CBH(Native): CBH activity in native plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.CBH(Invasive): CBH activity in invaded plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.
File: Soil_microbial_food_web_node_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
Description: Node counts of soil microbial food webs in native and invasive plant communities at different altitudes.
Variables
Elevation: altitude in metres (1400, 2000, 2350).Native: number of nodes in native plots; six replicates per elevation.Invasive: number of nodes in invaded plots; six replicates per elevation.
File: Soil_NAG_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
Description: Soil β-1,4-N-acetylglucosaminidase (NAG) activity in native and invasive plant communities at different altitudes.
Variables
Elevation: altitude in metres (1400, 2000, 2300).NAG(Native): NAG activity in native plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.NAG(Invasive): NAG activity in invaded plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.
File: Soil_LAP_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
Description: Soil L-leucine aminopeptidase (LAP) activity in native and invasive plant communities at different altitudes.
Variables
Elevation: altitude in metres (1400, 2000, 2300).LAP(Native): LAP activity in native plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.LAP(Invasive): LAP activity in invaded plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.
File: Soil_nitrogen-acquiring_enzyme_activity_data_of_native_and_invasive_plant_communities_at_different_elevations.xlsx
Description: Soil nitrogen-acquiring enzyme activities (NAG + LAP) in native and invasive plant communities at different elevations.
Variables
Elevation: altitude in metres (1400, 2000, 2300).N-acquiring enzyme activities(Native): combined NAG + LAP activity in native plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.N-acquiring enzyme activities(Invasive): combined NAG + LAP activity in invaded plots; six replicate columns; unit nmol g⁻¹ soil h⁻¹.
File: Soil_total_nitrogen_data_of_native_and_invasive_plant_communities_at_different_altitudes.xlsx
Description: Soil total nitrogen (TN) in native and invasive plant communities at different altitudes.
Variables
Elevation: altitude in metres (1400, 2000, 2300).TN(Native): total nitrogen in native plots; six replicate columns.TN(Invasive): total nitrogen in invaded plots; four replicate columns as provided.
Code/software
File: Soil_micro-food_web_analysis.R
Description: R script for constructing and analysing soil micro-food web co-occurrence networks. It uses Hmisc, igraph, and psych to calculate Spearman correlations among OTUs/ASVs, applies BH correction, retains significant correlations (|r| ≥ 0.60, P < 0.05), and builds weighted undirected networks. The script also generates Erdős–Rényi random networks to calculate expected average path length, clustering coefficient, and modularity. Finally, it reads a network adjacency matrix and sample representative OTU table, extracts sample-specific subgraphs, and calculates subnetwork topological properties.
File: Structural_Equation_Model_Analysis.R
Description: R script for piecewise structural equation modeling using the piecewiseSEM package. It reads sem2026.XLSX and fits a set of linear models describing direct and indirect pathways linking elevation-related environmental factors, plant diversity, multitrophic diversity, soil nutrient status, soil nutrient cycling capacity, and soil micro-food web complexity. The script prints model summaries and produces a simple path diagram.
Access information
Other publicly accessible locations of the data:
- Dryad Digital Repository: https://doi.org/10.5061/dryad.ns1rn8q8s
(Jiao et al., 2026, dataset associated with this study.)
Data was derived from the following sources:
- Field sampling conducted in April 2024 in the Gaoligong Mountains, Lushui County, Nujiang Lisu Autonomous Prefecture, Yunnan Province, China.
- Sampling plots were established at low (1400 m), moderate (2000 m), and high (2300/2350 m) elevations, comparing native herbaceous plant communities with communities invaded by Ageratina adenophora.
- Soil physicochemical analyses included soil moisture, SOC, DOC, TN, and available nitrogen (NH₄⁺-N + NO₃⁻-N).
- Soil enzyme activities included carbon-acquiring enzymes (BG and CBH) and nitrogen-acquiring enzymes (NAG and LAP).
- Soil micro-food web data were derived from high-throughput sequencing of bacteria (16S V4), fungi (ITS), protists (18S V4), and nematodes (18S), followed by co-occurrence network construction and topological analysis.
- Plant diversity data were based on Margalef and Shannon indices of native herbaceous plant communities.
- Meta-analysis data used in the manuscript are provided in Supplementary Table S1.
- Statistical analyses were performed in R, SPSS, GraphPad Prism, and Origin, as described in the manuscript.