Ecology

To calculate total root biomass C colonized by AM and EcM fungi, we developed a workflow that combines multiple publicly available datasets to ultimately link fine root stocks to mycorrhizal colonization estimates (Fig. 1). These estimates were individually derived for 881 different spatial units that were constructed by combining 28 different ecoregions, 15 land cover types and six continents. In a given spatial unit, the relationship between the proportion of AM- and EcM-plants aboveground biomass and the proportion of AM- and EcM-associated root biomass depends on the prevalence of distinct growth forms. Therefore, to increase the accuracy of our estimates, calculations were made separately for woody and herbaceous vegetation and combined in the final step and subsequently mapped. Below we detail the specific methodologies we followed within the workflow and the main assumptions and uncertainties associated.Fig. 1Workflow used to create maps of mycorrhizal fine root biomass carbon. The workflow consists of two main steps: (1) Estimation of total fine root stock capable to form mycorrhizal associations with AM and EcM fungi and (2) estimation of the proportion of fine roots colonized by AM and EcM fungi.Full size imageDefinition of spatial unitsAs a basis for mapping mycorrhizal root abundances at a global scale, we defined spatial units based on a coarse division of Bailey’s ecoregions23 After removing regions of permanent ice and water bodies, we included 28 ecoregions defined according to differences in climatic regimes and elevation (deposited at Dryad-Table S1). A map of Bailey’s ecoregions was provided by the Oak Ridge National Laboratory Distributed Active Archive Center24 at 10 arcmin spatial resolution. Due to potential considerable differences in plant species identities, ecoregions that extended across multiple continents were split for each continent. The continent division was based upon the FAO Global Administrative Unit Layers (http://www.fao.org/geonetwork/srv/en/). Finally, each ecoregion-continent combination was further divided according to differences in land cover types using the 2015 Land Cover Initiative map developed by the European Space Agency at 300 m spatial resolution (https://www.esa-landcover-cci.org/). To ensure reliability, non-natural areas (croplands and urban areas), bare areas and water bodies were discarded (Table 1). In summary, a combination of 28 ecoregions, 15 land cover types and six continents were combined to define a total of 881 different spatial units (deposited at Dryad-Table S2). The use of ecoregion/land cover/continent combination provided a much greater resolution than using a traditional biome classification and allowed to account for human-driven transformations of vegetation, the latter based on the land cover data.Table 1 List of land cover categories within the ESA CCI Land Cover dataset, used to assemble maps of mycorrhizal root biomass.Full size tableMycorrhizal fine root stocksTotal root C stocksEstimation of the total root C stock in each of the spatial units was obtained from the harmonized belowground biomass C density maps of Spawn et al.20. These maps are based on continental-to-global scale remote sensing data of aboveground biomass C density and land cover-specific root-to-shoot relationships to generate matching belowground biomass C maps. This product is the best up-to-date estimation of live root stock available. For subsequent steps in our workflow, we distinguished woody and herbaceous belowground biomass C as provided by Spawn et al.20. As the tundra belowground biomass C map was provided without growth form distinction, it was assessed following a slightly different workflow (see Section 2.2.3 for more details). To match the resolution of other input maps in the workflow, all three belowground biomass C maps were scaled up from the original spatial resolution of 10-arc seconds (approximately 300 m at the equator) to 10 arc‐minutes resolution (approximately 18.5 km at the equator) using the mean location of the raster cells as aggregation criterion.As the root biomass C maps do not distinguish between fine and coarse roots and mycorrhizal fungi colonize only the fine fractions of the roots, we considered the fine root fraction to be 88,5% and 14,1% of the total root biomass for herbaceous and woody plants, respectively. These constants represent the mean value of coarse/fine root mass ratios of herbaceous and woody plants provided by the Fine-Root Ecology Database (FRED) (https://roots.ornl.gov/)25 (deposited at Dryad-Table S3). Due to the non-normality of coarse/fine root mass ratios, mean values were obtained from log-transformed data and then back-transformed for inclusion into the workflow.Finally, the belowground biomass C maps consider the whole root system, but mycorrhizal colonization occurs mainly in the upper 30 cm of the soil18. Therefore, we estimated the total fine root stocks in the upper 30 cm by applying the asymptotic equation of vertical root distribution developed by Gale & Grigal26:$$y=1-{beta }^{d}$$where y is the cumulative root fraction from the soil surface to depth d (cm), and β is the fitted coefficient of extension. β values of trees (β = 0.970), shrubs (β = 0.978) and herbs (β = 0.952) were obtained from Jackson et al.27. A mean value was then calculated for trees and shrubs to obtain a woody vegetation β value of 0.974. As a result, we estimated that 54.6% of the total live root of woody vegetation and 77.1% of herbaceous vegetation is stored in the upper 30 cm of the soil. In combination, this allowed deriving fine root C stocks in the upper 30 cm of woody and herbaceous vegetation.The proportion of root stocks colonized by AM and EcMThe proportion of root stock that forms associations with AM or EcM fungi was obtained from the global maps of aboveground biomass distribution of dominant mycorrhizal types published by Soudzilovskaia et al.14. These maps provide the relative abundance of EcM and AM plants based on information about the biomass of grass, shrub and tree vegetation at 10arcmin resolution. To match with belowground root woody plants biomass data, proportions of AM trees and shrubs underlying the maps of Soudzilovskaia et al.14 were summed up to obtain the proportion of AM woody vegetation. The same was done for EcM trees and shrubs.Our calculations are subjected to the main assumption that, within each growth form, the proportion of aboveground biomass associated with AM and EcM fungi reflects the proportional association of AM and EM fungi to belowground biomass. We tested whether root:shoot ratios were significantly different between AM and EcM woody plants (the number of EcM herbaceous plants is extremely small17). Genera were linked to growth form based on the TRY database (https://www.try-db.org/)19 and the mycorrhizal type association based on the FungalRoots database17. Subsequently, it was tested whether root:shoot ratios of genera from the TRY database (https://www.try-db.org/)19 were significantly different for AM vs EcM woody plants. No statistically significant differences (ANOVA-tests p-value = 0.595) were found (Fig. 2).Fig. 2Mean and standar error of root to shoot ratios of AM and EcM woody plant species.Full size imageEstimation of mycorrhizal fine root stocksWe calculated the total biomass C of fine roots that can potentially be colonized by AM or EcM fungi by multiplying the total woody and herbaceous fine root C biomass in the upper 30 cm of the soil by the proportion of AM and EcM of woody and herbaceous vegetation. In the case of tundra vegetation, fine root C stocks were multiplied by the relative abundance of AM and EcM vegetation without distinction of growth forms (for simplicity, this path was not included in Fig. 1, but can be seen in Fig. 3. As tundra vegetation consists mainly of herbs and small shrubs, the distinction between woody and herbaceous vegetation is not essential in this case.Fig. 3Workflow used to create mycorrhizal fine root biomass C maps specific for tundra areas.Full size imageFinally, we obtained the mean value of mycorrhiza growth form fine root C stocks in each of the defined spatial units. These resulted in six independent estimations: AM woody, AM herbaceous, EcM woody, EcM herbaceous, AM tundra and EcM tundra total fine root biomass C (Fig. 4).Fig. 4Fine root biomass stocks capable to form association with AM (a) and EcM (b) fungi for woody, herbaceous and tundra vegetation. Final AM and EcM stock result from the sum of the growth form individual maps. There were no records of fine root biomass of EcM herbaceous vegetation.Full size imageThe intensity of root colonization by mycorrhizal fungiColonization databaseThe FungalRoot database is the largest up-to-date compilation of intensity of root colonization data, providing 36303 species observations for 14870 plant species. Colonization data was filtered to remove occurrences from non-natural conditions (i.e., from plantations, nurseries, greenhouses, pots, etc.) and data collected outside growing seasons. Records without explicit information about habitat naturalness and growing season were maintained as colonization intensity is generally recorded in the growing season of natural habitats. When the intensity of colonization occurrences was expressed in categorical levels, they were converted to percentages following the transformation methods stated in the original publications. Finally, plant species were distinguished between woody and herbaceous species using the publicly available data from TRY (https://www.trydb.org/)19. As a result, 9905 AM colonization observations of 4494 species and 521 EcM colonization observations of 201 species were used for the final calculations (Fig. 5).Fig. 5Number of AM (a) and EcM (b) herbaceous and woody plant species and total observations obtained from FungalRoot database.Full size imageThe use of the mean of mycorrhizal colonization intensity per plant species is based on two main assumptions:

1)

The intensity of root colonization is a plant trait: It is known that the intensity of mycorrhizal infections of a given plant species varies under different climatic and soil conditions28,29, plant age30 and the identity of colonizing fungal species31. However, Soudzilovskaia et al.9 showed that under natural growth conditions the intraspecific variation of root mycorrhizal colonization is lower than interspecific variation, and is within the range of variations in other plant eco-physiological traits. Moreover, recent literature reported a positive correlation between root morphological traits and mycorrhizal colonization, with a strong phylogenetic signature of these correlations32,33. These findings provide support for the use of mycorrhizal root colonization of plants grown in natural conditions as a species-specific trait.

2)

The percentage of root length or root tips colonized can be translated to the percentage of biomass colonized: intensity of root colonization is generally expressed as the proportion of root length colonized by AM fungi or proportion of root tips colonized by EcM fungi (as EcM infection is restricted to fine root tips). Coupling this data with total root biomass C stocks requires assuming that the proportion of root length or proportion of root tips colonized is equivalent to the proportion of root biomass colonized. While for AM colonization this equivalence can be straightforward, EcM colonization can be more problematic as the number of root tips varies between tree species. However, given that root tips represent the terminal ends of a root network34, the proportion of root tips colonized by EcM fungi can be seen as a measurement of mycorrhizal infection of the root system and translated to biomass independently of the number of root tips of each individual. Yet, it is important to stress that estimations of fine root biomass colonized by AM and EcM as provided in this paper might not be directly comparable.

sPlot databaseThe sPlotOpen database21 holds information about the relative abundance of vascular plant species in 95104 different vegetation plots spanning 114 countries. In addition, sPlotOpen provides three partially overlapping resampled subset of 50000 plots each that has been geographically and environmentally balanced to cover the highest plant species variability while avoiding rare communities. From these three available subsets, we selected the one that maximizes the number of spatial units that have at least one vegetation plot. We further checked if any empty spatial unit could be filled by including sPlot data from other resampling subsets.Plant species in the selected subset were classified as AM and EcM according to genus-based mycorrhizal types assignments, provided in the FungalRoot database17. Plant species that could not be assigned to any mycorrhizal type were excluded. Facultative AM species were not distinguished from obligated AM species, and all were considered AM species. The relative abundance of species with dual colonization was treated as 50% AM and 50% ECM. Plant species were further classified into woody and herbaceous species using the TRY database.Estimation of the intensity of mycorrhizal colonizationThe percentage of AM and EcM root biomass colonized per plant species was spatially upscaled by inferring the relative abundance of AM and EcM plant species in each plot. For each mycorrhizal-growth form and each vegetation plot, the relative abundance of plant species was determined to include only the plant species for which information on the intensity of root colonization was available. Then, a weighted mean intensity of colonization per mycorrhizal-growth form was calculated according to the relative abundance of the species featuring that mycorrhizal-growth form in the vegetation plot. Lastly, the final intensity of colonization per spatial unit was calculated by taking the mean value of colonization across all plots within that spatial unit. These calculations are based on 38127 vegetation plots that hold colonization information, spanning 384 spatial units.The use of vegetation plots as the main entity to estimate the relative abundance of AM and EcM plant species in each spatial unit assumes that the plant species occurrences and their relative abundances in the selected plots are representative of the total spatial unit. This is likely to be true for spatial units that are represented by a high number of plots. However, in those spatial units where the number of plots is low, certain vegetation types or plant species may be misrepresented. We addressed this issue in our uncertainty analysis. Details are provided in the Quality index maps section.Final calculation and maps assemblyThe fraction of total fine root C stocks that is colonized by AM and EcM fungi was estimated by multiplying fine root C stocks by the mean root colonization intensity in each spatial unit. This calculation was made separately for tundra, woody and herbaceous vegetation.To generate raster maps based on the resulting AM and EcM fine root biomass C data, we first created a 10 arcmin raster map of the spatial units. To do this, we overlaid the raster map of Bailey ecoregions (10 arcmin resolution)24, the raster of ESA CCI land cover data at 300 m resolution aggregated to 10 arcmin using a nearest neighbour approach (https://www.esa-landcover-cci.org/) and the FAO polygon map of continents (http://www.fao.org/geonetwork/srv/en/), rasterized at 10 arcmin. Finally, we assigned to each pixel the corresponding biomass of fine root colonized by mycorrhiza, considering the prevailing spatial unit. Those spatial units that remained empty due to lack of vegetation plots or colonization data were filled with the mean value of the ecoregion x continent combination.Quality index mapsAs our workflow comprises many different data sources and the extracted data acts in distinct hierarchical levels (i.e plant species, plots or spatial unit level), providing a unified uncertainty estimation for our maps is particularly challenging. Estimates of mycorrhizal fine root C stocks are related mainly to belowground biomass C density maps and mycorrhizal aboveground biomass maps, which have associated uncertainties maps provided by the original publications. In contrast, estimates of the intensity of root colonization in each spatial unit have been associated with three main sources of uncertainties:

1)

The number of observations in the FungalRoot database. The mean species-level intensity of mycorrhizal colonization in the vegetation plots has been associated with a number of independent observations of root colonization for each plant species. We calculated the mean number of observations of each plant species for each of the vegetation plots and, subsequently the mean number of observations (per plant species) from all vegetation plots in each spatial unit. These spatial unit averaged number of observations ranged from 1 to 14 in AM and from 1 to 26 in EcM. A higher number of observations would indicate that the intraspecific variation in the intensity of colonization is better captured and, therefore, the species-specific colonization estimates are more robust.

2)

The relative plant coverage that was associated with colonization data. From the selected vegetation plots, only a certain proportion of plant species could be associated with the intensity of colonization data in FungalRoot database. The relative abundance of the plant species with colonization data was summed up in each vegetation plot. Then, we calculated the average values for each spatial unit. Mean abundance values ranged from 0.3 to 100% in both AM and EcM spatial units. A high number indicates that the dominant plant species of the vegetation plots have colonization data associated and, consequently, the community-averaged intensity of colonization estimates are more robust.

3)

The number of vegetation plots in each spatial unit. Each of the spatial units differs in the number of plots used to calculate the mean intensity of colonization, ranging from 1 to 1583 and from 1 to 768 plots in AM and EcM estimations, respectively. A higher number of plots is associated with a better representation of the vegetation variability in the spatial units, although this will ultimately depend on plot size and intrinsic heterogeneity (i.e., a big but homogeneous spatial unit may need fewer vegetation plots for a good representation than a small but very heterogeneous spatial unit).

We provide independent quality index maps of the spatial unit average of these three sources of uncertainty. These quality index maps can be used to locate areas where our estimates have higher or lower robustness. More

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Real-world dataThe dataset consisted of 2986 observations from 902 freshwater shallow lakes in Denmark and North America (data extracted from the LAGOSNE database on 22 February 2022 via R LAGOSNE package version 2.0.2)56 (Supplementary Fig. 9). The Danish lakes were sampled for one or several years from 1984 to 2020 (data extracted in October 2021 from https://odaforalle.au.dk/main.aspx) (Supplementary Fig. 10). Prerequisites for inclusion in the analysis were that lakes had been sampled for physical and chemical variables at least four times or at least three times over the growing season (May to September) for the Danish or North American lakes, respectively, had a mean depth of less than 3 m and were freshwater. Water chemistry samples were analysed using standard methods and data for total phosphorus (TP), total nitrogen (TN) and chlorophyll-a are included here57. The mean and range of TP, TN and chlorophyll-a for the combined sites is given in Table 1, along with the values for each region separately.To gain a longer-term perspective on the relationship between nutrients and chlorophyll-a, we calculated the across-year averages of the summer means of TP, TN and chlorophyll-a, sequentially increasing numbers of years included in the mean up to a total of a five-year mean, at which point there were only 99 lakes left in the dataset. In calculating the multi-year means we allowed a maximum gap of 2 years between observations (i.e. two observations could cover 3 years) to avoid including time series with too many missing years in between. Hence, only lakes with sufficient numbers of sequential data were included, resulting in a large drop in lake numbers as the length of the multi-year mean increased (Table 2).Numerical methodsDiagnostic tests or proxies of alternative equilibriaWe modelled the response of chlorophyll-a to TP and TN using generalised-linear models58 with Gamma distribution and an identity link on untransformed data for single-year and multiple-year means up to 5-year means. We used the Gamma distribution, as chlorophyll fit this significantly better than a normal or log-normal distribution. We used psuedo R2 of the model along with the patterns of residuals, and finally, we plotted the kernel density of the chlorophyll-a values as diagnostics of the presence, absence or prevalence of alternative equilibria in the simulated and real work data.To test how appropriate these diagnostics or proxies of alternative stable states in terms of how well they identify the existence of alternative stable states in randomly sampled multi-year data, we

1.

Simulated two scenarios for the main manuscript, with and without alternative stable states in the data, which were as close to the real-life data as possible. The results of these scenarios appear in the main text (please see details below in the “Data Simulation” section).

2.

We provide multiple scenarios with different degrees, or prevalence, of alternative stable states in the data, see simulations of alternative stable state scenarios. The results of these scenarios appear in Supplementary note 2.

Hierarchical bootstrap approachThere are a large number of permutations of data, both real-world and simulated, that can provide a mean of the two to five sequential years from each lake in the time series data. It was vital to have a method that selects the data for analysis that provides a valid and comparable representation of both real work and simulated data and the models’ errors. In order to provide this we used a non-parametric hierarchical bootstrap procedure38. The flowchart shows the data preparation and data analysis steps of the hierarchical bootstrap procedure (Fig. 4). In the first step (step 1 in Fig. 4), all possible longer-term means are calculated for each lake. To keep as much data as possible, we decided to allow for up to 2 years of gap in the data between years. Taking the 5-year mean data as an example, if data from a lake existed for the years 1991 and 1994−1997, a 5-year mean would be calculated for the years 1991, 1994, 1995, 1996 and 1997. However, if the time series would contain a larger gap, e.g. data would only exist for the years 1991 and 1995–1998, no 5-year mean could be calculated. After the selection procedure, all the 2-year, 3-year and 5-year means are transferred into a new table (step 2 in Fig. 4).Fig. 4Data preparation and analysis steps of the hierarchical bootstrap procedure.Full size imageThe procedure is the same for each temporal scale from 2-year means to 5-year means. For the example of 5 mean years, lakes are randomly sampled from the full 5-year mean dataset in step 2 (Fig. 4) with replacement up to the number of lakes as in the original dataset, for the 5-year means 99 (step 3a). Here, the same lake can appear multiple times or not at all. This step is common for every bootstrap procedure59. However, since we have nested data (5-year means within lakes), we need a second step, in which for every resampled lake in step 3a, one 5-year mean is chosen (step 3b in Fig. 4). Then the three GLM models are produced from the randomly selected data in step 3c (Fig. 4). These steps are then repeated 1000 times to get a good representation of the uncertainties of the model. To ensure a fair comparison between single-year data and their equivalent multi-year mean data, we repeated the bootstrap procedure with single years only using only the lakes for which we also calculated multi-year means. To take the five-year mean as an example, there were 99 lakes where we could calculate at least one 5-year mean observation. First, we ran the bootstrap procedure to calculate 5-year mean values of TP, TN and chlorophyll-a (1000 times) and then took single years’ values of TP, TN and chlorophyll-a (1000 times) from exactly the same 99 lakes. With this approach, exactly the same datasets with the same lakes and observations within lakes are used for the calculation of the multi-year means and their single-year counterparts, making for a robust analysis. The GLM models did not always converge. If either the TP, TN or TP*TN model with interaction did not converge, the iteration was not used in further analysis. The number of converging models equal for each iteration of random samples is given in the results.The described hierarchical approach is the best way to reflect the structure of the original data. A simple, non-hierarchical bootstrap would favour lakes with more five-year means over lakes with fewer five-year means, simply because these make up a larger part of the data. Furthermore, sampling without replacement at the lake level would result in five-year means from lakes with few data dominating the produced random dataset, as every lake would be sampled every time, which then would result in high model leverage of 5-year means from lakes with less data. In contrast, the hierarchical procedure ensures that every lake has the same chance to end up in the randomly sampled bootstrap, in the second step, it ensures that of each sampled lake, every 5-year mean has the same chance to end up in the random dataset. These notions are in agreement with the findings of an assessment on how to properly resample hierarchical data by non-parametric bootstrap38.Data simulationGeneral approach of simulation assumptions and proceduresWe generated random scatter for the generalised-linear model based on Gamma distributions for two different “populations” of lakes with two different intercepts and slopes. At first, we calculated the linear equations for the two populations:For each population i and j, 99 samples (equalling the number of lakes in real-life data with 5-year means, nlake) were generated with a specific number of data points depending on the scenario (nyear) each, hence nlake = 1−99 for each population of lakes, e.g. with 20 years (nyear = 20) each.We found the real nutrient data to be normally distributed, with total nitrogen (TN) having a range between 0.33 and 4.93 mg/L and a constant coefficient of variation (CV, with a mean CV of 0.35) across this range (the same is true for total phosphorus (TP) at a shorter range). Hence, for each nlake, the x for the nyear = 20 were generated based on the mean range (mean per lake of the real-life data) and CV (0.35) from the real-life TN concentration data, hence with a range of 0.33 to 4.33 mg/L. Therefore the values and random variability of x in the simulations are close to the true values of the TN concentrations. The x is then fed into the linear equations above.To the resulting yi and yj we added random noise based on the Gamma distribution (using the rgamma function in R). We used a Gamma distribution because the Chlorophyll-a concentration also follows a Gamma distribution. The variability of a Gamma distribution is expressed by the shape variable. The variability of chlorophyll-a, its shape value, equals 2.63. This shape value was used in the Gamma distribution of yi and yj. The final calculated yi and yj had therefore a random rate calculated as shape/yi or shape/yj. Hence, their variability in the y dimension was close to the true chlorophyll-a variability.The data from both lake populations were then pooled and randomly sampled using the same hierarchical bootstrap procedure with 500 iterations for the scenarios in the supplementary materials and with 1000 iterations for main text simulation scenarios, which is identical to what was done for the real-world data.Simulation scenarios based on characteristics of real-world dataThe real-world 5-year mean data consisted of 99 lakes with 5–20 years of data for each lake. For the simulation scenario in the main text, we therefore randomly sampled between 5 and 20 data points for each of the 99 simulated lakes based on the x distribution described above. Intercepts and slopes of the simulation, resembled the range of the true data (see scatter plots in Fig. 2 of the main manuscript).In the alternative stable state scenario, we chose two slopes and intercepts for different populations of lakes:

Population i: ai = 0, bi = 40

Population j: aj = 50, bj = 120

We based the slopes and intercepts of the ASS scenarios on the diagnostic combination defined by Scheffer and Carpenter7 which propose an abrupt shift in (a) the time series, (b) the multimodal distribution of states and (c) the dual relationship to a controlling factor. Here, the idea is that an ecosystem will jump from one state to the next at the same (nutrient) conditions (different intercept and/or slope, condition a within ref. 7), where any change in the nutrient will have different effects on algae or macrophytes (best represented by different slope, condition c), resulting in a multimodal distribution of the response (condition b). Hence, simulations are in line with what is predicted for ASS, but we took great lengths to also show other possibilities with the simulations in the Supplementary information to ensure we did not overlook any occasional occurrence of alternative equilibria.Here, the appearance of alternative stable states in the data could happen at any point in the time series of a single lake, or the entire time series could include only one of the two alternative stable states. To accommodate these alternative stable state constellations (for each of which we made a separate simulation scenario, (see Supplementary Note 2, “Simulations of alternative stable state constellations”), we forced the alternative stable state scenario to be constructed of 1/3 of data with one state, 1/3 of data with the second state and 1/3 of data where both alternative states could occur. In the latter case, the alternative stable state appeared after the first 20% but before the last 20% of the time series. Since the variability and range of x (nutrient) and y (chlorophyll -a response) is simulated as close as possible to the real-world data in all scenarios, the measures taken here (variable time series and combination of different alternative stable state scenario constellations) produce a simulation as close to the real-world data as possible. Specifically, we found the real-world nutrient data to be normally distributed, with total nitrogen (TN) having a range between 0.33 and 4.93 mg/L and a constant coefficient of variation (CV, with a mean CV of 0.35) across this range (the same is true for total phosphorus (TP) at a shorter range). Hence, for each simulated lake, the x were generated based on this mean range and CV. Furthermore, the resulting yi and yj were randomised by using a Gamma distribution (using the rgamma function in R). We used a Gamma distribution because the chlorophyll-a concentration also follows a Gamma distribution. The variability of a Gamma distribution is expressed by the shape variable. The variability of chlorophyll-a, its shape value, equals 2.63. This shape value was used in the Gamma distribution of yi and y. The final calculated yi and yj had, therefore a random rate calculated as shape/yi or shape/y. Hence, their variability in the y dimension was close to the true chlorophyll-a variability.For the scenario without alternative stable states, both populations of data had the same intercept and slope:

Population i: ai = 0, bi = 40

Population j: aj = 0, bj = 40.

Please see Supplementary Note 2 for further simulations of different potential constellations of alternative states. There we show that our approach finds alternative stable states in response to nutrient concentration, even if they appear in time series from different lakes.Assessment of diagnostic tests or proxies of alternative equilibriaWe modelled the response of chlorophyll-a to TP and TN using generalised-linear models3 with Gamma distribution and an identity link on untransformed data for single-year and multiple-year means up to 5-year means. We used the Gamma distribution, as chlorophyll fit this significantly better than a normal or log-normal distribution. We used R2 of the model along with the patterns of residuals, and finally, we plotted the kernel density of the chlorophyll-a values as diagnostics of the presence, absence or prevalence of alternative equilibria in the simulated and real work data.The comparison of how the diagnostics/proxies of alternative stable states respond to the variation in the prevalence of alternative equilibria in the simulated datasets provides a robust assessment of their ability to identify both the presence and absence of alternative equilibria. It is the response of these diagnostic tests over time, with the increase in the temporal perspective as more years are added to the mean values of TP, TN and chlorophyll-a, that are key to the identification of the presence and or absence of alternative equilibria in a given dataset. The simulations show that a dataset which contains alternative equilibria will show (1) no improvement in R2 as the temporal perspective of the data increases (more years in the multi-year mean); (2) an increased bimodality in the residuals of the models of nutrients predicting chlorophyll-a will increase as more years are added to the multi-year mean and (3) the kernel density function of chlorophyll-a will display increasingly bimodality as more years are added to the mean. In the absence of alternative equilibria, the patterns differ with an R2, and increase in unimodality of residuals and a consistent unimodal pattern in the kernel density function. Thus, the diagnostic tests provide a robust test of both the presence and absence of alternative equilibria in a given dataset.Alternative stable state assessment for real data with limited data rangeIt could be the case that alternative stable states do not appear in the full dataset but only in a limited TN and TP concentration range. We filtered and re-analyzed the data, only keeping data points within the following two ranges: – TN concentration = 0.5−2 mg/L–TP concentration = 0.05−0.4 mg/L. In the filtered data, 1329 out of the original 2876 single-year data points, 289 out of 1028 3-year mean data points and 212 out of the 864 five-mean year data points remained. The filtered data consisted of data points from 550, 48 and 27 lakes for the single-year data, 3-year means and 5-year means, respectively. The smaller range resulted in lower R² of the models, yet the pattern that multi-year means result in higher R² compared to single-year data was largely consistent, apart from the 5-year mean TN models for which both, the single-year and mean data resulted in very low R² (Supplementary Fig. 6). Furthermore, due to the lower number of samples, the errors of all proxies are higher, making conclusions more difficult than for the full data. Still, we do not see any clear indication of alternative stable states in the scatter plots (two groups of dots are not appearing (Supplementary Fig. 5), the Kernel density plots (or model residuals (Supplementary Fig. 6)). i.e. no signs of bimodality in residuals or Kernel density plots. Please see details on this analysis in the supplementary material.Details and the R code for the steps for the random multi-year sampling can be found in the supplementary materials.Reporting summaryFurther information on research design is available in the Nature Portfolio Reporting Summary linked to this article. More

Game theory is a framework for analysing the outcome of the strategic interaction between decision makers1. The fundamental concept is that of a Nash equilibrium where no player can improve her payoff by a unilateral strategy change. Typically, the Nash equilibrium is considered to be the optimal outcome of a game, however in social dilemmas the individual optimal outcome is at odds with the collective optimal outcome2. This means that one player can improve her payoff at the expense of the other by unilaterally deviating, but if both deviate, they end up with lower payoffs. In this type of games, the mutually beneficial, but non-Nash equilibrium strategy is called cooperation. However, in this context cooperation should not be interpreted as an interest in the welfare of others, as players only aim to secure a high payoff for themselves.In this framework, payoff maximisation is considered to be rational, but when such rational players then seize every opportunity to gain at the opponent’s expense, they may counterintuitively both end up with low payoffs. A game that clearly exhibits this contradiction is the Traveler’s Dilemma. Since its formulation in 1994 by the economist Kaushik Basu3, the game has become one of the most studied in the economics literature. Additionally, it has been discussed in theoretical biology in the context of evolutionary game theory.In general, the dilemma relies on the individuals’ incentive to undercut the opponent. To be more specific, players are motivated to claim a lower value than their opponent to reach a higher payoff at the opponent’s expense. Such incentive leads players to a systematic mutual undercutting until the lowest possible payoff is reached, which is the unique Nash equilibrium. It seems paradoxical that players defined as rational in a game theoretical sense end up with such a poor outcome. Therefore, the question that naturally arises is how can this poor outcome be prevented and how cooperation can be achieved.To address these questions, it can be helpful to better understand price wars, which consist in the mutual undercutting of prices to gain market share. In addition, it can provide information about human behaviour, because economic experiments have shown that individuals prefer to choose the cooperative high payoff action, instead of the Nash equilibrium4.Our analysis focuses on showing that the Traveler’s Dilemma can be decomposed into a local and a global game. If the payoff optimisation is constrained to the local game, then players will inevitably end up in the Nash equilibrium. However, if players escape the local maximisation and optimise their payoff for the global game, they can reach the cooperative high payoff equilibrium.Here, we show that the cooperative equilibrium can be reached in a game like the Traveler’s Dilemma due to diversity, which we define as the presence of suboptimal strategies. The appearance of strategies far from those of the residents allows for the local maximisation process to be escaped, such that an optimisation at a global level takes place. Overall this can lead to cooperation because by considering “suboptimal strategies” that play against each other it is possible to reach higher payoffs, both collectively and individually.GameThe Traveler’s Dilemma is a two-player game. Player i has to choose a claim, (n_i), from the action space, consisting of all integers on the interval [L, U], where (0 le L < U). The payoffs are determined as follows: If both players, i and j, choose the same value ((n_i = n_j)), both get paid that value. There is a reward parameter (R >1), such that if (n_i < n_j), then i receives (n_i + R) and j gets (n_i- R) Thus, the payoff of player i playing against player j is$$begin{aligned} pi _{ij} = {left{ begin{array}{ll} n_i& text { if } n_i = n_j\ n_i + R& text { if } n_i < n_j\ n_j - R& text { if } n_i > n_j end{array}right. } end{aligned}$$
(1)
Thus, a player is better off by choosing a slightly lower value than the opponent: when j plays (n_j), then it is best for i to play (n_j-1). The iteration of this reasoning, which we will call the stairway to hell, leads to the only Nash equilibrium of the game, ({L,L}), where both players choose the lowest possible claim. The classical game theory method to arrive to this equilibrium is called iterative elimination of dominated strategies5.The game can be visualised through its payoff matrix (Fig. 1). For simplicity, we use the values from the original formulation: (L=2), (U=100) and (R=2). The payoff matrix shows that the Traveler’s Dilemma can be decomposed into a local and a global game. Let us begin with the local game. When the action space of the game is reduced to two adjacent actions n and (n+1) (black boxes in Fig. 1), the Traveler’s Dilemma with (R=2) is equivalent to the Prisoner’s Dilemma6. In general, for any value of R, the Traveler’s Dilemma becomes a Prisoner’s Dilemma for any pair of actions n and (n+s), where ( 1 le s le R-1 ). For example, for (R=4) the pair of actions n and (n+1), n and (n+2), n and (n+3) follow the same game structure as the Prisoner’s Dilemma. Therefore, the Traveler’s Dilemma consists of many embedded Prisoners’ Dilemmas. This means that at a local level the game is a Prisoner’s Dilemma.If we now consider actions that are distant from each other in the action space, e.g. 2 and 100, we can observe a coordination game structure (gray boxes in Fig. 1), where ({100,100}) is payoff and risk dominant7,8. In general, any pair of actions n and (n+s), where ( R le s le U-n), construct a coordination game. As a result, the Traveler’s Dilemma becomes a coordination game at a global level, which has different equilibria than the local game.Figure 1Payoff matrix of the Traveler’s Dilemma. Visualisation of the payoff scheme described by Eq. (1). For simplicity, the action space is ( {n_i in {mathbb {N}} mid 2 le n_i le 100}) and the reward parameter is (R=2). The Traveler’s Dilemma can be decomposed into a local and a global game. At a local level the game is a Prisoner’s Dilemma (black boxes). This happens when the action space is reduced to any pair of actions n and (n+s), where ( 1 le s le R-1 ). While at the global level, we can observe a coordination game (gray boxes). This level is defined as any pair of actions n and (n+s), where ( R le s le U-n).Full size imageParadoxSocial dilemmas appear paradoxical in the sense that self-interested competing players, when rationally playing the Nash equilibrium, end up with a payoff that clearly goes against their self-interest. But with the Traveler’s Dilemma, the paradox goes further, as suggested in its original formulation3. Classical game theory proposes ({L,L}) as the Nash equilibrium of the game. However, it seems unlikely and implausible that, with R being moderately low, say (R=2), for individuals to play the Nash equilibrium. This has been confirmed in economic experiments where individuals rather choose values close to the upper bound of the interval. Such experiments have also shown that the chosen value depends on the reward parameter (R), where an increasing value of R shifts players’ decision towards ({L,L})4. Nonetheless, classical game theory states that the Nash equilibrium of the game is independent of R.Consequently, the aim of this paper is to seek and explore simple mechanisms through which the apparent non-rational cooperative behaviour can come about. We also examine the effect of the reward parameter on the game’s outcome. Given that the Traveler’s Dilemma paradox emerges in the classical game theory framework, we analyse the game using evolutionary game theory tools5,9,10. This dynamical approach allows us to explore adaptive behaviour outside of the stationary classical game theory framework. To be more precise, for this approach individuals dynamically adjust their actions according to their payoffs.The key point of course is to understand how the system can converge to high claims. We show that this behaviour is possible because the Traveler’s Dilemma can be decomposed into a local and a global game. If the payoff maximisation is constrained to the local level, then the stairway to hell leads the system to the Nash equilibrium; given that locally the game is a Prisoner’s Dilemma. On the other hand, at a global level the game follows a coordination game structure, where the high claim actions are payoff dominant. Thus, for the system to reach a high claim equilibrium the maximisation process needs to jump from the local to the global level.Our analysis led us to identify the mechanism of diversity as responsible for enabling this jump and preventing players from going down the stairway to hell. This mechanism works on the idea that to reach a high claim equilibrium, players have to benefit from playing a high claim. For a population setting, it means that players need to have the chance to encounter opponents also playing high. From a learning model point of view, it refers to the belief that the opponent will also play high, at least with a certain probability. If the belief is shared by both players, they should both play high and reach the cooperative equilibrium. Here, we explore these two types of models to unveil the mechanism leading to cooperation.Population based models unveil diversity as the cooperative mechanism via the effect of mutations on the game’s outcome. This is shown for the replicator-mutator equation and the Wright–Fisher model. Similarly, a two-player learning model approach, more in line with human reasoning, shows that if players are free to adopt a higher payoff action from a diverse action set during their introspection process, they can reach the cooperative equilibrium. This result is obtained using introspection dynamics.Finally, we explain how diversity is the underlying mechanism that enables the convergence to high claims in previously proposed models. To be more precise, we show that diversity is required because it allows for the maximisation process to jump from the local to the global level. More

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There is a growing impetus to leverage our fundamental understanding of microbial community assembly towards applied problems. With microbes contributing to diverse physiological, biogeochemical, and agricultural processes, the potential to control and optimise microbial communities holds promise for interventions ranging from industrial and environmental remediation to human medicine and biofuel production [1, 2]. Realising this goal is contingent on high fidelity between theory, experiments, and the natural dynamics of target systems.Theoretical and experimental research in microbial community optimisation has largely proceeded along two parallel paths. Theoretical approaches leverage mathematical models and metabolic networks to predict which species combinations are stable and how they can optimise a given function (e.g., maximum biomass, waste degradation or host health) [3,4,5,6,7]. Experimental studies often take a combinatorial approach, iteratively assembling different species combinations in vitro and evaluating their stability and functional attributes [8,9,10,11]. Both theory and experiments are valuable but they are also susceptible to their own modus operandi that may limit their correspondence and their translation to real-world systems. On the one hand, theoretical approaches typically adopt the analytical tractability of steady state dynamics, where microbial consumers and the resources on which they depend are assumed to establish a stable equilibrium. On the other hand, experimental approaches almost exclusively embrace the high-throughput efficiency of serial-batch culture, where consumers and resources are made to fluctuate over several orders of magnitude with each serial passage. This raises an important question: should we expect unity in the composition of optimised communities emerging under continuous resource supply (e.g., chemostat) versus the discrete pulsed resource supply of, for example, serial-batch culture?To explore how microbial community composition varies under contrasting resource supply dynamics, we performed simulations of a classical resource-competition model:$$frac{{dN_i}}{{dt}} = N_ileft( {mathop {sum}limits_{j = 1}^n {mu _{ij}left( {R_j} right) – m} } right)$$
(1)
$$frac{{dR_j}}{{dt}} = {Psi}_jleft( {R_j} right) – mathop {sum }limits_{i = 1}^n Q_{ij}mu _{ij}left( {R_j} right)N_i,$$
(2)
where Ni is the population density of consumer i, Rj is the concentration of resource j, μij(Rj) is the per capita functional response of consumer i, m is the per capita mortality rate due to dilution, Ψj(Rj) is the resource supply function, and Qij is the resource quota of consumer i on resource j (amount of resource per unit consumer). The consumer functional response is given by the Monod function, (mu _{ij}(R_j) = mu _{max_{ij}}frac{{R_j}}{{K_{s_{ij}} + R_j}}) , where (mu _{max_{ij}}) is the maximum growth rate and (K_{s_{ij}}) is the half saturation constant for consumer i on resource j.To set up the simulations, we randomly sampled the parameters of the Monod growth functions, (μmax and Ks) for five species competing for five substitutable resources (essential resources are treated separately in the supplementary information, with similar findings). In one set of parametrisations (n = 100 unique competitor combinations) we used both random μmax and Ks, and in another set (n = 100) we imposed a trade-off in maximum growth rate and substrate affinity (( {frac{{mu _{max}}}{{K_s}}} )) (Fig. 1a). The rationale for imposing a trade-off is that metabolic theory predicts that organisms that invest energy into a high maximum growth rate will have lower substrate affinities and vice versa [12, 13]. To ensure reasonable growth rates relative to the time-scale of resource pulsing, we sampled μmax such that minimum doubling times spanned from 21 to 52 min (when all resources are non-limiting). For each of the random competitor combinations, we simulated resources under continuous or pulsed resource supply with resource replenishment every 1/2, 1, 2, 4, 12, or 24 h. Under pulsed resource supply, Ψj(Rj) and m are removed from Eq. (1) and (2) and replaced by discontinuous resource pulsing and cell transfer at fixed intervals. The total resource flux (and mortality) was held constant under all frequencies of resource supply i.e., less frequent replenishment corresponds to larger resource pulses (see Supplementary Information for full model/simulation specifications).Fig. 1: Quantifying compositional overlap between communities assembled under continuous vs. pulsed resource supply.a Per capita growth responses (Monod functions) from a single iteration of the model assuming a trade-off between maximum growth rate and resource affinity (colours correspond to individual consumers). b Time series of consumers in a under different resource supply regimes. Numbers above individual panels reflect pulsing intervals in hours. The amplitude of population fluctuations increases with longer intervals between pulses, with distinct phases of growth, saturation, and instantaneous mortality visible at a finer temporal resolution (Fig. S10). c Example measure of compositional overlap (Jaccard similarity index) between communities assembled under continuous resource supply (far left panel in b) vs. pulsing every two hours (centre panel in b).Full size imageAfter allowing the competitors to reach a steady state (time-averaged over 24 h under pulsed treatments), we quantified the correspondence between the continuous supply treatment and the pulsed treatments using the Jaccard similarity index, (Jleft( {A,B} right) = frac{{left| {A cap B} right|}}{{left| {A cup B} right|}}) (0 ≤ J(A,B) ≤ 1), where the numerator gives the number of species (max = 5) that persist under continuous (A) and pulsed (B) resource supply, and the denominator gives the number of species (max = 5) that persist under continuous or pulsed resource supply (Fig. 1b, c).Under both sets of simulations (with and without enforcing a trade-off between maximal growth rate and resource affinity), we observe that the similarity in final community composition between continuous and pulsed resource supply decays with increasingly large intervals between resource replenishment (Fig. 2a). When no trade-off is imposed between maximum growth rate and resource affinity (orange line in Fig. 2a) the mean compositional similarity is only 0.68 when resources are pulsed every 2 h and down to 0.41 when resources are pulsed every 24 h (typical of serial-batch culture). The rate of decay in the Jaccard index is more severe when a trade-off is imposed between maximum growth rate and substrate affinity, to the extent that once pulsing intervals reach four hours there is almost zero overlap in community composition (blue line in Fig. 2a).Fig. 2: Impact of resource supply regime on community composition and abundance weighted mean trait values.a Compositional overlap (Jaccard similarity) between communities under continuous versus pulsed resource supply. Orange lines, points and circles denote model parametrisations with random sampling of both μmax and Ks; blue lines, points and circles denote model parametrisations with a trade-off imposed between μmax and resource affinity (( {frac{{mu _{max}}}{{K_s}}} )). Simulation parameters provided in the Supplementary Information. b Mean trait values for affinity and μmax averaged for each consumer across the five resources and weighted by their final abundance at the end of a simulation (cont. = continuous). In both a and b, small points (jittered for clarity) give the result of an individual simulation; large circles indicate the corresponding mean.Full size imageEcological theory provides an intuitive explanation for these observations. When resources are more continuously supplied, the better competitor is the one that can sustain a positive growth rate at the lowest concentrations of a limiting resource (i.e., has a higher resource affinity or lower R* in the language of resource competition theory [14]). In contrast, under increasingly pulsed resource supply, the better competitor is the one that can grow rapidly at higher resource concentrations. Having a high resource affinity (low R*) is of little benefit if resource concentrations fluctuate over large amplitudes because it only confers an ephemeral competitive advantage in the brief period before the resource is completely depleted (ahead of the next resource pulse). Instead, a high maximum growth rate is optimal because it allows the consumer to grow rapidly and quickly deplete a shared limiting resource. This high maximum growth strategy is, however, sub-optimal under continuous resource supply because a low R* strategist can draw the resource down and hold it at a concentration at which the maximum growth strategist is unable to maintain a positive growth rate.Looking at the mean trait values for resource affinity and μmax weighted by each consumer’s final abundance, it is indeed apparent that consumers with a higher affinity (averaged across the five resources) are favoured under continuous resource supply, while consumers with high maximum growth rates are favoured under pulsing intervals of increasing length (Fig. 2b). Enforcing this trade-off, therefore, leads to the rapid decline in compositional similarity we observe under resource pulsing. Notably, it also leads to a richness peak at intermediate pulsing intervals, where these alternative strategies have a higher probability of coexisting [15] (Fig. S1). At the same time, we still observe a decline in compositional similarity when μmax and Ks are randomly sampled independently of each other simply because the trade-off between maximum growth and resource affinity will emerge occasionally by chance. Two experimental tests of microbial community composition under continuous versus pulsed resource supply are consistent with these observations [16, 17].To evaluate the sensitivity of these observations to different assumptions, we ran additional simulations under various alternative model parameterisations and formulations. In brief, comparable trends to those described above are observed when: i) maximum growth rates are faster or slower than those presented in the main text (Figs. S2, S3); ii) all resources are assumed to be essential to growth (following Liebig’s law of the minimum) (Fig. S4); iii) a weaker trade-off is imposed between maximum growth and affinity (Figs. S5, S6); or iv) mortality is continuous rather than intermittent (Figs. S7, S8). We also investigated the relationship between observed compositional overlap and the dynamical stability under continuous resource supply, anticipating that more stable communities would tend to be more resistant to compositional shifts under resource pulsing. The reality appears more nuanced, namely that weaker dynamical stability at the limit of constant resource supply is associated with higher variance in compositional overlap under continuous vs. pulsed conditions (Fig. S9). In other words, systems with weaker stability are less predictable. A wide range of other microbial traits and trade-offs may interact unpredictably with the relationship between resource supply and community composition. The potential modulating role of system instabilities generated by cross-feeding interactions, non-convex trade-off functions, and the evolution of specialist versus generalist strategies present several especially valuable lines of enquiry [18,19,20].Although these observations are germane to any consumer-resource system, our emphasis here is on the emerging field of microbial community optimisation, where the practical implications are especially timely and important; namely, the resource supply regime must be tailored to the community being optimised. For example, wastewater treatment might be more appropriately modelled under continuous resource supply [21], whereas fermented food and beverage production may be more closely allied to the pulsed resource dynamics observed in batch culture [22]. Resource supply might also be manipulated to favourably modify the competitive hierarchy in an existing community (e.g., by regulating the rate of nutrient supply to the gut through meal timing). Indeed, there is emerging evidence that feeding frequency can drive significant changes in gut microbiota composition [23, 24]. Thus, resource supply dynamics should be considered both a constraint in the design of novel microbial communities and as a tuning mechanism for the optimisation of preexisting communities like those found in the human gut. More

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