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Ecological communities can be stable over multiple generations, or rapidly shift into structurally and functionally different configurations. In kelp forest ecosystems, overgrazing by sea urchins can abruptly shift forests into alternative states that are void of macroalgae and primarily dominated by actively grazing sea urchins. Beginning in 2014, a sea urchin outbreak along the central coast of California resulted in a patchy mosaic of remnant forests interspersed with sea urchin barrens. In this study, we used a 14-year subtidal monitoring dataset of invertebrates, algae, and fishes to explore changes in community structure associated with the loss of forests. We found that the spatial mosaic of barrens and forests resulted in a region-wide shift in community structure. However, the magnitude of kelp forest loss and taxonomic-level consequences were spatially heterogeneous. Taxonomic diversity declined across the region, but there were no declines in richness for any group, suggesting compositional redistribution. Baseline ecological and environmental conditions, and sea urchin behaviour, explained the persistence of forests through multiple stressors. These results indicate that spatial heterogeneity in preexisting ecological and environmental conditions can explain patterns of community change.

Tidal marsh plant communities in the Pacific Northwest are characterized by tall, perennial graminoids (TPGs), which provide forage for herbivores such as Canada geese. Excessive grazing by Canada geese leads to loss of marsh habitat, and removal of grazing pressure is required for the vegetation to recover. Grazing exclosures (fences) are used to allow time and space for vegetation to recover following intensive herbivory; however, their effects on native plant community recovery has not been tested. Generalized linear models were used to compare TPG abundance in aboveground vegetation and surface seed banks in 1-year-old and 10-year-old exclosures at Nanaimo River Estuary (NRE) and Little Qualicum River Estuary (LQRE), respectively, to areas of the marshes that had no known history of grazing (undisturbed) and areas still actively grazed (grubbed). Compared to undisturbed sites, grubbed sites had 187.3% less mean TPG vegetation cover and 190.7% lower proportion of TPG seeds. The 1-year-old exclosures at NRE had 105.0% less mean TPG vegetation cover and 193.2% lower proportion of TPG seeds. The 10-year-old exclosures at LQRE had 7.0% greater mean TPG cover and 55.7% greater proportion of TPG seed than all undisturbed sites; however, these exclosures had 110.0% greater mean relative abundance of non-native TPGs than undisturbed sites. These results indicate vegetation may not recover towards comparable historic conditions through grazing exclusion alone, and that active restoration methods may be required following intensive grazing, especially in estuaries where the vegetation community and surface seed bank has a high abundance of non-native, invasive species. [ABSTRACT FROM AUTHOR]

Warming climate impacts aquatic ectotherms by changes in individual vital rates and declines in body size, a phenomenon known as the temperature‐size rule (TSR), and indirectly through altered species interactions and environmental feedbacks. The relative importance of these effects in shaping community responses to environmental change is incompletely understood. We employ a tri‐trophic food chain model with size‐ and temperature‐dependent vital rates and species interaction strengths to explore the role of direct kinetic effects of temperature and TSR on community structure along resource productivity and temperature gradients. We find that community structure, including the propensity for sudden collapse along resource productivity and temperature gradients, is primarily driven by the direct kinetic effects of temperature on vital rates and thermal mismatches between the consumer and predator species, overshadowing the TSR‐mediated effects. Overall, our study enhances the understanding of the complex interplay between temperature, species traits and community dynamics in aquatic ecosystems. [ABSTRACT FROM AUTHOR]

Background and Aims Not all plant–pollinator interactions are mutualistic, and in fact deceptive pollination systems are widespread in nature. The genus Arisaema has a pollination system known as lethal deceptive pollination, in which plants not only attract pollinating insects without providing any rewards, but also trap them until they die. Many Arisaema species are endangered from various disturbances, including reduction in forest habitat, modification of the forest understorey owing to increasing deer abundance, and plant theft for horticultural cultivation. We aimed to theoretically investigate how lethal deceptive pollination can be maintained from a demographic perspective and how plant and pollinator populations respond to different types of disturbance. Methods We developed and analysed a mathematical model to describe the population dynamics of a deceptive plant species and its victim pollinator. Calibrating the model based on empirical data, we assessed the conditions under which plants and pollinators could coexist, while manipulating relevant key parameters. Key Results The model exhibited qualitatively distinct behaviours depending on certain parameters. The plant becomes extinct when it has a low capability for vegetative reproduction and slow transition from male to female, and plant–insect co-extinction occurs especially when the plant is highly attractive to male insects. Increasing deer abundance has both positive and negative effects because of removal of other competitive plants and diminishing pollinators, respectively. Theft for horticultural cultivation can readily threaten plants whether male or female plants are frequently collected. The impact of forest habitat reduction may be limited compared with that of other disturbance types. Conclusions Our results have emphasized that the demographic vulnerability of lethal deceptive pollination systems would differ qualitatively from that of general mutualistic pollination systems. It is therefore important to consider the demographics of both victim pollinators and deceptive plants to estimate how endangered Arisaema populations respond to various disturbances. [ABSTRACT FROM AUTHOR]

Forest and landscape restoration are increasingly popular nature‐based solutions to mitigate climate change and safeguard biodiversity. Restoration planning and monitoring implies that a reference ecosystem has been defined to which the restored site can be compared, but how to best select such reference? We tested three different potential natural vegetation (PNV) maps of the same areas in Kenya and Uganda for their utility as ecological references with independent data that were not used when those maps were made. These independent datasets included presence observations of woody species from 76 sites in forest reserves in Kenya and Uganda, and classification of surveyed species into a system that included "forest‐only" and "nonforest‐only" ecological types. Our tests show that (1) the three vegetation maps largely agree on the environmental envelopes/ranges within which forests occur. (2) There are large differences in how well the maps predict the presence of forest‐only species. (3) Two maps, based on empirical observations (V4A and White), predict forest types well, whereas the third, based on climate envelopes only (NS), performs poorly. (4) A large area in Uganda is potentially in one of two alternative stable states. We conclude that it is possible to evaluate the utility of PNV maps at a more detailed scale than the level of biome and ecoregion. This indicates that it is possible to map PNV at scales required for reference for restoration and management of forest vegetation. We recommend that empirically based maps of potential natural vegetation are used in restoration planning (biome and PNV maps based on climate envelopes alone may be unreliable tools) as a baseline model for predicting the distribution of reference ecosystems under current and future conditions. It could conveniently be done by deconstructing the existing biome maps, supported by rapid botanical surveys. [ABSTRACT FROM AUTHOR]

Ecosystem responses to disturbance depend on the nature of the perturbation and the ecological legacies left behind, making it critical to understand how climate‐driven changes in disturbance regimes modify resilience properties of ecosystems. For coral reefs, recent increases in severe marine heat waves now co‐occur with powerful storms, the historic agent of disturbance. While storms kill coral and remove their skeletons, heat waves bleach and kill corals but leave their skeletons intact. Here, we explored how the material legacy of dead coral skeletons modifies two key ecological processes that underpin coral reef resilience: the ability of herbivores to control macroalgae (spatial competitors of corals), and the replenishment of new coral colonies. Our findings, grounded by a major bleaching event at our long‐term study locale, revealed that the presence of structurally complex dead skeletons reduced grazing on turf algae by ~80%. For macroalgae, browsing was reduced by >40% on less preferred (unpalatable) taxa, but only by ~10% on more preferred taxa. This enabled unpalatable macroalgae to reach ~45% cover in 2 years. By contrast, herbivores prevented macroalgae from becoming established on adjacent reefs that lacked skeletons. Manipulation of unpalatable macroalgae revealed that the cover reached after 1 year (~20%) reduced recruitment of corals by 50%. The effect of skeletons on juvenile coral growth was contingent on the timing of settlement relative to the disturbance. If corals settled directly after bleaching (before macroalgae colonized), dead skeletons enhanced colony growth by 34%, but this benefit was lost if corals colonized dead skeletons a year after the disturbance once macroalgae had proliferated. These findings underscore how a material legacy from a changing disturbance regime can alter ecosystem resilience properties by disrupting key trophic and competitive interactions that shape post‐disturbance community dynamics. [ABSTRACT FROM AUTHOR]

A cellular automata model was developed and parameterized to test the effectiveness of application of biological control insects to water hyacinth (Pontederia crassipes), which is an invasive floating plant species in many parts of the world and outcompetes many submersed native aquatic species in southern Florida. In the model, P. crassipes was allowed to compete with Nuttall's waterweed (Elodea nuttallii). In the absence of biocontrol acting on the P. crassipes, E. nuttallii excluded P. crassipes at low concentrations of the limiting nutrient (nitrogen), and the reverse occurred at high nutrient concentrations. At intermediate values, alternative stable states could occur; either P. crassipes alone or a mixture of the two species. When the biocontrol agent, the weevil Neochetina eichhorniae, was applied in the model, there was initially a rapid reduction of the P. crassipes, however, over time a regular striped pattern of moving spatially alternating stripes of P. crassipes and E. nuttallii emerged. -This pattern of moving stripes emerged and persisted over thousands of days but could quickly transform into an irregular pattern at some apparently random time, when either external stochasticity (added adult weevils) or only the weak internal stochasticity of weevil movements occurred. The cause of the end of the long transient can be traced to a single slightly irregular pixel within the striped pattern. Model parameters were varied to study effects of plant growth rate, nutrient concentration and nutrient diffusion rate on the dynamics of the system. [ABSTRACT FROM AUTHOR]

Background and aims: Several lines of evidence indicate that arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) associations can have different effects on soil nutrient dynamics. Some lineages of ECM fungi can extract N from organic matter, with varying impacts on decomposers, soil carbon pools, mineral N availability, and plants that lack ECM. However, these effects are not always observed, and it is not clear how they are mediated by environmental factors. Methods: We used Plant Root Simulator probes to compare soil availability of a wide range of nutrients beneath replicated 30-yr old plantations of Chilean Nothofagus (ECM) and Cupressaceae (Austrocedrus, Fitzroya: AM) on a lowland temperate site. Probes were buried for two 8-week periods in early spring and late summer. We also compared understorey composition beneath plantations, to test for evidence of different successional trajectories beneath Nothofagus and Cupressaceae. Results: Soil organic carbon, total N and total phosphorus did not differ significantly between Nothofagus and Cupressaceae stands. Redundancy analysis revealed significant effects of both plantation type (Nothofagus vs. Cupressaceae) and season on overall mineral nutrient availability. Mineral N availability did not differ significantly between Nothofagus and Cupressaceae plots, but pH and calcium availability were significantly lower beneath Nothofagus. Manganese (Mn) was much more available beneath Nothofagus stands, which might reflect abundant Mn-peroxidase, a key enzyme involved in breakdown of lignin by ECM fungi. Understorey composition varied considerably between individual plantations, but did not differ significantly between Nothofagus and Cupressaceae plantations. Conclusions: Despite an overall effect on the stoichiometry of nutrient availability, we found little evidence of modification of the local N cycle by ECM fungi, or of divergent regeneration patterns beneath AM and ECM plantations. This might reflect the relatively N-rich character of this site, and/or mycorrhizal effects being counteracted by leaf trait differences between Chilean Cupressaceae and Nothofagus species. [ABSTRACT FROM AUTHOR]

Within communities, species are wrapped in a set of feedbacks with each other and with their environment. When such feedbacks are strong enough they can generate alternative stable states. So far, research on alternative stable states has mostly focused on systems with a small number of species and a limited diversity of interaction types. Here, we analyze a spatial model of plant community dynamics in stressed ecosystems such as drylands, where each species is characterized by a strategy, and the different species interact through facilitation and competition for space and resources, such as water. We identify three different types of multistability emerging from the interplay of competition and facilitation. Under low‐stress levels, plant communities organize in small groups of coexisting species, maintained by space, competition and facilitation ("cliques"). Under higher stress levels, positive feedback from facilitation lead to the dominance of a single facilitating species ("mutual exclusion states"). At the highest stress levels, the single facilitating species left in the system coexists with the desert state. By linking community ecology and alternative stable states theory using a spatial plant community model for stressed ecosystems, our study contributes to highlight the importance of positive feedback loops for the stability of ecological communities. [ABSTRACT FROM AUTHOR]

Summary: Strong disturbances may induce ecosystem transitions into new alternative states that sustain through plant–soil interactions, such as the transition of dwarf shrub‐dominated into graminoid‐dominated vegetation by herbivory in tundra. Little evidence exists on soil microbial communities in alternative states, and along the slow process of ecosystem return into the predisturbance state.We analysed vegetation, soil microbial communities and activities as well as soil physico‐chemical properties in historical reindeer enclosures in northernmost Finland in the following plot types: control heaths in the surrounding tundra; graminoid‐dominated; 'shifting'; and recovered dwarf shrub‐dominated vegetation inside enclosures.Soil fungal communities followed changes in vegetation, whereas bacterial communities were more affected by soil physico‐chemical properties. Graminoid plots were characterized by moulds, pathotrophs and dark septate endophytes. Ericoid mycorrhizal and saprotrophic fungi were typical for control and recovered plots. Soil microbial communities inside the enclosures showed historical contingency, as their spatial variation was high in recovered plots despite the vegetation being more homogeneous.Self‐maintaining feedback loops between plant functional types, soil microbial communities, and carbon and nutrient mineralization act effectively to stabilize alternative vegetation states, but once predisturbance vegetation reestablishes itself, soil microbial communities and physico‐chemical properties return back towards their predisturbance state. [ABSTRACT FROM AUTHOR]

The effects of species on one another sometimes depend on the order in which they arrive at a local site. This historical contingency, termed priority effects, can have a major influence on the assembly and functioning of ecological communities. Although historically studied within community ecology, phenomena consistent with priority effects appear in a variety of biological scenarios and across a wide range of spatial and temporal scales, but are referred to by many different but related terms. There exists a fragmented communication landscape between studies of priority effects across these disparate biological subfields, which is stifling a conceptual unification of how, when, and why priority effects occur. Our review provides a launchpad for developing a unified framework across a broad range of ecological contexts. Although primarily studied through the lens of community ecology, phenomena consistent with priority effects appear to be widespread across many different scenarios spanning a broad range of spatial, temporal, and biological scales. However, communication between these research fields is inconsistent and has resulted in a fragmented co-citation landscape, likely due to the diversity of terms used to refer to priority effects across these fields. We review these related terms, and the biological contexts in which they are used, to facilitate greater cross-disciplinary cohesion in research on priority effects. In breaking down these semantic barriers, we aim to provide a framework to better understand the conditions and mechanisms of priority effects, and their consequences across spatial and temporal scales. [ABSTRACT FROM AUTHOR]

Abstract Forest and landscape restoration are increasingly popular nature‐based solutions to mitigate climate change and safeguard biodiversity. Restoration planning and monitoring implies that a reference ecosystem has been defined to which the restored site can be compared, but how to best select such reference? We tested three different potential natural vegetation (PNV) maps of the same areas in Kenya and Uganda for their utility as ecological references with independent data that were not used when those maps were made. These independent datasets included presence observations of woody species from 76 sites in forest reserves in Kenya and Uganda, and classification of surveyed species into a system that included “forest‐only” and “nonforest‐only” ecological types. Our tests show that (1) the three vegetation maps largely agree on the environmental envelopes/ranges within which forests occur. (2) There are large differences in how well the maps predict the presence of forest‐only species. (3) Two maps, based on empirical observations (V4A and White), predict forest types well, whereas the third, based on climate envelopes only (NS), performs poorly. (4) A large area in Uganda is potentially in one of two alternative stable states. We conclude that it is possible to evaluate the utility of PNV maps at a more detailed scale than the level of biome and ecoregion. This indicates that it is possible to map PNV at scales required for reference for restoration and management of forest vegetation. We recommend that empirically based maps of potential natural vegetation are used in restoration planning (biome and PNV maps based on climate envelopes alone may be unreliable tools) as a baseline model for predicting the distribution of reference ecosystems under current and future conditions. It could conveniently be done by deconstructing the existing biome maps, supported by rapid botanical surveys.

Worldwide, large wildfires are becoming increasingly common, leading to economic damages and threatening ecosystems and human health. Under future climate change, more frequent fire disturbance may push ecosystems into non‐forested alternative stable states. Fire‐prone ecosystems such as those in the Mediterranean Basin are expected to be particularly vulnerable, but the position of tipping points is unclear.We compare long‐term palaeoecological data from Sardinia with output from a process‐based dynamic vegetation model to investigate the mechanisms controlling the complex interactions between fire, climate, and vegetation in the past and the future.Our results show that past vegetation changes from Erica‐shrublands to mixed evergreen‐broadleaved Quercus ilex‐dominated forests were driven by a climate‐induced fire regime shift. By simulating vegetation dynamics under varying fire regimes, we could reproduce Holocene vegetation trajectories and mechanistically identify tipping points.Without an immediate reduction of greenhouse gas emissions, we simulate future expansion of fire‐prone Mediterranean maquis and increasing fire occurrence. Similarly, high anthropogenic ignition frequencies and plantations of non‐native, highly flammable trees could induce a shift to fire‐adapted Erica shrublands. However, our simulations indicate that if global warming can be kept below 2°C, Quercus ilex forests will be able to persist and effectively reduce fire occurrences and impacts, making them a valuable restoration target in Mediterranean ecosystems.Synthesis. By combining long‐term records of ecosystem change with a dynamic vegetation model, we show that past climate‐driven fire regime shifts were the main driver of vegetation change, creating alternative stable states that persisted over centuries. Projected future climate change exceeding Holocene variability leads to pronounced vegetation changes and increased fire risks in our simulations, requiring new fire management strategies to maintain current ecosystem services. [ABSTRACT FROM AUTHOR]

Rotational closures have potential fisheries benefits, yet their impact on coral cover is unknown. Research has shown that permanent closures can protect herbivorous fish, indirectly benefiting corals, but these observations may not apply when closed periods alternate with fishing. Here, we examine how rotational closures affect coral, focusing on systems with the potential to switch between alternative stable states, a context in which temporary closures may have persistent effects. We show that rotational closures can trigger coral recovery, and in some contexts lead to better coral recovery than fixed closures of similar size. Such benthic effects are only possible if closures last long enough for change to occur. We also note that very large fixed or rotating closures may concentrate fishing effort in areas where fishing remains permitted, leading to lower overall coral cover. Our findings offer crucial guidance to managers regarding rotational closures' potential advantages and drawbacks. [ABSTRACT FROM AUTHOR]

Eutrophication of lakes, as one of the most challenging global environmental problems for more than half a century has been addressed by a vast number of publications. Issues hitherto not considered or treated superficially have been discussed here. They concern: i. breakthrough phases in the 100-year period of development of the Eutrophication Concept (EC) and, ii. concepts and theories derived from EC and their complementarity in terms of assumptions and terminology. The paper traces the history of perception of the primary factors responsible for lake eutrophication. It presents the evolution of the approach to the problem, initially focusing on point and then non-point external sources of pollution, supplemented with internal nutrient supply, bottom-up and top-down regulation, with increasing emphasis on the role of interactions in the food web. The article addresses the justification of the Lake Aging Concept (LAC), assuming an inevitable increase in the trophic status during the development of a lake, and unjustly identifying eutrophication with progressing disappearance of lakes in a geologically-relevant timescale. It also discusses the assumptions of the Theory of Alternative Stable States (TASS) and discrepancies between EC and TASS regarding the application of different terminology in reference to the same phenomena and lake classifications. [ABSTRACT FROM AUTHOR]

Assessments of historical contingency have advanced our understanding of adaptive radiation and community ecology, but little attention has been given to assessing the importance of historical contingency in population ecology. An obstacle has been the unmet need to conceptualize historical contingencies for populations in a manner that allows for their explanatory power to be assessed and quantified so that it can be directly compared with the explanatory power of statistical models representing other hypotheses or theory-based explanations. Here we conceptualize historical contingencies as a series of random events characterized by (1) significant legacy effects that are comparable in length to the waiting time between such events, and (2) the disparate nature of individual events in the series. From that conceptualization, we present a simple quantitative framework for assessing the explanatory power of historical contingencies in population ecology and apply it to an existing long-term dataset on the predator-prey system in Isle Royale National Park. The population-level phenomenon that we focused on was predation rate because it is a synthesis of three basic elements in population ecology (predator abundance, prey abundance and kill rate). We also compared the explanatory power of models of the historical contingency hypothesis to a wide-range of alternative, theory-based, statistical models used to assess underlying mechanisms or forecast future dynamics. Models of the historical contingency hypothesis explained over half of the interannual variation in predation rate and performed similarly, or better than, the vast majority of alternative, theory-based, models. Those findings highlight the potential value of reconsidering the way that population ecologists traditionally attempt to explain phenomena. We also discuss how this new conceptualization of the historical contingency hypothesis can also be valuable for synthesizing several other important ecological concepts of broad significance, especially reddened spectra, tipping points, alternative stable states, and ecological surprises. If the historical contingency hypothesis were found to be broadly applicable, then it would likely explain why ecologists are conspicuously poor at forecasting future dynamics. [ABSTRACT FROM AUTHOR]

Increased stress on coastal ecosystems, such as coral reefs, seagrasses, kelp forests, and other habitats, can make them shift toward degraded, often algae-dominated or barren communities. This has already occurred in many places around the world, calling for new approaches to identify where such regime shifts may be triggered. Theoretical work predicts that the spatial structure of habitat-forming species should exhibit changes prior to regime shifts, such as an increase in spatial autocorrelation. However, extending this theory to marine systems requires theoretical models connecting field-supported ecological mechanisms to data and spatial patterns at relevant scales. To do so, we built a spatially explicit model of subtropical coral communities based on experiments and long-term datasets from Rapa Nui (Easter Island, Chile), to test whether spatial indicators could signal upcoming regime shifts in coral communities. Spatial indicators anticipated degradation of coral communities following increases in frequency of bleaching events or coral mortality. However, they were generally unable to signal shifts that followed herbivore loss, a widespread and well-researched source of degradation, likely because herbivory, despite being critical for the maintenance of corals, had comparatively little effect on their self-organization. Informative trends were found under both equilibrium and nonequilibrium conditions but were determined by the type of direct neighbor interactions between corals, which remain relatively poorly documented. These inconsistencies show that while this approach is promising, its application to marine systems will require detailed information about the type of stressor and filling current gaps in our knowledge of interactions at play in coral communities. [ABSTRACT FROM AUTHOR]

Choosing restoration strategies may depend on ecosystem's stability properties. When degraded ecosystems do not self‐perpetuate, natural regeneration can lead to system recovery, and restoration interventions are often designed to accelerate the natural regeneration process. However, when degraded systems self‐perpetuate, reestablishing functional ecosystems depends on overcoming resistance thresholds that impede recovery. In both scenarios, concentrating restoration efforts in patches of the desired state may enhance ecosystem recovery. Introducing patches of a desired state has been motivated by two frameworks: autocatalytic nucleation and the analogy to nucleation. When restoration depends on overcoming resistance thresholds, autocatalytic nucleation lowers restoration barriers by initiating a local positive feedback mechanism that is only successful when desired patches are introduced above a critical patch size. In contrast, the analogy to nucleation accelerates natural regeneration whereby desired patches interact with landscape scale factors often through directed dispersal. We compare nucleation frameworks, and discuss their applications for restoration practices. [ABSTRACT FROM AUTHOR]

Background The unprecedented influence of human activities on natural ecosystems in the 21st century has resulted in increasingly frequent large-scale changes in ecological communities. This has heightened interest in understanding such changes and effective means to manage them. Accurate interpretation of state changes is challenging because of difficulties translating theory to empirical study, and most theory emphasizes systems near equilibrium, which may not be relevant in rapidly changing environments. Scope We review concepts of long-transient stages and phase shifts between stable community states, both smooth, continuous and discontinuous shifts, and the relationships among them. Three principal challenges emerge when applying these concepts. The first is how to interpret observed change in communities – distinguishing multiple stable states from long transients, or reversible shifts in the phase portrait of single attractor systems. The second is how to quantify the magnitudes of three sources of variability that cause switches between community states: (1) 'noise' in species' abundances, (2) 'wiggle' in system parameters and (3) trends in parameters that affect the topography of the basin of attraction. The third challenge is how variability of the system shapes evidence used to interpret community changes. We outline a novel approach using critical length scales to potentially address these challenges. These concepts are highlighted by a review of recent examples involving macroalgae as key players in marine benthic ecosystems. Conclusions Real-world examples show three or more stable configurations of ecological communities may exist for a given set of parameters, and transient stages may persist for long periods necessitating their respective consideration. The characteristic length scale (CLS) is a useful metric that uniquely identifies a community 'basin of attraction', enabling phase shifts to be distinguished from long transients. Variabilities of CLSs and time series data may likewise provide proactive management measures to mitigate phase shifts and loss of ecosystem services. Continued challenges remain in distinguishing continuous from discontinuous phase shifts because their respective dynamics lack unique signatures. [ABSTRACT FROM AUTHOR]

Abstract Rotational closures have potential fisheries benefits, yet their impact on coral cover is unknown. Research has shown that permanent closures can protect herbivorous fish, indirectly benefiting corals, but these observations may not apply when closed periods alternate with fishing. Here, we examine how rotational closures affect coral, focusing on systems with the potential to switch between alternative stable states, a context in which temporary closures may have persistent effects. We show that rotational closures can trigger coral recovery, and in some contexts lead to better coral recovery than fixed closures of similar size. Such benthic effects are only possible if closures last long enough for change to occur. We also note that very large fixed or rotating closures may concentrate fishing effort in areas where fishing remains permitted, leading to lower overall coral cover. Our findings offer crucial guidance to managers regarding rotational closures’ potential advantages and drawbacks.

ABSTRACTArchaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1–42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird’s-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.

Assessments of historical contingency have advanced our understanding of adaptive radiation and community ecology, but little attention has been given to assessing the importance of historical contingency in population ecology. An obstacle has been the unmet need to conceptualize historical contingencies for populations in a manner that allows for their explanatory power to be assessed and quantified so that it can be directly compared with the explanatory power of statistical models representing other hypotheses or theory-based explanations. Here we conceptualize historical contingencies as a series of random events characterized by (1) significant legacy effects that are comparable in length to the waiting time between such events, and (2) the disparate nature of individual events in the series. From that conceptualization, we present a simple quantitative framework for assessing the explanatory power of historical contingencies in population ecology and apply it to an existing long-term dataset on the predator-prey system in Isle Royale National Park. The population-level phenomenon that we focused on was predation rate because it is a synthesis of three basic elements in population ecology (predator abundance, prey abundance and kill rate). We also compared the explanatory power of models of the historical contingency hypothesis to a wide-range of alternative, theory-based, statistical models used to assess underlying mechanisms or forecast future dynamics. Models of the historical contingency hypothesis explained over half of the interannual variation in predation rate and performed similarly, or better than, the vast majority of alternative, theory-based, models. Those findings highlight the potential value of reconsidering the way that population ecologists traditionally attempt to explain phenomena. We also discuss how this new conceptualization of the historical contingency hypothesis can also be valuable for synthesizing several other important ecological concepts of broad significance, especially reddened spectra, tipping points, alternative stable states, and ecological surprises. If the historical contingency hypothesis were found to be broadly applicable, then it would likely explain why ecologists are conspicuously poor at forecasting future dynamics.

Previous work indicates that tropical forest can exist as an alternative stable state to savanna. Therefore, perturbation by climate change or human impact may lead to crossing of a tipping point beyond which there is rapid forest dieback that is not easily reversed. A hypothesized mechanism for such bistability is feedback between fire and vegetation, where fire spreads as a contagion process on grass patches. Theoretical models have largely implemented this mechanism implicitly, by assuming a threshold dependence of fire spread on flammable vegetation. Here, we show how the nonlinear dynamics and bistability emerge spontaneously, without assuming equations or thresholds for fire spread. We find that the forest geometry causes the nonlinearity that induces bistability. We demonstrate this in three steps. First, we model forest and fire as interacting contagion processes on grass patches, showing that spatial structure emerges due to two counteracting effects on the forest perimeter: forest expansion by dispersal and forest erosion by fires originating in adjacent grassland. Then, we derive a landscape-scale balance equation in which these two effects link forest geometry and dynamics: Forest expands proportionally to its perimeter, while it shrinks proportionally to its perimeter weighted by adjacent grassland area. Finally, we show that these perimeter quantities introduce nonlinearity in our balance equation and lead to bistability. Relying on the link between structure and dynamics, we propose a forest resilience indicator that could be used for targeted conservation or restoration. [ABSTRACT FROM AUTHOR]

Alternative stable ecosystem states are possible under the same environmental conditions in models of two or three interacting species and an array of feedback loops. However, multispecies food webs might weaken the feedbacks loops that can create alternative stable states. To test how this potential depends on food web properties, we develop a many-species model where consumer Allee effects emerge from consumer-resource interactions. We evaluate the interactive effects of food web connectance, interspecific trait diversity, and two classes of feedbacks: specialized feedbacks, where consumption of individual resources declines at high resource abundance (e.g., from schooling or reaching size refugia), and aggregate feedbacks, where overall resource abundance reduces consumer recruitment (e.g., from resources enhancing competition or mortality experienced by recruits). We find that aggregate feedbacks maintain, and specialized feedbacks reduce, the potential for alternative states. Interspecific trait diversity decreases the prevalence of alternative stable states more for specialized than for aggregate feedbacks. Increasing food web connectance increases the potential for alternative stable states for aggregated feedbacks but decreases it for specialized feedbacks, where losing vulnerable consumers can cascade into food web collapses. Altogether, multispecies food webs can limit the set of processes that create alternative stable states and impede consumer recovery from disturbance. [ABSTRACT FROM AUTHOR]

The concepts of ecological thresholds and alternative stable states were proposed to explain nonlinear changes. However, the greatest obstacle to advance these theories and their managerial applications is a lack of data and research experience. There are almost all types of ecosystems in China, and various ecological degradation and catastrophe events occurred at the end of the 20th century. Considerable monitoring data and research cases that focus on the ecological thresholds are published in Chinese, limiting their dissemination around the world. We integrate Chinese cases and data that refer to the framework of Threshold Database and Regime Shifts Database. We introduce the China Ecological Thresholds and Alternative Stable States Database (CETASSD), developed by the Chinese Research Academy of Environmental Sciences, which mainly collects research cases. The CETASSD uses a unified description framework to integrate key information from past 110 case studies from China. This paper summarizes relevant case studies with intrinsic consistency to ecological thresholds and alternative stable states in social-ecological systems. We collate and analyze 26 potential alternative stable states and 60 potential ecological thresholds in CETASSD, covering 14 types of ecosystems. We found several peculiarities of the Chinese case studies. First, more types of alternative stable states were identified in arid areas and Qinghai-Tibet Plateau. Second, critical thresholds research related to spatial gradient has received great attention. Third, methods of constructing highly generalized "stress-response" process lines are mainly used for threshold analysis. We suggest re-examining past research cases and methods with the latest theories of ecological thresholds and alternative stable states; strengthening research on the detection of threshold and mechanism establishment of certain ecosystems, such as the ocean in China; and further applying ecological thresholds to ecological assessment and early warning. [ABSTRACT FROM AUTHOR]

Parental care patterns differ enormously among and even within species. This is exemplified by Chinese penduline tits Remiz consobrinus, where biparental care, female‐only care, male‐only care and biparental desertion all occur in the same population; moreover, the distribution of these care patterns differs systematically between populations. The eco‐evolutionary determinants of this diversity are largely unknown.We developed an individual‐based model that allows us to investigate the effects of season length and offspring needs (expressed by the efficacy with which a clutch can be raised by a single parent) on the evolution of parental care patterns. The model is largely conceptual, aiming at general conclusions. However, to keep the model realistic, its set‐up and the choice of parameters are motivated by field studies on Chinese penduline tits. Exploring a wide range of parameters, we investigate how parental care patterns are affected by season length and offspring needs and whether and under what conditions diverse parental care patterns can stably coexist.We report five main findings. First, under a broad range of conditions, different care patterns (e.g. male care and biparental care) coexist at equilibrium. Second, for the same parameters, alternative evolutionary equilibria are possible; this can explain differences in care patterns across populations. Third, rapid evolutionary transitions can occur between alternative equilibria; this can explain the often‐reported evolutionary lability of parental care patterns. Fourth, season length has a strong but nonmonotonic effect on the evolved care patterns. Fifth, when uniparental care efficacy is low, biparental care tends to evolve; however, in many scenarios uniparental care is still common at equilibrium. In addition, our study sheds new light on Trivers' hypothesis that the sex with the highest prezygotic investment is predestined to invest more postzygotically as well.Our study highlights that diversity in parental care can readily evolve and it shows that even in the absence of environmental change parental care patterns can be evolutionary labile. In the presence of directional environmental change, systematic shifts in care patterns are to be expected. [ABSTRACT FROM AUTHOR]

The growing shortfall in wild seafood and expansion of aquaculture can involve ecological and economic feedback between wild and farmed fish populations such as disease transmission and market competition. Here, we investigate the resilience of bioeconomically interacting fisheries and aquaculture systems by developing and analyzing mathematical models that capture the ecological suppression of wild fish survival by aquaculture, the management of fisheries for maximum sustainable yield, and aquaculture growth via two regulatory scenarios: perfect competition or rent optimization. Stability analysis of the models indicates that coexistence of productive fisheries and aquaculture is stable if the ecological impacts of aquaculture on wild fish are held below a bioeconomic threshold. Otherwise, the dynamics involve regime shifts between alternative stable states of fishery dominance with little aquaculture versus aquaculture dominance with collapsed fisheries. These regime shifts are difficult to reverse due to hysteresis. Coexistence and alternative stable states occur in both regulatory scenarios, but resilience is higher under rent optimization than perfect competition. Our results indicate that bioeconomic feedback can have important consequences for the resilience of aquaculture-fishery systems. [ABSTRACT FROM AUTHOR]

Self‐reinforcing differences in fire frequency help closed‐canopy forests, which resist fire, and open woodlands, which naturally burn often, to co‐occur stably at landscape scales. Forest tree seedlings, which could otherwise encroach and overgrow woodlands, are killed by regular fire, yet fire has other effects that may also influence these feedbacks. In particular, many forest trees require symbiotic ectomycorrhizal fungi in order to establish. By restructuring soil fungal communities, fire might affect the availability of symbionts or the potential for symbiont sharing between encroaching trees and woodland vegetation.To investigate this possibility, we performed a soil bioassay experiment using inoculum from burned and unburned oak woodlands and Douglas‐fir forests. We examined how fire, ecosystem type, and neighboring heterospecific seedlings affect fungal root community assembly of Douglas‐firs and oaks. We asked whether heterospecific seedlings facilitated fungal colonization of seedling roots in non‐native soil, and if so, whether fire influenced this interaction.External fungal colonization of oak roots was more influenced by fire and ecosystem type than by the presence of a Douglas‐fir, and oaks increased the likelihood that Douglas‐fir roots would be colonized by fungi in oak woodland soil. Yet, fire increased colonization of Douglas‐fir in oak soil, diminishing the otherwise crucial role played by oak facilitation. Fire also strengthened the positive effect of Douglas‐firs on oak root‐associated fungal diversity in Douglas‐fir forest soil.Prior work shows that fire supports woodland ecosystems by stemming recruitment of encroaching seedlings. Here, we find evidence that it may contrastingly reduce fungal limitation of invasive seedling growth and establishment, otherwise relieved only by facilitation. Future work can investigate how these opposing effects might contribute to the net impact of changes in fire regime on landcover stability. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Mixotrophs are ubiquitous and integral to microbial food webs, but their impacts on the dynamics and functioning of broader ecosystems are largely unresolved.Here, we show that mixotrophy produces a unique type of food web module that exhibits unusual ecological dynamics, with surprising consequences for carbon flux under warming. We develop a generalizable model of a mixotrophic food web module that incorporates dynamic switching between phototrophy and phagotrophy to assess ecological dynamics and total system CO2 flux.We find that warming switches mixotrophic systems between alternative stable carbon states—including a phototrophy‐dominant carbon sink state, a phagotrophy‐dominant carbon source state and cycling between these two. Moreover, warming always shifts this mixotrophic system from a carbon sink state to a carbon source state, but a coordinated increase in nutrients can erase early warning signals of this transition and expand hysteresis.This suggests that mixotrophs can generate critical carbon tipping points under warming that will be more abrupt and less reversible when combined with increased nutrient levels, having widespread implications for ecosystem functioning in the face of rapid global change. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Fertilizers, pesticides and global warming are threatening freshwater aquatic ecosystems. Most of these are shallow ponds or slow-flowing streams or ditches dominated by submerged macrophytes, periphyton or phytoplankton. Regime shifts between the dominance of these primary producers can occur along a gradient of nutrient loading, possibly triggered by specific disturbances influencing their competitive interactions. However, phytoplankton dominance is less desirable due to lower biodiversity and poorer ecosystem function and services. In this study, we combined a microcosm experiment with a processbased model to test three hypotheses: 1) agricultural run-off (ARO), consisting of nitrate and a mixture of organic pesticides and copper, differentially affects primary producers and enhances the risk of regime shifts, 2) warming increases the risk of an ARO-induced regime shift to phytoplankton dominance and 3) custom-tailored process-based models support mechanistic understanding of experimental results through scenario comparison. Experimentally exposing primary producers to a gradient of nitrate and pesticides at 22°C and 26°C supported the first two hypotheses. ARO had direct negative effects on macrophytes, while phytoplankton gained from warming and indirect effects of ARO like a reduction in the competitive pressure exerted by other groups. We used the process-based model to test eight different scenarios. The best qualitative fit between modeled and observed responses was reached only when taking community adaptation and organism acclimation into account. Our results highlight the importance of considering such processes when attempting to predict the effects of multiple stressors on natural ecosystems. [ABSTRACT FROM AUTHOR]

Fire–vegetation feedbacks potentially maintain global savanna and forest distributions. Accordingly, vegetation in savanna and forest ecosystems should have differential responses to fire, but fire response data for herbaceous vegetation have yet to be synthesized across biomes. Here, we examined herbaceous vegetation responses to experimental fire at 30 sites spanning four continents. Across a variety of metrics, herbaceous vegetation increased in abundance where fire was applied, with larger responses to fire in wetter and in cooler and/or less seasonal systems. Compared to forests, savannas were associated with a 4.8 (±0.4) times larger difference in herbaceous vegetation abundance for burned versus unburned plots. In particular, grass cover decreased with fire exclusion in savannas, largely via decreases in C4 grass cover, whereas changes in fire frequency had a relatively weak effect on grass cover in forests. These differential responses underscore the importance of fire for maintaining the vegetation structure of savannas and forests. [ABSTRACT FROM AUTHOR]

Submerged macrophytes have attracted increasing attention in lake restoration due to the importance of their structuring communities and stabilizing functions in lake ecosystems. However, there is still a lack of systematic reviews on lake restoration with submerged macrophytes. Thus, we performed a systematic review based on a bibliometric analysis via analyzing and visualizing 934 published works from 1996 to 2023 from the Web of Science core collection. Publication characteristics were summarized, and keyword co-occurrence networks, reference co-citation analysis, and keyword burst tests were conducted. Our results suggest that the increasing attention in this field has partly resulted from the many water treatments and scientific schemes in Europe, China, and the USA and extensive international cooperation. The development of this field was divided into three stages based on keyword bursts (e.g., early, turning, and recent stages). Alternative stable states and biomanipulation laid the foundations of this field in the early stage. Progress in the field was discussed based on four aspects, the influence of environmental factors on submerged macrophytes, theory and mechanisms, targets, and evaluation and methods. Therefore, our results provide a new and comprehensive understanding of lake restoration with submerged macrophytes. [ABSTRACT FROM AUTHOR]

For most of Earth's history, the ocean's interior was pervasively anoxic and showed occasional shifts in ocean redox chemistry between iron-buffered and sulfide-buffered states. These redox transitions are most often explained by large changes in external inputs, such as a strongly altered delivery of iron and sulfate to the ocean, or major shifts in marine productivity. Here, we propose that redox shifts can also arise from small perturbations that are amplified by nonlinear positive feedbacks within the internal iron and sulfur cycling of the ocean. Combining observational evidence with biogeochemical modeling, we show that both sedimentary and aquatic systems display intrinsic iron-sulfur bistability, which is tightly linked to the formation of reduced iron-sulfide minerals. The possibility of tipping points in the redox state of sediments and oceans, which allow large and nonreversible geochemical shifts to arise from relatively small changes in organic carbon input, has important implications for the interpretation of the geological rock record and the causes and consequences of major evolutionary transitions in the history of Earth's biosphere.

Abstract Background Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as “dysbiosis” in human microbiomes. Methods We integrated theoretical frameworks and empirical analyses with the aim of anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We analyzed the time-series data based on statistical physics and non-linear mechanics to describe the characteristics of the microbiome dynamics and to examine the predictability of major shifts in microbial community structure. Results We confirmed that the abrupt community changes observed through the time-series could be described as shifts between “alternative stable states“ or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the “energy landscape” analysis of statistical physics or that of a stability index of nonlinear mechanics. Conclusions The results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems. Video Abstract

Abstract Background In aquatic ecosystems, the health and performance of fish depend greatly on the dynamics of microbial community structure in the background environment. Nonetheless, finding microbes with profound impacts on fish’s performance out of thousands of candidate species remains a major challenge. Methods We examined whether time-series analyses of microbial population dynamics could illuminate core components and structure of fish-associated microbiomes in the background (environmental) water. By targeting eel-aquaculture-tank microbiomes as model systems, we reconstructed the population dynamics of the 9605 bacterial and 303 archaeal species/strains across 128 days. Results Due to the remarkable increase/decrease of constituent microbial population densities, the taxonomic compositions of the microbiome changed drastically through time. We then found that some specific microbial taxa showed a positive relationship with eels’ activity levels even after excluding confounding effects of environmental parameters (pH and dissolved oxygen level) on population dynamics. In particular, a vitamin-B12-producing bacteria, Cetobacterium somerae, consistently showed strong positive associations with eels’ activity levels across the replicate time series of the five aquaculture tanks analyzed. Network theoretical and metabolic modeling analyses further suggested that the highlighted bacterium and some other closely-associated bacteria formed “core microbiomes” with potentially positive impacts on eels. Conclusions Overall, these results suggest that the integration of microbiology, ecological theory, and network science allows us to explore core species and interactions embedded within complex dynamics of fish-associated microbiomes. Video Abstract

The global rise in anthropogenic reactive nitrogen and the negative impacts of N deposition on terrestrial plant diversity are well documented. The R* theory of resource competition predicts reversible decreases in plant diversity in response to N loading. However, empirical evidence for the reversibility of N-induced biodiversity loss is mixed. In a long-term N-enrichment experiment in Minnesota, a low-diversity state that emerged during N addition has persisted for decades after additions ceased. Hypothesized mechanisms preventing recovery of biodiversity include nutrient recycling, insufficient external seed supply, and litter inhibition of plant growth. Here, we present an ordinary differential equation model that unifies these mechanisms, produces bistability at intermediate N inputs, and qualitatively matches the observed hysteresis at Cedar Creek. Key features of the model, including native species' growth advantage in low-N conditions and limitation by litter accumulation, generalize from Cedar Creek to North American grasslands. Our results suggest that effective biodiversity restoration in these systems may require management beyond reducing N inputs, such as burning, grazing, haying, and seed additions. By coupling resource competition with an additional interspecific inhibitory process, the model also illustrates a general mechanism for bistability and hysteresis that may occur in multiple ecosystem types. [ABSTRACT FROM AUTHOR]

Biodiversity may increase ecosystem resilience. However, we have limited understanding if this holds true for ecosystems that respond to gradual environmental change with abrupt shifts to an alternative state. We used a mathematical model of anoxic–oxic regime shifts and explored how trait diversity in three groups of bacteria influences resilience. We found that trait diversity did not always increase resilience: greater diversity in two of the groups increased but in one group decreased resilience of their preferred ecosystem state. We also found that simultaneous trait diversity in multiple groups often led to reduced or erased diversity effects. Overall, our results suggest that higher diversity can increase resilience but can also promote collapse when diversity occurs in a functional group that negatively influences the state it occurs in. We propose this mechanism as a potential management approach to facilitate the recovery of a desired ecosystem state. [ABSTRACT FROM AUTHOR]

Although savanna woody encroachment has become a global phenomenon, relatively little is known about its effects on multiple dimensions and levels of savanna biodiversity.Using a combination of field surveys, a species‐level phylogeny, and functional metrics drawn from a morphological dataset, we evaluated how the progressive increase in tree cover in a fire‐suppressed savanna landscape affects the taxonomic, functional, and phylogenetic diversity of neotropical ant communities, at both the alpha and beta levels. Ants were sampled along an extensive tree cover gradient, ranging from open savannas to forests established in former savanna areas.Variation in tree cover had a significant influence on all facets of diversity at the beta level, whereas at the alpha level tree cover variation affected the taxonomic and functional but not the phylogenetic diversity of the ant communities.In general, ant community responses to variation in tree cover were largely non‐linear as differences in taxonomic alpha diversity and in the taxonomic, functional, and phylogenetic composition of the sampled communities were often much stronger at the savanna/forest transition than at any other part of the gradient. This indicates that savanna ant communities switch rapidly to an alternative state once the savanna turns into forest.Ant communities in the newly formed forest areas lacked many of the species typical of the savanna habitats, suggesting that the maintenance of a fire suppression policy is likely to result in a decrease in ant diversity and in the homogenisation of the ant fauna at the landscape scale. [ABSTRACT FROM AUTHOR]

Fynbos and afrotemperate forest exist as alternate stable states in the Cape Floristic Region of South Africa. In parts of Table Mountain National Park, afrotemperate forest has expanded in recent decades. The aim of this project was to explore the drivers of this change and distinguish whether this expansion represents a recovery of forest after previous clearance during the 18th century or is a novel expansion of forest range that resulted from policies of fire suppression in the 20th century. To determine the relationships between forest and fynbos and its key drivers, pollen, non-pollen palynomorphs, charcoal, stable isotope ratios (δ13C) and major and trace elements were analysed from late-Holocene sediments extracted from Orange Kloof. Pollen data show that forest cover has fluctuated over the past 3690 years. At the start of the record, under drier conditions from 1670 BCE to ~170 CE, forests contracted, and dry, asteraceous fynbos dominated the landscape. Around ~170 CE there was a shift to ericaceous fynbos as water availability increased. Weak signals of Khoekhoen pastoralists may be visible in the record around 50 CE, indicated by increased spores and charcoal. A regime shift towards increased dominance of the forest occurred ~250 CE, associated with wetter climate. Clear anthropogenic signals are associated with European settlement from 1650 CE. Reinforced by human clearance of forest, fynbos expanded during the cool conditions of the late phase of Little Ice Age (~1750–1850 CE). Forest expansion in the 20th century likely reflects fire suppression and recovery from past forest clearance. Fire needs to be managed accordingly if further expansion of forest into fynbos is to be curbed. [ABSTRACT FROM AUTHOR]

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Standing dead structures of habitat‐forming organisms (e.g., dead trees, coral skeletons, oyster shells) killed by a disturbance are material legacies that can affect ecosystem recovery processes. Many ecosystems are subject to different types of disturbance that either remove biogenic structures or leave them intact. Here we used a mathematical model to quantify how the resilience of coral reef ecosystems may be differentially affected following structure‐removing and structure‐retaining disturbance events, focusing in particular on the potential for regime shifts from coral to macroalgae. We found that dead coral skeletons could substantially diminish coral resilience if they provided macroalgae refuge from herbivory, a key feedback associated with the recovery of coral populations. Our model shows that the material legacy of dead skeletons broadens the range of herbivore biomass over which coral and macroalgae states are bistable. Hence, material legacies can alter resilience by modifying the underlying relationship between a system driver (herbivory) and a state variable (coral cover). [ABSTRACT FROM AUTHOR]

Tree species of Eurasian broadleaved forest possess two divergent trait syndromes with contrasting patterns of resource allocation adapted to different selection environments: short‐stature basal resprouters that divert resources to a bud bank adapted to frequent and severe disturbances such as fire and herbivory, and tall trees that delay reproduction by investing in rapid height growth to escape shading. Drawing on theory developed in savanna ecosystems, we propose a conceptual framework showing that the possession of contrasting trait syndromes is essential for the persistence of broadleaved trees in an open ecosystem that burns. Consistent with this hypothesis, trees of modern Eurasian broadleaved forest bear a suite of traits that are adaptive to surface and crown‐fire regimes. We contend that limited opportunities in grassland restricts recruitment to disturbance‐free refugia, and en masse establishment creates a wooded environment where shade limits the growth of light‐demanding savanna plants. Rapid height growth, which involves investment in structural support and the switch from a multi‐stemmed to a monopodial growth form, is adaptive in this shaded environment. Although clustering reduces surface fuel loads, these establishment nuclei are vulnerable to high‐intensity crown fires. The lethal effects of canopy fire are avoided by seasonal leaf shedding, and aerial resprouting enhances rapid post‐fire recovery of photosynthetic capacity. While these woody formations satisfy the structural definition of forest, their constituents are clearly derived from savanna. Contrasting trait syndromes thus represent the shift from consumer to resource regulation in savanna ecosystems. Consistent with global trends, the diversification of most contemporary broadleaved taxa coincided with the spread of grasslands, a surge in fire activity and a decline in wooded ecosystems in the late Miocene–Pliocene. Recognition that Eurasian broadleaved forest has savanna origins and persists as an alternative state with adjacent grassy ecosystems has far‐reaching management implications in accordance with functional rather than structural criteria. Shade is a severe constraint to the regeneration and growth of both woody and herbaceous growth forms in consumer‐regulated ecosystems. However, these ecosystems are highly resilient to disturbance, an essential process that maintains diversity especially among the species‐rich herbaceous component that is vulnerable to shading when consumer behaviour is altered. [ABSTRACT FROM AUTHOR]

With increased pressure from anthropogenic climate change, boreal forests are suspected to be approaching tipping points which could cause large-scale changes in tree cover and affect global climatic feedback. However, evidence for this proposed tipping is sparse and relies heavily on observations on short time scales from remote sensing data and space-for-time substitutions. Here we make use of an extensive pollen data set including 239 records of large lakes to investigate the existence of alternative stable forest cover states in the boreal forest and its adjacent biomes during the last 8000 years. By using a multimodality measure on time series of reconstructed tree cover we find very little multimodality in pollen data. To test whether this lack of multimodality is caused by limitations in the paleo data set we perform surrogate experiments. Surrogate data with alternative stable states based on the paleo vegetation–climate relationship were generated and significant multimodality was found more often than for the pollen-based tree cover (24.7% and 5.3% respectively). The response of tree cover to climate may, therefore, be more gradual and not as abrupt as would be expected from remote sensing analyses on stability. The apparent alternative stability hypothesized in the analyses of climate–vegetation relationships could be due to the strong spatial heterogeneity of environmental factors and vegetation responses as an artifact of space-for-time substitutions. Even though current and upcoming shifts in the boreal forest are indisputable and a reason for strong concern, these changes could happen gradually without going through large-scale tipping between alternative stable states. To aid adaptation and conservation measures, more knowledge is needed about boreal forest drivers and their spatial heterogeneity.

It is hypothesised that ecological restoration in grasslands can induce an alternative stable state shift in vegetation. The change in vegetation influences insect community assemblages and allows for greater functional redundancy in pollination and refuge for native insect species. 2. Insect community assemblages at eight coastal California grassland sites were evaluated. Half of these sites had undergone restoration through active revegetation of native grassland flora and half were non-restored. Insects were collected from Lupinus bicolor (Fabaceae) within 2 × 2-m2 plots in spring 2017. Lupinus bicolor is a common native species that is used in California restoration projects, and home and state landscaping projects. 3. Ordination demonstrated that insect community assemblages were different between restored and non-restored sites. These differences were seen in insect functional groups as well as taxa-specific differences and were found to be driven by environmental characteristics such as non-native forb cover. 4. Functional redundancy of herbivores decreased at restored sites, while pollinators became more redundant compared with non-restored sites. The assemblages of the common species found at restoration sites contained more native insects than those found at non-restored sites, including species such as Bombus vosnesenskii. 5. Local grassland restoration has the potential to induce an alternative stable state change and affect insect community assemblages. Additionally, it was found that grassland restoration can be a potential conservation tool to provide refugia for bumblebees (Bombus), but additional studies are required to fully understand its broader applicability.

Understanding why some renewable resources are overharvested while others are conserved remains an important challenge. Most explanations focus on institutional or ecological differences among resources. Here, we provide theoretical and empirical evidence that conservation and overharvest can be alternative stable states within the same exclusive-resource management system because of path-dependent processes, including slow institutional adaptation. Surprisingly, this theory predicts that the alternative states of strong conservation or overharvest are most likely for resources that were previously thought to be easily conserved under optimal management or even open access. Quantitative analyses of harvest rates from 217 intensely managed fisheries supports the predictions. Fisheries harvest rates also showed transient dynamics characteristic of path dependence, as well as convergence to the alternative stable state after unexpected transitions. This statistical evidence for path dependence differs from previous empirical support that was based largely on case studies, experiments, and distributional analyses. Alternative stable states in conservation appear likely outcomes for many cooperatively managed renewable resources, which implies that achieving conservation outcomes hinges on harnessing existing policy tools to navigate transitions.

Fertilizers, pesticides and global warming are threatening freshwater aquatic ecosystems. Most of these are shallow ponds or slow-flowing streams or ditches dominated by submerged macrophytes, periphyton or phytoplankton. Regime shifts between the dominance of these primary producers can occur along a gradient of nutrient loading, possibly triggered by specific disturbances influencing their competitive interactions. However, phytoplankton dominance is less desirable due to lower biodiversity and poorer ecosystem function and services. In this study, we combined a microcosm experiment with a process-based model to test three hypotheses: 1) agricultural run-off (ARO), consisting of nitrate and a mixture of organic pesticides and copper, differentially affects primary producers and enhances the risk of regime shifts, 2) warming increases the risk of an ARO-induced regime shift to phytoplankton dominance and 3) custom-tailored process-based models support mechanistic understanding of experimental results through scenario comparison. Experimentally exposing primary producers to a gradient of nitrate and pesticides at 22°C and 26°C supported the first two hypotheses. ARO had direct negative effects on macrophytes, while phytoplankton gained from warming and indirect effects of ARO like a reduction in the competitive pressure exerted by other groups. We used the process-based model to test eight different scenarios. The best qualitative fit between modeled and observed responses was reached only when taking community adaptation and organism acclimation into account. Our results highlight the importance of considering such processes when attempting to predict the effects of multiple stressors on natural ecosystems.

Functional and structural regime shifts have been observed among many ecosystems. Understanding regime shifts in watershed ecosystems is crucial for landscape management and sustainable development. We propose the perspective that the relationship dynamics of ecosystem services (ESs) can reflect watershed ecosystem regime shifts. An assessment of the critical transitions in watershed landscape patterns is integrated to support the regime shift analysis. The downstream basin of the Nu-Salween River (NSR) was selected as the study area to demonstrate regime shifts occurring from 1999 to 2019. To detect the functional critical transition, changes in the relationships among various ESs, including in the habitat quality for biodiversity (HQ), carbon storage (CS), water yield (WY), soil conservation (SC) and grain production (GP), were revealed using time series correlation analysis. To identify the critical structural transitions of watershed, the Pettitt test and principal component analysis (PCA) were used to display changes in landscape patterns. The results showed that (1) WY and GP were key ESs that could define watershed stable states; (2) three states, the “coordinated state” from 1999 to 2008, the “transient state” from 2009 to 2013 and the “trade-off state” from 2014 to 2019, were identified in the downstream basin of the NSR; and (3) the watershed functional critical transition had a 1-year time lag with the structural critical transition. This research revealed the nonlinear dynamics of a complex system in watersheds, and the detection of regime shifts that integrate the interaction dynamics of ESs can better serve watershed management to cope with abrupt changes.

Background: Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes. Methods: We integrated theoretical frameworks and empirical analyses with the aim of anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We analyzed the time-series data based on statistical physics and non-linear mechanics to describe the characteristics of the microbiome dynamics and to examine the predictability of major shifts in microbial community structure. Results: We confirmed that the abrupt community changes observed through the time-series could be described as shifts between "alternative stable states" or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the "energy landscape" analysis of statistical physics or that of a stability index of nonlinear mechanics. Conclusions: The results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems. BZtjfqfgm5MWSae9EkdSwR Video Abstract [ABSTRACT FROM AUTHOR]

Background: In aquatic ecosystems, the health and performance of fish depend greatly on the dynamics of microbial community structure in the background environment. Nonetheless, finding microbes with profound impacts on fish's performance out of thousands of candidate species remains a major challenge. Methods: We examined whether time-series analyses of microbial population dynamics could illuminate core components and structure of fish-associated microbiomes in the background (environmental) water. By targeting eel-aquaculture-tank microbiomes as model systems, we reconstructed the population dynamics of the 9605 bacterial and 303 archaeal species/strains across 128 days. Results: Due to the remarkable increase/decrease of constituent microbial population densities, the taxonomic compositions of the microbiome changed drastically through time. We then found that some specific microbial taxa showed a positive relationship with eels' activity levels even after excluding confounding effects of environmental parameters (pH and dissolved oxygen level) on population dynamics. In particular, a vitamin-B12-producing bacteria, Cetobacterium somerae, consistently showed strong positive associations with eels' activity levels across the replicate time series of the five aquaculture tanks analyzed. Network theoretical and metabolic modeling analyses further suggested that the highlighted bacterium and some other closely-associated bacteria formed "core microbiomes" with potentially positive impacts on eels. Conclusions: Overall, these results suggest that the integration of microbiology, ecological theory, and network science allows us to explore core species and interactions embedded within complex dynamics of fish-associated microbiomes. 2gKjfWoBRNSUwrepeh_GG8 Video Abstract [ABSTRACT FROM AUTHOR]