From competition to facilitation and mutualism: a general theory of the niche

Increased density of conspecifics caused niche contraction in a multispecific passerine assemblage

Competition is a prominent mechanism driving population dynamics and structuring community assemblage, which can be investigated by linking shifts in species' ecological niche and the densities of sympatric species because the ecological release from competitive constraints is a density-dependent process. In this work we determine how a steppe passerine community segregates their ecological niches and evaluate the role of competition in inducing changes in the ecological niche of species. We built multidimensional ecological niches (with Gaussian kernel density estimators) using data on the habitat features used by 10 bird species collected from seven sites in the natural steppes of Central Spain over 2 consecutive years. We computed distance and niche similarity metrics to explore the ecological niche partitioning of the bird community. Next, we ran multivariate linear regression models to evaluate the effects of conspecific and heterospecific density (as proxies of intraspecific and interspecific competition, respectively) on niche breadth and/or position of the three most abundant species. We found low niche overlap in the community assemblage but varying levels of niche similarity among pairs of species, which could increase the likelihood of current competition operating in the community. However, we found no effect of heterospecific density on niche breadth or position, although conspecific density was negatively related to niche breadth. Contrary to predictions of competition theory, increased density of conspecifics caused niche contraction. Our results from a multispecies system contribute to advanced knowledge of the biotic mechanisms structuring wildlife communities within the framework of ecological niche theory.

Nitrification Control by Plants and Preference for Ammonium versus Nitrate: Positive Feedbacks Increase Productivity but Undermine Resilience

AbstractSome plants, via their action on microorganisms, control soil nitrification (i.e., the transformation of ammonium into nitrate). We model how the covariation between plant control of nitrification and preference for ammonium versus nitrate impacts ecosystem properties such as productivity, nitrogen (N) losses, and overall resilience. We show that the control of nitrification can maximize productivity by minimizing total inorganic N losses. We initially predicted that plants with an ammonium preference should achieve the highest biomass when inhibiting nitrification, and conversely that plants preferring nitrate should achieve the highest biomass by stimulating nitrification. With a parametrization derived from the Lamto savanna (Ivory Coast), we find that productivity is maximal for plants that slightly prefer ammonium and inhibit nitrification. Such situations, however, lead to strong positive feedbacks that can cause abrupt shifts from a highly to a lowly productive ecosystem. The comparison with other parameter sets (Pawnee short-grass prairie [United States], intensively cultivated field, and a hypothetical parameter set in which ammonium is highly volatilized and nitrate inputs are high) shows that strategies yielding the highest biomass may be counterintuitive (i.e., preferring nitrate but inhibiting nitrification). We argue that the level of control yielding the highest productivity depends on ecosystem properties (quantity of N deposition, leaching rates, and baseline nitrification rates), not only preference. Finally, while contrasting N preferences offer, as expected, the possibility of coexistence through niche partitioning, we stress how control of nitrification can be framed as a niche construction process that adds an additional dimension to coexistence conditions.

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.

A taxonomy of multiple stable states in complex ecological communities

Natural systems are built from multiple interconnected units, making their dynamics, functioning and fragility notoriously hard to predict. A fragility scenario of particular relevance concerns so-called regime shifts: abrupt transitions from healthy to degraded ecosystem states. An explanation for these shifts is that they arise as transitions between alternative stable states, a process that is well-understood in few-species models. However, how multistability upscales with system complexity remains a debated question. Here, we identify that four different multistability regimes generically emerge in models of species-rich communities and other archetypical complex biological systems assuming random interactions. Across the studied models, each regime consistently emerges under a specific interaction scheme and leaves a distinct set of fingerprints in terms of the number of observed states, their species richness and their response to perturbations. Our results help clarify the conditions and types of multistability that can be expected to occur in complex ecological communities.

Reciprocal facilitation between ants and small mammals in tidal marshes

The role of facilitation in shaping natural communities has primarily been studied in the context of plant assemblages, while its relevance for mobile animals remains less understood. Our study investigates whether reciprocal interspecific facilitation may exist between fire ants (Solenopsis richteri) and cavies (Cavia aperea), two mobile animals, in the SW Atlantic coast brackish marshes. Field samples showed a spatial association between ant mounds and cavies, and that ants prefer to use cavy runways for movement within the marsh. Through experiments involving transplanting the dominant plant, cordgrass (Spartina densiflora), and manipulating cavy presence in areas with and without ant mounds, we observed that cavies forage extensively (and defecate more) near ant mounds. The ants actively remove cavy droppings in their mound vicinity. These ant activities and interactions with cavy droppings led to reduced moisture and organic content while increasing nitrate and phosphate levels in marsh sediment. Consequently, this enhanced plant growth, indirectly facilitating the cavies, which preferred consuming vegetation near ant mounds. These cascading indirect effects persisted over time; even four months after cavies left the marshes, transplanted plants near ant mounds remained larger and exhibited more leaf senescence when exposed to cavy herbivory. Therefore, the networks of positive interactions appear to generate simultaneous selection among species (populations), promoting coexistence within the community. Although complex, these reciprocal facilitative effects among mobile animals may be more common than currently believed and should be further studied to gain a better understanding of the underlying mechanisms driving species coexistence in natural communities.

Oxidative stress changes interactions between 2 bacterial species from competitive to facilitative

Knowing how species interact within microbial communities is crucial to predicting and controlling community dynamics, but interactions can depend on environmental conditions. The stress-gradient hypothesis (SGH) predicts that species are more likely to facilitate each other in harsher environments. Even if the SGH gives some intuition, quantitative modeling of the context-dependency of interactions requires understanding the mechanisms behind the SGH. In this study, we show with both experiments and a theoretical analysis that varying the concentration of a single compound, linoleic acid (LA), modifies the interaction between 2 bacterial species, Agrobacterium tumefaciens and Comamonas testosteroni, from competitive at a low concentration, to facilitative at higher concentrations where LA becomes toxic for one of the 2 species. We demonstrate that the mechanism behind facilitation is that one species is able to reduce reactive oxygen species (ROS) that are produced spontaneously at higher concentrations of LA, allowing for short-term rescue of the species that is sensitive to ROS and longer coexistence in serial transfers. In our system, competition and facilitation between species can occur simultaneously, and changing the concentration of a single compound can alter the balance between the two.

Plant interaction networks reveal the limits of our understanding of diversity maintenance

Species interactions are key drivers of biodiversity and ecosystem stability. Current theoretical frameworks for understanding the role of interactions make many assumptions which unfortunately, do not always hold in natural, diverse communities. This mismatch extends to annual plants, a common model system for studying coexistence, where interactions are typically averaged across environmental conditions and transitive competitive hierarchies are assumed to dominate. We quantify interaction networks for a community of annual wildflowers in Western Australia across a natural shade gradient at local scales. Whilst competition dominated, intraspecific and interspecific facilitation were widespread in all shade categories. Interaction strengths and directions varied substantially despite close spatial proximity and similar levels of local species richness, with most species interacting in different ways under different environmental conditions. Contrary to expectations, all networks were predominantly intransitive. These findings encourage us to rethink how we conceive of and categorize the mechanisms driving biodiversity in plant systems.

Bridging theory and experiments of priority effects

Priority effects play a key role in structuring natural communities, but considerable confusion remains about how they affect different ecological systems. Synthesizing previous studies, we show that this confusion arises because the mechanisms driving priority and the temporal scale at which they operate differ among studies, leading to divergent outcomes in species interactions and biodiversity patterns. We suggest grouping priority effects into two functional categories based on their mechanisms: frequency-dependent priority effects that arise from positive frequency dependence, and trait-dependent priority effects that arise from time-dependent changes in interacting traits. Through easy quantification of these categories from experiments, we can construct community models representing diverse biological mechanisms and interactions with priority effects, therefore better predicting their consequences across ecosystems.

Myths of past biases and progress in biology

Two ideas are popular among biologists. The first idea is concerned with the biased nature of biology, especially the idea that biologists have overemphasized the importance of competition in the past. The second idea is concerned with progress in correcting for biases, namely, that the biased nature of biology decreases with time. To test these ideas, data on the popularity of interaction topics, such as competition, predation, and mutualism, was collected from articles published in biology journals. Research biases should be visible in publication data as systematic over- and underemphases regarding the popularity of alternative, viable research topics. Were the two ideas correct, data should show that the popularity of a historically dominant topic(s) diminishes with time, whereas the popularity of historically marginal, alternative topics increases with time. The data show that the two ideas are false. According to publication data, the biased nature of biology increases with time, which is a sign of regress rather than progress in biology.

Microbial interactions in theory and practice: when are measurements compatible with models?

Most predictive models of ecosystem dynamics are based on interactions between organisms: their influence on each other's growth and death. We review here how theoretical approaches are used to extract interaction measurements from experimental data in microbiology, particularly focusing on the generalised Lotka-Volterra (gLV) framework. Though widely used, we argue that the gLV model should be avoided for estimating interactions in batch culture - the most common, simplest and cheapest in vitro approach to culturing microbes. Fortunately, alternative approaches offer a way out of this conundrum. Firstly, on the experimental side, alternatives such as the serial-transfer and chemostat systems more closely match the theoretical assumptions of the gLV model. Secondly, on the theoretical side, explicit organism-environment interaction models can be used to study the dynamics of batch-culture systems. We hope that our recommendations will increase the tractability of microbial model systems for experimentalists and theoreticians alike.

A Theoretical Framework for Trait-Based Eco-Evolutionary Dynamics: Population Structure, Intraspecific Variation, and Community Assembly

AbstractHow is trait diversity in a community apportioned between and within coevolving species? Disruptive selection may result in either a few species with large intraspecific trait variation (ITV) or many species with different mean traits but little ITV. Similar questions arise in spatially structured communities: heterogeneous environments could result in either a few species that exhibit local adaptation or many species with different mean traits but little local adaptation. To date, theory has been well-equipped to either include ITV or to dynamically determine the number of coexisting species, but not both. Here, we devise a theoretical framework that combines these facets and apply it to the above questions of how trait variation is apportioned within and between species in unstructured and structured populations, using two simple models of Lotka-Volterra competition. For unstructured communities, we find that as the breadth of the resource spectrum increases, ITV goes from being unimportant to crucial for characterizing the community. For spatially structured communities on two patches, we find no local adaptation, symmetric local adaptation, or asymmetric local adaptation, depending on how much the patches differ. Our framework provides a general approach to incorporate ITV in models of eco-evolutionary community assembly.

Ecological forces dictate microbial community assembly processes in bioreactor systems

Microbial communities are indispensable for future biotechnology to produce valuable platform chemicals and reduce the exploitation of fossil resources. Yet, the stability of microbial communities in classical continuous reactor setups is best brief or non-existent. This is due to ecological forces such as stochastic and deterministic properties of communities that contribute to rapid changes in structure and function to varying degrees. The review highlights the differences between these two properties, provides tools for their estimation, and gives an outlook on overcoming instabilities of microbial communities in biotechnological reactor systems.

Niche theory for positive plant-soil feedbacks

Interactions between plants and the soil are an important ecological process in terrestrial ecosystems as they affect plant community structure: when and where we find different plant species. Those interactions are typically thought of as one-directional: local soil conditions filter through dispersing species to produce a community of locally adapted plants. However, plants can modify local physicochemical soil conditions via their roots and associations with soil microbes. These may in turn affect the local fitness of other plants, making plant-soil interactions bidirectional. In order to understand how they differ from other ecological processes that structure plant communities, we need a theory connecting these individual-level plant-soil feedbacks to community-level patterns. Here, we build this theory with a mathematical model of plant community dynamics in which soil conditioning is explicitly modeled over time and depends on the density of the plants. We analyze this model to describe the long-term composition and spatial distribution of the plant community. Our main result is that positive plant-soil feedbacks will create clustering of species with similar soil preferences. The composition of these clusters is further influenced by niche width and conditioning strength. In contrast with competitive dynamics driven by niche overlap, only species belonging to the same cluster can maintain high relative abundance in the community. Spatial heterogeneity in the form of an environmental gradient generates patches, each representing a single cluster. However, such patchiness is disfavored when species differ in dispersal ability. We show that stronger dispersers cannot take over the habitat as long as an exogenous driver favors soil conditions that benefit the other species. If exogenous drivers supersede soil conditioning by plants, we retrieve classic habitat filtering, where species are selected based on their suitability to the local environment. Overall, we provide a novel mathematical model for positive plant-soil feedback that we use to describe the spatial patterns of plant abundance and traits related to soil preference and conditioning ability.

Coexistence in diverse communities with higher-order interactions

A central assumption in most ecological models is that the interactions in a community operate only between pairs of species. However, two species may interactively affect the growth of a focal species. Although interactions among three or more species, called higher-order interactions, have the potential to modify our theoretical understanding of coexistence, ecologists lack clear expectations for how these interactions shape community structure. Here we analytically predict and numerically confirm how the variability and strength of higher-order interactions affect species coexistence. We found that as higher-order interaction strengths became more variable across species, fewer species could coexist, echoing the behavior of pairwise models. If interspecific higher-order interactions became too harmful relative to self-regulation, coexistence in diverse communities was destabilized, but coexistence was also lost when these interactions were too weak and mutualistic higher-order effects became prevalent. This behavior depended on the functional form of the interactions as the destabilizing effects of the mutualistic higher-order interactions were ameliorated when their strength saturated with species' densities. Last, we showed that more species-rich communities structured by higher-order interactions lose species more readily than their species-poor counterparts, generalizing classic results for community stability. Our work provides needed theoretical expectations for how higher-order interactions impact species coexistence in diverse communities.

Predicting the distribution of plant associations under climate change: A case study on Larix gmelinii in China

Association is the basic unit of plant community classification. Exploring the distribution of plant associations can help improve our understanding of biodiversity conservation. Different associations depend on different habitats and studying the association level is important for ecological restoration, regional ecological protection, regulating the ecological balance, and maintaining biodiversity. However, previous studies have only focused on suitable distribution areas for species and not on the distribution of plant associations. Larix gmelinii is a sensitive and abundant species that occurs along the southern margin of the Eurasian boreal forests, and its distribution is closely related to permafrost. In this study, 420 original plots of L. gmelinii forests were investigated. We used a Maxent model and the ArcGIS software to project the potential geographical distribution of L. gmelinii associations in the future (by 2050 and 2070) according to the climate scenarios RCP 2.6, RCP 4.5, and RCP 8.5. We used the multi‐classification logistic regression analysis method to obtain the response of the suitable area change for the L. gmelinii alliance and associations to climate change under different climate scenarios. Results revealed that temperature is the most crucial factor affecting the distribution of L. gmelinii forests and most of its associations under different climate scenarios. Suitable areas for each association type are shrinking by varying degrees, especially due to habitat loss at high altitudes in special terrains. Different L. gmelinii associations should have different management measures based on the site conditions, composition structure, growth, development, and renewal succession trends. Subsequent research should consider data on biological factors to obtain more accurate prediction results.

Stability criteria for the consumption and exchange of essential resources

Models of consumer effects on a shared resource environment have helped clarify how the interplay of consumer traits and resource supply impact stable coexistence. Recent models generalize this picture to include the exchange of resources alongside resource competition. These models exemplify the fact that although consumers shape the resource environment, the outcome of consumer interactions is context-dependent: such models can have either stable or unstable equilibria, depending on the resource supply. However, these recent models focus on a simplified version of microbial metabolism where the depletion of resources always leads to consumer growth. Here, we model an arbitrarily large system of consumers governed by Liebig’s law, where species require and deplete multiple resources, but each consumer’s growth rate is only limited by a single one of these resources. Resources that are taken up but not incorporated into new biomass are leaked back into the environment, possibly transformed by intracellular reactions, thereby tying the mismatch between depletion and growth to cross-feeding. For this set of dynamics, we show that feasible equilibria can be either stable or unstable, again depending on the resource environment. We identify special consumption and production networks which protect the community from instability when resources are scarce. Using simulations, we demonstrate that the qualitative stability patterns derived analytically apply to a broader class of network structures and resource inflow profiles, including cases where multiple species coexist on only one externally supplied resource. Our stability criteria bear some resemblance to classic stability results for pairwise interactions, but also demonstrate how environmental context can shape coexistence patterns when resource limitation and exchange are modeled directly.

Conceptualizing the 3D niche and vertical space use

Spatial partitioning in ecological communities has predominantly been described in two dimensions, yet habitat is complex and 3D. Complex space use mediates community structure and interaction strength by expanding spatial, temporal, and dietary dimensions. Vertical stratification of resources provides opportunities for novel specializations, creating a 3D niche. Competition and predation are mediated by 3D space use, as individuals use the vertical axis to access prey, flee predators, or avoid competitors. The 3D niche is important for long-term conservation strategies as species must navigate tradeoffs in habitat use between strata-specific threats and suboptimal habitat patches. Ultimately, elucidating the 3D niche has implications for protected area management and corridor design that directly influence species persistence and ecosystem function in a rapidly changing world.

Indirect facilitation between prey promotes asymmetric apparent competition

Apparent competition is one mechanism that can contribute to the complex dynamics observed in natural systems, yet it remains understudied in empirical systems. Understanding the dynamics that shape the outcome of processes like apparent competition is vital for appreciating how they influence natural systems.

We empirically evaluated the role of indirect trophic interactions in driving apparent competition in a model laboratory system. Our experimental system was designed to let us evaluate combined direct and indirect interactions among species.

Here we describe the results of a factorial experiment using two noncompeting prey (Colpidium kleini, a heterotroph, and Chlamydomonas reinhardtii, an autotroph) consumed by a generalist predator Euplotes eurystomus to explore the dynamics of apparent competition. To gain intuition into the potential mechanism driving the asymmetry in the observed results, we further explored the system using structural equation modelling.

Our results show an important role of positive interactions and indirect effects contributing to apparent competition in this system with a marked asymmetrical outcome favouring one prey, Chlamydomonas. The selected structural equation supports a role of indirect facilitation; although Chlamydomonas (a photoautotroph) and Colpidium (a bacterivore) use different resources and therefor do not directly compete, Colpidium reduces bacteria that may compete with Chlamydomonas. In addition, formation of colonies by Chlamydomonas in response to predation by Euplotes provides an antipredator defence not available to Colpidium.

Asymmetric apparent competition may be more common in natural systems than the symmetric interaction originally proposed in classic theory, suggesting that exploration of the mechanisms driving the asymmetry of the interaction can be a fruitful area of further research to better our understanding of interspecific interactions and community dynamics.

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.