Vegetation type mediates how urbanization reshapes the structure, function, and spatial variation of soil food webs
Data files
Jan 28, 2026 version files 117.87 KB
-
NB_SFW.xlsx
64.40 KB
-
README.md
8.78 KB
-
Soil_food_web_reconstruction.Rmd
22.57 KB
-
statistical_analysis.Rmd
22.11 KB
Abstract
Urbanization represents one of the major anthropogenic alterations of the Earth's surface, with significant impacts on biodiversity and its functions. Soil animals are essential components of biodiversity, playing integral roles in terrestrial ecosystems. How urbanization reshapes soil food webs and affects their function and stability is largely unknown. We assessed the structure and function of soil food webs using stable isotope analysis and the energy flux approach in urban grasslands and woodlands in a subtropical city in China, using natural ecosystems with the same vegetation type as the reference. In urban woodlands, total biomass was 6 times higher, and energy flux was 2 times higher than in the reference natural forests, resulting in a 50 % lower energy turnover (energy flux to biomass ratio), and supporting longer food chains. By contrast, urban grasslands had similar total biomass, total energy flux, and turnover to wild grasslands, but both the bacterial-to-fungal ratio and soil consumption-to-feces production ratio increased, suggesting accelerated soil carbon cycling. Further, we found that urbanization reduced the stability of trophic connections between food-web nodes (i.e., increased variation in trophic interaction strengths), especially in woodlands, probably related to the strong specific predator-prey interactions and higher environmental heterogeneity of urban green spaces. Overall, against the generally assumed negative impacts of land-use changes on soil communities, our study demonstrates that urbanization enhances energy flux in soil food webs but increases the risk of declining energy flux balance between different channels and trophic interaction stability. In addition, the divergent responses to urbanization between different vegetation emphasize the importance of vegetation-specific management to improve soil ecosystem functioning (such as C sequestration).
Dataset DOI: 10.5061/dryad.j3tx95xs3
Description of the data and file structure
Urbanization represents one of the major anthropogenic alterations of the Earth's surface, with significant impacts on biodiversity and its functions. Soil animals are essential components of biodiversity, playing integral roles in terrestrial ecosystems. How urbanization reshapes soil food webs and affects their function and stability is largely unknown. Here, we explore the structure and function of the soil food web by combining stable isotope analysis and an energy flux approach to provide quantitative insights into how urbanization affects the soil biodiversity-ecosystem functioning relationships under different vegetation types. We collected soil animals from two major types of urban green space - urban woodland and urban grassland - alongside natural forest and wild grassland as reference sites in Ningbo, China. We recorded the abundance and biomass of all major soil animal taxa and used stable isotope analysis (δ15N values) and food web reconstruction with an energy flux approach to evaluate the structure and function of soil food webs. We have submitted our raw data (NB_SFW.xlsx) and R script ( Soil_food_web_reconstruction.Rmd, statistical analysis.Rmd).
Files and variables
File: Soil_food_web_reconstruction.Rmd
Description: R code for soil food web reconstruction
File: NB_SFW.xlsx
Description: Original dataset for soil food web reconstruction.
- Sheet 1: Animal traits used for soil food web reconstruction
- Plot: Site ID, in total 16 sites were assessed
- Guild: Name of the trophic guild (=food-web node)
- Group: Broad ecological category of animals
- Abbreviation: Short name
- Metabolic Type: Name of broad phylogenetic category to account for in metabolism calculation
- P: Feeds on living vascular plant shoots and/or (fine) roots and/or photoautotrophic microorganisms
- A: Feeds on algae
- L: Feeds on dead leaves and dead fine roots
- W: Feeds on dead tree trunks, twigs, branches, large roots, etc
- S: Feeds on animal faeces, residues of microorganisms, and other transformed organic matter associated with mineral soil fractions
- B: Feeds on free-living prokaryotes, here traditionally includes domains Bacteria and Archaea
- F: Feeds on fungi, including free-living saprotrophs, mycorrhizal fungi, and lichen-associated fungi, predominantly mycelium and spores, but also fruiting bodies
- Invt: Feeds on invertebrates
- Vert: Feeds on vertebrates
- PPMR: PPMR = Predator–prey mass ratio. Here, traits modifying the PPMR are listed
- PPMRopt: Multiplying coefficient modifying the optimum PPMR (higher values = ratio is larger; lower values = ratio is smaller)
- PPMRwidth: Multiplying coefficient modifying the PPMR distribution breadth (higher values = wide size spectrum of prey; lower values = narrow size spectrum of prey)
- Predatory: Organism is a carnivore and may strike back while being attacked (for organisms in the same size class)
- Agility: Organisms may escape predators by jumping away. Potentially reduces predation pressure
- Physical.protection: Organism is physically protected from predators (e.g., by a cuticle or shell). Reduces predation and increases PPMR
- Metabolites: The organism produces protective metabolites, such as e.g. poison. Requires specific adaptations to overcome and thus, on average, largely reduces predation
- Protection: The overall protection across multiple mechanisms (multiplication of protection coefficients)
- Proportion.C: Proportion of carbon in the body, average value
- Proportion.N: Proportion of nitrogen in the body, average value
- above: Organisms that spend at least part of their life cycle aboveground (e.g., flying or living on green vegetation, including canopies)
- epi: Organisms that are active on litter, wood, and stone surfaces. Usually actively moving. Only occasionally climbing understorey. Can use coarse detritus as a shelter
- hemi: Organisms that inhabit coarse detritus, found predominantly inside decomposing litter or wood
- eu: Organisms that inhabit lower organic and mineral soil layers, including rhizosphere
- MassMean_mg: Mean log10-transformed fresh body mass of the guild in milligrams; information is directly collected
- MassSD_mg: Standard deviation of mean log10-transformed fresh body mass of the guild in milligrams; information is directly collected
- Biomass_mg_sqm: Biomass per square meter, expressed in milligrams
- d.15N.adj: Leaf-calibrated 15N stable isotope values of animals
- System: Ecosystem types, in total 4 types were assessed
- Feedingguild: The animal's feeding group
- Sheet 2: Resource characteristics
- Group: Broad ecological category (resources)
- Taxon: Resource types
- Abbreviation: Short name
- Metabolic Type: Broad ecological category (resources)
- Biomass_g_sqm: Biomass. Arbitrary value, NOT used in the reconstruction and energy flux calculations. The steady-state assumption implies that there are enough resources
- P: Feeds on living vascular plant shoots and/or (fine) roots and/or photoautotrophic microorganisms
- L: Feeds on dead leaves and dead fine roots
- S: Feeds on animal faeces, residues of microorganisms, and other transformed organic matter associated with mineral soil fractions
- B: Feeds on free-living prokaryotes, here traditionally includes domains Bacteria and Archaea
- F: Feeds on fungi, including free-living saprotrophs, mycorrhizal fungi, and lichen-associated fungi, predominantly mycelium and spores, but also fruiting bodies
- Invt: Feeds on invertebrates
- Vert: Feeds on vertebrates
- PPMR: PPMR = Predator–prey mass ratio. Here, traits modifying the PPMR are listed
- PPMRopt: Multiplying coefficient modifying the optimum PPMR (higher values = ratio is larger; lower values = ratio is smaller)
- PPMRwidth: Multiplying coefficient modifying the PPMR distribution breadth (higher values = wide size spectrum of prey; lower values = narrow size spectrum of prey)
- MassMean_mg: Mean log10-transformed fresh body mass of the guild in milligrams
- MassSD_mg: Standard deviation of mean log10-transformed fresh body mass of the guild in milligrams
- Predatory: Organism is a carnivore and may strike back while being attacked (for organisms in the same size class)
- Agility: Organisms may escape predators by jumping away. Potentially reduces predation pressure
- Physical.protection: Organism is physically protected from predators (e.g., by a cuticle or shell). Reduces predation and increases PPMR
- Metabolites: The organism produces protective metabolites, such as e.g. poison. Requires specific adaptations to overcome and thus, on average, largely reduces predation
- Protection: The overall protection across multiple mechanisms (multiplication of protection coefficients)
- Proportion.C: Proportion of carbon in the body, average value
- Proportion.N: Proportion of nitrogen in the body, average value
- above: Organisms that spend at least part of their life cycle aboveground (e.g., flying or living on green vegetation, including canopies)
- epi: Organisms that are active on litter, wood, and stone surfaces. Usually actively moving. Only occasionally climbing understorey. Can use coarse detritus as a shelter
- hemi: Organisms that inhabit coarse detritus, found predominantly inside decomposing litter or wood
- eu: Organisms that inhabit lower organic and mineral soil layers, including rhizosphere
- PreySD: Arbitrary value, is not used in the reconstruction
- PreyMean: Arbitrary value, is not used in the reconstruction
- efficiencies: Assimilation efficiency while feeding on these resources (based on %N)
- Empty cells have been filled with n/a, indicating that this cell is not applicable in this table.
- Sheet 3: Related indices used to calculate metabolic rate
- Metabolic Type: Metabolic type to link with the raw data table
- Reference: Source of the coefficients
- a: Scaling coefficient
- PerMass_Exponent: Exponent coefficient (per unit body mass)
- E: Activation energy
- ln_i0_watt: Intercept
- Boltzmann_eVK: Boltzmann constant
File: statistical_analysis.Rmd
Description: R code for statistical analysis
Code/software
All analyses were performed in R version 4.3.2.
