DOI: 10.5061/dryad.j3tx95xs3
title: Vegetation type mediates how urbanization reshapes the structure, function, and spatial variation of soil food webs

description: 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).
description: # Vegetation type mediates how urbanization reshapes the structure,
 function, and spatial variation of soil food webs Dataset DOI:
 [10.5061/dryad.j3tx95xs3](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 (δ^15^N 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.