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Coastal ecosystems, such as estuaries, salt marshes, mangroves and seagrass meadows, comprise some of the world’s most productive and ecologically significant ecosystems. Currently, the predominant factor considered in valuing coastal wetlands as fish habitats is the contribution they make to offshore, adult fish stocks via ontogenetic migrations. However, the true value of coastal nurseries for fish is much more extensive, involving several additional, fundamentally important ecosystem processes. Overlooking these broader aspects when identifying and valuing habitats risks suboptimal conservation outcomes, especially given the intense competing human pressures on coastlines and the likelihood that protection will have to be focussed on specific locations rather than across broad sweeps of individual habitat types. We describe 10 key components of nursery habitat value grouped into three types: (1) connectivity and population dynamics (includes connectivity, ontogenetic migration and seascape migration), (2) ecological and ecophysiological factors (includes ecotone effects, ecophysiological factors, food/predation trade-offs and food webs) and (3) resource dynamics (includes resource availability, ontogenetic diet shifts and allochthonous inputs). By accounting for ecosystem complexities and spatial and temporal variation, these additional components offer a more comprehensive account of habitat value. We explicitly identify research needs and methods to support a broader assessment of nursery habitat value. We also explain how, by better synthesising results from existing research, some of the seemingly complex aspects of this broader view can be addressed efficiently.

Fragmentation is a major driver of ecosystem degradation, reducing the capacity of habitats to provide many important ecosystem services. Mangrove ecosystem services, such as erosion prevention, shoreline protection and mitigation of climate change (through carbon sequestration), depend on the size and arrangement of forest patches, but we know little about broad-scale patterns of mangrove forest fragmentation. Here we conduct a multi-scale analysis using global estimates of mangrove density and regional drivers of mangrove deforestation to map relationships between habitat loss and fragmentation. Mangrove fragmentation was ubiquitous; however, there are geographic disparities between mangrove loss and fragmentation; some regions, like Cambodia and the southern Caribbean, had relatively little loss, but their forests have been extensively fragmented. In Southeast Asia, a global hotspot of mangrove loss, the conversion of forests to aquaculture and rice plantations were the biggest drivers of loss (>50%) and fragmentation. Surprisingly, conversion of forests to oil palm plantations, responsible for >15% of all deforestation in Southeast Asia, was only weakly correlated with mangrove fragmentation. Thus, the management of different deforestation drivers may increase or decrease fragmentation. Our findings suggest that large scale monitoring of mangrove forests should also consider fragmentation. This work highlights that regional priorities for conservation based on forest loss rates can overlook fragmentation and associated loss of ecosystem functionality.

To promote the sequestration of blue carbon, resource managers rely on best-management practices that have historically included protecting and restoring vegetated coastal habitats (seagrasses, tidal marshes, and mangroves), but are now beginning to incorporate catchment-level approaches. Drawing upon knowledge from a broad range of environmental variables that influence blue carbon sequestration, including warming, carbon dioxide levels, water depth, nutrients, runoff, bioturbation, physical disturbances, and tidal exchange, we discuss three potential management strategies that hold promise for optimizing coastal blue carbon sequestration: (1) reducing anthropogenic nutrient inputs, (2) reinstating top-down control of bioturbator populations, and (3) restoring hydrology. By means of case studies, we explore how these three strategies can minimize blue carbon losses and maximize gains. A key research priority is to more accurately quantify the impacts of these strategies on atmospheric greenhouse-gas emissions in different settings at landscape scales.

Coastal Ecosystem Values, Threats, and Decline Coastal wetlands, such as seagrass beds, mangrove wetlands, salt marshes, macroalgal, and seaweed beds, shellfish reefs, tidal freshwater wetlands, and coral reefs, are remarkable features of tropical and temperate coastlines. [...]these systems are subject to what may be called “a triple whammy” of increasing industrialization and urbanization, an increased loss of biological and physical resources (fish, water, energy, space), and a decreased resilience to the consequences of a warming climate and sea level rise (Elliott et al., 2016). Trans-Disciplinary Teams Looking forward into the next decade, coastal habitat restoration will truly require a trans-disciplinary approach with skills drawn from engineering, modeling, ecology, chemistry, hydrology, social sciences including economics, financial, and project planning, governance, and integrated land, and sea spatial planning and management. Coastal ecosystems are at least as complex as terrestrial ecosystems, although arguably more dynamic, with the added gravity of the “triple whammy”—future development expansion that further alters shoreline ecosystems, loss of biodiversity and environmental conditions (e.g., water quality), and changing climate which alters sea level in many complex ways.

Aquatic ecologists routinely count animals to provide critical information for conservation and management. Increased accessibility to underwater recording equipment such as action cameras and unmanned underwater devices has allowed footage to be captured efficiently and safely, without the logistical difficulties manual data collection often presents. It has, however, led to immense volumes of data being collected that require manual processing, and thus significant time, labour and money. The use of deep learning to automate image processing has substantial benefits but has rarely been adopted within the field of aquatic ecology. To test its efficacy and utility, we compared the accuracy and speed of deep learning techniques against human counterparts for quantifying fish abundance in underwater images and video footage. We collected footage of fish assemblages in seagrass meadows in Queensland, Australia. We produced three models using an object detection framework to detect the target species, an ecologically important fish, luderick (Girella tricuspidata). Our models were trained on three randomised 80:20 ratios of training:validation datasets from a total of 6,080 annotations. The computer accurately determined abundance from videos with high performance using unseen footage from the same estuary as the training data (F1 = 92.4%, mAP50 = 92.5%), and from novel footage collected from a different estuary (F1 = 92.3%, mAP50 = 93.4%). The computer’s performance in determining abundance was 7.1% better than human marine experts, and 13.4% better than citizen scientists in single image test datasets, and 1.5% and 7.8% higher in video datasets, respectively. We show that deep learning can be a more accurate tool than humans at determining abundance, and that results are consistent and transferable across survey locations. Deep learning methods provide a faster, cheaper and more accurate alternative to manual data analysis methods currently used to monitor and assess animal abundance and have much to offer the field of aquatic ecology.

This Perspective considers the influence of marine predators on carbon cycling in salt marshes, seagrass meadows, and mangroves, and the potential role that these carbon-rich vegetated coastal ecosystems could play in climate change mitigation. Predators continue to be harvested unsustainably throughout most of the Earth's ecosystems. Recent research demonstrates that the functional loss of predators could have far-reaching consequences on carbon cycling and, by implication, our ability to ameliorate climate change impacts. Yet the influence of predators on carbon accumulation and preservation in vegetated coastal habitats (that is, salt marshes, seagrass meadows and mangroves) is poorly understood, despite these being some of the Earth's most vulnerable and carbon-rich ecosystems. Here we discuss potential pathways by which trophic downgrading affects carbon capture, accumulation and preservation in vegetated coastal habitats. We identify an urgent need for further research on the influence of predators on carbon cycling in vegetated coastal habitats, and ultimately the role that these systems play in climate change mitigation. There is, however, sufficient evidence to suggest that intact predator populations are critical to maintaining or growing reserves of 'blue carbon' (carbon stored in coastal or marine ecosystems), and policy and management need to be improved to reflect these realities.

Animal movement studies are conducted to monitor ecosystem health, understand ecological dynamics, and address management and conservation questions. In marine environments, traditional sampling and monitoring methods to measure animal movement are invasive, labor intensive, costly, and limited in the number of individuals that can be feasibly tracked. Automated detection and tracking of small‐scale movements of many animals through cameras are possible but are largely untested in field conditions, hampering applications to ecological questions. Here, we aimed to test the ability of an automated object detection and object tracking pipeline to track small‐scale movement of many individuals in videos. We applied the pipeline to track fish movement in the field and characterize movement behavior. We automated the detection of a common fisheries species (yellowfin bream, Acanthopagrus australis) along a known movement passageway from underwater videos. We then tracked fish movement with three types of tracking algorithms (MOSSE, Seq‐NMS, and SiamMask) and evaluated their accuracy at characterizing movement. We successfully detected yellowfin bream in a multispecies assemblage (F1 score =91%). At least 120 of the 169 individual bream present in videos were correctly identified and tracked. The accuracies among the three tracking architectures varied, with MOSSE and SiamMask achieving an accuracy of 78% and Seq‐NMS 84%. By employing this integrated object detection and tracking pipeline, we demonstrated a noninvasive and reliable approach to studying fish behavior by tracking their movement under field conditions. These cost‐effective technologies provide a means for future studies to scale‐up the analysis of movement across many visual monitoring systems. We applied automatic object detection and object tracking to track fish movement in the field and characterise movement behaviour.

1. In light of the global extent and cascading effect of our impact on the environment, we design and manage reserves to restore biodiversity and the functioning of ecosystems. Mobile organisms link important processes across ecosystems, however, their roles in providing these services are often overlooked and we need to know how they influence ecosystem functions in reserves. Herbivorous fish play a key role in coral reef seascapes. By removing algae, they promote coral growth and recruitment, and help to increase resilience. 2. We examined how connectivity with mangroves affected herbivore populations and benthic succession on reefs in eastern Australia. We surveyed fish assemblages, examined reef composition and characterised benthic recruitment on reefs at multiple levels of connectivity with mangroves, in a no-take reserve and areas open to fishing. 3. Our results show that connectivity enhanced herbivore biomass and richness in reserves, and that these connectivity and reserve effects interacted to promote herbivory on protected reefs near mangroves. 4. Connectivity and reserve protection combined to double the biomass of roving herbivorous fish on protected reefs near mangroves. The increase in grazing intensity drove a trophic cascade that reduced algal cover and enhanced coral recruitment and reef resilience. 5. Synthesis and applications. Our findings demonstrate that ecosystem resilience can be improved by managing both reefs and adjacent habitats together as functional seascape units. By understanding how landscapes influence resilience, and explicitly incorporating these effects into conservation decision-making, we may have greater success with environmental restoration and preservation actions.

Food webs near the interface of adjacent ecosystems are potentially subsidised by the flux of organic matter across system boundaries. Such subsidies, including carrion of marine provenance, are predicted to be instrumental on open-coast sandy shores where in situ productivity is low and boundaries are long and highly permeable to imports from the sea. We tested the effect of carrion supply on the structure of consumer dynamics in a beach-dune system using broad-scale, repeated additions of carcasses at the strandline of an exposed beach in eastern Australia. Carrion inputs increased the abundance of large invertebrate scavengers (ghost crabs, Ocypode spp.), a numerical response most strongly expressed by the largest size-class in the population, and likely due to aggregative behaviour in the short term. Consumption of carrion at the beach-dune interface was rapid and efficient, driven overwhelmingly by facultative avian scavengers. This guild of vertebrate scavengers comprises several species of birds of prey (sea eagles, kites), crows and gulls, which reacted strongly to concentrations of fish carrion, creating hotspots of intense scavenging activity along the shoreline. Detection of carrion effects at several trophic levels suggests that feeding links arising from carcasses shape the architecture and dynamics of food webs at the land-ocean interface.

Mangroves are traditionally considered to provide important nutrition to tropical estuarine consumers. However, there is still controversy about this, and the extent and importance of these inputs are largely unquantified. In particular, there is no information for food webs of small estuaries that dominate wet–dry tropical coasts, where freshwater inflow is intermittent, leading to highly seasonal inputs of nutrients from terrestrial systems. Since the relative importance of the different sources depends on the type and extent of different habitats and on hydrological and topographic conditions, results from other regions/type of systems cannot be extrapolated to these estuaries. Here, δ¹³C is used to determine the importance of mangrove-derived carbon for Penaeus merguiensis (detritivore; shrimp), Ambassis vachellii (planktivore; fish), and Leiognathus equulus (benthivore; fish) from six small wet–dry tropical estuaries that differ in mangrove (C₃) cover and in type of terrestrial vegetation adjacent to the estuary. Bayesian mixing models confirmed that mangrove material was important to consumers in all estuaries. There was a gradient in this importance that agreed with the extent of mangrove forests in the estuaries, as C₃sources were the most important contributors to animals from the three estuaries with the greatest (>40 %) mangrove cover. There was also evidence of incorporation of C₃material for the three estuaries with lower (<30 %) mangrove cover. Since these latter estuaries had no adjacent terrestrial C₃forests, the detected C₃influence can only be of mangrove origin. This shows that mangroves are important contributors to these food webs, underlining the importance of mangroves in supporting estuarine nursery ground value and fisheries productivity.