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Taking a coordinated, holistic approach to the governance of coastal ecosystems is widely advocated in recognition of the need to manage ecosystems as a whole. Despite commitment to approaches such as integrated coastal zone management and ecosystem-based management of fisheries, governance remains fragmented, with sectors such as environment, fisheries and forestry maintaining separate systems of governance from the national to village level. These systems include the formation of separate community-based structures, reporting directly to the respective sectoral ministry. This raises questions about how this collaborative governance approach aligns with taking a more integrated, holistic approach to management. The paper draws on findings from research in Kenya and Zanzibar-Tanzania in coastal villages where forest and fisheries management groups have been formed. The research found that the groups operate in compartmentalised ‘silos’, in contrast to the interrelated ecosystems on which they depend, with little coordination of plans and priorities. In addition, these groups are not consistent in their relationship to local government, answering directly to the sectoral ministry rather than democratic local government, raising issues for accountability and sustainability. These dual challenges of a sectoral-focus and long-term sustainability must be addressed for management of ecosystems to be integrated and effective.

Aim As a step towards providing support for an ecological approach to strengthening marine protected areas (MPAs) and meeting international commitments, this study combines cumulative impact assessment and conservation planning approach to undertake a large‐scale spatial prioritization. Location Exclusive Economic Zone (EEZ) of Brazil, Southwest Atlantic Ocean. Methods We developed a prioritization approach to protecting different habitat types, threatened species ranges and ecological connectivity, while also mitigating the impacts of multiple threats on biodiversity. When identifying priorities for conservation, we accounted for the co‐occurrence of 24 human threats and the distribution of 161 marine habitats and 143 threatened species, as well as their associated vulnerabilities. Additionally, we compared our conservation priorities with MPAs proposed by local stakeholders. Results We show that impacts to habitats and species are widespread and identify hot spots of cumulative impacts on inshore and offshore areas. Industrial fisheries, climate change and land‐based activities were the most severe threats to biodiversity. The highest priorities were mostly found towards the coast due to the high cumulative impacts found in nearshore areas. As expected, our systematic approach showed a better performance on selecting priority sites when compared to the MPAs proposed by local stakeholders without a typical conservation planning exercise, increasing the existing coverage of MPAs by only 7.9%. However, we found that proposed MPAs still provide some opportunities to protect areas facing high levels of threats. Main conclusions The study presents a blueprint of how to embrace a comprehensive ecological approach when identifying strategic priorities for conservation. We advocate protecting these crucial areas from degradation in emerging conservation efforts is key to maintain their biodiversity value.

Marine ecosystems are prone to tipping points, particularly in coastal zones where dramatic changes are associated with interactions between cumulative stressors (e.g., shellfish harvesting, eutrophication and sediment inputs) and ecosystem functions. A common feature of many degraded estuaries is elevated turbidity that reduces incident light to the seafloor, resulting from multiple factors including changes in sediment loading, sea-level rise and increased water column algal biomass. To determine whether cumulative effects of elevated turbidity may result in marked changes in the interactions between ecosystem components driving nutrient processing, we conducted a large-scale experiment manipulating sediment nitrogen concentrations in 15 estuaries across a national-scale gradient in incident light at the seafloor. We identified a threshold in incident light that was related to distinct changes in the ecosystem interaction networks (EIN) that drive nutrient processing. Above this threshold, network connectivity was high with clear mechanistic links to denitrification and the role of large shellfish in nitrogen processing. The EIN analyses revealed interacting stressors resulting in a decoupling of ecosystem processes in turbid estuaries with a lower capacity to denitrify and process nitrogen. This suggests that, as turbidity increases with sediment load, coastal areas can be more vulnerable to eutrophication. The identified interactions between light, nutrient processing and the abundance of large shellfish emphasizes the importance of actions that seek to manage multiple stressors and conserve or enhance shellfish abundance, rather than actions focusing on limiting a single stressor.

Bottom fishing such as trawling and dredging may pose serious risks to the seabed and benthic habitats, calling for a quantitative assessment method to evaluate the impact and guide management to develop mitigation measures. We provide a method to estimate the sensitivity of benthic habitats based on the longevity composition of the invertebrate community. We hypothesize that long-lived species are more sensitive to trawling mortality due to their lower pace of life (i.e., slower growth, late maturation). We analyze data from box-core and grab samples taken from 401 stations in the English Channel and southern North Sea to estimate the habitat-specific longevity composition of the benthic invertebrate community and of specific functional groups (i.e., suspension feeders and bioturbators), and examine how bottom trawling affects the longevity biomass composition. The longevity biomass composition differed between habitats governed by differences in sediment composition (gravel and mud content) and tidal bed-shear stress. The biomass proportion of long-lived species increased with gravel content and decreased with mud content and shear stress. Bioturbators had a higher median longevity than suspension feeders. Trawling, in particular by gears that penetrate the seabed >2 cm, shifted the community toward shorter-lived species. Changes from bottom trawling were highest in habitats with many long-lived species (hence increasing with gravel content, decreasing with mud content). Benthic communities in high shear stress habitats were less affected by bottom trawling. Using these relationships, we predicted the sensitivity of the benthic community from bottom trawling impact at large spatial scale (the North Sea). We derived different benthic sensitivity metrics that provide a basis to estimate indicators of trawling impact on a continuous scale for the total community and specific functional groups. In combination with high resolution data of trawling pressure, our approach can be used to monitor and assess trawling impact and seabed status at the scale of the region or broadscale habitat and to compare the environmental impact of bottom-contacting fishing gears across fisheries.

Time can be a limiting constraint for consumers, particularly when resource phenology mediates foraging opportunity. Though a large body of research has explored how resource phenology influences trophic interactions, this work has focused on the topics of trophic mismatch or predator swamping, which typically occur over short periods, at small spatial extents or coarse resolutions. In contrast many consumers integrate across landscape heterogeneity in resource phenology, moving to track ephemeral food sources that propagate across space as resource waves. Here we provide a conceptual framework to advance the study of phenological diversity and resource waves. We define resource waves, review evidence of their importance in recent case studies, and demonstrate their broader ecological significance with a simulation model. We found that consumers ranging from fig wasps (Chalcidoidea) to grizzly bears (Ursus arctos) exploit resource waves, integrating across phenological diversity to make resource aggregates available for much longer than their component parts. In model simulations, phenological diversity was often more important to consumer energy gain than resource abundance per se. Current ecosystem‐based management assumes that species abundance mediates the strength of trophic interactions. Our results challenge this assumption and highlight new opportunities for conservation and management. Resource waves are an emergent property of consumer–resource interactions and are broadly significant in ecology and conservation.

Pacific salmon influence temperate terrestrial and freshwater ecosystems through the dispersal of marine-derived nutrients and ecosystem engineering of stream beds when spawning. They also support large fisheries, particularly along the west coast of North America. We provide a comprehensive synthesis of relationships between the densities of Pacific salmon and terrestrial and aquatic ecosystems, summarize the direction, shape, and magnitude of these relationships, and identify possible ecosystem-based management indicators and benchmarks. We found 31 studies that provided 172 relationships between salmon density (or salmon abundance) and species abundance, species diversity, food provisioning, individual growth, concentration of marine-derived isotopes, nutrient enhancement, phenology, and several other ecological responses. The most common published relationship was between salmon density and marine-derived isotopes (40%), whereas very few relationships quantified ecosystem-level responses (5%). Only 13% of all relationships tended to reach an asymptote (i.e., a saturating response) as salmon densities increased. The number of salmon killed by bears and the change in biomass of different stream invertebrate taxa between spawning and nonspawning seasons were relationships that usually reached saturation. Approximately 46% of all relationships were best described with linear or curved nonasymptotic models, indicating a lack of saturation. In contrast, 41% of data sets showed no relationship with salmon density or abundance, including many of the relationships with stream invertebrate and biofilm biomass density, marine-derived isotope concentrations, or vegetation density. Bears required the highest densities of salmon to reach their maximum observed food consumption (i.e., 9.2 kg/m² to reach the 90% threshold of the relationship’s asymptote), followed by freshwater fish abundance (90% threshold = 7.3 kg/m² of salmon). Although the effects of salmon density on ecosystems are highly varied, it appears that several of these relationships, such as bear food consumption, could be used to develop indicators and benchmarks for ecosystem-based fisheries management.

Marine environmental management policies seek to ensure that fishing impacts on fished populations and other components of the ecosystem are sustainable, to simultaneously meet objectives for fisheries and conservation. For example, in Europe, targets for (i) biodiversity, (ii) food web structure as indicated by the proportion of large fish and (iii) fishing mortality rates for exploited species that lead to maximum sustainable yield, FMSY, are being proposed to support implementation of the Marine Strategy Framework Directive. Efforts to reconcile any trade‐offs among objectives need to be informed by knowledge on the consequences of alternate management actions. We develop, calibrate and apply a multispecies size spectrum model of the North Sea fish community to assess the response of populations and the community to fishing. The model predicts species' size distributions, abundance, productivity and interactions and therefore provides a single framework for evaluating trade‐offs between population status, community and food web structure, biodiversity and fisheries yield. We show that the model can replicate realistic fish population and community structure and past responses to fishing. We assess whether meeting management targets for exploited North Sea populations (fishing species at FMSY) will be sufficient to meet proposed targets for biodiversity and food web indicators under two management scenarios (status quo and FMSY). The recovery in biodiversity indicators is 60% greater when fishing populations at FMSY than if status quo (2010) fishing rates are maintained. The probability of achieving a food web target was 60% under both scenarios in spite of major community restructuring revealed by other indicators of community size structure. Synthesis and applications. Our model can be applied to evaluate indicator targets and trade‐offs among fisheries and conservation objectives. There is a significant probability that reductions in fishing mortality below FMSY would be needed in Europe if managers make a binding commitment to a proposed large fish indicator target, with concomitant reductions in fisheries yield.

Unsustainable fishing is a major driver of change in marine ecosystems. The ways that fishing gears target fishes with different ecological functions are unclear, particularly in complex multispecies fisheries. Here, we examine whether artisanal fishing gears selectively target fishes with unique combinations of ecological traits (diet, body size, depth, position in water column, period of activity, schooling behaviour) in a coral reef ecosystem. We use coral reef fish landing data from 25 sites along the Kenyan coast collected over a 7‐year period. All fishing gears targeted a wide diversity of traits, but with some differentiation among gears. Fish assemblages captured by spearguns were significantly different from the other gear types, specializing on diurnal species that feed on sessile invertivores. Nets, including gillnets and beachseines, targeted the most functional diversity. Escape slot traps targeted the least functionally diverse assemblages. Basket traps and escape slot traps targeted the most functionally similar species of all two‐gear combinations. There were 163 functional entities (unique combinations of traits) captured in the fishery; however, 50% of the catch by each gear was from only two to six functional entities. Most of the differences in gear selectivity were due to unique and rarely targeted functional entities, that made up only a small proportion of the catch. Synthesis and applications. Coral reef fisheries target a breadth of functional entities (unique combinations of traits), but catches are heavily skewed towards relatively few functional entities. While banning specific gears will benefit rare functional entities in the catch, effort reductions will be necessary to alleviate pressure on commonly targeted functional entities. Coral reef fisheries target a breadth of functional entities (unique combinations of traits), but catches are heavily skewed towards relatively few functional entities. While banning specific gears will benefit rare functional entities in the catch, effort reductions will be necessary to alleviate pressure on commonly targeted functional entities.

Identifying organisms that play an important role in maintaining ecosystem function is a key aspect of resilience‐based management. For Australia's Great Barrier Reef (GBR), we found that the recovery ability of shallow exposed fore‐reefs is more than 14 times higher when tabular Acropora are present. The disproportionate role that tabular Acropora play appears to be driven by a combination of traits including high recruitment, high growth rate and, importantly, large maximum colony sizes. Despite this key role, tabular Acropora are highly sensitive to most pressures. We compile evidence suggesting that if tabular corals were to decline or disappear on the GBR, the potential for reef recovery on exposed fore‐reefs would be considerably slowed. We then consider the merits of placing special emphasis on the protection of tabular Acropora within the management of the GBR. Importantly, we recognise that an analysis of costs and benefits of such recognition is vital before any change is implemented. Actions might include targeted crown‐of‐thorns starfish control, anchoring restrictions and protection for tabular corals on reefs identified as essential for their larval dispersal. In addition, targeted communications about the critical importance of these highly recognisable corals may boost community support and participation in their protection.

Coral reefs provide food and livelihoods for hundreds of millions of people as well as harbour some of the highest regions of biodiversity in the ocean. However, overexploitation, land‐use change and other local anthropogenic threats to coral reefs have left many degraded. Additionally, coral reefs are faced with the dual emerging threats of ocean warming and acidification due to rising CO2 emissions, with dire predictions that they will not survive the century. This review evaluates the impacts of climate change on coral reef organisms, communities and ecosystems, focusing on the interactions between climate change factors and local anthropogenic stressors. It then explores the shortcomings of existing management and the move towards ecosystem‐based management and resilience thinking, before highlighting the need for climate change‐ready marine protected areas (MPAs), reduction in local anthropogenic stressors, novel approaches such as human‐assisted evolution and the importance of sustainable socialecological systems. It concludes that designation of climate change‐ready MPAs, integrated with other management strategies involving stakeholders and participation at multiple scales such as marine spatial planning, will be required to maximise coral reef resilience under climate change. However, efforts to reduce carbon emissions are critical if the long‐term efficacy of local management actions is to be maintained and coral reefs are to survive. Coral reefs are degraded by human activities, and are now faced with ocean warming and acidification. This review summarizes current knowledge on the impacts of climate change on coral reefs, synergies with other stressors, and the move toward ecosystem‐based management of coral reefs. Climate change‐ready MPAs, integrated management at various spatial scales, novel approaches, and efforts to reduce greenhouse gas emissions are critical if coral reefs are to survive.