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At certain nutrient concentrations, shallow freshwater lakes are generally characterized by two contrasting ecological regimes with disparate patterns of biodiversity and biogeochemical cycles: a macrophyte-dominated regime (MDR) and a phytoplankton-dominated regime (PDR). To reveal ecological mechanisms that affect bacterioplankton along the regime shift, Illumina MiSeq sequencing of the 16S rRNA gene combined with a novel network clustering tool (Manta) were used to identify patterns of bacterioplankton community composition across the regime shift in Taihu Lake, China. Marked divergence in the composition and ecological assembly processes of bacterioplankton community was observed under the regime shift. The alpha diversity of the bacterioplankton community consistently and continuously decreased with the regime shift from MDR to PDR, while the beta diversity presents differently. Moreover, as the regime shifted from MDR to PDR, the contribution of deterministic processes (such as environmental selection) to the assembly of bacterioplankton community initially decreased and then increased again as regime shift from MDR to PDR, most likely as a consequence of differences in nutrient concentration. The topological properties, including modularity, transitivity and network diameter, of the bacterioplankton co-occurrence networks changed along the regime shift, and the co-occurrences among species changed in structure and were significantly shaped by the environmental variables along the regime transition from MDR to PDR. The divergent environmental state of the regimes with diverse nutritional status may be the most important factor that contributes to the dissimilarity of bacterioplankton community composition along the regime shift.

Ocean warming linked to anthropogenic climate change is impacting the ecology of marine species around the world. In 2010, the Gulf of Maine and Scotian Shelf regions of the Northwest Atlantic underwent an unprecedented regime shift. Forced by climate-driven changes in the Gulf Stream, warm slope waters entered the region and created a less favorable foraging environment for the endangered North Atlantic right whale population. By mid-decade, right whales had shifted their late spring/summer foraging grounds from the Gulf of Maine and the western Scotian Shelf to the Gulf of St. Lawrence. The population also began exhibiting unusually high mortality in 2017. Here, we report that climate-driven changes in ocean circulation have altered the foraging environment and habitat use of right whales, reducing the population’s calving rate and exposing it to greater mortality risks from ship strikes and fishing gear entanglement. The case of the North Atlantic right whale provides a cautionary tale for the management of protected species in a changing ocean.

Opportunities to study community-level responses to extreme natural pulse disturbances in unaltered ecosystems are rare. Lake sediment records that span thousands of years can contain well-resolved sediment pulses, triggered by earthquakes. These palaeorecords provide a means to study repeated pulse disturbances and processes of resistance (insensitivity to disturbance) and ecological resilience (capacity to regain structure, function and process). In this study, sedimentary DNA was extracted from a sediment core from Lake Paringa (New Zealand) that is situated in a near natural catchment. Metabarcoding and inferred functions were used to assess the lake microbial community over the past 1100 years - a period that included four major earthquakes. Microbial community composition and function differed significantly between highly perturbed (postseismic, ~50 years) phases directly after the earthquakes and more stable (interseismic, ~250 years) phases, indicating a lack of community resistance. Although community structure differed significantly in successive postseismic phases, function did not, suggesting potential functional redundancy. Significant differences in composition and function in successive interseismic phases demonstrate that communities are not resilient to large-scale natural pulse disturbances. The clear difference in structure and function, and high number of indicator taxa (responsible for driving differences in communities between phases) in the fourth interseismic phase probably represents a regime shift, possibly due to the two-fold increase in sediment and terrestrial biospheric organic carbon fluxes recorded following the fourth earthquake. Large pulse disturbances that enhance sediment inputs into lake systems may produce an underappreciated mechanism that destabilises lake ecosystem processes.

Coral reefs across the globe are facing threats from a variety of anthropogenic disturbances. Consequently, the proportional representation of live scleractinian corals in the benthic community has declined substantially in many regions. In contrast, parts of the reef ecosystem around Mo’orea (French Polynesia) have displayed remarkable rebound potential. Nevertheless, detailed studies of when, where, and to what extent reefs have been disturbed and subsequently recovered in the different reef habitats are lacking. Using long-term monitoring data (2004-2018), we reveal that the spatiotemporal dynamics of benthic communities differ markedly between the contiguous inner (fringing and barrier) and outer (fore) reefs. Coral communities on inner reefs vary spatially but were remarkably stable over 15 yr, exhibiting consistent levels of coral and algal cover, with no evidence for disturbance-driven regimes or community transitions. In contrast, the outer reefs showed marked declines in coral cover following consecutive acute disturbances, but coral recovered rapidly thereafter. Nevertheless, community composition changed significantly, with Pocillopora replacing Acropora as the dominant genus at several sites, indicating a more subtle but potentially critical transition into an alternative state defined by the prevalence of a single, fast-growing genus. Inner reef stability and outer reef recovery provide evidence that the effects of environmental disturbances and chronic anthropogenic stressors can manifest in fundamentally different ways, depending on prevailing conditions. Our results suggest important ecological and physical links between inner and outer reef systems that influence the observed dynamics, emphasizing that reef ecosystem management and conservation strategies need to consider all habitats.

Climate change is expected to impact on marine-capture fisheries around the world. The Korea Strait showes the highest fisheries production among the adjacent seas of Korea, but studies on changes in the fish community related with climate change are scarce. We evaluated the spatio-temporal changes in fish assemblages, and their relationships with oceanic conditions in the Korea Strait (KS, 126°–129°5′E, 33°5′–35°N) to provide a scientific basis for developing fisheries policies to adapt to climate change and global warming. We used the inflow indices of the Korea Strait Bottom Cold Water and the Tsushima Warm Current, water temperature and salinity, and commercial fisheries catch data from 1986 to 2010. To detect temporal shifts in the oceanic conditions, we applied a sequential t test of regime shift. To evaluate spatio-temporal changes of the fish assemblage structure by year, month, and fishing block, we graphically summarized the species compositions of the commercial fisheries catch data by correspondence analysis (CA). We conducted cross-correlation and canonical CA to evaluate the relationship between the oceanic conditions and fish assemblages. Sardine and filefish dominated in spring and were mainly distributed far away from the coast. Anchovy were mostly caught in summer near the southeast coast of Korea, and their annual catch steadily increased. Squid and hairtail dominated in autumn–winter, and were mainly distributed from the northern part off Jeju Island to the southeast water of Korea. Chub mackerel were relatively constant in annual and seasonal catch. CA detected a shift in the fish assemblage between 1990 and 1991, which we speculated was triggered by the 1988–1989 regime shift in the North Pacific. Surface temperatures at 0–20 m depths, especially with a time lag of 1 year, were significantly correlated with the 1990–1991 shift in fish assemblage structure. We concluded that (1) the KS is an intermediate area between the waters of Ieodo and the East Sea with respect to the timing of shift in fish assemblage structure, (2) the regional shifts were characterized by the replacement of dominant fish species from sardine and filefish to chub mackerel and squid. We hope that further multidisciplinary studies between regional oceanographers and fisheries scientists will contribute to the development of fisheries policies through better understanding of the interactions between oceanographic processes and fishes at the regional scale in adaptation to climate change.

We drilled a core in Tingming Lake (located at the tree line) to conduct pollen and diatom analyses. The pollen record shows that the vegetation ecosystem is very stable and has no obvious regime shift signals, although the vegetable belt has moved gradually upward or downward under the backdrop of climate change. There may be a positive relationship between the vegetation ecosystem stability and the turnover component (βsim). Diatoms, which record the lake ecosystem, show an obvious regime shift signal in 1929 AD, which was possibly was due to environmental changes or decreased nutrient inputs. However, there were fluctuations in species richness and species dissimilarity and there was a slightly increased β diversity (βsor), which was mainly interpreted by the increased turnover component (βsim). It is difficult to determine the relationship between the unstable stability and diversity fluctuations. Therefore, the relationships between diversity and stability in the adjacent vegetation and lake ecosystems are different. It is possible that β diversity partitioning may lead to an improved understanding of ecosystem stability.

Deterioration of aquatic ecosystems, as a consequence of human-induced disturbances, is a critical global concern. To fully understand the responses of aquatic systems to anthropogenic impacts, it is crucial to assess long-term changes in lakes. The water quality of Jili Lake, a large water body in northwest China, has deteriorated recently, owing to the growing impacts of regional warming and human activities. Thus, Jili Lake was a prime candidate for evaluation of historical multi-stressor impacts. Meteorological data, historical documents, and assemblages of cladoceran microfossils in the sediments of Jili Lake were employed to investigate changes in the cladoceran community over the past century, and to evaluate the response of that aquatic community to human activities. From the 1920s to the 1950s, species richness of the cladoceran community was high, which reflected conditions of relatively low human impact. From the 1960s to 1970s, a sharp decrease in Bosmina longirostris, a planktonic cladoceran species, suggested a decrease in water level as a result of dam construction and intensified water exploitation. Since the 1980s, the water level in the lake has been restored, but increased fish farming and construction of a water storage facility caused salinisation and eutrophication of Jili Lake. Accordingly, the cladoceran community displayed distinct signs of a regime shift, with a gradual transition to dominance of B. longirostris and a sharp decrease in littoral species (e.g. Leydigia leydigi, L. acanthocercoides, Alona quadrangularis, Alona affinis). Our results suggest that human-induced disturbances were the main factor that drove changes in the cladoceran community since about the mid-20th century.

Global warming is facilitating the range expansion of tropical herbivores, causing a tropicalization of temperate marine ecosystems, where tropical herbivores can suppress habitat‐forming macrophytes, supporting the resilience of canopy‐free ecosystem states. However, currently we lack a thorough understanding of the mechanisms that, on one hand, support the persistence of tropical herbivores and on the other support the recovery of temperate foundation species in tropicalized ecosystems, a required knowledge to predict potential regime shifts and reversals to the baseline state of the ecosystem. This study tested processes behind the persistence of the tropicalization of temperate reefs which experienced a complete loss of their kelp forests and an influx of tropical herbivores following a marine heatwave in 2011. For this, we assessed the feedback mechanisms that maintain turf‐dominated states (recruitment of tropical herbivores, browsing and grazing rates and turf cover) and those that resist it (kelp recruitment, survival and reproductiveness). We found that the reefs remained tropicalized with high abundances of turf and tropical herbivores after 9 years from the regime shift. The rabbitfish Siganus fuscescens and the chub Kyphosus bigibbus were the most important herbivores whose persistence was supported by the adjacent reef lagoon, where seagrass meadows and the backreef habitats hosted juveniles of both species, particularly rabbitfish. Tropical herbivores exerted a strong top–down control on turf seaweed and kelp during herbivory assays, rapidly consuming kelp individuals in open areas. However, in topographical refuges in the reefs, herbivory was low and kelp individuals survived, with some having reproductive tissue. Synthesis. Our findings incorporate the importance of nursery grounds for tropical herbivores and herbivory refugia for kelp individuals into the tropicalization model, where the former increases the resilience of canopy‐free states and the latter might facilitate recovering kelp populations. The restoration of abundant warm‐resistant kelp populations in shelters could provide local sources of propagules to recolonize open spaces; however, our results suggest that the reduction of herbivory and the provision of turf‐free substratum would be necessary to boost the recovery of kelp forests.

The enhanced or reduced growth of juvenile masu salmon (Oncorhynchus masou masou) may result from climate changes to their environment and thus impact on the eco-evolutionary dynamics of their life-history choices. Male juveniles with status, i.e., if their body size is larger than a threshold, stay in the stream and become resident males reproducing for multiple years, while those with smaller status, i.e., their body size is below the threshold, migrate to the ocean and return to the stream one year later to reproduce only once. Since juvenile growth is suppressed by the density of resident males, the fraction of resident males may stay in equilibrium or fluctuate wildly over a 2-year period. When the threshold value evolves, the convergence stable strategy may generate either an equilibrium or large fluctuations of male residents. If environmental changes occur faster than the rate of evolutionary adaptation, the eco-evolutionary dynamics exhibit a qualitative shift in the population dynamics. We also investigated the relative assessment models, in which individual life-history choices are made based on the individual’s relative status within the juvenile population. The eco-evolutionary dynamics are very different from the absolute assessment model, demonstrating the importance of understanding the mechanisms of life history choices when predicting the impacts of climate change.

Modified fish behaviors in response to anthropogenic stressors, such as chemicals, microplastics, acoustic emissions and fisheries, are a debated driver of change in freshwater ecosystems and oceans. Our ability to judge the severity of observed behavioral responses is hampered by limited knowledge regarding how subtle behavior modifications in prey fish affect ecosystems. Here we show that anthropogenic stressors affecting fish boldness, are not expected to cause population collapse, but rather elusive effects on fish length, population biomass, reproduction and ecosystem state shifts. We use a physiologically structured population model (three trophic levels), well fed with empirical data, to simulate how previously suggested alterations of fish boldness traits due to anthropogenic stressors affect ecosystem structure. Our results suggest that these stressors may cause ecosystem structure effects, such as skewed size distributions, reduced fish biomass and reduced reproduction success, by altering the foraging behavior of fish. However, the specific structure effects depend on where the boldness‐shyness continuum change occurs and on the species‐specific life‐stages. The model also highlights somewhat counterintuitive effects leading to possible extinction of predators when the foraging behavior of the prey is hampered. We conclude that anthropogenic forcing of fish behavior may be a hidden mechanism behind ecosystem structure changes in both freshwater and marine ecosystems.

The swap in abundance between two Calanus species in the North Sea during the 1980s constitutes a quintessential example of regime shift, with important ecosystemic and economic repercussions because these copepods constitute a major component of the diet of larval and juvenile cods. It is hypothesized that this transition was driven by gradual changes in primary productivity, the North Atlantic Oscillation (NAO) and sea surface temperatures (SST), and yet how these factors contribute to the population dynamics of these two species and the overall regime shift remains unclear. Here, we combine a highly resolved and spatially structured longitudinal dataset with population dynamics theory-based models to obtain a thorough and more detailed description of populations' responses to the regime shift observed in the North Sea. Our analyses highlight that this transition exhibits a clear spatial structure and involved a decoupling between the dynamics of Calanus finmarchicus and the NAO in western regions and between Calanus helgolandicus and SST in the eastern regions of the North Sea. Consequently, the observed switch in abundance between these species reflects the interaction between species-specific attributes, a well-defined spatial structure with a marked east-west axis and a decoupling between the ecological drivers and Calanus population dynamics following the shift. Succinctly, we suspect that higher water temperatures have favored C. helgolandicus and resulted in restrictive conditions for C. finmarchicus, eventually overshadowing the effects of NAO detected in historical records. Overall, our study illustrates how population dynamics theory can be successfully employed to disentangle the complex and multifactorial nature of a regime shift in response to gradually changing environmental conditions.

Regime shifts of climatic and environmental conditions potentially affect productivity of fisheries resources, posing challenging issues to stock management. The stocks of the Japanese flying squid (Todarodes pacificus) are suspected to suffer from regime shifts, but their detection is difficult and possibly doubtful because the nature of short-lived species readily makes the effect of regime shifts confounded with observation errors. Here we developed a new state-space assessment model to evaluate the influence of regime shifts on spawner-recruitment relationship of the Japanese flying squid. The model simultaneously estimates the population dynamics of multiple stocks that could share some life history parameters, making parameter inference stable. We demonstrate that two-time regime shifts of productivity around 1991 and 2015 caused two-to three-fold changes of maximum sustinabile yields. The model with regime shifts clarifies the relationship between fishing pressure and spawner abudance that is difficult to detect in a model with no regime shift. The state-space approach will be a promising tool to accurately assess stock status by separating recruitment process from observation errors and contribute tothe management of marine biological resources sensitive to regime shifts.

The complexity and spatio–temporal scale of populations’ dynamics influence how populations respond to large‐scale ecological pressures. Detecting and attributing synchrony (i.e. temporally coincident fluctuations in populations’ parameters) is key as synchronous populations can become more vulnerable to stochastic events that can affect the viability of harvest and have profound consequences to community structure. Here, we aimed to estimate the level of synchrony in fish growth within and among species across 1 million km2 and identify the environmental drivers contributing to synchronous population fluctuations. We developed otolith increment‐based growth chronologies for two deep‐sea scorpaenid fishes (Helicolenus dactylopterus and Pontinus kuhlii) from geographically and bathymetrically disjunct populations in the northeast Atlantic (one species in three locations; two species with different depth preferences). We used hierarchical models to partition variation in growth within and between populations attributing it to intrinsic (age, species, population) and extrinsic (environmental variables) drivers. We assessed synchrony in growth variation within and among species and identified common change points in population specific growth patterns. We documented time‐variant synchrony in growth variation of geographically and bathymetrically segregated deep‐sea fish populations, lasting 25 and 18 years, respectively. The observed synchrony was likely driven by shared environmental forcing (Moran effect) as large‐scale climate indices (East Atlantic pattern and North Atlantic Oscillation) were important environmental drivers of overall growth variation while the onset of synchrony in growth variation was likely related to marine regime shifts occurring in a wide area of the northeast Atlantic that affected the entire ecosystem. However, our capacity to extrapolate growth information across species and locations was dependent on the timing and magnitude of environmental change. Developing a better understanding of the mechanisms driving growth synchrony is key to ensure sustainable management of populations in habitats that are fragile and highly sensible to environmental change, such as the deep‐sea.

Habitat alterations that result from anthropogenic disturbance impact both the abiotic and biotic conditions of ecosystems, causing changes in biodiversity in many parts of the world. Recently, the use of functional diversity has been suggested as an approach to better evaluate the effects of such disturbance on particular communities. Here, we investigated the temporal changes in species and functional diversities of fish communities in the downstream area of the Three Gorges Dam (TGD) before, during, and after impoundment. We found two regime shifts in the fish community in 2004 and 2013 following impoundment. Although taxonomic diversity declined sharply at the first regime shift, it increased at the second shift. On the other hand, functional diversity declined throughout the same period, indicating the loss of functional diversity despite increased species diversity. Our analysis also showed that the fish communities shifted from under‐dispersion to over‐dispersion due to both a decrease in the relative abundance of migratory fish and an increase in the number of fish adapted to the new hydrologic conditions. Our results indicated that the impacts of dams on downstream fish communities may change over time. Interactions between species may become more important when the environment is stable., We investigated the temporal changes in taxonomic and functional diversities of fish communities in the downstream area of the Three Gorges Dam (TGD).We found two regime shifts in the fish community and the opposite trends in taxonomic and functional diversities.

Strong physical disturbance from hurricanes can disrupt coral reef ecosystems and precipitate a regime shift toward algal dominance, particularly in the absence of grazing pressure to regulate algal growth post-storm. Here, we examine the influence of Hurricane Irma on a keystone grazer, Diadema antillarum, and the surrounding coral reef benthic community in the Florida Keys. D. antillarum densities and test diameters, as well as percent cover of coral reef benthic groups, were measured at 10 sites in the middle and upper Keys before and after Irma. Significant decreases in mean D. antillarum density and median test diameter were observed following the storm. There was a correlation between the magnitude of decline in D. antillarum density and the magnitude of sediment deposition on reefs, suggesting that abrasion or burial from sediment transport may have contributed to D. antillarum mortality. We detected significant decreases in the percent cover of sponges and hydrocorals following the storm, but no change in scleractinian coral cover, which was very low (3% mean cover) at the onset of the study. Macroalgal cover increased at sites in the upper Keys and decreased at sites in the middle Keys. There was no relationship between post-storm D. antillarum density and the change in percent cover of macroalgae or turf-algal-sediment matrix (TAS), likely due to low overall abundance of the grazer. We predict that coral reefs will remain in an algal-dominated ecosystem state due to, among other factors, increasing frequency of strong hurricanes that impact the D. antillarum population.

The origin of the nucleus remains a great mystery in life science, although nearly two centuries have passed since the discovery of nuclei. To date, studies of eukaryogenesis have focused largely on micro-evolutionary explanations. Here, we examined macro-patterns of C-values (the total amount of DNA within the haploid chromosome set of an organism) for over 110,000 species and the chromosome numbers for over 11,000 species and their potential links with the state of atmospheric oxidation over geological time. Eukaryogenesis was in sync with an over 2.5 order-of-magnitude increase in genome size from prokaryote to eukaryote, and also with a rapid rise of atmospheric oxidation, suggesting that eukaryogenesis would have resulted from a regime shift of genomes driven by the oxidation-driven complexification and structuralization (e.g. chromatin packing).

This paper examines the character of phytoplankton blooms in a restricted sub-tropical lagoon along the Atlantic coast of central Florida. The results of the 23-year study (1997–2020) provide evidence for multiple types of variability in bloom activity, including cyclical patterns, stochastic events, and most prominently a regime shift in composition and intensity. Cyclical patterns (e.g., El Niño/La Niña periods) and stochastic events (e.g., tropical storms) influenced rainfall levels, which in turn impacted nutrient concentrations in the water column and the timing and intensity of blooms. In 2011, a major change occurred in the character of blooms, with a dramatic increase in peak biomass levels of blooms and the appearance of new dominant taxa, including the brown tide speciesAureoumbra lagunensisand other nanoplanktonic species. Results of quantitative analyses reveal system behavior indicative of a regime shift. The shift coincided with widespread losses of seagrass community and reduced drift algae biomass. A combination of exceptionally low water temperatures in the winters of 2009/2010 and 2010/2011, hypersaline conditions associated with drought conditions, and high light attenuation caused by blooms appear to have contributed to the widespread and protracted decline in seagrass and drift macroalgal communities in the lagoon, leading to shifts in distribution of internal and external nutrient sources toward phytoplankton.

Replacement of coral by macroalgae in post-disturbance reefs, also called a “coral-macroalgal regime shift”, is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02, p = 0.001), especially in herbivorous fishes (R2 = 0.07, p = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (Rikenella, Akkermensia, Desulfovibrio, Brachyspira) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of Scarinae and Siganidae fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions.

Climate extremes are becoming more frequent with global climate change and have the potential to cause major ecological regime shifts. Along the northern Gulf of Mexico, a coastal wetland in Texas suffered sudden vegetation dieback following an extreme precipitation and flooding event associated with Hurricane Harvey in 2017. Historical salt marsh dieback events have been linked to climate extremes, such as extreme drought. However, to our knowledge, this is the first example of extreme precipitation and flooding leading to mass mortality of the salt marsh foundation species, Spartina alterniflora. Here, we investigated the relationships between baseline climate conditions, extreme climate conditions, and large-scale plant mortality to provide an indicator of ecosystem vulnerability to extreme precipitation events. We identified plant zonal boundaries along an elevation gradient with plant species tolerant of hypersaline conditions, including succulents and graminoids, at higher elevations, and flood-tolerant species, including S. alterniflora, at lower elevations. We quantified a flooding threshold for wetland collapse under baseline conditions characterized by incremental increases in flooding (i.e., sea level rise). We proposed that the sudden widespread dieback of S. alterniflora following Hurricane Harvey was the result of extreme precipitation and flooding that exceeded this threshold for S. alterniflora survival. Indeed, S. alterniflora dieback occurred at elevations above the wetland collapse threshold, illustrating a heightened vulnerability to flooding that could not be predicted from baseline climate conditions. Moreover, the spatial pattern of vegetation dieback indicated that underlying stressors may have also increased susceptibility to dieback in some S. alterniflora marshes.Collectively, our results highlight a new mechanism of sudden vegetation dieback in S. alterniflora marshes that is triggered by extreme precipitation and flooding. Furthermore, this work emphasizes the importance of considering interactions between multiple abiotic and biotic stressors that can lead to shifts in tolerance thresholds and incorporating climate extremes into climate vulnerability assessments to accurately characterize future climate threats.

A reaction-diffusion-advection model is proposed to describe the growth of algae depending on both nutrients and inorganic carbon in a poorly mixed water column. Nutrients from the water bottom and inorganic carbon from the water surface form an asymmetric resource supply mechanism for the algal growth. The existence and stability of semi-trivial steady state and positive steady state of the model are proved, and a threshold condition for the regime shift from extinction to survival of algae is established. The influence of environmental parameters on the vertical distribution of algae is investigated in the water column. It is shown that the vertical distribution of algae can exhibit many different profiles under the combined limitation of nutrients and inorganic carbon.

Seagrasses are threatened worldwide due to anthropogenic and natural disturbances disrupting the multiple feedbacks needed to maintain these ecosystems. If the disturbance is severe enough, seagrass systems may undergo a regime shift to a degraded system state that is resistant to recovery. In Florida Bay, Florida, United States, two recent, large-scale disturbances (a drought-induced seagrass die-off in 2015 and Hurricane Irma in 2017) have caused 8,777 ha of seagrass beds to degrade into a turbid, unvegetated state, causing a large sediment plume. Using satellite imagery digitization and long-term seagrass cover data, we investigate the expansion of this sediment plume between 2008 and 2020 and the potential interaction of this sediment plume with seagrass recovery in two focal basins in Florida Bay affected by the die-off, Johnson and Rankin. The average size of the sediment plume increased by 37% due to the die-off and Hurricane Irma, increasing from an average of 163.5 km2 before the disturbances to an average of 223.5 km2. The expansion of the plume was basin-specific, expanding into Johnson after the 2015 seagrass die-off with expansive and long-lasting effects, but only expanding into Rankin after Hurricane Irma with less severe and short-term effects. Furthermore, the sediment plume was negatively correlated with seagrass cover in Johnson, but held no relationship with seagrass cover in Rankin. Thus, different disturbances can act upon seagrass ecosystems at varying scales with varying consequences. This study illustrates the advantage of combining satellite imagery with field data to monitor disturbances as well as highlights the importance of investigating disturbances of seagrass ecosystems at various scales to comprehend seagrass resilience in the context of future extreme events.

Temperate reefs are being tropicalized worldwide. In temperate Western Australia, a marine heatwave led to a regime shift from kelp (Ecklonia radiata) dominated to canopy-free reefs, together with an increase in tropical herbivorous fishes that contribute to keeping low kelp abundances and even prevent kelp reestablishment in northern regions. However, whether tropical herbivorous fishes prefer kelps over other seaweeds and/or whether this preference changes with latitude remains untested. Multiple-choice experiments (young kelp vs. other seaweeds) with tropical, subtropical and temperate herbivorous fishes show shifting species-specific preferences and fish-to-fish interference shifting with latitude (assays replicated in two regions four degrees of latitude apart). Against expectations, only the temperate Kyphosus sydneyanus preferred kelp over other seaweeds, but only in the lower latitude region. Siganus fuscescens, the most abundant tropical herbivore in both regions, preferred grazing on turf, suggesting that tropical fish might reduce kelp recruitment by consuming microscopic sporophytes in turf matrix.

Due to persistent fishing expansion in the China Seas over the past six decades, fisheries resources have been over-exploited; as a result, exploited fish have become smaller in size and younger in age. Marine piscivorous fish constituted a large portion of Chinese fisheries catch, long-term variability of which has rarely been investigated despite intense fishing pressure and climate change. In this study, we attempt to identify their responses to climate change and fishing activities and to provide scientific basis for sustainable exploitation of these resources. Seven taxa from pelagic to demersal species inhabiting either cold-water or warm-water were selected to represent the piscivorous fish assemblage in the China Seas. Total catch of these piscivorous fish in the China Seas increased during the early 1990s, stabilizing around 1.2 million tons after 1997. Principal component analysis (PCA) showed evident interannual-decadal variabilities in the catch of these fish with step changes around 1985/86 and 1997/98. Individual taxa, however, showed different trends in catches with sharks, rays, and lizardfishes manifesting downward trends while Pacific cod, eels, and hairtail increasing. Common dolphinfish and Japanese-Spanish mackerel increased largely in the 1990s but declined slightly during the 2000s. Although there were temporal overlaps between climate change and fishing variabilities, results of gradient forest analyses indicated that fishing effort imposed the most important influence on piscivorous fish. And among all climate variables explored in this study, sea surface temperature (SST) especially that of the East China Sea, had greatest impacts on variations in piscivorous fish catch, which may have been gradually exacerbated by the continued high fishing intensity. In addition, significant changes were identified in the life history traits in the species we evaluated, such as reduced average body sizes and truncated age compositions, strongly indicating the effect of fishing. We therefore advocate precautionary fishery practices under climate change.

The Dutch coastal zone is a region of the North Sea with a marked interannual and long-term abiotic and phytoplankton variability. To investigate the relationship between abiotic variability and phytoplankton composition, two routine water monitoring data sets (1991-2005) were examined. Multivariate statistics revealed two significant partitions in the data. The first consisted of interannual abiotic fluctuations that were correlated to Rhine discharge that affected the abundance of summer and autumn diatom species. The second partition was caused by a shift in the abiotic data from 1998 to 1999 that was followed by a shift in phytoplankton composition from 1999 to 2000. Important factors in the abiotic shift were decreases in suspended matter (SPM) and phosphate (DIP) concentrations, as well as in pH. The decrease in SPM was caused by a reduction in wind speed. The increase in water column daily irradiance from the decrease in SPM led to increases in the abundance of winter-spring species, notably the prymnesiophyte Phaeocystis globosa. Because wind speed is related to the North Atlantic Oscillation (NAO) index it was possible to correlate NAO index and P. globosa abundance. Only five abiotic variables representing interannual and long-term variability, including Rhine discharge and NAO index, were needed to model the observed partitions in phytoplankton composition. It was concluded that interannual variability in the coastal phytoplankton composition was related to year-to-year changes in river discharge while the long-term shift was caused by an alternating large-scale meteorological phenomenon.

Sea urchins have the capacity to destructively overgraze kelp beds and cause a wholesale shift to an alternative and stable 'urchin barren' reef state. However, destructive grazing appears labile and contingent on behavioural shift. Changes in supply of allochthonous 'drift-kelp' food are hypothesised as a trigger of change in urchin grazing behaviour, yet field tests are lacking. Here we conduct a suite of in situ behavioural surveys and manipulative experiments within kelp beds and on urchin barrens to examine foraging movements and evidence for a behavioural switch to an 'overgrazing mode' by the Australian urchin Heliocidaris erythrogramma (Echinometridae). Tracking urchins using time-lapse photography revealed urchin foraging to conform to a random walk model within kelp beds and on barrens. However, many individuals tended towards local movement within proximal crevices and movement was reduced in kelp beds compared to barrens. Directional movement of urchins toward newly available kelp was experimentally inducible, consistent with locally observed 'mobile-feeding-fronts' that develop at barrens-kelp interfaces. Habitat-specific feeding modes were also evidenced by herbivory assays which revealed urchin grazing rates to be high on both drift-kelp and standing kelp on barren grounds, while drift-kelp but not standing kelp was consumed at high rates within kelp beds. Time-lapse tracking of urchin foraging before/after addition of drift-kelp revealed a reduction in foraging across the reef surface after drift-kelp capture. Collectively, results indicate that the availability of drift-kelp is a pivotal trigger in determining urchin feeding modes which thus mediates the shift between alternative stable states for rocky reef ecosystems.

Mechanisms underlying the loss of ecological resilience and a shift to an alternate regime with lower ecosystem service provisioning continues to be a leading debate in ecology, particularly in cases where evidence points to human actions and decision-making as the primary drivers of resilience loss and regime change. In this paper, we introduce the concept of coerced resilience as a way to explore the interplay among social power, ecological resilience, and fire management, and to better understand the unintended and undesired regime changes that often surprise ecosystem managers and governing officials. Philosophically, coercion is the opposite of freedom, and uses influence or force to gain compliance among local actors. The coercive force imposed by societal laws and policies can either enhance or reduce the potential to manage for essential structures and functions of ecological systems and, therefore, can greatly alter resilience. Using a classical fire-dependent regime shift from North America (tallgrass prairie to juniper woodland), and given that coercion is widespread in fire management today, we quantify relative differences in resilience that emerge in a policy-coerced fire system compared to a theoretical, policy-free fire system. Social coercion caused large departures in the fire conditions associated with alternative grassland and juniper woodland states, and the potential for a grassland state to emerge to dominance became increasingly untenable with fire as juniper cover increased. In contrast, both a treeless, grassland regime and a co-dominated grass-tree regime emerged across a wide range of fire conditions in the absence of policy controls. The severe coercive forcing present in fire management in the Great Plains, and corresponding erosion of grassland resilience, points to the need for transformative environmental governance and the rethinking of social power structures in modern fire policies.

Extensive dieback in dominant plant species in response to climate change is increasingly common. Climatic conditions and related variables, such as evapotranspiration, vary in response to topographical complexity. This complexity plays an important role in the provision of climate refugia. In 2008/2009, an island-wide dieback event of the keystone cushion plant Azorella macquariensis Orchard (Apiaceae) occurred on sub-Antarctic Macquarie Island. This signalled the start of a potential regime shift, suggested to be driven by increasing vapour pressure deficit. Eight years later, we quantified cover and dieback across the range of putative microclimates to which the species is exposed, with the aim of explaining dieback patterns. We test for the influence of evapotranspiration using a suite of topographic proxies and other variables as proposed drivers of change. We found higher cover and lower dieback towards the south of the island. The high spatial variation in A. macquariensis populations was best explained by latitude, likely a proxy for macroscale climate gradients and geology. Dieback was best explained by A. macquariensis cover and latitude, increasing with cover and towards the north of the island. The effect sizes of terrain variables that influence evapotranspiration rates were small. Island-wide dieback remains conspicuous. Comparison between a subset of sites and historical data revealed a reduction of cover in the north and central regions of the island, and a shift south in the most active areas of dieback. Dieback remained comparatively low in the south. The presence of seedlings was independent of dieback. This study provides an empirical baseline for spatial variation in the cover and condition of A. macquariensis, both key variables for monitoring condition and ‘cover-debt’ in this critically endangered endemic plant species. These findings have broader implications for understanding the responses of fellfield ecosystems and other Azorella species across the sub-Antarctic under future climates.

Population dynamics of small pelagic fishes (SPF) and their management in Japan were reviewed for Japanese sardine Sardinops melanostictus, Japanese anchovy Engraulis japonicus, chub mackerel Scomber japonicus, and Pacific saury Cololabis saira. The catch and biomass of SPF generally showed decadal-scale variability with prominent species replacements since the 1900s. The causes of species replacements were generally associated with climatic/oceanic variability, particularly “regime shifts,” of which the 1988/89 regime shift was the most influential since the 1970s. Variability in the early survival rate is a key factor for population fluctuations, and the proposed hypothetical mechanisms of recruitment variability are summarized herein. Although overfishing during the 1990s and early 2000s prevented the recovery of Pacific stocks of sardine and chub mackerel, they have been recovering since the mid-2000s owing to strong year classes and reduced exploitation rates. The fundamental cause of overfishing was derived from a mismatch between investments in larger purse seine fleets during the 1980s and poor ocean productivity since the 1988/89 regime shift, when dominant SPF began to shift from sardine to anchovy. Recommendations for fisheries management of SPF around the Japanese Archipelago are proposed, considering climate change and naturally and drastically changing SPF populations.

Owing to rapid socio-economic development and climate warming, lakes even in remote areas have experienced marked changes in the last century. However, there are few studies revealing the multi-faceted biogeochemical changes and disentangling impacts of human and climate in relatively remote lakes in China. In this study we reconstructed historical changes of geochemistry, nutrition, primary production, ecology, and pollution in an alpine lake (Gonghai) in central North China, and revealed coherent changes and drivers in relatively remote Chinese lakes by compiling other records. Results show that Lake Gonghai has experienced considerably biogeochemical changes since the 1980s induced mainly by increased regional human activities, with detected human-related changes occurring in the 1950s-70s. The most important change is a shift of diatom primary producers in the 1980s, caused mainly by an increase of regional atmospheric N and P deposition associated with rapid socio-economic development. Another remarkable change is the increase of pollution levels since the 1980s, represented by heavy metals, also caused by atmospheric deposition. Compiled sediment records demonstrate similar biogeochemical changes in most lakes from relatively remote areas of China since the 1970s-80s, associated closely with increased inputs of human-induced atmospheric N, P and pollutants, whereas the influence of climate warming is likely limited. This study highlights markedly human-related biogeochemical changes in relatively remote Chinese lakes during the Anthropocene epoch.

Small pelagic fishes such as sardine and anchovy play an important role in marine ecosystem and are affected largely by environmental changes because of their character as r-strategists and their low trophic levels. Small pelagic fishes are crucial targets of Chinese fisheries, accounting for 26% of the total catch in 2014. Their catches show an increasing trend since the 1950s. However, there is still little information on small pelagic species inhabiting Chinese waters. Catch trends and impacts of climatic regime shifts for six typical commercially important small pelagic species, chub mackerel (Scomber japonicus), Japanese scad (Decapterus maruadsi), Pacific herring (Clupea pallasi), Japanese anchovy (Engraulis japonicus), Japanese sardine (Sardinops melanostictus) and horse mackerel (Trachurus japonicus), are analyzed using Chinese Fishery Statistics, FAO data, climatic indices and sea surface temperature (SST) data. The aim is to explore the interannual to decadal variability of their catches in China Seas and their responses to climatic regime shifts. Decadal variability is evident in the catches of the six small pelagic fishes with different variation patterns between warm- and cold-water species. Step changes in catches of the six species were observed in 1976/77, 1986/87, 1995/96, 2001/02 and 2005/06, while regime shifts in climatic/SST indices occurred around 1976/77, the late 1980s and the mid-1990s. This indicates that decadal variations in small pelagic fishes respond strongly to the climatic regime shifts, and the different response patterns of warm- and cold-water species reflect their different life strategies. Marine thermal variation patterns during the period 1981–2000 were well explained by different phase changes in the SSTs between summer and winter and were consistent with the step change in the catches of small pelagic fishes. The double-integration hypothesis, which indicates that cumulative integrations of atmospheric forcing can generate marine population responses, is useful both to understand the process from climate forcing to fish and the controlling mechanism of climate variability on small pelagic fishes in China Seas.

Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: this loss may hamper ecosystems’ ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of climate and human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. Here, we investigate the effects of a nutrient pulse on the resistance, resilience and elasticity of a tritrophic—and thus more realistic—plankton food web model depending on its functional diversity. We compare a non-adaptive food chain with no diversity to a highly diverse food web with three adaptive trophic levels. The species fitness differences are balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occured. Importantly, we found that a more diverse food web was generally more resistant, resilient, and elastic. Particularly, functional diversity dampened the probability of a regime shift towards a non-desirable alternative state. In addition, despite the complex influence of the shape and type of the dynamical attractors, the basal-intermediate interaction determined the robustness against a nutrient pulse. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience and elasticity as functional diversity declines.

An increasing number of studies have been examining the functional configuration of biological communities or ecosystems using biological traits. Here, we investigated the temporal dynamics and resilience of the traits composition in Mediterranean fisheries landings over 31 years (1985-2015). We transcribed the FAO Mediterranean landings dataset for 101 marine species into a dataset of 23 traits related to the life cycle, distribution, ecology and behaviour. Mediterranean mean Sea Surface Temperature (SST) was evaluated as a potential driver of the traits composition. Trait dynamics were evaluated both individually and holistically by developing an Integrated Traits Resilience Assessment (ITRA). ITRA is a variation of the Integrated Resilience Assessment (IRA), a method to infer resilience dynamics and build stability landscapes of complex natural systems. Changes in landings trait dynamics were documented both for individual traits and for the entire traits 'system', and a relevant regime shift was detected in the second half of the 1990s. The traits system switched to higher optimal temperature, more summer spawning, shorter life span, smaller maximum size, shallower optimal depth and planktivorous diet. This shift was found to be a lagged discontinuous response to sea warming, which gradually eroded the resilience of the original state of the traits system, leading it into a new basin of attraction. The inclusion of ecological/response traits (related to environmental preferences) in our analyses indicates potential mechanisms that explain the observed shift, while changes in functional/effect traits indicate potential impacts on ecosystem functioning. Our findings suggest that changes in the Mediterranean ecosystems are evidently larger than previously thought, with profound implications for the management of this highly impacted sea. ​.

Animal populations at northern latitudes may have cyclical dynamics that are degraded by climate change leading to trophic cascade. Hare populations at more southerly latitudes are characterized by dramatic declines in abundance associated with agricultural intensification. We focus on the impact of historical climatic and agricultural change on a mid-latitude population of mountain hares, Lepus timidus hibernicus. Using game bag records from multiple sites throughout Ireland, the hare population index exhibited a distinct regime shift. Contrary to expectations, there was a dynamical structure typical of northern latitude hare populations from 1853 to 1908, during which numbers were stable but cyclic with a periodicity of 8 years. This regime was replaced by dynamics more typical of southern latitude hare populations from 1909 to 1970, in which cycles were lost and numbers declined dramatically. Destabilization of the autumn North Atlantic Oscillation (NAO) led to the collapse of similar cycles in the hare population, coincident with the onset of agricultural intensification (a shift from small-to-large farms) in the first half of the 20th century. Similar, but more recent regime shifts have been observed in Arctic ecosystems and attributed to anthropogenic climate change. The present study suggests such shifts may have occurred at lower latitudes more than a century ago during the very early 20th century. It seems likely that similar tipping points in the population collapse of other farmland species may have occurred similarly early but went undocumented. As northern systems are increasingly impacted by climate change and probable expansion of agriculture, the interaction of these processes is likely to disrupt the pulsed flow of resources from cyclic populations impacting ecosystem function.

This study and the sampling at sea was funded by a grant from the UK Natural Environment Research Council (NE/E010350/1) to ASB and VAS. EGM was funded by a NERC grant (NE/P002412/1) and Independent Research Fellowship (NE/S014756/1). Robust time-series of direct observations of jellyfish abundance are not available for many ecosystems, leaving it difficult to determine changes in jellyfish abundance, the possible causes (e.g. climate change) or the consequences (e.g. trophic cascades). We sought an indirect ecological route to reconstruct jellyfish abundance in the Irish Sea: since zooplankton are jellyfish prey, historic variability in zooplankton communities may provide proxies for jellyfish abundance. We determined the Bayesian ecological network of jellyfish–zooplankton dependencies using jellyfish- and zooplankton-abundance data obtained using nets during a 2-week cruise to the Irish Sea in 2008. This network revealed that Aurelia aurita abundance was dependent on zooplankton groups Warm Temperate and Temperate Oceanic as defined by previous zooplankton ecology work. We then determined historic zooplankton networks across the Irish Sea from abundance data from Continuous Plankton Recorder surveys conducted between 1970 and 2000. Transposing the 2008 spatial dependencies onto the historic networks revealed that Aurelia abundance was more strongly dependent over time on sea surface temperature than on the zooplankton community. The generalist predatory abilities of Aurelia may have insulated this jellyfish over the 1985 regime shift when zooplankton composition in the Irish Sea changed abruptly, and also help explain its globally widespread distribution. Publisher PDF

In coral reefs, dissolved organic matter (DOM) cycling is a critical process for sustaining ecosystem functioning. However, global and local stressors have caused persistent shifts from coral- to algae-dominated benthic communities. The influence of such phase shifts on DOM nature and its utilization by heterotrophic bacterioplankton remains poorly studied. Every second month for one year, we retrieved seawater samples enriched in DOM produced by coral- and algae-dominated benthic communities in a central Red Sea reef during a full annual cycle. Seawater incubations were conducted in the laboratory under in situ temperature and light conditions by inoculating enriched DOM samples with bacterial assemblages collected in the surrounding waters. Dissolved organic carbon (DOC) concentrations were higher in the warmer months (May-September) in both communities, resulting in higher specific growth rates and bacterial growth efficiencies (BGE). However, these high summer values were significantly enhanced in algal-DOM relative to coral-DOM, suggesting the potential for bacterioplankton biomass increase in reefs with algae replacing healthy coral cover under warmer conditions. The potential exacerbation of heterotrophic bacterial activity in the ongoing widespread regime shift from coral- to algae-dominated communities may have detrimental consequences for the overall health of tropical coral reefs. (C) 2020 The Authors. Published by Elsevier B.V.

The detection and prediction of lake ecosystem responses to environmental changes are pressing scientific challenge of major global relevance. Specifically, an understanding of lake ecosystem stability over long-term scales is urgently needed to identify impending ecosystem regime shifts induced by human activities and improve lake ecosystem protection. This study investigated regime shifts in cyanobacterial and eukaryotic algal communities in a large shallow lake over a century in response to nutrient enrichment and hydrologic regulation using evidence from empirical state indicators and ecological network analyses of sedimentary-inferred communities. The diversity and structure of cyanobacterial and eukaryotic algal communities were investigated from sedimentary DNA records and used, for the first time, as state variables of the lake ecosystem to detect lake stability. Two regime shifts were inferred in the 1970s and 2000s based on temporal analysis of empirical indicators. Co-occurrence network analysis based on taxonomic abundance distributions and presence/absence patterns also supported the two regime shifts based on architectural features of the ecological networks. Moreover, the associations of cyanobacterial and eukaryotic algal taxa were observed to be non-random across time. The abrupt driver-mediated regime shift in the 1970s is characterized by the disappearance of submerged vegetation, significantly increased relative abundances of Microcystis and Chlorophyta taxa, and was primarily caused by sluice construction. The critical transition observed in the 2000s was manifested by the occurrence of serious cyanobacterial blooms and was triggered by increased nutrient loading with the development of urbanization and agricultural intensification. This study reveals the important roles of hydrologic regulation and nutrient loading in the temporal successional dynamics of a shallow lake ecosystem, providing new insights into regime shifts of lake ecosystems that can help inform future efforts to predict important lake ecosystem state changes.

Sub-Antarctic Macquarie Island has been the location of a rapid ecosystem collapse in its most dominant vegetation assemblage, the Macquarie Island alpine mosaic, beginning around 2008 and continuing today. An ecosystem engineer and endemic, keystone species, the cushion plant, Azorella macquariensis (Apiaceae), and associated bryophyte species have undergone sudden and widespread dieback. Additional species, particularly the megaherb daisy, Pleurophyllum hookeri (Asteraceae), are currently also showing widespread mortality. Initially, water stress linked to long-term changes in climate appeared to be the primary pressure causing dieback, with a secondary putative pathogen emerging. However, over the last 10 years there has been a shift in fundamental ecosystem processes with the pathogenic system appearing to be the current predominant cause of dieback. This change suggests that a threshold has been crossed into a new operating state. Furthermore, an ecosystem regime shift with two clear new states (grassland and bare ground) appears to be emerging with the loss of the ecosystem engineering species from many areas of fellfield. Modelling suggests that cold refugia may allow current elements to survive into the future, but as interstitial species, rather than as dominants present at the start of the twenty-first century. This ecosystem presents a potential exemplar for climate change response in patchy, resource-concentrated ecosystems elsewhere. In particular, showing how interactions change in response to climate change and how longer-term consequences may emerge following short-term effects.

A key pursuit in contemporary ecology is to differentiate regime shifts that are truly irreversible from those that are hysteretic. Many ecological regime shifts have been labeled as irreversible without exploring the full range of variability in stabilizing feedbacks that have the potential to drive an ecological regime shift back towards a desirable ecological regime. Removing fire from grasslands can drive a regime shift to juniper woodlands that cannot be reversed using typical fire frequency and intensity thresholds, and has thus been considered irreversible. This study uses a unique, long-term experimental fire landscape co-dominated by grassland and closed-canopy juniper woodland to determine whether extreme fire can shift a juniper woodland regime back to grassland dominance using aboveground herbaceous biomass as an indicator of regime identity. We use a space-for-time substitute to quantify herbaceous biomass following extreme fire in juniper woodland up to 15 years post-fire and compare these with (i) 15 years of adjacent grassland recovery post-fire, (ii) unburned closed-canopy juniper woodland reference sites and (iii) unburned grassland reference sites. Our results show grassland dominance rapidly emerges following fires that operate above typical fire intensity thresholds, indicating that grassland-juniper woodlands regimes are hysteretic rather than irreversible. One year following fire, total herbaceous biomass in burned juniper stands was comparable to grasslands sites, having increased from 5 ± 3 g m−2 to 142 ± 42 g m−2 (+2785 ± 812 percent). Herbaceous dominance in juniper stands continued to persist 15-years after initial treatment, reaching a maximum of 337 ± 42 g m−2 eight years post-fire. In juniper encroached grasslands, fires that operate above typical fire intensity thresholds can provide an effective method to reverse juniper woodland regime shifts. This has major implications for regions where juniper encroachment threatens rancher-based economies and grassland biodiversity and provides an example of how to operationalize resilience theory to disentangle irreversible thresholds from hysteretic system behavior.

Algal blooms in lakes and reservoirs can be considered regime shifts from a clear‐water to algae‐dominated state that often occurs abruptly. Under experimental conditions, these regime shifts have been predicted from rises in variance and autocorrelation (generic resilience indicators) of state variables monitored at a high frequency. The goal of this study was to evaluate the behavior of resilience indicators prior to a critical transition in lakes that naturally experience algal blooms. Ambient lake conditions provide several potential hurdles that could inhibit the detection of meaningful changes in resilience indicators prior to a critical transition such as stochastic nutrient loading, spatial complexity, and decreased resilience due to higher baseline nutrient concentrations. We compiled five lake‐years of high‐frequency monitoring of chlorophyll a, phycocyanin, dissolved oxygen, and pH from four hypereutrophic lakes. Despite the factors that might hinder detecting statistical indicators of changing resilience in hypereutrophic ecosystems, we found that a rise in resilience indicators did occur prior to a critical transition in three out of four possible lake‐years, with rise beginning between 5 and 33 d prior. In one lake‐year, a critical transition occurred soon after the monitoring began, preventing detection of rising variance or autocorrelation signals which are calculated using a 21‐d rolling window. These results add to the growing body of evidence that rises in resilience indicators can be detected in ecosystems prior to a regime shift if monitoring programs are properly designed to capture the dynamics; however, continued research is needed to better understand the conditions under which resilience indicators may be useful as an early warning detection tool for lake management.

Ocean warming, ocean acidification and overfishing are major threats to the structure and function of marine ecosystems. Driven by increasing anthropogenic emissions of CO2, ocean warming is leading to global redistribution of marine biota and altered ecosystem dynamics, while ocean acidification threatens the ability of calcifying marine organisms to form skeletons due to decline in saturation state of carbonate Ω and pH. In Tasmania, the interaction between overfishing of sea urchin predators and rapid ocean warming has caused a phase-shift from productive kelp beds to overgrazed sea urchin barren grounds, however potential impacts of ocean acidification on this system have not been considered despite this threat for marine ecosystems globally. Here we use automated loggers and point measures of pH, spanning kelp beds and barren grounds, to reveal that kelp beds have the capacity to locally ameliorate effects of ocean acidification, via photosynthetic drawdown of CO2, compared to unvegetated barren grounds. Based on meta-analysis of anticipated declines in physiological performance of grazing urchins to decreasing pH and assumptions of nil adaptation, future projection of OA across kelp-barrens transition zones reveals that kelp beds could act as important pH refugia, with urchins potentially becoming increasingly challenged at distances >40 m from kelp beds. Using spatially explicit simulation of physicochemical feedbacks between grazing urchins and their kelp prey, we show a stable mosaicked expression of kelp patches to emerge on barren grounds. Depending on the adaptative capacity of sea urchins, future declines in pH appear poised to further alter phase-shift dynamics for reef communities; thus, assessing change in spatial-patterning of reef-scapes may indicate cascading ecological impacts of ocean acidification.

Die-offs of seabirds in Alaska have occurred with increased frequency since 2015. In 2018, on St. Lawrence Island, seabirds were reported washing up dead on beaches starting in late May, peaking in June, and continuing until early August. The cause of death was documented to be starvation, leading to the conclusion that a severe food shortage was to blame. We use physiology and colony-based observations to examine whether food shortage is a sufficient explanation for the die-off, or if evidence indicates an alternative cause of starvation such as disease. Specifically, we address what species were most affected, the timing of possible food shortages, and food shortage severity in a historical context. We found that thick-billed murres (Uria lomvia) were most affected by the die-off, making up 61% of all bird carcasses encountered during beach surveys. Thick-billed murre carcasses were proportionately more numerous (26:1) than would be expected based on ratios of thick-billed murres to co-occurring common murres (U. aalge) observed on breeding study plots (7:1). Concentrations of the stress hormone corticosterone, a reliable physiological indicator of nutritional stress, in thick-billed murre feathers grown in the fall indicate that foraging conditions in the northern Bering Sea were poor in the fall of 2017 and comparable in severity to those experienced by murres during the 1976-1977 Bering Sea regime shift. Concentrations of corticosterone in feathers grown during the pre-breeding molt indicate that foraging conditions in late winter 2018 were similar to previous years. The 2018 murre egg harvest in the village of Savoonga (on St. Lawrence Is.) was one-fifth the 1993-2012 average, and residents observed that fewer birds laid eggs in 2018. Exposure of thick-billed murres to nutritional stress in August, however, was no different in 2018 compared to 2016, 2017, and 2019, and was comparable to levels observed on St. George Island in 2003-2017. Prey abundance, measured by the National Oceanic and Atmospheric Administration in bottom-trawl surveys, was also similar in 2018 to 2017 and 2019, supporting the evidence that food was not scarce in the summer of 2018 in the vicinity of St. Lawrence Island. Of two moribund thick-billed murres collected at the end of the mortality event, one tested positive for a novel re-assortment H10 strain of avian influenza with Eurasian components, likely contracted during the non-breeding season. It is not currently known how widely spread infection of murres with the novel virus was, thus insufficient evidence exists to attribute the die-off to an outbreak of avian influenza. We conclude that food shortage alone is not an adequate explanation for the mortality of thick-billed murres in 2018, and highlight the importance of rapid response to mortality events in order to document alternative or confounding causes of mortality.

The population dynamics of fish in northern lakes is strongly influenced by climatic factors. In this study, we investigated whether there is a link between the late 1980s climate regime shift in Europe and the collapse of vendace (Coregonus albula) population at the same time in Lake Peipsi. Until the end of the 1980s, vendace was very abundant in the lake, but then its catches sharply declined. This decline inspired investigations into the extreme weather events preceding the vendace collapse using data on daily water temperatures and ice phenology together with commercial fishery statistics since 1931 and test catch data since 1986. We identified using advanced statistical methods that the hot summer of 1988, which was accompanied by a severe cyanobacterial bloom and extensive fish kill, and the subsequent non-permanent ice cover and early ice-offs in 1989 and 1990 in Lake Peipsi were the main reasons for the disappearance of vendace from catches in 1991. Moreover, a negative correlation appeared between catches of the predatory pikeperch (Sander lucioperca) and vendace. Predation pressure as well as fish habitat degradation caused by lake eutrophication may contribute to the instability of the vendace population too. Our study showed that extreme weather events such as heat waves in summer and non-permanent ice-cover in winter in consecutive years may have long-lasting harmful effects on the population abundance of cool-water fish species such as vendace whose eggs usually develop under an ice cover in north-temperate lakes.

Algae, as primary producers in riverine ecosystems, are found in two distinct habitats: benthic and pelagic algae typically prevalent in shallow/small and deep/large streams, respectively. Over an entire river continuum, spatiotemporal patterns of the two algal communities reflect specificity in habitat preference determined by geomorphic structure, hydroclimatic controls, and spatiotemporal heterogeneity in nutrient loads from point- and diffuse-sources. By representing these complex interactions between geomorphic, hydrologic, geochemical, and ecological processes, we present here a new river-network-scale dynamic model (CnANDY) for pelagic (A) and benthic (B) algae competing for energy and one limiting nutrient (phosphorus, P). We used the urbanized Weser River Basin in Germany (7th-order; ~8.4 million population; ~46 K km2) as a case study and analyzed simulations for equilibrium mass and concentrations under steady median river discharge. We also examined P, A, and B spatial patterns in four sub-basins. We found an emerging pattern characterized by scaling of P and A concentrations over stream-order ω, whereas B concentration was described by three distinct phases. Furthermore, an abrupt algal regime shift occurred in intermediate streams from B dominance in ω≤3 to exclusive A presence in ω≥6. Modeled and long-term basin-scale monitored dissolved P concentrations matched well for ω>4, and with overlapping ranges in ω

Fens and bogs are distinct in terms of their biogeochemistry, water table behavior, and net peat-accumulation regimes. While most peatlands start developing as fens, a large fraction of them eventually shift to bogs in a step-like ecosystem shift. This transition has traditionally been assumed to be primarily controlled by the ecosystem itself (autogenic control). Here we use 90 peat profiles from southernmost South America as a case study that illustrates a synchronous, regional-scale shift from fen to bog around 4200 years ago. In light of these results, we propose and discuss conceptual models that link environmental change (allogenic control) as a trigger to the fen-bog transition. In addition, our stratigraphic analyses show that Sphagnum deposits are associated with greater peat masses, larger soil-carbon stocks, and higher rates of peat-carbon accumulation than their non-Sphagnum counterparts, with Sphagnum bogs being characterized by soil-carbon densities over twice that of non-Sphagnum peatlands (medians = 141 vs. 56 kgC/m2). Since fens and bogs also behave differently in terms of their carbon exchanges with the atmosphere, a better appraisal of the processes involved in the fen-bog transition could help elucidate the role of this critical ecosystem shift in the past and future global carbon cycle.

Microbial engineering forces flux redistribution to accommodate higher production rates, straining the cellular supply chain and leading to growth deficiency. Thus, there is a selective pressure to alleviate metabolic burden and revert towards the innate flux distribution (‘flux memory’) via mutations. Suboptimal fermentation exacerbates this phenomenon as increased number of generations prolong the selection window for the underlying flux memory to generate faster growing non-producers. New strategies to mitigate host genetic instability include laboratory evolution, high-resolution genome resequencing combined with phenotype screening, mismatch repair protein engineering, and advanced synthetic biology approaches (e.g. oscillators and biosensor regulators). Moreover, 13C-metabolic flux analysis can quantify flux suboptimality driven by metabolic burdens and cultivation stresses. Elucidation of correlations between metabolic suboptimality and host mutation rates/spectra may lead to early stage risk assessments of culture-population’s regime shift during process scale-up as well as strategies to boost bioproductions.

Regime shifts of climatic and environmental conditions potentially affect productivity of fisheries resources, posing challenging issues to stock management. The stocks of the Japanese flying squid (Todarodes pacificus) are suspected to suffer from regime shifts, but their detection is difficult and possibly doubtful because the nature of short-lived species readily makes the effect of regime shifts confounded with observation errors. Here we developed a new state-space assessment model to evaluate the influence of regime shifts on spawner-recruitment relationship of the Japanese flying squid. The model simultaneously estimates the population dynamics of multiple stocks that could share some life history parameters, making parameter inference stable. We demonstrate that two-time regime shifts of productivity around 1991 and 2015 caused two-to three-fold changes of maximum sustinabile yields. The model with regime shifts clarifies the relationship between fishing pressure and spawner abudance that is difficult to detect in a model with no regime shift. The state-space approach will be a promising tool to accurately assess stock status by separating recruitment process from observation errors and contribute tothe management of marine biological resources sensitive to regime shifts.