Ecosystems in Action: Lessons from Marine Ecology about Recovery, Resistance, and Reversibility

The concepts of irreversibility and reversibility in research on anthropogenic environmental changes

The concept of "irreversibility" and its counterpart "reversibility" have become prominent in environmental and ecological research on human-induced changes, thresholds, climate tipping points, ecosystem degradation, and losses in the cryosphere and biosphere. Through a systematic literature review, we show that in these research fields, these notions are not only descriptive terms, but can have different semantic functions and normative aspects. The results suggest that, in the context of environmental and ecological research the concepts of irreversibility and reversibility have taken on additional usages in comparison to their contexts in theoretical thermodynamics and mechanics. Irreversible as a classification of anthropogenic environmental change can be used categorically, in the sense of a finite end, or relatively, i.e. on time or spatial scales of interest. Surprisingly, most of the analyzed scientific articles that use the terminology of (ir)reversibility substantively do not provide an explicit conceptualization or definition (74.7%). The research on potential (ir)reversibility of environmental change may affect the social and political willingness to bear the costs of interventions to mitigate or prevent undesirable environmental change. In particular, classifying a change as reversible or irreversible and determining the timescale(s) and spatial scale(s) involved has implications for policy and ecosystem management decisions, as suggested by its use in several high-level scientific and policy reports on ecosystem and climate change. Therefore, it is important to explicitly present a clear definition of irreversibility or reversibility for the readers from other fields, even if it could be the case that within a specific community an implicit definition was considered to be sufficient. We propose further recommendations for inter- and transdisciplinary reflection and conceptual use in the context of environmental, ecological, and sustainability research.

Diversity and future perspectives of Mediterranean deep-water oyster reefs

Anthropogenic and climate factors are increasingly affecting the composition and functions of many marine biogenic reefs globally, leading to a decline in associated biodiversity and ecosystem services. Once dominant ecological component, modern oyster reefs in the Mediterranean and Black Sea and the Atlantic Ocean have already been profoundly altered by overharvesting, habitat loss and the introduction of alien species. Far less known are deep-water oyster reefs, which can however form substantial biogenic structures below 30 m depth. Here we analyze the diversity of benthic assemblages associated with deep-water oyster reefs formed by the gryphaeid Neopycnodonte cochlear, and other mesophotic habitats in the central Mediterranean Sea using a taxonomic and functional approach. Our findings suggest that deep-water oyster reefs may act as hotspots of biodiversity and ecological functions in the Mediterranean Sea under current conditions, having also an edge in survival in a changing ocean.

Changes in the Diet of an Invasive Predatory Crab, Chionoecetes opilio, in the Degrading Benthic Community of an Arctic Fjord

The introduction of a new species can lead to substantial changes in a new ecosystem. Local and introduced species' survival depends on their ability to adapt to the new environment. Studying such adaptations is often hindered by multiple factors affecting the ecosystem. The introduction of a large predatory snow crab, Chionoecetes opilio, into the Kara Sea, is a unique invasive species affecting an otherwise undisturbed ecosystem. The crab has caused drastic changes in the macro- and megabenthic taxonomic structure, abundance, and biomass of the most common species in an Arctic fjord, Blagopoluchiya Bay. Stomach content and stable isotope analysis were applied to study crabs' feeding habits. As the abundance of the most common prey items diminished, the crabs switched to other less accessible food. Prior to substantial changes in benthic communities, the diet of the snow crabs was similar to that of other invaded and native areas, where animal food predominates. However, with the degradation of the ecosystem, detritus contribution has substantially increased. The changes in prey items did not change the crab's trophic status, and they continued to feed within the same trophic niche. In the depleted benthic communities of Blagopoluchiya Bay, the snow crab is forced to use all available food sources.

Genome analysis reveals three distinct lineages of the cosmopolitan white shark

The white shark (Carcharodon carcharias) (Linnaeus, 1758), an iconic apex predator occurring in all oceans,1,2 is classified as Vulnerable globally3-with global abundance having dropped to 63% of 1970s estimates,4-and as Critically Endangered in Europe.5 Identification of evolutionary significant units and their management are crucial for conservation,6 especially as the white shark is facing various but often region-specific anthropogenic threats.7,8,9,10,11 Assessing connectivity in a cosmopolitan marine species requires worldwide sampling and high-resolution genetic markers.12 Both are lacking for the white shark, with studies to date typified by numerous but geographically limited sampling, and analyses relying largely on relatively small numbers of nuclear microsatellites,13,14,15,16,17,18,19 which can be plagued by various genotyping artefacts and thus require cautious interpretation.20 Sequencing and computational advances are finally allowing genomes21,22,23 to be leveraged into population studies,24,25,26,27 with datasets comprising thousands of single-nucleotide polymorphisms (SNPs). Here, combining target gene capture (TGC)28 sequencing (89 individuals, 4,000 SNPs) and whole-genome re-sequencing (17 individuals, 391,000 SNPs) with worldwide sampling across most of the distributional range, we identify three genetically distinct allopatric lineages (North Atlantic, Indo-Pacific, and North Pacific). These diverged 100,000-200,000 years ago during the Penultimate Glaciation, when low sea levels, different ocean currents, and water temperatures produced significant biogeographic barriers. Our results show that without high-resolution genomic analyses of samples representative of a species' range,12 the true extent of diversity, presence of past and contemporary barriers to gene flow, subsequent speciation, and local evolutionary events will remain enigmatic.

Shifts in dominance of benthic communities along a gradient of water temperature and turbidity in tropical coastal ecosystems

Tropical coastal benthic communities will change in species composition and relative dominance due to global (e.g., increasing water temperature) and local (e.g., increasing terrestrial influence due to land-based activity) stressors. This study aimed to gain insight into possible trajectories of coastal benthic assemblages in Raja Ampat, Indonesia, by studying coral reefs at varying distances from human activities and marine lakes with high turbidity in three temperature categories (<31 °C, 31-32 °C, and >32 °C). The benthic community diversity and relative coverage of major benthic groups were quantified via replicate photo transects. The composition of benthic assemblages varied significantly among the reef and marine lake habitats. The marine lakes <31 °C contained hard coral, crustose coralline algae (CCA), and turf algae with coverages similar to those found in the coral reefs (17.4-18.8% hard coral, 3.5-26.3% CCA, and 15-15.5% turf algae, respectively), while the higher temperature marine lakes (31-32 °C and >32 °C) did not harbor hard coral or CCA. Benthic composition in the reefs was significantly influenced by geographic distance among sites but not by human activity or depth. Benthic composition in the marine lakes appeared to be structured by temperature, salinity, and degree of connection to the adjacent sea. Our results suggest that beyond a certain temperature (>31 °C), benthic communities shift away from coral dominance, but new outcomes of assemblages can be highly distinct, with a possible varied dominance of macroalgae, benthic cyanobacterial mats, or filter feeders such as bivalves and tubeworms. This study illustrates the possible use of marine lake model systems to gain insight into shifts in the benthic community structure of tropical coastal ecosystems if hard corals are no longer dominant.

Speed and degree of functional and compositional recovery varies with latitude and community age

Rates at which a community recovers after disturbance, or its resilience, can be accelerated by increased net primary productivity and recolonization dynamics such as recruitment. These mechanisms can vary across biogeographic gradients, such as latitude, suggesting that biogeography is likely important to predicting resilience. To test whether community resilience, informed by functional and compositional recovery, hinges on geographic location, we employed a standardized replicated experiment on marine invertebrate communities across four regions from the tropics to the subarctic zone. Communities assembled naturally on standardized substrate while experiencing distinct levels of biomass removal (no removal, low disturbance, and high disturbance), which opened space for new colonizers, thereby providing a pulse of limited resource to these communities. We then quantified functional (space occupancy and biomass) and compositional recovery from these repeated pulse disturbances across two community assembly timescales (early and late at 3 and 12 months, respectively). We documented latitudinal variation in resilience across 47° latitude, where speed of functional recovery was higher toward lower latitudes yet incomplete at late assembly in the tropics and subtropics. The degree of functional recovery did not coincide with compositional recovery, and regional differences in recruitment and growth likely contributed to functional recovery in these communities. While biogeographic variation in community resilience has been predicted, our results are among the first to examine functional and compositional recovery from disturbance in a single large-scale standardized experiment.

Decline in Size-at-Maturity of European Hake in Relation to Environmental Regimes: A Case in the Eastern Ionian Sea

European hake, Merluccius merluccius L. 1758, is a highly valuable demersal fish species exploited in both the east Atlantic and the Mediterranean Sea. Changes in the size-at-maturity of this species have been reported in various geographic areas. Size-at-maturity is a key parameter in fishery management. Our main goal was to study the trend of the size-at-maturity of European hake in the eastern Ionian Sea (Central Mediterranean) over the last five decades. Utilizing a multi-decadal series of data for various environmental variables, we employed multivariate analyses and non-additive modeling in an attempt to identify shifts in the climatic environment of the eastern Ionian Sea and whether the maturation of the hake population could be affected by these changes. The analyses used suggest a plausible environmental regime shift in the study area in the late 1990s/early 2000s. The decrease in size-at-maturity that was detected in the last two decades may, thus, be associated with environmental changes. However, as many fish stocks already experience fishery-induced evolution, further investigation is necessary to determine whether this environmental effect is an additional stressor on a possibly already fishery-impacted population. The outcomes of this study highlight the importance of investigating the relationship between fish reproductive traits and altered environmental conditions, as the latter are generally ignored during assessments, affecting the robustness of fishery management.

Extensive and Continuing Loss of Seagrasses in Florida's Big Bend (USA)

Florida's Big Bend in the northeastern Gulf of Mexico contains the second-largest contiguous seagrass meadow in the continental United States, providing numerous ecosystem functions and services, including carbon cycling and storage. We present 21 years of mapping data and 13 years of annual in-water monitoring that reveal extensive declines in area, species frequency of occurrence (FO), and percent cover of seagrass. Seagrass area declined by 15% to 85,170 ha in 2022. Subregions in the southern Big Bend experienced extensive seagrass losses of 90-100%. North of the Steinhatchee River, the Northern Big Bend contained 85% of the total seagrass area and experienced losses of only 8.4%. The FO of seagrass and bare quadrats exhibited similar trends to areal coverage. The lowest FO along with complete loss of species was observed near the mouth of the Suwannee River. At a distance from the Suwannee River, FO also declined, but no species were lost. In the remainder of the Big Bend, FO remained stable except for short-term reductions in 2013-2014, which were likely related to anomalously high runoff from rainfall and tropical storm activity. Mean percent cover, however, declined throughout Big Bend, reaching minimal levels in 2014, with little to no recovery through 2019. The persistence of low percent cover may increase vulnerability of beds to continuing areal losses, but the persistence of seagrass species at a distance from the Suwannee River mouth may allow recovery if environmental conditions improve.

Considerations on the programmed functional life (one generation) of a green artificial reef in terms of the sustainability of the modified ecosystem

The installation of artificial reefs serves to enhance marine ecosystems, although it also modifies them. These changes do not have to be irreversible, since it is possible to treat the functional life of an artificial reef (AR) as a variable factor to be determined, with the objective of contributing to the sustainability of the ecosystem. The quest for sustainability does not end with the manufacture and installation of the AR units. It is also necessary to analyse the sustainability of the modified ecosystem, through the production of services. This leads to consider the medium-term return of the ecosystem to its initial state, once the functional life of the ARs expires. This paper presents and justifies an AR design/composition for limited functional life. It is the result of acting on the base material, the concrete, with the objective of limiting the useful life to one social generation. Four different dosages were proposed for such a purpose. They were subjected to mechanical tests (compressive strength and absorption after immersion), including an innovative abrasion-resistant one. The results allow estimating the functional life of the four types of concrete from the design variables (density, compactness, and quantity of water and cement as well as its relation). To this end linear regression models and clustering techniques were applied. The described procedure leads to an AR design for limited functional life.

The Gut Microbiota of Naturally Occurring and Laboratory Aquaculture Lytechinus variegatus Revealed Differences in the Community Composition, Taxonomic Co-Occurrence, and Predicted Functional Attributes

Sea urchins, in many instances, are collected from the wild, maintained in the laboratory aquaculture environment, and used as model animals for various scientific investigations. It has been increasingly evident that diet-driven dysbiosis of the gut microbiome could affect animal health and physiology, thereby impacting the outcome of the scientific studies. In this study, we compared the gut microbiome between naturally occurring (ENV) and formulated diet-fed laboratory aquaculture (LAB) sea urchin Lytechinus variegatus by amplicon sequencing of the V4 region of the 16S rRNA gene and bioinformatics tools. Overall, the ENV gut digesta had higher taxa richness with an abundance of Propionigenium, Photobacterium, Roseimarinus, and Flavobacteriales. In contrast, the LAB group revealed fewer taxa richness, but noticeable abundances of Arcobacter, Agarivorans, and Shewanella. However, Campylobacteraceae, primarily represented by Arcobacter spp., was commonly associated with the gut tissues of both ENV and LAB groups whereas the gut digesta had taxa from Gammaproteobacteria, particularly Vibrio spp. Similarly, the co-occurrence network displayed taxonomic organizations interconnected by Arcobacter and Vibrio as being the key taxa in gut tissues and gut digesta, respectively. Predicted functional analysis of the gut tissues microbiota of both ENV and LAB groups showed a higher trend in energy-related metabolisms, whereas amino acids, carbohydrate, and lipid metabolisms heightened in the gut digesta. This study provides an outlook of the laboratory-formulated diet-fed aquaculture L. variegatus gut microbiome and predicted metabolic profile as compared to the naturally occurring animals, which should be taken into consideration for consistency, reproducibility, and translatability of scientific studies.

Natural recovery of a marine foundation species emerges decades after landscape-scale mortality

Globally, the conditions and time scales underlying coastal ecosystem recovery following disturbance remain poorly understood, and post-disturbance examples of resilience based on long-term studies are particularly rare. Here, we documented the recovery of a marine foundation species (turtlegrass) following a hypersalinity-associated die-off in Florida Bay, USA, one of the most spatially extensive mortality events for seagrass ecosystems on record. Based upon annual sampling over two decades, foundation species recovery across the landscape was demonstrated by two ecosystem responses: the range of turtlegrass biomass met or exceeded levels present prior to the die-off, and turtlegrass regained dominance of seagrass community structure. Unlike reports for most marine taxa, recovery followed without human intervention or reduction to anthropogenic impacts. Our long-term study revealed previously uncharted resilience in subtropical seagrass landscapes but warns that future persistence of the foundation species in this iconic ecosystem will depend upon the frequency and severity of drought-associated perturbation.

Messaging on Slow Impacts: Applying Lessons Learned from Climate Change Communication to Catalyze and Improve Marine Nutrient Communication

Building publics' understanding about human-environmental causes and impacts of nutrient pollution is difficult due to the diverse sources and, at times, extended timescales of increasing inputs, consequences to ecosystems, and recovery after remediation. Communicating environmental problems with "slow impacts" has long been a challenge for scientists, public health officials, and science communicators, as the time delay for subsequent consequences to become evident dilutes the sense of urgency to act. Fortunately, scientific research and practice in the field of climate change communication has begun to identify best practices to address these challenges. Climate change demonstrates a delay between environmental stressor and impact, and recommended practices for climate change communication illustrate how to explain and motivate action around this complex environmental problem. Climate change communication research provides scientific understanding of how people evaluate risk and scientific information about climate change. We used a qualitative coding approach to review the science communication and climate change communication literature to identify approaches that could be used for nutrients and how they could be applied. Recognizing the differences between climate change and impacts of nutrient pollution, we also explore how environmental problems with delayed impacts demand nuanced strategies for effective communication and public engagement. Applying generalizable approaches to successfully communicate the slow impacts related to nutrient pollution across geographic contexts will help build publics' understanding and urgency to act on comprehensive management of nutrient pollution, thereby increasing protection of coastal and marine environments.

Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont

Coral microbiomes are critical to holobiont health and functioning, but the stability of host–microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, “bleaching”), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont’s diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.

The timing and causality of ecological shifts on Caribbean reefs

Caribbean reefs have experienced unprecedented changes in the past four decades. Of great concern is the perceived widespread shift from coral to macroalgal dominance and the question of whether it represents a new, stable equilibrium for coral-reef communities. The primary causes of the shift-grazing pressure (top-down), nutrient loading (bottom-up) or direct coral mortality (side-in)-still remain somewhat controversial in the coral-reef literature. We have attempted to tease out the relative importance of each of these causes. Four insights emerge from our analysis of an early regional dataset of information on the benthic composition of Caribbean reefs spanning the years 1977-2001. First, although three-quarters of reef sites have experienced coral declines concomitant with macroalgal increases, fewer than 10% of the more than 200 sites studied were dominated by macroalgae in 2001, by even the most conservative definition of dominance. Using relative dominance as the threshold, a total of 49 coral-to-macroalgae shifts were detected. This total represents ~35% of all sites that were dominated by coral at the start of their monitoring periods. Four shifts (8.2%) occurred because of coral loss with no change in macroalgal cover, 15 (30.6%) occurred because of macroalgal gain without coral loss, and 30 (61.2%) occurred owing to concomitant coral decline and macroalgal increase. Second, the timing of shifts at the regional scale is most consistent with the side-in model of reef degradation, which invokes coral mortality as a precursor to macroalgal takeover, because more shifts occurred after regional coral-mortality events than expected by chance. Third, instantaneous observations taken at the start and end of the time-series for individual sites showed these reefs existed along a continuum of coral and macroalgal cover. The continuous, broadly negative relationship between coral and macroalgal cover suggests that in some cases coral-to-macroalgae phase shifts may be reversed by removing sources of perturbation or restoring critical components such as the herbivorous sea urchin Diadema antillarum to the system. The five instances in which macroalgal dominance was reversed corroborate the conclusion that macroalgal dominance is not a stable, alternative community state as has been commonly assumed. Fourth, the fact that the loss in regional coral cover and concomitant changes to the benthic community are related to punctuated, discrete events with known causes (i.e. coral disease and bleaching), lends credence to the hypothesis that coral reefs of the Caribbean have been under assault from climate-change-related maladies since the 1970s.

Resilience of seamount benthic communities to trawling disturbance

Despite bottom trawling being the most widespread, severe disturbance affecting deep-sea environments, it remains uncertain whether recovery is possible once trawling has ceased. Here, we review information regarding the resilience of seamount benthic communities to trawling. We focus on seamounts because benthic communities associated with these features are especially vulnerable to trawling as they are often dominated by emergent, sessile epifauna, and trawling on seamounts can be highly concentrated. We perform a meta-analysis to investigate whether any taxa demonstrate potential for recovery once trawling has ceased. Our findings indicate that mean total abundance can gradually increase after protection measures are placed, although taxa exhibit various responses, from no recovery to intermediate/high recovery, resistance, or signs of early colonisation. We use our results to recommend directions for future research to improve our understanding of the resilience of seamount benthic communities, and thereby inform the management of trawling impacts on these ecosystems.

Resilience of aquatic systems: Review and management implications

Our understanding of how ecosystems function has changed from an equilibria-based view to one that recognizes the dynamic, fluctuating, nonlinear nature of aquatic systems. This current understanding requires that we manage systems for resilience. In this review, we examine how resilience has been defined, measured and applied in aquatic systems, and more broadly, in the socioecological systems in which they are embedded. Our review reveals the importance of managing stressors adversely impacting aquatic system resilience, as well as understanding the environmental and climatic cycles and changes impacting aquatic resources. Aquatic resilience may be enhanced by maintaining and enhancing habitat connectivity as well as functional redundancy and physical and biological diversity. Resilience in aquatic socioecological system may be enhanced by understanding and fostering linkages between the social and ecological subsystems, promoting equity among stakeholders, and understanding how the system is impacted by factors within and outside the area of immediate interest. Management for resilience requires implementation of adaptive and preferably collaborative management. Implementation of adaptive management for resilience will require an effective monitoring framework to detect key changes in the coupled socioecological system. Research is needed to (1) develop sensitive indicators and monitoring designs, (2) disentangle complex multi-scalar interactions and feedbacks, and (3) generalize lessons learned across aquatic ecosystems and apply them in new contexts.

Examining Community Stability in the Face of Mass Extinction in Communities of Digital Organisms

Digital evolution is a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve. It is an excellent platform for addressing topics in long-term evolution and paleobiology, such as mass extinction and recovery, with experimental evolutionary approaches. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an alteration of the abiotic environment to which the communities had to adapt. These treatments were applied at two different strengths, along with unperturbed control experiments. We examined how stability in the digital communities was affected from the perspectives of division of labor, relative shift in rank abundance, and genealogical connectedness of the community's component ecotypes. Mass extinction that was due to a Strong Press treatment was most effective in producing reshaped communities that differed from the pre-treatment ones in all of the measured perspectives; weaker versions of the treatments did not generally produce significant departures from a Control treatment; and results for the Strong Pulse treatment generally fell between those extremes. The Strong Pulse treatment differed from others in that it produced a slight but detectable shift towards more generalized communities. Compared to Press treatments, Pulse treatments also showed a greater contribution from re-evolved ecological doppelgangers rather than new ecotypes. However, relatively few Control communities showed stability in any of these metrics over the whole course of the experiment, and most did not represent stable states (by some measure of stability) that were disrupted by the extinction treatments. Our results have interesting, broad qualitative parallels with findings from the paleontological record, and show the potential of digital evolution studies to illuminate many aspects of mass extinction and recovery by addressing them in a truly experimental manner.

Functional roles and redundancy of demersal Barents Sea fish: Ecological implications of environmental change

When facing environmental change and intensified anthropogenic impact on marine ecosystems, extensive knowledge of how these systems are functioning is required in order to manage them properly. However, in high-latitude ecosystems, where climate change is expected to have substantial ecological impact, the ecosystem functions of biological species have received little attention, partly due to the limited biological knowledge of Arctic species. Functional traits address the ecosystem functions of member species, allowing the functionality of communities to be characterised and the degree of functional redundancy to be assessed. Ecosystems with higher functional redundancy are expected to be less affected by species loss, and therefore less sensitive to disturbance. Here we highlight and compare typical functional characteristics of Arctic and boreal fish in the Barents Sea and address the consequences of a community-wide reorganization driven by climate warming on functional redundancy and characterization. Based on trait and fish community composition data, we assessed functional redundancy of the Barents Sea fish community for the period 2004-2012, a period during which this northern region was characterized by rapidly warming water masses and declining sea ice coverage. We identified six functional groups, with distinct spatial distributions, that collectively provide a functional characterization of Barents Sea fish. The functional groups displayed different prevalence in boreal and Arctic water masses. Some functional groups displayed a spatial expansion towards the northeast during the study period, whereas other groups showed a general decline in functional redundancy. Presently, the observed patterns of functional redundancy would seem to provide sufficient scope for buffering against local loss in functional diversity only for the more speciose functional groups. Furthermore, the observed functional reconfiguration may affect future ecosystem functioning in the area. In a period of rapid environmental change, monitoring programs integrating functional traits will help inform management on ecosystem functioning and vulnerability.

Salinity shifts in marine sediment: Importance of number of fluctuation rather than their intensities on bacterial denitrifying community

The sensitivity of denitrifying community to salinity fluctuations was studied in microcosms filled with marine coastal sediments subjected to different salinity disturbances over time (sediment under frequent salinity changes vs sediment with "stable" salinity pattern). Upon short-term salinity shift, denitrification rate and denitrifiers abundance showed high resistance whatever the sediment origin is. Denitrifying community adapted to frequent salinity changes showed high resistance when salinity increases, with a dynamic nosZ relative expression level. Marine sediment denitrifying community, characterized by more stable pattern, was less resistant when salinity decreases. However, after two successive variations of salinity, it shifted toward the characteristic community of fluctuating conditions, with larger proportion of Pseudomonas-nosZ, exhibiting an increase of nosZ relative expression level. The impact of long-term salinity variation upon bacterial community was confirmed at ribosomal level with a higher percentage of Pseudomonas and lower proportion of nosZII clade genera.

A resilience framework for chronic exposures: water quality and ecosystem services in coastal social-ecological systems

Water quality degradation is a chronic problem which influences the resilience of a social-ecological system differently than acute disturbances, such as disease or storms. Recognizing this, we developed a tailored resilience framework that applies ecosystem service concepts to coastal social-ecological systems affected by degraded water quality. We present the framework as a mechanism for coordinating interdisciplinary research to inform long-term community planning decisions pertaining to chronic challenges in coastal systems. The resulting framework connects the ecological system to the social system via ecological production functions and ecosystem services. The social system then feeds back to the ecological system via policies and interventions to address declining water quality. We apply our resilience framework to the coastal waters and communities of Cape Cod (Barnstable County, Massachusetts, USA) which are affected by nitrogen over-enrichment. This approach allowed us to design research to improve the understanding of the effectiveness and acceptance of water quality improvement efforts and their effect on the delivery of ecosystem services. This framework is intended to be transferable to other geographical settings and more generally applied to systems exposed to chronic disturbances in order to coordinate interdisciplinary research planning and inform coastal management.

Resilience of benthic deep-sea fauna to mining activities

With increasing demand for mineral resources, extraction of polymetallic sulphides at hydrothermal vents, cobalt-rich ferromanganese crusts at seamounts, and polymetallic nodules on abyssal plains may be imminent. Here, we shortly introduce ecosystem characteristics of mining areas, report on recent mining developments, and identify potential stress and disturbances created by mining. We analyze species' potential resistance to future mining and perform meta-analyses on population density and diversity recovery after disturbances most similar to mining: volcanic eruptions at vents, fisheries on seamounts, and experiments that mimic nodule mining on abyssal plains. We report wide variation in recovery rates among taxa, size, and mobility of fauna. While densities and diversities of some taxa can recover to or even exceed pre-disturbance levels, community composition remains affected after decades. The loss of hard substrata or alteration of substrata composition may cause substantial community shifts that persist over geological timescales at mined sites.

Preparing for the unprecedented - Towards quantitative oil risk assessment in the Arctic marine areas

The probability of major oil accidents in Arctic seas is increasing alongside with increasing maritime traffic. Hence, there is a growing need to understand the risks posed by oil spills to these unique and sensitive areas. So far these risks have mainly been acknowledged in terms of qualitative descriptions. We introduce a probabilistic framework, based on a general food web approach, to analyze ecological impacts of oil spills. We argue that the food web approach based on key functional groups is more appropriate for providing holistic view of the involved risks than assessments based on single species. We discuss the issues characteristic to the Arctic that need a special attention in risk assessment, and provide examples how to proceed towards quantitative risk estimates. The conceptual model presented in the paper helps to identify the most important risk factors and can be used as a template for more detailed risk assessments.

Understanding the Spatio-Temporal Response of Coral Reef Fish Communities to Natural Disturbances: Insights from Beta-Diversity Decomposition

Understanding how communities respond to natural disturbances is fundamental to assess the mechanisms of ecosystem resistance and resilience. However, ecosystem responses to natural disturbances are rarely monitored both through space and time, while the factors promoting ecosystem stability act at various temporal and spatial scales. Hence, assessing both the spatial and temporal variations in species composition is important to comprehensively explore the effects of natural disturbances. Here, we suggest a framework to better scrutinize the mechanisms underlying community responses to disturbances through both time and space. Our analytical approach is based on beta diversity decomposition into two components, replacement and biomass difference. We illustrate this approach using a 9-year monitoring of coral reef fish communities off Moorea Island (French Polynesia), which encompassed two severe natural disturbances: a crown-of-thorns starfish outbreak and a hurricane. These disturbances triggered a fast logistic decline in coral cover, which suffered a 90% decrease on all reefs. However, we found that the coral reef fish composition remained largely stable through time and space whereas compensatory changes in biomass among species were responsible for most of the temporal fluctuations, as outlined by the overall high contribution of the replacement component to total beta diversity. This suggests that, despite the severity of the two disturbances, fish communities exhibited high resistance and the ability to reorganize their compositions to maintain the same level of total community biomass as before the disturbances. We further investigated the spatial congruence of this pattern and showed that temporal dynamics involved different species across sites; yet, herbivores controlling the proliferation of algae that compete with coral communities were consistently favored. These results suggest that compensatory changes in biomass among species and spatial heterogeneity in species responses can provide further insurance against natural disturbances in coral reef ecosystems by promoting high levels of key species (herbivores). They can also allow the ecosystem to recover more quickly.

Taking action against ocean acidification: a review of management and policy options

Ocean acidification has emerged over the last two decades as one of the largest threats to marine organisms and ecosystems. However, most research efforts on ocean acidification have so far neglected management and related policy issues to focus instead on understanding its ecological and biogeochemical implications. This shortfall is addressed here with a systematic, international and critical review of management and policy options. In particular, we investigate the assumption that fighting acidification is mainly, but not only, about reducing CO2 emissions, and explore the leeway that this emerging problem may open in old environmental issues. We review nine types of management responses, initially grouped under four categories: preventing ocean acidification; strengthening ecosystem resilience; adapting human activities; and repairing damages. Connecting and comparing options leads to classifying them, in a qualitative way, according to their potential and feasibility. While reducing CO2 emissions is confirmed as the key action that must be taken against acidification, some of the other options appear to have the potential to buy time, e.g. by relieving the pressure of other stressors, and help marine life face unavoidable acidification. Although the existing legal basis to take action shows few gaps, policy challenges are significant: tackling them will mean succeeding in various areas of environmental management where we failed to a large extent so far.

Genomic basis for coral resilience to climate change

Recent advances in DNA-sequencing technologies now allow for in-depth characterization of the genomic stress responses of many organisms beyond model taxa. They are especially appropriate for organisms such as reef-building corals, for which dramatic declines in abundance are expected to worsen as anthropogenic climate change intensifies. Different corals differ substantially in physiological resilience to environmental stress, but the molecular mechanisms behind enhanced coral resilience remain unclear. Here, we compare transcriptome-wide gene expression (via RNA-Seq using Illumina sequencing) among conspecific thermally sensitive and thermally resilient corals to identify the molecular pathways contributing to coral resilience. Under simulated bleaching stress, sensitive and resilient corals change expression of hundreds of genes, but the resilient corals had higher expression under control conditions across 60 of these genes. These "frontloaded" transcripts were less up-regulated in resilient corals during heat stress and included thermal tolerance genes such as heat shock proteins and antioxidant enzymes, as well as a broad array of genes involved in apoptosis regulation, tumor suppression, innate immune response, and cell adhesion. We propose that constitutive frontloading enables an individual to maintain physiological resilience during frequently encountered environmental stress, an idea that has strong parallels in model systems such as yeast. Our study provides broad insight into the fundamental cellular processes responsible for enhanced stress tolerances that may enable some organisms to better persist into the future in an era of global climate change.

Resilience of a beef cow-calf farming system to variations in demographic parameters

Beef cow-calf farming systems are assumed to be resilient to biological disturbances that induce variations in herd demography; however, this hypothesis has not been fully investigated to date. Modeling is an interesting approach to study farming system resilience and to evaluate the impact of biological disturbances, taking into account interactions between system components, including biological variability and management practices. Our objective was to evaluate the resilience of beef cow-calf farming systems to variations in fertility and mortality using a modeling approach. We studied the direct effect of variations in demographic parameters on production objectives without explicitly representing the causes of the variations. We developed a stochastic model to represent the population dynamics of a beef cow-calf herd with breeding by natural service and biological processes occurring at the animal level. The model was validated by comparing observed and simulated distributions of the calving-to-calving interval, which were found to be consistent. Resistance was evaluated by the proportion of simulations where the objective in terms of number of weaned calves is reached even when there is a disturbance that persists for 10 yr. Reversibility was evaluated by the time needed to return to the predisturbance production level. Beef cow-calf farming systems did not appear to be resistant to variations in mortality and infertility rates except when increases in the infertility rates were low (0.02 for cows and 0.03 for heifers). Critical situations, consequently, may emerge with regard to farm production if management practices are not adapted. Reversibility was observed for disturbances that persist for up to 5 yr. However, the system needed 2 to 3 yr to recover its predisturbance production level and up to 4 yr after an increase in cow infertility of 0.12.

Rarity and genetic diversity in Indo-Pacific Acropora corals

Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo-Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome.

Efficient species-level monitoring at the landscape scale

Monitoring the population trends of multiple animal species at a landscape scale is prohibitively expensive. However, advances in survey design, statistical methods, and the ability to estimate species presence on the basis of detection-nondetection data have greatly increased the feasibility of species-level monitoring. For example, recent advances in monitoring make use of detection-nondetection data that are relatively inexpensive to acquire, historical survey data, and new techniques in genetic evaluation. The ability to use indirect measures of presence for some species greatly increases monitoring efficiency and reduces survey costs. After adjusting for false absences, the proportion of sample units in a landscape where a species is detected (occupancy) is a logical state variable to monitor. Occupancy monitoring can be based on real-time observation of a species at a survey site or on evidence that the species was at the survey location sometime in the recent past. Temporal and spatial patterns in occupancy data are related to changes in animal abundance and provide insights into the probability of a species' persistence. However, even with the efficiencies gained when occupancy is the monitored state variable, the task of species-level monitoring remains daunting due to the large number of species. We propose that a small number of species be monitored on the basis of specific management objectives, their functional role in an ecosystem, their sensitivity to environmental changes likely to occur in the area, or their conservation importance.

Sponge ecology in the molecular era

Knowledge of the functioning, health state, and capacity for recovery of marine benthic organisms and assemblages has become essential to adequately manage and preserve marine biodiversity. Molecular tools have allowed an entirely new way to tackle old and new questions in conservation biology and ecology, and sponge science is following this lead. In this review, we discuss the biological and ecological studies of sponges that have used molecular markers during the past 20 years and present an outlook for expected trends in the molecular ecology of sponges in the near future. We go from (1) the interface between inter- and intraspecies studies, to (2) phylogeography and population level analyses, (3) intra-population features such as clonality and chimerism, and (4) environmentally modulated gene expression. A range of molecular markers has been assayed with contrasting success to reveal cryptic species and to assess the genetic diversity and connectivity of sponge populations, as well as their capacity to respond to environmental changes. We discuss the pros and cons of the molecular gene partitions used to date and the prospects of a plentiful supply of new markers for sponge ecological studies in the near future, in light of recently available molecular technologies. We predict that molecular ecology studies of sponges will move from genetics (the use of one or some genes) to genomics (extensive genome or transcriptome sequencing) in the forthcoming years and that sponge ecologists will take advantage of this research trend to answer ecological and biological questions that would have been impossible to address a few years ago.

Recovery of marine animal populations and ecosystems

Many marine populations and ecosystems have experienced strong historical depletions, yet reports of recoveries are increasing. Here, we review the growing research on marine recoveries to reveal how common recovery is, its magnitude, timescale and major drivers. Overall, 10-50% of depleted populations and ecosystems show some recovery, but rarely to former levels of abundance. In addition, recovery can take many decades for long-lived species and complex ecosystems. Major drivers of recovery include the reduction of human impacts, especially exploitation, habitat loss and pollution, combined with favorable life-history and environmental conditions. Awareness, legal protection and enforcement of management plans are also crucial. Learning from historical recovery successes and failures is essential for implementing realistic conservation goals and promising management strategies.

Second-generation environmental sequencing unmasks marine metazoan biodiversity

Biodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude and organization of marine diversity at a range of spatial and taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Richness estimates from the current benchmarked Operational Clustering of Taxonomic Units from Parallel UltraSequencing analyses are broadly aligned with those derived from morphological assessments. However, the slope of taxon rarefaction curves for many phyla remains incomplete, suggesting that the true alpha diversity is likely to exceed current perceptions. The approaches provide a rapid, objective and cost-effective taxonomic framework for exploring links between ecosystem structure and function of all hitherto intractable, but ecologically important, communities.

Recent developments in sequencing technologies have provided the opportunity to investigate the biodiversity of ecosystems. Such a metagenomic approach, combined with taxon clustering, is used here to demonstrate that the species richness of a marine community in Scotland is much greater than anticipated.

Climate change, coral reef ecosystems, and management options for marine protected areas

Marine protected areas (MPAs) provide place-based management of marine ecosystems through various degrees and types of protective actions. Habitats such as coral reefs are especially susceptible to degradation resulting from climate change, as evidenced by mass bleaching events over the past two decades. Marine ecosystems are being altered by direct effects of climate change including ocean warming, ocean acidification, rising sea level, changing circulation patterns, increasing severity of storms, and changing freshwater influxes. As impacts of climate change strengthen they may exacerbate effects of existing stressors and require new or modified management approaches; MPA networks are generally accepted as an improvement over individual MPAs to address multiple threats to the marine environment. While MPA networks are considered a potentially effective management approach for conserving marine biodiversity, they should be established in conjunction with other management strategies, such as fisheries regulations and reductions of nutrients and other forms of land-based pollution. Information about interactions between climate change and more "traditional" stressors is limited. MPA managers are faced with high levels of uncertainty about likely outcomes of management actions because climate change impacts have strong interactions with existing stressors, such as land-based sources of pollution, overfishing and destructive fishing practices, invasive species, and diseases. Management options include ameliorating existing stressors, protecting potentially resilient areas, developing networks of MPAs, and integrating climate change into MPA planning, management, and evaluation.

Scleractinian coral population size structures and growth rates indicate coral resilience on the fringing reefs of North Jamaica

Coral reefs throughout the world are under severe challenges from many environmental factors. This paper quantifies the size structure of populations and the growth rates of corals from 2000 to 2008 to test whether the Discovery Bay coral colonies showed resilience in the face of multiple acute stressors of hurricanes and bleaching. There was a reduction in numbers of colonies in the smallest size class for all the species at all the sites in 2006, after the mass bleaching of 2005, with subsequent increases for all species at all sites in 2007 and 2008. Radial growth rates (mm yr(-1)) of non-branching corals and linear extension rates (mm yr(-1)) of branching corals calculated on an annual basis from 2000-2008 showed few significant differences either spatially or temporally. At Dairy Bull reef, live coral cover increased from 13+/-5% in 2006 to 20+/-9% in 2007 and 31+/-7% in 2008, while live Acropora species increased from 2+/-2% in 2006 to 10+/-4% in 2007 and 22+/-7% in 2008. These studies indicate good levels of coral resilience on the fringing reefs around Discovery Bay in Jamaica.