Sediment DNA Records the Critical Transition of Bacterial Communities in the Arid Lake.

It is necessary to predict the critical transition of lake ecosystems due to their abrupt, non-linear effects on social-economic systems. Given the promising application of paleolimnological archives to tracking the historical changes of lake ecosystems, it is speculated that they can also record the lake's critical transition. We studied Lake Dali-Nor in the arid region of Inner Mongolia because of the profound shrinking the lake experienced between the 1300 s and the 1600 s. We reconstructed the succession of bacterial communities from a 140-cm-long sediment core at 4-cm intervals and detected the critical transition. Our results showed that the historical trajectory of bacterial communities from the 1200 s to the 2010s was divided into two alternative states: state1 from 1200 to 1300 s and state2 from 1400 to 2010s. Furthermore, in the late 1300 s, the appearance of a tipping point and critical slowing down implied the existence of a critical transition. By using a multi-decadal time series from the sedimentary core, with general Lotka-Volterra model simulations, local stability analysis found that bacterial communities were the most unstable as they approached the critical transition, suggesting that the collapse of stability triggers the community shift from an equilibrium state to another state. Furthermore, the most unstable community harbored the strongest antagonistic and mutualistic interactions, which may imply the detrimental role of interaction strength on community stability. Collectively, our study showed that sediment DNA can be used to detect the critical transition of lake ecosystems.

Trajectories and state changes of a grassland stream and riparian zone after a decade of woody vegetation removal.

Riparian zones and the streams they border provide vital habitat for organisms, water quality protection, and other important ecosystem services. These areas are under pressure from local (land use/land cover change) to global (climate change) processes. Woody vegetation is expanding in grassland riparian zones worldwide. Here we report on a decade-long watershed-scale mechanical removal of woody riparian vegetation along 4.5 km of stream channel in a before-after control impact experiment. Prior to this removal, woody plants had expanded into grassy riparian areas, associated with a decline in streamflow, loss of grassy plant species, and other ecosystem-scale impacts. We confirmed some expected responses, including rapid increases in stream nutrients and sediments, disappearance of stream mosses, and decreased organic inputs to streams via riparian leaves. We were surprised that nutrient and sediment increases were transient for 3 years, that there was no recovery of stream discharge, and that areas with woody removal did not shift back to a grassland state, even when reseeded with grassland species. Rapid expansion of shrubs (Cornus drummondii, Prunus americana) in the areas where trees were removed allowed woody vegetation to remain dominant despite repeating the cutting every 2 years. Our results suggest woody expansion can fundamentally alter terrestrial and aquatic habitat connections in grasslands, resulting in inexorable movement toward a new ecosystem state. Human pressures, such as climate change, atmospheric CO2 increases, and elevated atmospheric nitrogen deposition, could continue to push the ecosystem along a trajectory that is difficult to change. Our results suggest that predicting relationships between riparian zones and the streams they border could be difficult in the face of global change in all biomes, even in well-studied sites.

Contact tracing-induced Allee effect in disease dynamics.

Contact tracing, case isolation, quarantine, social distancing, and other non-pharmaceutical interventions (NPIs) have been a cornerstone in managing the COVID-19 pandemic. However, their effects on disease dynamics are not fully understood. Saturation of contact tracing caused by the increase of infected individuals has been recognized as a crucial variable by healthcare systems worldwide. Here, we model this saturation process with a mechanistic and a phenomenological model and show that it induces an Allee effect which could determine an infection threshold between two alternative states-containment and outbreak. This transition was considered elsewhere as a response to the strength of NPIs, but here we show that they may be also determined by the number of infected individuals. As a consequence, timing of NPIs implementation and relaxation after containment is critical to their effectiveness. Containment strategies such as vaccination or mobility restriction may interact with contact tracing-induced Allee effect. Each strategy in isolation tends to show diminishing returns, with a less than proportional effect of the intervention on disease containment. However, when combined, their suppressing potential is enhanced. Relaxation of NPIs after disease containment--e.g. because vaccination--have to be performed in attention to avoid crossing the infection threshold required to a novel outbreak. The recognition of a contact tracing-induced Allee effect, its interaction with other NPIs and vaccination, and the existence of tipping points contributes to the understanding of several features of disease dynamics and its response to containment interventions. This knowledge may be of relevance for explaining the dynamics of diseases in different regions and, more importantly, as input for guiding the use of NPIs, vaccination campaigns, and its combination for the management of epidemic outbreaks.

Regime shifts in a shallow lake over 12 years: Consequences for taxonomic and functional diversities, and ecosystem multifunctionality.

Under increasing nutrient loading, shallow lakes may shift from a state of clear water dominated by submerged macrophytes to a turbid state dominated by phytoplankton or a shaded state dominated by floating macrophytes. How such regime shifts mediate the relationship between taxonomic and functional diversities (FD) and lake multifunctionality is poorly understood. We employed a detailed database describing a shallow lake over a 12-year period during which the lake has displayed all the three states (clear, turbid and shaded) to investigate how species richness, FD of fish and zooplankton, ecosystem multifunctionality and five individual ecosystem functions (nitrogen and phosphorus concentrations, standing fish biomass, algae production and light availability) differ among states. We also evaluated how the relationship between biodiversity (species richness and FD) and multifunctionality is affected by regime shifts. We showed that species richness and the FD of fish and zooplankton were highest during the clear state. The clear state also maintained the highest values of multifunctionality as well as standing fish biomass production, algae biomass and light availability, whereas the turbid and shaded states had higher nutrient concentrations. Functional diversity was the best predictor of multifunctionality. The relationship between FD and multifunctionality was strongly positive during the clear state, but such relationship became flatter after the shift to the turbid or shaded state. Our findings illustrate that focusing on functional traits may provide a more mechanistic understanding of how regime shifts affect biodiversity and the consequences for ecosystem functioning. Regime shifts towards a turbid or shaded state negatively affect the taxonomic diversity and FD of fish and zooplankton, which in turn impairs the multifunctionality of shallow lakes.

Cascading effects of benthic fish impede reinstatement of clear water conditions in lakes: A mesocosm study.

In shallow eutrophic lakes, submersed macrophytes are essential for maintaining a clear water state, and they are affected markedly by fishes directly through herbivory and indirectly by fish-invertebrate-periphyton complexity, a pathway that presently is not well understood in subtropical lakes but probably vital to lake managements. We conducted a mesocosm study involving benthic fish (Misgurnus anguillicaudatus), snails (Radix swinhoei) and submersed macrophyte (Vallisneria natans), aiming to examine whether benthic fish is detrimental to reestablishment of clear-water macrophyte-dominated state in eutrophic degraded lakes. In addition, we aimed to investigate the cascading effect that benthic fish might have on periphyton and phytoplankton and to what extent snails can alleviate this effect. Our results showed that benthic fish promoted nutrient release from the sediment and thereby facilitated the growth of phytoplankton and periphyton, leading to reduced growth of submerged macrophytes due to shading. Snails consumed the periphyton attached on the leaves of macrophytes, thereby being beneficial to the plant growth, albeit it could not fully counteract the adverse effects from benthic fish. The water quality indicators in terms of nutrients concentrations, phytoplankton biomass and light extinction coefficient along the water column was affected primarily by benthic fish, followed by macrophytes and snails. To target a clear-water condition, the water quality was best at the presence of macrophytes alone or in combination with snails, and worst at the presence of benthic fish. Our results implied that the removal of benthic fish should be a useful ecological restoration method for rehabilitation of submersed macrophytes and water quality improvement in subtropic, eutrophic, shallow lakes following external nutrient loading reduction.

Disease and fire interact to influence transitions between savanna-forest ecosystems over a multi-decadal experiment.

Global change is shifting disturbance regimes that may rapidly change ecosystems, sometimes causing ecosystems to shift between states. Interactions between disturbances such as fire and disease could have especially severe effects, but experimental tests of multi-decadal changes in disturbance regimes are rare. Here, we surveyed vegetation for 35 years in a 54-year fire frequency experiment in a temperate oak savanna-forest ecotone that experienced a recent outbreak of oak wilt. Different fire regimes determined whether plots were savanna or forest by regulating tree abundance (r2  = 0.70), but disease rapidly reversed the effect of fire exclusion, increasing mortality by 765% in unburned forests, but causing relatively minor changes in frequently burned savannas. Model simulations demonstrated that disease caused unburned forests to transition towards a unique woodland that was prone to transition to savanna if fire was reintroduced. Consequently, disease-fire interactions could shift ecosystem resilience and biome boundaries as pathogen distributions change.

Basin Transition and Alternative States: Role of Multi-species Herbivores-Induced Volatile in Plant-Insect Interactions.

A simple model on volatile organic compound (VOC)-mediated plant-insect interactions is proposed and examined here, when two different classes of herbivorous insects competing for a common resource (plant) in the presence of a specialist carnivorous enemy, which only predates one of the herbivore species. We, particularly, emphasize the impact of VOCs on plant's growth fitness. The system experiences several local and global bifurcations with emergent alternative states for variations in recruitment factors and predation rate. Basin transitions and basin of attractions have provided detail descriptions on the selectivity of the alternative states, when only one of the herbivore species can survive depending on the choice of initial population densities of the interacting species and how it provides a steady growth in plant. Additionally, our results support the concept of competitive exclusion principle in an indirect interspecific competition between the two herbivore types for the common resource, plant.

Temporal clustering of extreme climate events drives a regime shift in rocky intertidal biofilms.

Research on regime shifts has focused primarily on how changes in the intensity and duration of press disturbances precipitate natural systems into undesirable, alternative states. By contrast, the role of recurrent pulse perturbations, such as extreme climatic events, has been largely neglected, hindering our understanding of how historical processes regulate the onset of a regime shift. We performed field manipulations to evaluate whether combinations of extreme events of temperature and sediment deposition that differed in their degree of temporal clustering generated alternative states in rocky intertidal epilithic microphytobenthos (biofilms) on rocky shores. The likelihood of biofilms to shift from a vegetated to a bare state depended on the degree of temporal clustering of events, with biofilm biomass showing both states under a regime of non-clustered (60 d apart) perturbations while collapsing in the clustered (15 d apart) scenario. Our results indicate that time since the last perturbation can be an important predictor of collapse in systems exhibiting alternative states and that consideration of historical effects in studies of regime shifts may largely improve our understanding of ecosystem dynamics under climate change.

Experimental evidence of spatial signatures of approaching regime shifts in macroalgal canopies.

Developing early warning signals to predict regime shifts in ecosystems is a central issue in current ecological research. While there are many studies addressing temporal early warning indicators, research into spatial indicators is far behind, with field experiments even more rare. Here, we tested the performance of spatial early warning signals in an intertidal macroalgal system, where removal of algal canopies pushed the system toward a tipping point (corresponding to approximately 75% of canopy loss), marking the transition between a canopy- to a turf-dominated state. We performed a two-year experiment where spatial early warning indicators were assessed in transects where the canopy was differentially removed (from 0 to 100%). Unlike Moran correlation coefficient at lag-1, spatial variance, skewness, and spatial spectra at low frequency increased along the gradient of canopy degradation and dropped, or did not show any further increase beyond the transition point from a canopy- to a turf-dominated state (100% canopy removal). Our study provides direct evidence of the suitability of spatial early warning signals to anticipate regime shifts in natural ecosystems, emphasizing the importance of field experiments as a powerful tool to establish causal relationships between environmental stressors and early warning indicators.

Reduced resistance to sediment-trapping turfs with decline of native kelp and establishment of an exotic kelp.

Understanding the strength and type of interactions among species is vital to anticipate how ecosystems will respond to ongoing anthropogenic stressors. Here, we examine the ecological function of native (Ecklonia radiata) and invasive (Undaria pinnatifida) kelps in resisting shifts to sediment-trapping turf on reefs within the highly urbanized temperate Port Phillip Bay (PPB), Australia. Short-term (30 days) and long-term (232 days) manipulations demonstrated that kelp laminae can clear and maintain the substratum free of turfs, while conversely, removal of kelp leads to a proliferation of turfs. Analyses looking at the relationship between total length of E. radiata and U. pinnatifida and the area cleared of turf algae showed that the clearing effect of E. radiata over a year was greater than that of U. pinnatifida due to the annual die-back of the invasive. A natural experiment (608 days) identified that ongoing sea urchin (Heliocidaris erythrogramma) grazing led to native kelp bed decline, facilitating turf dominance. Even though U. pinnatifida establishes once native beds are disturbed, its ecological function in clearing turf is weaker than E. radiata, given its annual habit. In PPB, turfs represent the more persistent and problematic algal group and are likely changing the structure, function, and energy flows of shallow temperate reefs in this urbanised embayment.

The present is the key to the past: linking regime shifts in kelp beds to the distribution of deep-living sea urchins.

Understanding processes that drive sudden shifts in ecosystem structure and function has become an important research focus for coastal management. In kelp bed ecosystems, regime shifts occur when high densities of sea urchins destructively graze kelp and create coralline algal barrens. While the importance of predation and disease in mediating shifts between kelp beds and barrens on shallow rocky reefs has been well documented, little is known about the role of deep-living urchins in these alternative stable-state dynamics. In this study, we test the hypothesis that deep-living urchins along the central Atlantic coast of Nova Scotia move onshore and trigger shifts from kelp beds to barrens on shallow rocky reefs. We documented urchin distribution and abundance using tow-camera surveys down to 140 m depth and spanning 140 km of coast and created a predictive species-distribution model using these observations and spatial data on environmental factors that likely delineate suitable habitat for urchins. We used a random forest model to generate our predictions, which correctly classified 91% of observations into a positive or negative occurrence of urchins. Sea urchins predominantly occurred within 1.5 km of shore, in depressions and flat habitats between 40 and 85 m depth. We found that shallow regions where destructive grazing fronts have been documented over the past four decades were closer to deep-living sea urchin habitats compared to regions that remained in a kelp bed state during the same period. This supports our prediction that deep-living urchins play an important role in driving shallow regime shift dynamics, and indicates that their distribution can help identify areas of coast that are most vulnerable to a collapse to barrens.

Integrating the invisible fabric of nature into fisheries management.

Overfishing and environmental change have triggered many severe and unexpected consequences. As existing communities have collapsed, new ones have become established, fundamentally transforming ecosystems to those that are often less productive for fisheries, more prone to cycles of booms and busts, and thus less manageable. We contend that the failure of fisheries science and management to anticipate these transformations results from a lack of appreciation for the nature, strength, complexity, and outcome of species interactions. Ecologists have come to understand that networks of interacting species exhibit nonlinear dynamics and feedback loops that can produce sudden and unexpected shifts. We argue that fisheries science and management must follow this lead by developing a sharper focus on species interactions and how disrupting these interactions can push ecosystems in which fisheries are embedded past their tipping points.

Historical contingency in species interactions: towards niche-based predictions.

The way species affect one another in ecological communities often depends on the order of species arrival. The magnitude of such historical contingency, known as priority effects, varies across species and environments, but this variation has proven difficult to predict, presenting a major challenge in understanding species interactions and consequences for community structure and function. Here, we argue that improved predictions can be achieved by decomposing species' niches into three components: overlap, impact and requirement. Based on classic theories of community assembly, three hypotheses that emphasise related, but distinct influences of the niche components are proposed: priority effects are stronger among species with higher resource use overlap; species that impact the environment to a greater extent exert stronger priority effects; and species whose growth rate is more sensitive to changes in the environment experience stronger priority effects. Using nectar-inhabiting microorganisms as a model system, we present evidence that these hypotheses complement the conventional hypothesis that focuses on the role of environmental harshness, and show that niches can be twice as predictive when separated into components. Taken together, our hypotheses provide a basis for developing a general framework within which the magnitude of historical contingency in species interactions can be predicted.

Community assembly history alters relationships between biodiversity and ecosystem functions during restoration.

Relationships between biodiversity and ecosystem functioning depend on the processes structuring community assembly. However, predicting biodiversity-ecosystem functioning (BEF) relationships based on community assembly remains challenging because assembly outcomes are often contingent on history and the consequences of history for ecosystem functions are poorly understood. In a grassland restoration experiment, we isolated the role of history for the relationships between plant biodiversity and multiple ecosystem functions by initiating assembly in three different years, while controlling for all other aspects of community assembly. We found that two aspects of assembly history-establishment year and succession-altered species and trait community trajectories, which in turn altered net primary productivity, decomposition rates, and floral resources. Moreover, history altered BEF relationships (which ranged from positive to negative), both within and across functions, by modifying the causal pathways linking species identity, traits, diversity, and ecosystem functions. Our results show that the interplay of deterministic succession and environmental stochasticity during establishment mediate historical contingencies that cause variation in biodiversity and ecosystem functions, even under otherwise identical assembly conditions. An explicit attention to history is needed to understand why biodiversity-ecosystem function relationships vary in natural ecosystems: a critical question at the intersection of fundamental theory and applications to environmental change biology and ecosystem restoration.

Temperature response of aquatic greenhouse gas emissions differs between dominant plant types.

Greenhouse gas (GHG) emissions from small inland waters are disproportionately large. Climate warming is expected to favor dominance of algae and free-floating plants at the expense of submerged plants. Through different routes these functional plant types may have far-reaching impacts on freshwater GHG emissions in future warmer waters, which are yet unknown. We conducted a 1,000 L mesocosm experiment testing the effects of plant type and warming on GHG emissions from temperate inland waters dominated by either algae, free-floating or submerged plants in controls and warmed (+4 °C) treatments for one year each. Our results show that the effect of experimental warming on GHG fluxes differs between dominance of different functional plant types, mainly by modulating methane ebullition, an often-dominant GHG emission pathway. Specifically, we demonstrate that the response to experimental warming was strongest for free-floating and lowest for submerged plant-dominated systems. Importantly, our results suggest that anticipated shifts in plant type from submerged plants to a dominance of algae or free-floating plants with warming may increase total GHG emissions from shallow waters. This, together with a warming-induced emission response, represents a so far overlooked positive climate feedback. Management strategies aimed at favouring submerged plant dominance may thus substantially mitigate GHG emissions.

Functional attractors in microbial community assembly.

For microbiome biology to become a more predictive science, we must identify which descriptive features of microbial communities are reproducible and predictable, which are not, and why. We address this question by experimentally studying parallelism and convergence in microbial community assembly in replicate glucose-limited habitats. Here, we show that the previously observed family-level convergence in these habitats reflects a reproducible metabolic organization, where the ratio of the dominant metabolic groups can be explained from a simple resource-partitioning model. In turn, taxonomic divergence among replicate communities arises from multistability in population dynamics. Multistability can also lead to alternative functional states in closed ecosystems but not in metacommunities. Our findings empirically illustrate how the evolutionary conservation of quantitative metabolic traits, multistability, and the inherent stochasticity of population dynamics, may all conspire to generate the patterns of reproducibility and variability at different levels of organization that are commonplace in microbial community assembly.

Stoichiometric mismatch causes a warming-induced regime shift in experimental plankton communities.

In many ecosystems, consumers respond to warming differently than their resources, sometimes leading to temporal mismatches between seasonal maxima in consumer demand and resource availability. A potentially equally pervasive, but less acknowledged threat to the temporal coherence of consumer-resource interactions is mismatch in food quality. Many plant and algal communities respond to warming with shifts toward more carbon-rich species and growth forms, thereby diluting essential elements in their biomass and intensifying the stoichiometric mismatch with herbivore nutrient requirements. Here we report on a mesocosm experiment on the spring succession of an assembled plankton community in which we manipulated temperature (ambient vs. +3.6°C) and presence versus absence of two types of grazers (ciliates and Daphnia), and where warming caused a dramatic regime shift that coincided with extreme stoichiometric mismatch. At ambient temperatures, a typical spring succession developed, where a moderate bloom of nutritionally adequate phytoplankton was grazed down to a clear-water phase by a developing Daphnia population. While warming accelerated initial Daphnia population growth, it speeded up algal growth rates even more, triggering a massive phytoplankton bloom of poor food quality. Consistent with the predictions of a stoichiometric producer-grazer model, accelerated phytoplankton growth promoted the emergence of an alternative system attractor, where the extremely low phosphorus content of the abundant algal food eventually drove Daphnia to extinction. Where present, ciliates slowed down the phytoplankton bloom and the deterioration of its nutritional value, but this only delayed the regime shift. Eventually, phytoplankton also grew out of grazer control in the presence of ciliates, and the Daphnia population crashed. To our knowledge, the experiment is the first empirical demonstration of the "paradox of energy enrichment" (grazer starvation in an abundance of energy-rich but nutritionally imbalanced food) in a multispecies phytoplankton community. More generally, our results support the notion that warming can exacerbate the stoichiometric mismatch at the plant-herbivore interface and limit energy transfer to higher trophic levels.

Pelagic energy flow supports the food web of a shallow lake following a dramatic regime shift driven by water level changes.

Across the globe, lake ecosystems are exposed to a variety of human disturbances. A notable example is shallow lakes where human-induced eutrophication or water level fluctuation may result in a switch from a clear-water, macrophyte-dominated state to a turbid, phytoplankton-dominated state. Yet, few investigations have described synchronous changes in biotic assemblage composition and food web framework under such a shift between alternative states. We used stable carbon and nitrogen isotopes to test the extent to which switching from macrophyte to phytoplankton dominance in Lake Gucheng, triggered by a water level increase, would alter ecosystem structure and change the basal resources supporting the food web. We found that invertebrates and fish compensated for a reduction of macrophyte and epiphyte resources by deriving more energy from the alternative pelagic energy channel, where benthic invertebrates act as crucial links between primary producers and higher consumers by transporting δ13C-depleted pelagic algae to the benthic zone. Although consumers can respond to large shifts in energy allocation and stabilize food web dynamics through their ability to feed across multiple energy pathways, our study suggest that energy subsidies may promote trophic cascades and enhance the stability of the turbid regime.

Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states.

A major challenge for advancing our understanding of the functional role of soil microbial communities is to link changes in their structure and function under climate change. To address this challenge requires new understanding of the mechanisms that underlie the capacity of soil microbial communities to resist and recover from climate extremes. Here, we synthesize emerging understanding of the intrinsic and extrinsic factors that influence the resistance and resilience of soil microbial communities to climate extremes, with a focus on drought, and identify drivers that might trigger abrupt changes to alternative states. We highlight research challenges and propose a path for advancing our understanding of the resistance and resilience of soil microbial communities to climate extremes, and of their vulnerability to transitions to alternative states, including the use of trait-based approaches. We identify a need for new approaches to quantify resistance and resilience of soil microbial communities, and to identify thresholds for transitions to alternative states. We show how high-resolution time series coupled with gradient designs will enable detecting response patterns to interacting drivers. Finally, to account for extrinsic factors, we suggest that future studies should use environmental gradients to track soil microbial community responses to climate extremes in space and time. This article is part of the theme issue 'Climate change and ecosystems: threats, opportunities and solutions'.

Modifying connectivity to promote state change reversal: the importance of geomorphic context and plant-soil feedbacks.

Alternative states maintained by feedbacks are notoriously difficult, if not impossible, to reverse. Although positive interactions that modify soil conditions may have the greatest potential to alter self-reinforcing feedbacks, the conditions leading to these state change reversals have not been resolved. In a 9-yr study, we modified horizontal connectivity of resources by wind or water on different geomorphic surfaces in an attempt to alter plant-soil feedbacks and shift woody-plant-dominated states back toward perennial grass dominance. Modifying connectivity resulted in an increase in litter cover regardless of the vector of transport (wind, water) followed by an increase in perennial grass cover 2 yr later. Modifying connectivity was most effective on sandy soils where wind is the dominant vector, and least effective on gravelly soils on stable surfaces with low sediment movement by water. We found that grass cover was related to precipitation in the first 5 yr of our study, and plant-soil feedbacks developed following 6 yr of modified connectivity to overwhelm effects of precipitation on sandy, wind-blown soils. These feedbacks persisted through time under variable annual rainfall. On alluvial soils, either plant-soil feedbacks developed after 7 yr that were not persistent (active soils) or did not develop (stable soils). This novel approach has application to drylands globally where desertified lands have suffered losses in ecosystem services, and to other ecosystems where connectivity-mediated feedbacks modified at fine scales can be expected to impact plant recovery and state change reversals at larger scales, in particular for wind-impacted sites.