Trophic compensation stabilizes soil nematode beta diversity despite increased plant beta diversity under long-term nitrogen enrichment

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Description of the data and file structureThe above-ground vegetation from each plot was harvested in August, using a 1 m × 1 m quadrat. After harvest, the vegetation was sorted to species, oven-dried at 65 ℃ for 48 hours, and then weighed to determine above-ground biomass. Plants were categorized into grasses, forbs, and sedges based on their life forms.We collected five soil cores (5 cm diameter) from the top 0-10 cm of each plot, sieved through a 2-mm mesh. The composite soil sample was separated into two parts: One part of the fresh soil was stored in a refrigerator at 4 ℃ for measurements of soil inorganic N, soil moisture and nematode community structure. Soil moisture was measured after drying at 105 ℃ for 24 hours.Nematodes were extracted from 100 g of fresh soil using the Baermann funnel method. After heat-killing in a 60°C water bath for approximately 3 minutes, the specimens were preserved in 4% formalin and then transferred to the laboratory for microscopy analysis.Nematode counts were conducted under a stereoscopic microscope, identifying up to the first 100 individuals or the entire sample if fewer. Classification into trophic groups (bacterivores, fungivores, herbivores, omnivores-predators) was based on feeding habits and morphological traits.Code/softwareAll statistical analyses were conducted using R version 4.3.1 (R Development Core team, 2023):1.For both nematode and plant communities, overall β-diversity (βsor) and its additive components, spatial turnover (βsim) and nestedness (βnes), were calculated based on pairwise Sørensen dissimilarity index among plots (Baselga, 2010). Here, βsor is Sørensen dissimilarity, βsim is Simpson dissimilarity ( = turnover component of Sørensen dissimilarity), and βnes is the nestedness component of Sørensen dissimilarity. The indices were computed as follows: βsor=(b+c)/(2a+b+c)where “a” is the number of species shared by two plots, “b” is the number of species present in the first plot but not in the second, and “c” is the number of species present in the second plot but not in the first. βsim=(min⁡(b,c))/(a+min⁡(b,c))This metric quantifies pure species turnover between sites, independent of richness differences. βnes=βsor-βsimThis metric quantifies the nestedness component resulting from differences in species richness, where species in the poorer site are a subset of those in the richer site. The interannual patterns of β-diversity and its components for aboveground (plant) and belowground (nematode) communities across different N addition levels were visualized using the ggplot2 package.2.To identify key drivers of β-diversity, we examined the temporal differences in β-diversity indices and their components (βsor, βsim, βnes) among plant communities, nematode communities, and their different groups. We calculated β-diversity indices and their components among plots within each N level and the control in each block, for each year and for the three-year average period. This allowed us to analyze factors driving community dissimilarity for both nematode and plant communities. 3.To assess the potential coupling or decoupling of aboveground and belowground communities, we analyzed correlations between the β-diversity indices (and their components) of plant and nematode communities. We also examined relationships between community attributes (species richness and abundance/biomass) for total communities and individual trophic groups to determine whether β-diversity differences were primarily driven by variation in species numbers or abundance/biomass.4.Following Legendre and De Cáceres (2013), nematode abundance data were compiled across a three-year period. The community data matrix was Hellinger-transformed (square root of relative abundances) to reduce the influence of extreme values. The SCBD was then calculated for each nematode taxon within each trophic group and for the entire nematode community using the ‘beta.div’ function in the ‘adespatial’ package (Dray et al., 2018). SCBD indicates the relative importance of each trophic group in driving overall β-diversity. We analyzed how the contributions of different trophic groups to β-diversity shifted under long-term N addition at different rates.5.From the same analysis, we obtained the total sum of squares (SST) and total beta diversity (βtotal) of the community matrix. The magnitude of βtotal was used to evaluate the extent of compositional differences among years.6.Finally, we analyzed the correlation between nematode abundance and its corresponding SCBD value to assess whether the influence of N deposition on nematode abundance followed a deterministic pattern.

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