Detecting Nonadditive Biotic Interactions and Assessing Their Biological Relevance among Temperate Rainforest Trees

AbstractInteractions between and within abiotic and biotic processes generate nonadditive density-dependent effects on species performance that can vary in strength or direction across environments. If ignored, nonadditivities can lead to inaccurate predictions of species responses to environmental and compositional changes. While there are increasing empirical efforts to test the constancy of pairwise biotic interactions along environmental and compositional gradients, few assess both simultaneously. Using a nationwide forest inventory that spans broad ambient temperature and moisture gradients throughout New Zealand, we address this gap by analyzing the diameter growth of six focal tree species as a function of neighbor densities and climate, as well as neighbor × climate and neighbor × neighbor statistical interactions. The most complex model featuring all interaction terms had the highest predictive accuracy. Compared with climate variables, biotic interactions typically had stronger effects on diameter growth, especially when subjected to nonadditivities from local climatic conditions and the density of intermediary species. Furthermore, statistically strong (or weak) nonadditivities could be biologically irrelevant (or significant) depending on whether a species pair typically interacted under average or more extreme conditions. Our study highlights the importance of considering both the statistical potential and the biological relevance of nonadditive biotic interactions when assessing species performance under global change.

Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence

Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.

Trophic tug-of-war: Coexistence mechanisms within and across trophic levels

Ecological communities encompass rich diversity across multiple trophic levels. While modern coexistence theory has been widely applied to understand community assembly, its traditional formalism only allows assembly within a single trophic level. Here, using an expanded definition of niche and fitness differences applicable to multitrophic communities, we study how diversity within and across trophic levels affects species coexistence. If each trophic level is analysed separately, both lower- and higher trophic levels are governed by the same coexistence mechanisms. In contrast, if the multitrophic community is analysed as a whole, different trophic levels are governed by different coexistence mechanisms: coexistence at lower trophic levels is predominantly limited by fitness differences, whereas coexistence at higher trophic levels is predominantly limited by niche differences. This dichotomy in coexistence mechanisms is supported by theoretical derivations, simulations of phenomenological and trait-based models, and a case study of a primeval forest ecosystem. Our work provides a general and testable prediction of coexistence mechanism operating in multitrophic communities.

Intransitivity in plant-soil feedbacks is rare but is associated with multispecies coexistence

Although plant-soil feedback (PSF) is being recognized as an important driver of plant recruitment, our understanding of its role in species coexistence in natural communities remains limited by the scarcity of experimental studies on multispecies assemblages. Here, we experimentally estimated PSFs affecting seedling recruitment in 10 co-occurring Mediterranean woody species. We estimated weak but significant species-specific feedback. Pairwise PSFs impose similarly strong fitness differences and stabilizing-destabilizing forces, most often impeding species coexistence. Moreover, a model of community dynamics driven exclusively by PSFs suggests that few species would coexist stably, the largest assemblage with no more than six species. Thus, PSFs alone do not suffice to explain coexistence in the studied community. A topological analysis of all subcommunities in the interaction network shows that full intransitivity (with all species involved in an intransitive loop) would be rare but it would lead to species coexistence through either stable or cyclic dynamics.

Eutrophication increases the similarity of cyanobacterial community features in lakes and reservoirs

Eutrophication of inland waters is a mostly anthropogenic phenomenon impacting aquatic biodiversity worldwide, and might change biotic community structure and ecosystem functions. However, little is known about the patterns of cyanobacterial community variations and changes both on alpha and beta diversity levels in response to eutrophication. Here, we investigated cyanobacterial communities sampled at 140 sites from 59 lakes and reservoirs along a strong eutrophication gradient in eastern China through using CPC-IGS and 16S rRNA gene amplicon sequencing. We found that taxonomic diversity increased, but phylogenetic diversity decreased significantly along the eutrophication gradient. Both niche width and niche overlap of cyanobacteria significantly decreased from low- to high-nutrient waterbodies. Cyanobacterial community distance-decay relationship became weaker from mesotrophic to hypereutrophic waterbodies, while ecological uniqueness (i.e., local contributions to beta diversity) tended to increase in high-nutrient waterbodies. Latitude and longitude were more important in shaping cyanobacterial community structure than other environmental variables. These findings suggest that eutrophication affects alpha and beta diversity of cyanobacterial communities, leading to increasingly similar community structures in lakes and reservoirs with a higher level of eutrophication. Our work highlights how cyanobacterial communities respond to anthropogenic eutrophication and calls for an urgent need to develop conservation and management strategies to control lake eutrophication and protect freshwater biodiversity.

Building modern coexistence theory from the ground up: The role of community assembly

Modern coexistence theory (MCT) is one of the leading methods to understand species coexistence. It uses invasion growth rates-the average, per-capita growth rate of a rare species-to identify when and why species coexist. Despite significant advances in dissecting coexistence mechanisms when coexistence occurs, MCT relies on a 'mutual invasibility' condition designed for two-species communities but poorly defined for species-rich communities. Here, we review well-known issues with this component of MCT and propose a solution based on recent mathematical advances. We propose a clear framework for expanding MCT to species-rich communities and for understanding invasion resistance as well as coexistence, especially for communities that could not be analysed with MCT so far. Using two data-driven community models from the literature, we illustrate the utility of our framework and highlight the opportunities for bridging the fields of community assembly and species coexistence.

The unimodal intransitivity-fertility relationship is not mediated by demographic trade-offs in a subtropical forest

Intransitive competition has long been acknowledged as a potential mechanism favoring species coexistence. However, its prevalence, variance along environmental gradients, and possible underlying mechanisms (trade-offs) in plant communities (especially in forests) has seldom been examined. A recently developed "reverse-engineering" approach based on Markov Chain allowed us to estimate the competitive transition matrices and competitive intransitivity from observational abundance data. Using this approach, we estimated competitive intransitivity of five dominant species in a subtropical forest and then related it to soil fertility (soil organic matter and soil pH) and demographic trade-offs (growth-survival and stature-recruitment trade-offs). In our forest plot, intransitive competition was common among the dominant species and peaked at the intermediate level of soil organic matter. Neither the growth-survival trade-off nor the stature-recruitment trade-off was positively related to competitive intransitivity. Our study for the first time empirically supported the unimodal intransitivity-fertility relationship in forests, which, however, was not mediated by the two demographic trade-offs in our plot.

Mechanistic Models of Trophic Interactions: Opportunities for Species Richness and Challenges for Modern Coexistence Theory

AbstractMany potential mechanisms promote species coexistence, but we know little about their relative importance. To compare multiple mechanisms, we modeled a two-trophic planktonic food web based on mechanistic species interactions and empirically measured species traits. We simulated thousands of possible communities under realistic and altered interaction strengths to assess the relative importance of three potential drivers of phytoplankton and zooplankton species richness: resource-mediated coexistence mechanisms, predator-prey interactions, and trait trade-offs. Next, we computed niche and fitness differences of competing zooplankton to obtain a deeper understanding of how these mechanisms determine species richness. We found that predator-prey interactions were the most important driver of phytoplankton and zooplankton species richness and that large zooplankton fitness differences were associated with low species richness, but zooplankton niche differences were not associated with species richness. However, for many communities we could not apply modern coexistence theory to compute niche and fitness differences of zooplankton because of conceptual issues with the invasion growth rates arising from trophic interactions. We therefore need to expand modern coexistence theory to fully investigate multitrophic-level communities.

A spatially explicit trait-based approach uncovers changes in assembly processes under warming

The re-assembly of plant communities during climate warming depends on several concurrent processes. Here, we present a novel framework that integrates spatially explicit sampling, plant trait information and a warming experiment to quantify shifts in these assembly processes. By accounting for spatial distance between individuals, our framework allows separation of potential signals of environmental filtering from those of different types of competition. When applied to an elevational transplant experiment in the French Alps, we found common signals of environmental filtering and competition in all communities. Signals of environmental filtering were generally stronger in alpine than in subalpine control communities, and warming reduced this filter. Competition signals depended on treatments and traits: Symmetrical competition was dominant in control and warmed alpine communities, while hierarchical competition was present in subalpine communities. Our study highlights how distance-dependent frameworks can contribute to a better understanding of transient re-assembly dynamics during environmental change.

Effects of Stage Structure on Coexistence: Mixed Benefits

The properties of competition models where all individuals are identical are relatively well-understood; however, juveniles and adults can experience or generate competition differently. We study here less well-known structured competition models in discrete time that allow multiple life history parameters to depend on adult or juvenile population densities. A numerical study with Ricker density-dependence suggested that when competition coefficients acting on juvenile survival and fertility reflect opposite competitive hierarchies, stage structure could foster coexistence. We revisit and expand those results. First, through a Beverton-Holt two-species juvenile-adult model, we confirm that these findings do not depend on the specifics of density-dependence or life cycles, and obtain analytical expressions explaining how this coexistence emerging from stage structure can occur. Second, we show using a community-level sensitivity analysis that such emergent coexistence is robust to perturbations of parameter values. Finally, we ask whether these results extend from two to many species, using simulations. We show that they do not, as coexistence emerging from stage structure is only seen for very similar life-history parameters. Such emergent coexistence is therefore not likely to be a key mechanism of coexistence in very diverse ecosystems, although it may contribute to explaining coexistence of certain pairs of intensely competing species.

Compensatory responses of vital rates attenuate impacts of competition on population growth and promote coexistence

Competition is among the most important factors regulating plant population and community dynamics, but we know little about how different vital rates respond to competition and jointly determine population growth and species coexistence. We conducted a field experiment and parameterised integral projection models to model the population growth of 14 herbaceous plant species in the absence and presence of neighbours across an elevation gradient (284 interspecific pairs). We found that suppressed individual growth and seedling establishment contributed the most to competition-induced declines in population growth, although vital rate contributions varied greatly between species and with elevation. In contrast, size-specific survival and flowering probability and seed production were frequently enhanced under competition. These compensatory vital rate responses were nearly ubiquitous (occurred in 92% of species pairs) and significantly reduced niche overlap and stabilised coexistence. Our study highlights the importance of demographic processes for regulating population and community dynamics, which has often been neglected by classic coexistence theories.

Effects of abiotic heterogeneity on species densities and interaction strengths lead to different spatial biodiversity patterns

During community assembly, abiotic factors can influence species at multiple stages during their life history, for example by affecting early settlement or establishment probabilities and thus initial densities (route 1: abiotic effects on density), or later by affecting the strength of biotic interactions during subsequent life stages (route 2: abiotic effects on interaction strengths). Since real abiotic landscapes are multivariate and complex, how these two distinct routes of abiotic influence affect community patterns has not been quantified. Using an individual-based spatially explicit simulation model, we compared scenarios where abiotic conditions shaped initial densities, interaction strengths, or both, of plant species with unique abiotic niches. We then partitioned the effect of the abiotic landscape on community patterns into components arising from variable density, variable interaction strengths, and their interaction. Even when plants responded to identical landscapes, variable density and variable interaction strengths led to different community patterns, and their combined effects were non-additive. Variable density promoted more spatial structure, while variable interaction strengths promoted higher local species richness. We highlight important implications these findings have in applied plant community ecology.

Does deterministic coexistence theory matter in a finite world?

Contemporary studies of species coexistence are underpinned by deterministic models that assume that competing species have continuous (i.e., noninteger) densities, live in infinitely large landscapes, and coexist over infinite time horizons. By contrast, in nature, species are composed of discrete individuals subject to demographic stochasticity and occur in habitats of finite size where extinctions occur in finite time. One consequence of these discrepancies is that metrics of species' coexistence derived from deterministic theory may be unreliable predictors of the duration of species coexistence in nature. These coexistence metrics include invasion growth rates and niche and fitness differences, which are now commonly applied in theoretical and empirical studies of species coexistence. In this study, we tested the efficacy of deterministic coexistence metrics on the duration of species coexistence in a finite world. We introduce new theoretical and computational methods to estimate coexistence times in stochastic counterparts of classic deterministic models of competition. Importantly, we parameterized this model using experimental field data for 90 pairwise combinations of 18 species of annual plants, allowing us to derive biologically informed estimates of coexistence times for a natural system. Strikingly, we found that for species expected to deterministically coexist, community sizes containing only 10 individuals had predicted coexistence times of more than 1000 years. We also found that invasion growth rates explained 60% of the variation in intrinsic coexistence times, reinforcing their general usefulness in studies of coexistence. However, only by integrating information on both invasion growth rates and species' equilibrium population sizes could most (>99%) of the variation in species coexistence times be explained. This integration was achieved with demographically uncoupled single-species models solely determined by the invasion growth rates and equilibrium population sizes. Moreover, because of a complex relationship between niche overlap/fitness differences and equilibrium population sizes, increasing niche overlap and increasing fitness differences did not always result in decreasing coexistence times, as deterministic theory would predict. Nevertheless, our results tend to support the informed use of deterministic theory for understanding the duration of species' coexistence while highlighting the need to incorporate information on species' equilibrium population sizes in addition to invasion growth rates.

Contrasting effects of dispersal network heterogeneity on ecosystem stability in rock-paper-scissors games

Intransitive competition, typically represented by the classic rock-paper-scissors game, provides an endogenous mechanism promoting species coexistence. As well known, species dispersal and interaction in nature might occur on complex patch networks, with species interacting in diverse ways. However, the effects of different interaction modes, combined with spatial heterogeneity in patch connectivities, have not been well integrated into our general understanding of how stable coexistence emerges in cyclic competition. We thus incorporate network heterogeneity into the classic rock-paper-scissors game, in order to compare ecosystem stability under two typical modes of interaction: species compete to fill empty sites, and species seize each other’s colony sites. On lattice-structured regular networks, the two interaction modes produce similar stability patterns through forming conspecific clusters to reduce interspecific competition. However, for heterogeneous networks, the interaction modes have contrasting effects on ecosystem stability. Specifically, if species compete for colony sites, increasing network heterogeneity stabilizes competitive dynamics. When species compete to fill empty sites, an increase in network heterogeneity leads to larger population fluctuations and therefore a higher risk of stochastic extinctions, in stark contrast to current knowledge. Our findings strongly suggest that particular attention should be devoted to testing which mode of interaction is more appropriate for modeling a given system.

Enhancing nutritional niche and host defenses by modifying the gut microbiome

The gut microbiome is essential for processing complex food compounds and synthesizing nutrients that the host cannot digest or produce, respectively. New model systems are needed to study how the metabolic capacity provided by the gut microbiome impacts the nutritional status of the host, and to explore possibilities for altering host metabolic capacity via the microbiome. Here, we colonized the nematode Caenorhabditis elegans gut with cellulolytic bacteria that enabled C. elegans to utilize cellulose, an otherwise indigestible substrate, as a carbon source. Cellulolytic bacteria as a community component in the worm gut can also support additional bacterial species with specialized roles, which we demonstrate by using Lactobacillus plantarum to protect C. elegans against Salmonella enterica infection. This work shows that engineered microbiome communities can be used to endow host organisms with novel functions, such as the ability to utilize alternate nutrient sources or to better fight pathogenic bacteria.

Towards a heuristic understanding of the storage effect

The storage effect is a general explanation for coexistence in a variable environment. Unfortunately, the storage effect is poorly understood, in part because the generality of the storage effect precludes an interpretation that is simultaneously simple, intuitive and correct. Here, we explicate the storage effect by dividing one of its key conditions-covariance between environment and competition-into two pieces, namely that there must be a strong causal relationship between environment and competition, and that the effects of the environment do not change too quickly. This finer-grained definition can explain a number of previous results, including (1) that the storage effect promotes annual plant coexistence when the germination rate fluctuates, but not when the seed yield fluctuates, (2) that the storage effect is more likely to be induced by resource competition than the apparent competition, and (3) why the storage effect arises readily in models with either stage structure or environmental autocorrelation. Additionally, our expanded definition suggests two novel mechanisms by which the temporal storage effect can arise-transgenerational plasticity and causal chains of environmental variables-thus suggesting that the storage effect is a more common phenomenon than previously thought.

Deciphering the diversity patterns and community assembly of rare and abundant bacterial communities in a wetland system

Water microorganisms that have distinct contributions to community dynamics, including many rare taxa and few abundant taxa, are crucial to the wetland ecosystem functions. In this study, we comprehensively investigated the diversity patterns and assembly processes of rare and abundant taxa to strengthen our understanding of ecosystem function and diversity in a wetland system. The results showed that TN and NH₃-N were the most significant factors affecting the community structure in this wetland. Functional Annotation of Prokaryotic Taxa (FAPROTAX) revealed that functions associated with nitrogen removal were the most prevalent metabolic pathways in samples of regenerated wetland (RW). Co-occurrence network analysis revealed that nonrare taxa exhibited more interactions with rare taxa than with conspecifics and some microbial hubs belonged to rare taxa, which might play an instrumental role in maintaining the stability of the community structure. We found that the assembly of rare taxa with a lower niche breadth was mainly governed by homogeneous selection, implying that their higher sensitivity of these to environmental disturbances and changes in TN played significant roles in community assembly of rare taxa. In contrast, the assembly of abundant taxa with higher niche breadth was dominated by stochastic processes (undominated process and dispersal limitation) indicating that abundant taxa had greater responsibility for maintaining community structure when exposed to environmental fluctuations. These results broaden our understanding of the microbial structure, interactions and ecological assembly mechanisms underlying microbial dynamics in aquatic ecosystems, which are crucial for the management of microorganisms in the wetlands.

Temporally auto-correlated predator attacks structure ecological communities

For species primarily regulated by a common predator, the P* rule of Holt & Lawton (Holt & Lawton, 1993. Am. Nat.142, 623–645. (doi:10.1086/285561)) predicts that the prey species that supports the highest mean predator density (P*) excludes the other prey species. This prediction is re-examined in the presence of temporal fluctuations in the vital rates of the interacting species including predator attack rates. When the fluctuations in predator attack rates are temporally uncorrelated, the P* rule still holds even when the other vital rates are temporally auto-correlated. However, when temporal auto-correlations in attack rates are positive but not too strong, the prey species can coexist due to the emergence of a positive covariance between predator density and prey vulnerability. This coexistence mechanism is similar to the storage effect for species regulated by a common resource. Negative or strongly positive auto-correlations in attack rates generate a negative covariance between predator density and prey vulnerability and a stochastic priority effect can emerge: with non-zero probability either prey species is excluded. These results highlight how temporally auto-correlated species’ interaction rates impact the structure and dynamics of ecological communities.

Accounting for demographic uncertainty increases predictions for species coexistence: A case study with annual plants

Natural systems contain more complexity than is accounted for in models of modern coexistence theory. Coexistence modelling often disregards variation arising from stochasticity in biological processes, heterogeneity among individuals and plasticity in trait values. However, these unaccounted‐for sources of uncertainty are likely to be ecologically important and have the potential to impact estimates of coexistence. We applied a Bayesian modelling framework to data from an annual plant community in Western Australia to propagate uncertainty in coexistence outcomes using the invasion criterion and ratio of niche to fitness differences. We found accounting for this uncertainty altered predictions of coexistence versus competitive exclusion for 3 out of 14 species pairs and yielded a probability of priority effects for an additional species pair. The propagation of uncertainty arising from sources of biological complexity improves our ability to predict coexistence more accurately in natural systems.

From surviving to thriving, the assembly processes of microbial communities in stone biodeterioration: A case study of the West Lake UNESCO World Heritage area in China

Serious concerns regarding stone biodeterioration have been raised due to the loss of aesthetic value and hidden dangers in stone cultural heritages and buildings. Stone biodeterioration involves a complex ecological interplay among organisms, however, the ecological mechanisms (deterministic or stochastic processes) that determine the microbial community on stone remain poorly understood. Here, using both amplicon and shotgun metagenomic sequencing approaches, we comprehensively investigated the biodiversity, assembly, and function of communities (including prokaryotes, fungi, microfauna, and plants) on various types of deteriorating limestone across different habitats in Feilaifeng. By generalizing classic ecological models to stone habitats, we further uncovered and quantified the mechanisms underlying microbial community assembly processes and microbial interactions within the biodeteriorated limestone. Community profiling revealed stable ecosystem functional potential despite high taxonomic variation across different biodeterioration types, suggesting non-random community assembly. Increased niche differentiation occurred in prokaryotes and fungi but not in microfauna and plant during biodeterioration. Certain microbial groups such as nitrifying archaea and bacteria showed wider niche breadth and likely contributing to the initiation, succession and expansion of stone biodeterioration. Consistently, prokaryotes were more strongly structured by selection-based deterministic processes, while micro-eukaryotes were more influenced by dispersal and drift-based stochastic processes. Importantly, microbial coexistence maintains network robustness within stone microbiotas, highlighting mutual cooperation among functional microorganisms. These results provide new insights into microbial community assembly mechanisms in stone ecosystems and may aid in the sustainable conservation of stone materials of interest.

Seed banks can help to maintain the diversity of interacting phytoplankton species

Seed formation is part of the reproductive cycle, leading to the accumulation of resistance stages that can withstand harsh environmental conditions for long periods of time. At the community level, multiple species with such long-lasting life stages can be more likely to coexist. While the implications of this process for biodiversity have been studied in terrestrial plants, seed banks are usually neglected in phytoplankton multispecies dynamic models, in spite of widespread empirical evidence for such seed banks. In this study, we build a metacommunity model of interacting phytoplankton species, including a resting stage supplying the seed bank. The model is parameterized with empirically-driven growth rate functions and field-based interaction estimates, which include both facilitative and competitive interactions. Exchanges between compartments (coastal pelagic cells, coastal resting cells on the seabed, and open ocean pelagic cells) are controlled by hydrodynamical parameters to which the sensitivity of the model is assessed. We consider two models, i.e., with and without a saturating effect of the interactions on the growth rates. Our results are consistent between models, and show that a seed bank allows to maintain all species in the community over 30 years. Indeed, a fraction of the species are vulnerable to extinction at specific times within the year, but this process is buffered by their survival in their resting stage. We thus highlight the potential role of the seed bank in the recurrent re-invasion of the coastal community, and of coastal environments in re-seeding oceanic regions. Moreover, the seed bank enables populations to tolerate stronger interactions within the community as well as more severe changes in the environment, such as those predicted within a climate change context. Our study therefore shows how a resting stage may help phytoplanktonic diversity maintenance.

Non-additive biotic interactions improve predictions of tropical tree growth and impact community size structure

Growth in individual size or biomass is a key demographic component in population models, with wide-ranging applications from quantifying species performance across abiotic or biotic conditions to assessing landscape-level dynamics under global change. In forest ecology, the responses of tree growth to biotic interactions are widely held to be crucial for understanding forest diversity, function, and structure. To date, most studies on plant-plant interactions only examine the additive competitive or facilitative interactions between species pairs; however, there is increasing evidence of non-additive, higher-order interactions (HOIs) impacting species demographic rates. When HOIs are present, the dynamics of a multispecies community cannot be fully understood or accurately predicted solely from pairwise outcomes because of how additional species "interfere" with the direct, pairwise interactions. Such HOIs should be particularly prevalent when species show non-linear functional responses to resource availability and resource-acquisition traits themselves are density dependent. With this in mind, we used data from a tropical secondary forest-a system that fulfills both of these conditions-to build an ontogenetic diameter growth model for individuals across 10 woody-plant species. We allowed both direct and indirect interactions within communities to influence the species-specific growth parameters in a generalized Lotka-Volterra model. Specifically, indirect interactions entered the model as higher-order quadratic terms, i.e., non-additive effects of conspecific and heterospecific neighbor size on the focal individual's growth. For the whole community and for four out of 10 focal species, the model that included HOIs had more statistical support than the model that included only direct interactions, despite the former containing a far greater number of parameters. HOIs had comparable effect sizes to direct interactions, and tended to further reduce the diameter growth rates of most species beyond what direct interactions had already reduced. In a simulation of successional stand dynamics, the inclusion of HOIs led to rank swaps in species' diameter hierarchies, even when community-level size distributions remained qualitatively similar. Our study highlights the implications, and discusses possible mechanisms, of non-additive density dependence in highly diverse and light-competitive tropical forests.

Species richness increases fitness differences, but does not affect niche differences

A key question in ecology is what limits species richness. Modern coexistence theory presents the persistence of species as a balance between niche differences and fitness differences that favour and hamper coexistence, respectively. With most applications focusing on species pairs, however, we know little about if and how this balance changes with species richness. Here, we apply recently developed definitions of niche and fitness differences, based on invasion analysis, to multispecies communities. We present the first mathematical proof that, for invariant average interaction strengths, the average fitness difference among species increases with richness, while the average niche difference stays constant. Extensive simulations with more complex models and analyses of empirical data confirmed these mathematical results. Combined, our work suggests that, as species accumulate in ecosystems, ever-increasing fitness differences will at some point exceed constant niche differences, limiting species richness. Our results contribute to a better understanding of coexistence multispecies communities.

Intraspecific variation mediates density dependence in a genetically diverse plant species

Interactions between neighboring plants are critical for biodiversity maintenance in plant populations and communities. Intraspecific trait variation and genome duplication are common in plant species and can drive eco-evolutionary dynamics through genotype-mediated plant-plant interactions. However, few studies have examined how species-wide intraspecific variation may alter interactions between neighboring plants. We investigate how subspecies and ploidy variation in a genetically diverse species, big sagebrush (Artemisia tridentata), can alter the demographic outcomes of plant interactions. Using a replicated, long-term common garden experiment that represents range-wide diversity of A. tridentata, we ask how intraspecific variation, environment, and stand age mediate neighbor effects on plant growth and survival. Spatially explicit models revealed that ploidy variation and subspecies identity can mediate plant-plant interactions but that the effect size varied in time and across experimental sites. We found that demographic impacts of neighbor effects were strongest during early stages of stand development and in sites with greater growth rates. Within subspecies, tetraploid populations showed greater tolerance to neighbor crowding compared to their diploid variants. Our findings provide evidence that intraspecific variation related to genome size and subspecies identity impacts spatial demography in a genetically diverse plant species. Accounting for intraspecific variation in studies of conspecific density dependence will improve our understanding of how local populations will respond to novel genotypes and biotic interaction regimes. As introduction of novel genotypes into local populations becomes more common, quantifying demographic processes in genetically diverse populations will help predict long-term consequences of plant-plant interactions.

Beyond direct neighbourhood effects: higher-order interactions improve modelling and predicting tree survival and growth

It is known that biotic interactions are the key to species coexistence and maintenance of species diversity. Traditional studies focus overwhelmingly on pairwise interactions between organisms, ignoring complex higher-order interactions (HOIs). In this study, we present a novel method of calculating individual-level HOIs for trees, and use this method to test the importance of size- and distance-dependent individual-level HOIs to tree performance in a 25-ha temperate forest dynamic plot. We found that full HOI-inclusive models improved our ability to model and predict the survival and growth of trees, providing empirical evidence that HOIs strongly influence tree performance in this temperate forest. Specifically, assessed HOIs mitigate the competitive direct effects of neighbours on survival and growth of focal trees. Our study lays a foundation for future investigations of the prevalence and relative importance of HOIs in global forests and their impact on species diversity.

Positively and Negatively Autocorrelated Environmental Fluctuations Have Opposing Effects on Species Coexistence

AbstractEnvironmental fluctuations can mediate coexistence between competing species via the storage effect. This fluctuation-dependent coexistence mechanism requires three conditions: (i) there is a positive covariance between species responses to environmental conditions and the strength of competition, (ii) there are species-specific environmental responses, and (iii) species are less sensitive to competition in environmentally unfavorable years. In serially uncorrelated environments, condition (i) occurs only if favorable environmental conditions immediately and directly increase the strength of competition. For many demographic parameters, this direct link between favorable years and competition may not exist. Moreover, many environmental variables are temporal autocorrelated, but theory has largely focused on serially uncorrelated environments. To address this gap, a model of competing species in autocorrelated environments is analyzed. This analysis shows that positive autocorrelations in demographic rates that increase fitness (e.g., maximal fecundity or adult survival) produce the positive environment-competition covariance in condition (i). Hence, when these demographic rates contribute to buffered population growth, positive temporal autocorrelations generate a storage effect; otherwise, they destabilize competitive interactions. For negatively autocorrelated environments, this theory highlights an alternative stabilizing mechanism that requires three conditions: (i') there is a negative environment-competition covariance, (ii) there are species-specific environmental responses, and (iii') species are less sensitive to competition in more favorable years. When the conditions for either of these stabilizing mechanisms are violated, temporal autocorrelations can generate stochastic priority effects or hasten competitive exclusion. Collectively, these results highlight that temporal autocorrelations in environmental conditions can play a fundamental role in determining ecological outcomes of competing species.

Experimental evidence of the importance of multitrophic structure for species persistence

Ecological theory predicts that species interactions embedded in multitrophic networks shape the opportunities for species to persist. However, the lack of experimental support of this prediction has limited our understanding of how species interactions occurring within and across trophic levels simultaneously regulate the maintenance of biodiversity. Here, we integrate a mathematical approach and detailed experiments in plant-pollinator communities to demonstrate the need to jointly account for species interactions within and across trophic levels when estimating the ability of species to persist. Within the plant trophic level, we show that the persistence probability of plant species increases when introducing the effects of plant-pollinator interactions. Across trophic levels, we show that the persistence probabilities of both plants and pollinators exhibit idiosyncratic changes when experimentally manipulating the multitrophic structure. Importantly, these idiosyncratic effects are not recovered by traditional simulations. Our work provides tractable experimental and theoretical platforms upon which it is possible to investigate the multitrophic factors affecting species persistence in ecological communities.

Demographic effects of interacting species: exploring stable coexistence under increased climatic variability in a semiarid shrub community

Population persistence is strongly determined by climatic variability. Changes in the patterns of climatic events linked to global warming may alter population dynamics, but their effects may be strongly modulated by biotic interactions. Plant populations interact with each other in such a way that responses to climate of a single population may impact the dynamics of the whole community. In this study, we assess how climate variability affects persistence and coexistence of two dominant plant species in a semiarid shrub community on gypsum soils. We use 9 years of demographic data to parameterize demographic models and to simulate population dynamics under different climatic and ecological scenarios. We observe that populations of both coexisting species may respond to common climatic fluctuations both similarly and in idiosyncratic ways, depending on the yearly combination of climatic factors. Biotic interactions (both within and among species) modulate some of their vital rates, but their effects on population dynamics highly depend on climatic fluctuations. Our results indicate that increased levels of climatic variability may alter interspecific relationships. These alterations might potentially affect species coexistence, disrupting competitive hierarchies and ultimately leading to abrupt changes in community composition.

Frequency-dependent tree growth depends on climate

Climate and competition interact to affect species' performance, such as growth and survival, and help determine species distributions and coexistence. However, it is unclear how climatic conditions modulate frequency-dependent performance, that is, how performance changes as a species becomes locally rare or common. This is critical because declines in performance as a species becomes more common (negative frequency dependence) is a signature of niche differences among species that stabilize coexistence, whereas positive frequency dependence leads to priority effects and hampers species coexistence. Here, we used dendrochronology and hierarchical models to test whether frequency-dependent growth of sugar pine (Pinus lambertiana) depends on climatic conditions. We found that growth rates were strongly dependent on annual precipitation, but no frequency dependence was evident across all years. However, there was a strong interaction between precipitation and frequency dependence, revealing stabilizing niche differences in dry years but positive frequency dependence in wet years. These differences emerged because of precipitation-driven changes in the direction and strength of both con- and heterospecific competition. Overall, these results show how stabilizing and destabilizing effects can be temporally dynamic for long-lived species and interact with climate variation.

Is Variation in Conspecific Negative Density Dependence Driving Tree Diversity Patterns at Large Scales?

Half a century ago, Janzen and Connell hypothesized that the high tree species diversity in tropical forests is maintained by specialized natural enemies. Along with other mechanisms, these can cause conspecific negative density dependence (CNDD) and thus maintain species diversity. Numerous studies have measured proxies of CNDD worldwide, but doubt about its relative importance remains. We find ample evidence for CNDD in local populations, but methodological limitations make it difficult to assess if CNDD scales up to control community diversity and thereby local and global biodiversity patterns. A combination of more robust statistical methods, new study designs, and eco-evolutionary models are needed to provide a more definite evaluation of the importance of CNDD for geographic variation in plant species diversity.

Dispersal network heterogeneity promotes species coexistence in hierarchical competitive communities

Understanding the mechanisms of biodiversity maintenance is a fundamental issue in ecology. The possibility that species disperse within the landscape along differing paths presents a relatively unexplored mechanism by which diversity could emerge. By embedding a classical metapopulation model within a network framework, we explore how access to different dispersal networks can promote species coexistence. While it is clear that species with the same demography cannot coexist stably on shared dispersal networks, we find that coexistence is possible on unshared networks, as species can surprisingly form self-organised clusters of occupied patches with the most connected patches at the core. Furthermore, a unimodal biodiversity response to an increase in species colonisation rates or average patch connectivity emerges in unshared networks. Increasing network size also increases species richness monotonically, producing characteristic species-area curves. This suggests that, in contrast to previous predictions, many more species can co-occur than the number of limiting resources.

Biotic rescaling reveals importance of species interactions for variation in biodiversity responses to climate change

Generality in understanding biodiversity responses to climate change has been hampered by substantial variation in the rates and even directions of response to a given change in climate. We propose that such context dependencies can be clarified by rescaling climate gradients in terms of the underlying biological processes, with biotic interactions as a particularly important process. We tested this rescaling approach in a replicated field experiment where entire montane grassland communities were transplanted in the direction of expected temperature and/or precipitation change. In line with earlier work, we found considerable variation across sites in community dynamics in response to climate change. However, these complex context dependencies could be substantially reduced or eliminated by rescaling climate drivers in terms of proxies of plant-plant interactions. Specifically, bryophytes limited colonization by new species into local communities, whereas the cover of those colonists, along with bryophytes, were the primary drivers of local extinctions. These specific interactions are relatively understudied, suggesting important directions for future work in similar systems. More generally, the success of our approach in explaining and simplifying landscape-level variation in climate change responses suggests that developing and testing proxies for relevant underlying processes could be a fruitful direction for building more general models of biodiversity response to climate change.

Interspecific competition reveals Raphidiopsis raciborskii as a more successful invader than Microcystis aeruginosa

As a successful invasive cyanobacterial species, Raphidiopsis raciborskii is distributed globally and shows a tendency to replace Microcystis aeruginosa in many subtropical and temperate waters, but the ecological traits that contribute to its invasiveness are still unclear. In this study, we found that R. raciborskii occurred in 149 sites in 42 lakes in eastern and central China and coexisted with M. aeruginosa at most sites. Based on field results, a combination of invasion and competition experiments using a biomass gradient to evaluate the invasiveness and competitiveness of R. raciborskii compared with M. aeruginosa was conducted. In invasive groups, both R. raciborskii and M. aeruginosa were shown to have positive specific growth rates, indicating that R. raciborskii could coexist with M. aeruginosa. Furthermore, R. raciborskii was shown to grow faster from invasion while M. aeruginosa reduced growth for invasion. In competitive groups, R. raciborskii reached a higher maximum biomass and grew longer than M. aeruginosa. The specific growth rate of R. raciborskii was not inhibited by M. aeruginosa biomass, whereas the growth of M. aeruginosa was inhibited by R. raciborskii biomass. It was shown during the whole experiment that R. raciborskii tended to replace M. aeruginosa to become dominant owing to its faster growth rate and the eventual decline in growth of M. aeruginosa. With an increase in biomass of M. aeruginosa, the vegetative cell size and filament length of R. raciborskii gradually increased. This study has demonstrated that the inherent invasive traits of R. raciborskii, size differences, niche differences, and relative fitness differences between R. raciborskii and M. aeruginosa are crucial reasons for the invasive success of R. raciborskii. Our results revealed the invasiveness and domination of R. raciborskii from a new perspective.

Movement-mediated community assembly and coexistence

Organismal movement is ubiquitous and facilitates important ecological mechanisms that drive community and metacommunity composition and hence biodiversity. In most existing ecological theories and models in biodiversity research, movement is represented simplistically, ignoring the behavioural basis of movement and consequently the variation in behaviour at species and individual levels. However, as human endeavours modify climate and land use, the behavioural processes of organisms in response to these changes, including movement, become critical to understanding the resulting biodiversity loss. Here, we draw together research from different subdisciplines in ecology to understand the impact of individual-level movement processes on community-level patterns in species composition and coexistence. We join the movement ecology framework with the key concepts from metacommunity theory, community assembly and modern coexistence theory using the idea of micro-macro links, where various aspects of emergent movement behaviour scale up to local and regional patterns in species mobility and mobile-link-generated patterns in abiotic and biotic environmental conditions. These in turn influence both individual movement and, at ecological timescales, mechanisms such as dispersal limitation, environmental filtering, and niche partitioning. We conclude by highlighting challenges to and promising future avenues for data generation, data analysis and complementary modelling approaches and provide a brief outlook on how a new behaviour-based view on movement becomes important in understanding the responses of communities under ongoing environmental change.

Trait convergence and niche differentiation of two exotic invasive free-floating plant species in China under shifted water nutrient stoichiometric regimes

The effects of eutrophication on the growth and phenotypic performance of macrophytes have been widely studied. Experimental evidence suggests that an increase in the water nutrient level would promote the performance of several invasive free-floating macrophytes. However, few studies have focused on how a shift in water nutrient (nitrogen and phosphorus) stoichiometric regimes may influence the performance of invasive free-floating macrophytes. In the present study, two exotic invasive plant species, free-floating Eichhornia crassipes and Pistia stratiotes, were subjected to different water nutrient stoichiometric regimes, and their phenotypic performance was studied. We found that the two species converged in several resource use traits and diverged in lateral root length. This implied that their similarities in fitness-correlated traits and their underwater niche differentiation probably contribute to their stable coexistence in the field. Additionally, the eutrophic conditions in the different N:P regimes scarcely altered the performance of both species compared to their performance in the oligotrophic condition. Based on previous studies, we predicted that moderate eutrophication with slight overloading of nitrogen and phosphorus would not improve the performance of several invasive free-floating plants and thus would scarcely alter the invasive status of these species. However, moderate eutrophication may cause other problems, such as the growth of phytoplankton and algae and increased pollution in the water.