Ecology

Direct injection method for ethylene and acetylene δ13C analyses by GC-C-IRMSFollowing the direct injection approach of classical ISARA12 with a few modifications, ARA samples with high ethylene yield ( > 500 ppmv) in 10% v/v acetylene were manually injected into a Thermo Scientific Trace GC Ultra-Isolink with an Agilent HP-PLOT/Q  capillary GC column (30 m, i.d. = 0.32 mm, f.t. = 20 μm) and a combustion reactor connected to a Thermo Scientific Delta V Plus isotope ratio mass spectrometer (GC-C-IRMS; Fig. 1a). Modifications include the replacement of silver ferrules in the GC oven with Valcon polymide (graphite reinforced polymer) ferrules to limit memory effects from acetylene. The combustion reactor was oxidized with pure oxygen for 1 h before each run and brief (15 min) seed oxidations were performed between measurement batches (i.e., required every ~ 6–8 ethylene injections, ~ 4–6 acetylene injections) to regenerate reactor oxidation capacity and minimize drift of δ13C values. See Supplementary Table S1a online for additional instrument settings.Ethylene Pre-Concentration (EPCon) methodARA samples with  More

Thermal requirements to develop PDWe examined the response of a wide spectrum of European grapevine varieties to XfPD infection in three independent experiments conducted in 2018, 2019, and 2020. Overall, 86.1% (n = 764) of 886 inoculated plants, comprising 36 varieties and 57 unique scion/rootstock combinations, developed PD symptoms 16 weeks after inoculation. European V. vinifera varieties exhibited significant differences in their susceptibility to XfPD (Supplementary Table S1). All varieties, however, showed PD symptoms to some extent, confirming previous field observations of general susceptibility to XfPD9,12,37. We also found significant differences in virulence (χ2 = 68.73, df = 1, P = 2.2 × 10−16) between two XfPD strains isolated from grapevines in Majorca across grapevine varieties (Supplementary Fig. S1). Full details on the results of the inoculation tests are available in “Methods”, Supplementary Note 1, Supplementary Table S1 and Supplementary Data 1.Growing degree days (GDD) have traditionally been used to describe and predict phenological events of plants and insect pests, but rarely in plant diseases58. We took advantage of data collated in the inoculation trials together with temperature to relate symptom development to the accumulated heat units at weeks eight, 10, 12, 14, and 16 after inoculation (Supplementary Data 1). Rather than counting GDDs linearly above a threshold temperature, we consider Xf ’s specific growth rate in vitro within its cardinal temperatures. The empirical growth rates come from the seminal work by Feil & Purcell38 shown in the inset of Fig. 1a. This Arrhenius plot was transformed, as explained in Supplementary Note 2A, to obtain a a piece-wise function f(T) Eq. (1). Our model and risk maps are based on f(T) (red line in Fig. 1a) because it provides the best fit to the experimental data when compared with the commonly used Beta function (blue line) for representing the thermal response in biological processes59,60. This Modified Growing Degree Day (MGDD) profile Eq. (1) enables to measure the thermal integral from hourly average temperatures, improving the prediction scale of the biological process61. MGDD also provides an excellent metric to link XfPD growth in culture with PD development as, once the pathogen is injected into the healthy vine, symptoms progression mainly depends upon the bacterial load (i.e., multiplication) and the movement through the xylem vessel network, which are fundamentally temperature-dependent processes38,62. Moreover, MGDD can be mathematically related to the exponential or logistic growth of the pathogen within the plant (Supplementary Note 2B).Fig. 1: Climatic and transmission layers composing the epidemiological model.a MGDD profile fitted to the in vitro data of Xf growth rate in Feil & Purcell 200138. The original Arrhenius plot in Kelvin degrees (inset) was converted to Celsius, as explained in (Supplementary Note 2A), to obtain the fit shown in the main plot red line; the blue line represents the fit with a Beta function. b Correlation between CDD and the average ({T}_{min }) of the coldest month between 1981 and 2019. Plotted black dots (worldwide) and yellow dots (main wine-producing zones) depict climatic data from 6,487,200 cells at 0.1∘ × 0.1∘ resolution, spread globally and retrieved from ERA5-Land dataset. The red solid line depicts the fitted exponential function for worldwide data and the blue solid line for main vineyard zones. c Nonlinear relationship between MGDD (red line) and CDD (blue line) and the likelihood of developing chronic infections. Black dots depict the cumulative proportion of grapevine plants in the population of 36 inoculated varieties showing five or more symptomatic leaves at each of the 15 MGDD levels (see Supplementary Information). Vertical bars are the 95% CI. d Combined ranges of MGDD and CDD on the likelihood of developing chronic infection. e Transmission layer in the dynamic equation (1) of the SIR compartmental model. f Relationship between the exponential growth of the number of infected plants with the risk index and their ranks.Full size imageInterannual infection survival in grapevines plays a relevant role when modelling PD epidemiology. In our model, we assumed a threshold of five or more symptomatic leaves for these chronic infections based on the relationship between the timing and severity of the infection during the growing season and the likelihood of winter recovery38,39,42. This five-leaf cut-off was grounded on: (i) the bimodal distribution in the frequency of the number of symptomatic leaves among the population of inoculated grapevines (Supplementary Fig. S1), whereby vines that generally show less than five symptomatic leaves at 12 weeks after inoculation remain so in the following weeks, while those that pass that threshold continue to produce symptomatic leaves, and (ii) the observed correlation between the acropetal and basipetal movement of Xf along the cane (Supplementary Fig. S1). The likelihood of developing chronic infections as a function of accumulated MGDD among the population of grapevine varieties was modelled using survival analysis with data fitted to a logistic distribution ({{{{{{{mathcal{F}}}}}}}}({{{{{rm{MGDD}}}}}})). A minimum window of MGDD = 528 was needed to develop chronic infections (var. Tempranillo), about 975 for a median estimate, while a cumulative MGDD  > 1159 indicate over 90% probability within a growing season (red curve in Fig. 1c and “Methods”).Next, we intended to model the probability of disease recovery by exposure to cold temperatures. Previous works had specifically modelled cold curing on Pinot Noir and Cabernet Sauvignon varieties in California as the effect of temperature and duration39 by assuming a progressive elimination of the bacterial load with cold temperatures42. In the absence of appropriate empirical data to formulate a general average pattern of winter curing among grapevine varieties, we combined the approach of Lieth et al.39 and the empirical observations of Purcell on the distribution of PD in the US related to the average minimum temperature of the coldest month, Tmin, isolines41. To consider the accumulation of cold units in an analogy of the MGDD, we searched for a general correlation between Tmin and the cold degree days (CDDs) with base temperature = 6 ∘C (see “Methods”). We found an exponential relation, ({{{{{rm{CDD}}}}}} sim 230exp (-0.26cdot {T}_{min })), where specifically, CDD ≳ 306 correspond to ({T}_{min } < -1.{1},^{circ }{{{{{rm{C}}}}}}) (Fig. 1b). To transform this exponential relationship to a probabilistic function analogous to ({{{{{{{mathcal{F}}}}}}}}({{{{{rm{MGDD}}}}}})), hereafter denoted ({{{{{{{mathcal{G}}}}}}}}({{{{{rm{CDD}}}}}})), ranging between 0 and 1, we considered the sigmoidal family of functions (f(x)=frac{A}{B+{x}^{C}}) with A = 9 × 106, B = A and C = 3 (Fig. 1c), fulfilling the limit ({{{{{{{mathcal{G}}}}}}}}({{{{{rm{CDD}}}}}}=0)=1), i.e., no winter curing when no cold accumulated, and a conservative 75% of the infected plants recovered at ({T}_{min }=-1.{1},^{circ }{{{{{rm{C}}}}}}) instead of 100% to reflect uncertainties on the effect of winter curing.MGDD/CDD distribution mapsMGDD were used to compute annual risk maps of developing PD during summer for the period 1981–2019 (see “Methods”). The resulting averaged map identifies all known areas with a recent history of severe PD in the US corresponding to ({{{{{{{mathcal{F}}}}}}}}({{{{{rm{MGDD}}}}}}) , > , 90 %) (i.e., high-risk), such as the Gulf Coast states (Texas, Alabama, Mississippi, Louisiana, Florida), Georgia and Southern California sites (e.g., Temecula Valley) (Fig. 2a), while captures areas with a steep gradation of disease endemicity in the north coast of California (({{{{{{{mathcal{F}}}}}}}}({{{{{rm{MGDD}}}}}} , > , 50 % )). Overall, more than 95% of confirmed PD sites (n = 155) in the US (Supplementary Data 2) fall in grid cells with ({{{{{{{mathcal{F}}}}}}}}({{{{{rm{MGDD}}}}}}) , > , 50 %).Fig. 2: Average thermal-dependent maps for Pierce’s disease (PD) development and recovery in North America and Europe.PD development during the growing season based on average ({{{{{{{mathcal{F}}}}}}}}({{{{{rm{MGDD}}}}}})) estimations between 1981 and 2019 in North America (a) and Europe (b) derived from the results of the inoculation experiments on 36 grapevine varieties. Large differences in the areal extension with favourable MGDDs can be observed between the US and Europe. The winter curing effect is reflected in the distribution of the average ({{{{{{{mathcal{G}}}}}}}}({{{{{rm{CDD}}}}}})) for the 1981–2019 period in the United States (c) and Europe (d). A snapshot of the temperature-driven probability of chronic infection averaged for the 1981–2019 period is obtained from the joint effect of MGDD and CDD in North America (e) and Europe (f). Warmer colours indicate more favourable conditions for chronic PD and the dashed line highlights the threshold of chronic infection probability being 0.5.Full size imageThe average MGDD-projected map for Europe during 1981–2019 spots a high risk for the coast, islands and major river valleys of the Mediterranean Basin, southern Spain, the Atlantic coast from Gibraltar to Oporto, and continental areas of central and southeast Europe (Fig. 2b). Of these, however, only some Mediterranean islands, such as Cyprus and Crete, show ({{{{{{{mathcal{F}}}}}}}}({{{{{rm{MGDD}}}}}}) , > , 99 %) comparable to areas with high disease incidence in the Gulf Coast states of the US and California. Almost all the Atlantic coast from Oporto (Portugal) to Denmark are below suitable MGDD, with an important exception in the Garonne river basin in France (Bordeaux Area) with low to moderate MGDD (Fig. 2b).Figure 2a shows how the area with high-risk MGDD values extends further north of the current known PD distribution in the southeastern US, suggesting that winter temperatures limit the expansion of PD northwards9. A comparison between MGDD and CDD maps (Fig. 2a vs. Fig. 2c, Fig. 2e) further supports the idea that winter curing is restricting PD northward migration from the southeastern US. However, consistent with growing concern among Midwest states winegrowers on PD northward migration led by climate change63, we found a mean increase of 0.12% y−1 in the areal extent with CDD  0.075) in 22.3% of the vineyards in Europe. However, no vineyard is in epidemic-risk zones with a high-risk index and only 2.9% of the vineyard surface is at moderate risk (Supplementary Table S8). The areas with the highest risk index (r(t) between 0.70 and 0.88) are mainly located in the Mediterranean islands of Crete, Cyprus and the Balearic Islands or at pronounced peninsulas like Apulia (Italy) and Peloponnese (Greece) in the continent (Fig. 6a and Supplementary Table S8). Most vineyards are in non-risk zones (42.1%), whereas 35.6% are located in transition zones with presently non-risk but where XfPD could become established in the next decades causing some sporadic outbreaks. In Supplementary Data 4 and Supplementary Table S8, we provide full details of the total vineyard areas currently at risk for each country and region.Fig. 6: Intersection between Corine-land-cover vineyard distribution map and PD-risk maps for 2020 and 2050.Data were obtained from Corine-land-cover (2018) and the layer of climatic suitability forP. spumarius in Europe from35. The surface of the vineyard contour has been enlarged to improve the visualisation of the risk zones and disease-incidence growth-rate ranks. a PD risk map for 2019 and its projection for 2050 (b). Blue colours represent non-risk zones and transient risk zones for chronic PD (R0  More

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Study species and pre-cultivationTo create the mesocosm communities, we selected nine herbaceous grassland species that are native to and widespread in Central Europe (Supplementary Table 9), where they can also co-occur. The species were Alopecurus pratensis L., Diplotaxis tenuifolia (L.) DC., Lolium perenne L., Poa pratensis L., Prunella vulgaris L., Sinapis arvensis L., Sonchus oleraceus L., Vicia cracca L., Vicia sativa L. To increase generalizability54, the species were selected from three functional groups (grasses, annual forbs, perennial forbs), and they represent five families.Seeds were obtained from different sources (Supplementary Table 9). For the transplanted-seedling community (see section ‘Experimental lay-out), seedlings were pre-cultivated in a greenhouse of the Botanical Garden of the University of Konstanz. As the species require different times for germination, they were sown on different dates (Supplementary Table 10) to ensure that seedlings of all species were at a similar developmental stage at transplantation. Seeds were sown separately per species in plastic trays filled with potting soil (Einheitserde®, Pikiererde CL P). The greenhouse had a regular day-night rhythm of c. 16:8 hours, and its ventilation windows automatically opened at 21 °C during the day and at 18 °C during the night. Two days before transplanting, the seedlings were placed outdoors to acclimatize. For the sown community, we sowed a seed mixture of the nine study species directly into the outdoor mesocosm pots.Experimental setupGlobal change treatmentsWe imposed six global change treatments: climate warming, light pollution, microplastic pollution, soil salinization, eutrophication, and fungicide accumulation, all of which frequently occur in the environment. These GCFs were chosen because they differ in their nature (i.e., physical, chemical), are likely to differ in their mode of action and effect direction21, and can be easily implemented. Each of the six GCFs have been shown to impact plants and their environment when applied on their own10,13,17,19,20,55,56,57,58,59,60. Furthermore, all of the chosen GCFs are likely to continue to increase in magnitude or extent in the near future61,62,63,64,65. For the climate-warming treatment, we used infrared-heater lamps (HS-2420; 240 V, 2000 W; Kalglo Electronics Co., Bethlehem, USA) set to 70% of their maximum capacity to achieve an average temperature increase of 2.0 °C (±SD = 0.2 °C) at plant level. This is within the range of temperature increases predicted by the RCP 4.5 scenario for the year 2100 [+1.1 − 2.6 °C; 63]. For the light-pollution treatment, we used LED spotlights (LED-Strahler Flare 10 W, IP 65, 900 lm, cool white 6500 K; REV Ritter GmbH, Mömbris, Germany), which were switched on daily from 9 pm to 5 am, corresponding to the times of sunset and -rise. The average light intensity was 24.5 lx at ground level, which is within the range of light intensities found below street lights, and matches the light intensities used in other light-pollution experiments14,56. For the microplastic pollution treatment, we used granules (1.0–2.5 mm diameter) of the synthetic rubber ethylene propylene diene monomer (EPDM Granulat, Gummi Appel GmbH + Co. KG, Kahl am Main, Germany) at a concentration of 1% (w/w, granules/dry soil, approximately corresponding to 1.5% v/v). EPDM granules are, for example, used in artificial sport turfs, from where they easily spread into the surroundings, and have been used previously to investigate the effects of microplastics on plants18. The chosen concentration is well within the range of concentrations used in previous studies18,66,67, and is at the low to intermediate range of concentrations found in sites polluted with plastics68. For the soil-salinization treatment, dissolved NaCl was added to the soil. Soil salinity is commonly measured as electrical conductivity, with a conductivity between 4 and 8 dS m−1 considered to be moderately saline69. For the experiment, we used a salinity of 6 dS m−1. To maintain a more or less constant salinity level, electrical conductivity was measured weekly, and, if required, adjusted by adding dissolved NaCl. For the eutrophication treatment, 3 g of a dissolved NPK fertilizer (Universol® blue oxide, ICL SF Germany & Austria, Nordhorn, Germany) was added per pot. For N, this corresponds to an input of 100 kg N ha−1, comparable to the yearly amounts of atmospheric N deposition in large parts of Europe52 and the yearly nitrogen input on agricultural field in the European Union70. To ensure a more or less constant nutrient availability during the experiments, we split total fertilizer input into three applications (directly after, 3 weeks after, and 6 weeks after starting the experiments) of 1 g fertilizer per pot per application. In addition, to avoid severe nutrient limitation in the other pots, all pots (irrespective of the eutrophication treatment) received basic fertilization. This was applied four times to the transplanted-seedling-community pots and five times to the sown community pots, with 0.2 g fertilizer per pot per application. For the pesticide treatment, we used the fungicide Landor® CT (Syngenta Agro GmbH, Maintal, Germany). This fungicide was chosen because it contains three azoles as active agents, which belong to the most widely used class of antifungal agents71. To each pot in this treatment, we added 1.5 μl fungicide dissolved in water (1‰). This corresponds to 60% of the maximum amount that should be used per hectare of cropland. A summary of the levels of the individual GCFs used in our experiment is provided in Supplementary Table 8.Combinations of simultaneously acting GCFsTo examine the potential effects of the numbers of simultaneously acting GCFs, we created five levels of increasing GCF numbers. These levels were: zero (i.e., the control without any GCF application), one (single), two, four and six GCFs. For the one-, two- and four-GCF levels, there were six different combinations, so that each of these levels included either six different GCFs in case of the one-factor, or six different GCF combinations in case of the two- and four-GCF levels. In the six-GCF level, all six factors were combined, so that there was only one combination. To avoid potential biases due to unequal representation of the different GCFs in each GCF-number level, we created the GCF combinations randomly but with the restriction that each GCF was present in an equal number of combinations for each GCF-number level (i.e., each GCF was included once in GCF-number levels 1 and 6, respectively, twice in GCF-number level 2, and four times in GCF-number level 4; Supplementary Table 11).Experimental lay-outThe experiment was conducted outdoors in the climate-warming-simulation facility of the Botanical Garden of the University of Konstanz, Germany (N: 47°69’19.56”, E: 9°17’78.42”). Twenty of the 2 m × 2 m plots of this facility were used for our experiment. As the climate-warming and light-pollution treatments could not be applied to each individual pot separately, we applied those treatments at the plot level. Therefore, we assigned four of the 20 plots to the climate-warming treatment, four plots to the light-pollution treatment and four plots to both climate-warming and light-pollution treatment combination. Each plot had a 145 cm high metal frame. The eight plots assigned to the climate-warming treatment were equipped with a 1.80 m long, horizontally hanging infrared-heating lamp at the top of the metal frame (i.e., at 145 cm above soil level). The heating lamp slowly oscillated along its longitudinal axis to ensure uniform heating of the whole 2 m × 2 m plot. The eight plots assigned to the light-pollution treatment, each had a LED spotlight attached to one of the sides of the metal frame at a height of 120 cm. To reduce illumination of the neighboring plots, light-pollution was only applied to the outer plots of the climate-warming-simulation facility (Supplementary Fig. 5), and LEDs were pointing away from the inner plots and were equipped with lamp shades made of black plastic pots (18 cm × 18 cm × 25.5 cm). Furthermore, to reduce the light intensity to a realistic light-pollution level (24.5 lx) as found below street lights, we covered the spotlight with a layer of white cloth (Supplementary Fig. 6). For further details on the artificial light treatment, see Supplementary Fig. 7.To create mesocosms with the transplanted-seedling and sown communities, we filled 10-L pots (CEP- Container, 10.0 F, Burger GmbH, Renningen-Malmsheim, Germany) with a mixture of 40% potting soil (see above), 40% quartz sand (0.5–0.8 mm), and—to inoculate the substrate with a natural soil community—20% top soil excavated from a seminatural grassland patch in the botanical garden. In total, the experiments with the transplanted-seedling and sown communities, each included 120 pots (i.e., 20 treatment combinations × six replicates × 2 experiments = 240 pots in total; see Supplementary Table 11), which were distributed across the 20 plots. To prevent leakage of fertilizer or salt solutions, each pot was placed onto a plastic dish. To reduce differences due to environmental variation within plots, the positions of pots within each plot were re-randomized every 14 days. Plants were watered regularly to avoid drought stress and to avoid differences in soil moisture due to application of fertilizer- and salt-solutions.For the sown community, we randomly distributed five seeds of each of the nine species on the substrate in each pot on 3 July 2020. For the transplanted-seedling community, two seedlings of each of the nine species were transplanted into each pot (i.e., 18 seedlings per pot) according to a fixed pattern (Supplementary Fig. 8) on 6 July 2020. Since there were a few seedlings missing for S. arvensis (six seedlings) and V. cracca (four seedlings), we re-sowed these species in germination trays on 6 July 2020. On 13 July 2020, dead seedlings, and the missing seedlings for S. arvensis were replaced. Since V. cracca took longer to germinate, the missing seedlings were transplanted on 17 July 2020.MeasurementsTo investigate the effects of single-GCFs and their number on the sown and transplanted-seedling communities, we used plant biomass as an indicator for plant performance72. As it was impossible to disentangle the roots, we only used aboveground biomass. On 14 and 15 September 2020, i.e., 10 weeks after transplanting, we harvested the transplanted-seedling communities. On 28 and 29 September, i.e., twelve weeks after sowing, we harvested the sown communities. For both community types, we harvested the plants separately by species. The harvested plants were stored in paper bags, dried at 70 °C for at least 72 hours and weighed.Statistical analysisAll analyses were done in R 3.6.273. As the transplanted-seedling and sown communities were harvested at different times, we treated them as separate experiments, and therefore analyzed them separately (but see the subsection “Community type specific responses” below).Community aboveground biomassTo analyze the effects GCF number on plant-community productivity, we fitted linear mixed-effects models separately for the transplanted-seedling and sown communities, using the lmer function in the “lme4” package74. Total aboveground biomass per pot was the response variable. To improve normality of the residuals, biomass of the transplanted-seedling and sown communities was square-root- and natural-log-transformed, respectively. We included GCF number as a continuous fixed variable. To account for non-independence of pots in the same GCF combination and of pots in the same plot, GCF combination and plot were included as random effects. The effects of the individual GCFs on biomass production were also assessed by fitting linear mixed-effects models, using only the data of the control and single-GCF treatments, and including GCF identity as fixed effect.Community compositionTo assess potential effects of single-GCFs and GCF number on the final composition of the transplanted-seedling and sown communities, we first assessed variation in species composition, based on biomass proportions, among pots using principal component analysis (PCA) [rda function of the “vegan” package75,]. For each PCA (Supplementary Fig. 1), we extracted the PC1 and PC2 values, which together explained more than 65% of the variation in community composition and included them as response variables in separate linear mixed models, as described above for community biomass.To evaluate whether GCF number affects the diversity and evenness of plant communities, we calculated the Shannon index (H)76, using the diversity function in the “vegan” package, and evenness index (J)77 based on species biomass proportions. Subsequently, the single-GCF and GCF-number effects on diversity and evenness of the sown and transplanted-seedling communities were analyzed using linear mixed-effects models, or—if adding random effects did not improve the model—more parsimonious linear models78,79. For all models, we used type II analysis of variance (ANOVA) tests (Anova function in the “car” package) to assess the significance of fixed effects.Hierarchical diversity-interaction modelingWhen there is a significant GCF-number effect, this could reflect that with increasing numbers of co-acting GCFs, there is a higher chance that it will include a GCF with a strong and dominant effect (i.e., sampling or selection effects). However, it could also be that the GCF-number effect is driven by interactions among the GCFs, and the effects of these interactions could be GCF-specific or general. As our experiment does not include all possible combinations of GCFs, it does not allow to test the contributions of each possible multi-way GCF interaction. Therefore, to gain insights into whether the GCF identities and specific or general GCF interactions underlie the significant GCF-number effects, we applied the hierarchical diversity-interaction modeling framework of Kirwan et al.80. This framework was originally developed for estimating contributions of species identities and their interactions to ecosystem functions, but we here applied it to GCF identities and interactions. For each of the response variables showing a significant GCF-number effect, we ran five hierarchical models specifying different assumptions about the potential contributions of individual GCFs and their interactions to the GCF-number effect, and compared them using likelihood ratio tests (Fig. 4). For these analyses, the data of the control treatment (i.e., GCF number zero) was excluded. Each of the five models specified different assumptions about the potential contributions of individual GCFs and their interactions to the GCF-number effect. The first model is the null model, which assumed that there were no GCF-specific contributions (i.e., all GCFs contributed equally) and that there were no contributions of GCF interactions. Therefore, the null model only included the centered sum of the GCFs of each treatment (M) as fixed effect. M accounts for differences in ‘initial abundances’ of GCFs—meaning that the other model terms are interpreted based on the average initial abundance—and was also included in the four other models80. This way, we could include the GCFs’ relative proportions in each GCF combination, instead of just considering GCF presence, while taking into account that, with increasing GCF number, the relative proportion of each individual GCF is automatically reduced. In the second model, the GCF identities (i.e., their proportions in the respective GCF combination) were added, assuming that individual GCFs contribute differently to the effect of GCF number. In the third model, separate-pairwise interactions between the GCFs were added, considering that, in addition to contributions of individual GCFs, specific pairwise interactions contributed to the GCF-number effect. In the fourth model, the average GCF-interaction model (which is also called the evenness model in Kirwan et al. 2009), the separate-pairwise GCF interactions were replaced by an average interaction effect. Thus, the average GCF-interaction model assumed equivalent contributions of all pairwise GCF interactions. In the fifth model, the additive GCF-specific interaction contributions model, the average interaction effect of the fourth model was replaced by average GCF-specific interaction effects. This model assumed that each GCF’s contribution to a pairwise interaction remains constant. For the calculation of the average GCF-specific and average interaction effect, we used the equations provided by Kirwan et al.80. For each of the response variables, we generally included the same random terms as in the main analyses of the GCF-number effect. However, as this resulted in singularity warnings for some of the hierarchical diversity-interaction models, e.g., those for species diversity and evenness measures, we used for these cases linear models instead of linear mixed models.Fig. 4: Hierarchical diversity-interaction-modeling framework to assess contributions of GCF identities and GCF interactions to GCF-number effects.The framework was adapted from Kirwan et al.80. The null model assumes equivalent contributions of all GCFs and no interactions between them. The subsequent models assume more complex effects of how the individual GCFs and their interactions determine the GCF-number effects. The questions that can be answered by comparing specific models are depicted next to the arrows connecting the two models.Full size imageCommunity type-specific responsesAs the transplanted-seedling and sown communities were harvested at different times, we treated them as separate experiments, and therefore analyzed them separately. However, to test explicitly whether both community types differed in their responses to single-GCFs and GCF number, we also analyzed them jointly. To this end, we fitted linear mixed-effects models for each response variable including GCF number (or single-factor treatments), community type and their interaction as fixed effects (Supplementary Table 5).Final number of plants per speciesTo test for effects of individual GCFs and GCF number on species presence, i.e., the number of individuals per species present at harvest, we fitted generalized linear mixed-effects models for the transplanted-seedling and sown communities separately. We included the survival rate (number of individuals present at harvest divided by the number of planted/sown individuals) as response variables. For the models testing the effects of GCF number, we included GCF combination, species, pot, and plot as random effects. For the models testing the effects of single-GCFs, the same random effects were included, except for GCF combination. Specific random effects were removed from the model if their incorporation resulted in singular fit warnings due to low variation. We assessed the effects of individual GCFs or GCF number using type III ANOVA tests (Anova function in the “car” package, Supplementary Table 7).Eutrophication effectsIn addition to the general assessment of individual GCF effects in the hierarchical diversity-interaction models, we specifically assessed the effects of eutrophication. This was done because eutrophication had the strongest effect on productivity as individual GCF, and this might also have dominated the GCF-number effect, indicating a sampling effect. To this end, we added a binary-coded variable to include information on whether eutrophication was included in the different GCF combinations. Subsequently, we fitted linear mixed-effects models for all response traits that were affected by GCF number. In these models, we included GCF number, community type, eutrophication, and the respective two-way interactions as fixed effects, and plot and GCF combination as random effects. Effects of fixed factors were assessed using type III ANOVA tests (Anova function in the “car” package; Supplementary Table 6).Reporting summaryFurther information on research design is available in the Nature Portfolio Reporting Summary linked to this article. More

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