Historical ecology with real numbers: past and present extent and biomass of an imperilled estuarine habitat

The effects of Mid-Holocene foragers on the European oyster in Denmark

Oysters (Ostreidae) play a pivotal role in the health and productivity of marine ecosystems. Their unique ability to filter water, provide habitat, and contribute to nutrient cycling has remained underused in many parts of Europe following the destruction of vast oyster beds in the 19th and 20th centuries. The burgeoning field of oyster restoration for aquaculture has recognized the potential of these bivalves in promoting ecosystem resilience and enhancing biodiversity. Restoring oysters to previous levels requires the establishment of ecological baselines that ideally take into account the long-term changes of animal behavior as well as the surrounding environment prior to significant human intervention, an extremely challenging task. Archaeological shell middens are invaluable baseline archives and provide exclusive insights into past ecosystems. Here, we use demographic information from over 2,000 analyzed European oyster (Ostrea edulis) shells dating from ~5,660 to 2,600 cal BCE (calibrated years BCE), the largest archaeological growth rate dataset of mollusks yet. Through the analysis of size as well as ontogenetic age, we decouple anthropogenic from environmental impacts throughout Denmark. Our data show definitive influence of oyster size-age structure through human harvesting during the Mid-Holocene, with older oysters in the Mesolithic (mean: 4.9 y) than the Neolithic (mean: 3.7 y), irrespective of changes in growth rate. Furthermore, we present the metrics for long-term sustainable harvesting of oysters across environmental and socioeconomic transitions, providing demographic targets for current oyster restoration projects and valuable context in mitigating the impact of modern climatic change.

Consequences of domestication in eastern oyster: Insights from whole genomic analyses

Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1-17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild - wild] < [wild - cultured] < [cultured - cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome-wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery-based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters.

High parasite prevalence in an ecosystem engineer correlated with both local- and landscape-level factors

Spatial variation in parasitic infection may have many physical and biological drivers. Uncovering these drivers may be especially important for parasites of ecosystem engineers because the engineers are foundational to their communities. Oysters are an important coastal ecosystem engineer that have declined drastically worldwide, in part due to enhanced cases of lethal oyster diseases, such as Dermo and MSX, caused by the protozoan parasites Perkinsus marinus and Haplosporidium nelsoni, respectively. Besides water quality and hydrodynamics, there is little information on how other variables influence the prevalence and intensity of these pathogens in oysters across a regional scale. To examine drivers of spatial variation in these oyster parasites-including host size, local reef properties, and landscape properties-we sampled 24 reefs systematically spread along the coast of Georgia, USA. Across sites, we found universally high prevalence of oysters with at least one of these parasites (91.02% ± 8.89, mean ± SD). Not only are high levels of parasite prevalence potentially problematic for a pivotal ecosystem engineer, but also low spatial variability may limit the explanatory power of variables across a regional scale. Our statistical models explained between 18 and 42% of the variation in spatial patterns of prevalence and intensity of these microparasites. Interestingly, landscape context was a positive predictor of P. marinus, but a negative predictor of H. nelsoni. Overall, our findings suggest that factors driving parasite prevalence and intensity operate across multiple spatial scales, and the same factor can both facilitate and hinder different parasites within the same host species.

In situ habitat clearance rates and particle size preference of indigenous Olympia oysters (Ostrea lurida) and non-native Pacific oysters (Magallana gigas) in North American Pacific coast estuaries

The Olympia oyster, Ostrea lurida, is the target of many restoration projects along estuaries on the North American Pacific coast, while the non-native Pacific oyster, Magallana gigas, dominates oyster aquaculture globally. Both species provide filtration functions that were investigated in three California bays using a whole-habitat, in situ approach, a laboratory particle selection experiment, and a regional physiological comparison. Measurements of chlorophyll α, temperature, salinity, and turbidity upstream and downstream, as well as point samples of seston total particulate matter and organic content to estimate habitat clearance rates (HCR, L hr-1 m-2) were collected. From February 2018 to June 2019, twenty-two trials were conducted across four sites. HCRs were highly variable within and among sites, ranging from site averages of -464 to 166 L hr-1 m-2, and not significantly different among sites, indicating field filtration performance of O. lurida habitat and M. gigas aquaculture is similar. Using a random forest regression, site was the most important predictor of HCR, with a variable importance score of 25.7 % (SD = 4.6 %). O. lurida and M. gigas had significantly different particle size selection preferences, likely affecting the quality of their filtration. This study's findings suggest that restoring O. lurida habitat may provide similar filtration benefits as M. gigas aquaculture, but the unique hydrodynamics and food quality of individual bays, as well as regional differences in filter feeder communities, must be considered in managing oyster habitat for filtration functions.

Using vulnerability assessment to characterize coastal protection benefits provided by estuarine habitats of a dynamic intracoastal waterway

The existence of coastal ecosystems depends on their ability to gain sediment and keep pace with sea level rise. Similar to other coastal areas, Northeast Florida (United States) is experiencing rapid population growth, climate change, and shifting wetland communities. Rising seas and more severe storms, coupled with the intensification of human activities, can modify the biophysical environment, thereby increasing coastal exposure to storm-induced erosion and inundation. Using the Guana Tolomato Matanzas National Estuarine Research Reserve as a case study, we analyzed the distribution of coastal protection services-expressly, wave attenuation and sediment control-provided by estuarine habitats inside a dynamic Intracoastal waterway. We explored six coastal variables that contribute to coastal flooding and erosion-(a) relief, (b) geomorphology, (c) estuarine habitats, (d) wind exposure, (e) boat wake energy, and (f) storm surge potential-to assess physical exposure to coastal hazards. The highest levels of coastal exposure were found in the north and south sections of the Reserve (9% and 14%, respectively) compared to only 4% in the central, with exposure in the south driven by low wetland elevation, high surge potential, and shorelines composed of less stable sandy and muddy substrate. The most vulnerable areas of the central Reserve and main channel of the Intracoastal waterway were exposed to boat wakes from larger vessels frequently traveling at medium speeds (10-20 knots) and had shoreline segments oriented towards the prevailing winds (north-northeast). To guide management for the recently expanded Reserve into vulnerable areas near the City of Saint Augustine, we evaluated six sites of concern where the current distribution of estuarine habitats (mangroves, salt marshes, and oyster beds) likely play the greatest role in natural protection. Spatially explicit outputs also identified potential elevation maintenance strategies such as living shorelines, landform modification, and mangrove establishment for providing coastal risk-reduction and other ecosystem-service co-benefits. Salt marshes and mangroves in two sites of the central section (N-312 and S-312) were found to protect more than a one-quarter of their cross-shore length (27% and 73%, respectively) from transitioning to the highest exposure category. Proposed interventions for mangrove establishment and living shorelines could help maintain elevation in these sites of concern. This work sets the stage for additional research, education, and outreach about where mangroves, salt marshes, and oyster beds are most likely to reduce risk to wetland communities in the region.

Using an ecosystem service model to inform restoration planning: A spatially explicit oyster filtration model for Pensacola Bay, Florida

The development of science-based restoration goals that reflect the primary motivation of stakeholders is a key factor leading to large-scale, long-term restoration successes. The ability to predict the potential ecosystem service delivery from restoration can inform the setting of appropriate goals and facilitate the strategic planning of restoration activities. While recovery of the ecosystem services provided by oyster reefs is a regularly cited reason for undertaking restoration, few examples exist where large-scale oyster habitat restoration plans have been informed using ecosystem service functions. Such an approach is currently being implemented in the Pensacola Bay System, Florida, where a broad coalition of partners and community stakeholders are utilizing a watershed approach to restoring oysters with the aim of restoring oysters for multiple objectives including habitat, ecosystem services, and wild harvest and aquaculture. Through the process of developing a habitat management plan, water filtration was identified as a key ecosystem service by the stakeholders. To support restoration planning we derived a spatially explicit estimate of water filtration services provided by the eastern oyster in the Pensacola Bay system by linking an oyster habitat suitability map to a hydrodynamic-oyster filtration model. This spatially explicit model allowed us to identify the areas where restored oyster reefs have the potential to provide the greatest increase in filtration service as well as provide spatially explicit estimates of the potential filtration provided by oyster habitat restored. Such information is useful in restoration planning and management and for stakeholder engagement, outreach, and education programs.

The genome sequence of the European flat oyster, Ostrea edulis (Linnaeus, 1758)

We present a genome assembly from an individual Ostrea edulis (the European flat oyster; Mollusca; Bivalvia; Ostreida; Ostreidae). The genome sequence is 894.8 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.35 kilobases in length.

Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas.

Importance

Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.

Utilizing historical maps in identification of long-term land use and land cover changes

Knowledge in the magnitude and historical trends in land use and land cover (LULC) is needed to understand the changing status of the key elements of the landscape and to better target management efforts. However, this information is not easily available before the start of satellite campaign missions. Scanned historical maps are a valuable but underused source of LULC information. As a case study, we used U-Net to automatically extract fields, mires, roads, watercourses, and water bodies from scanned historical maps, dated 1965, 1984 and 1985 for our 900 km[Formula: see text] study area in Southern Finland. We then used these data, along with the topographic databases from 2005 and 2022, to quantify the LULC changes for the past 57 years. For example, the total area of fields decreased by around 27 km[Formula: see text], and the total length of watercourses increased by around 2250 km in our study area.

Host genetic identity determines parasite community structure across time and space in oyster restoration

Intraspecific variation in host susceptibility to individual parasite species is common, yet how these effects scale to mediate the structure of diverse parasite communities in nature is less well understood. To address this knowledge gap, we tested how host genetic identity affects parasite communities on restored reefs seeded with juvenile oysters from different sources-a regional commercial hatchery or one of two wild progenitor lines. We assessed prevalence and intensity of three micro- and two macroparasite species for 4 years following restoration. Despite the spatial proximity of restored reefs, oyster source identity strongly predicted parasite community prevalence across all years, with sources varying in their relative susceptibility to different parasites. Oyster seed source also predicted reef-level parasite intensities across space and through time. Our results highlight that host intraspecific variation can shape parasite community structure in natural systems, and reinforce the importance of considering source identity and diversity in restoration design.

Meta-analysis of ecosystem services associated with oyster restoration

Restoration of foundation species promises to reverse environmental degradation and return lost ecosystem services, but a lack of standardized evaluation across projects limits understanding of recovery, especially in marine systems. Oyster reefs are restored to reverse massive global declines and reclaim valuable ecosystem services, but the success of these projects has not been systematically and comprehensively quantified. We synthesized data on ecosystem services associated with oyster restoration from 245 pairs of restored and degraded reefs and 136 pairs of restored and reference reefs across 3500 km of U.S. Gulf of Mexico and Atlantic coastlines. On average, restoration was associated with a 21-fold increase in oyster production (mean log response ratio = 3.08 [95% confidence interval: 2.58-3.58]), 34-97% enhancement of habitat provisioning (mean community abundance = 0.51 [0.41-0.61], mean richness = 0.29 [0.19-0.39], and mean biomass = 0.69 [0.39-0.99]), 54% more nitrogen removal (mean = 0.43 [0.13-0.73]), and 89-95% greater sediment nutrients (mean = 0.67 [0.27-1.07]) and organic matter (mean = 0.64 [0.44-0.84]) relative to degraded habitats. Moreover, restored reefs matched reference reefs for these ecosystem services. Our results support the continued and expanded use of oyster restoration to enhance ecosystem services of degraded coastal systems and match many functions provided by reference reefs.

Oyster reef restoration fails to recoup global historic ecosystem losses despite substantial biodiversity gain

Human activities have led to degradation of ecosystems globally. The lost ecosystem functions and services accumulate from the time of disturbance to the full recovery of the ecosystem and can be quantified as a "recovery debt," providing a valuable tool to develop better restoration practices that accelerate recovery and limit losses. Here, we quantified the recovery of faunal biodiversity and abundance toward a predisturbed state following structural restoration of oyster habitats globally. We found that while restoration initiates a rapid increase in biodiversity and abundance of reef-associated species within 2 years, recovery rate then decreases substantially, leaving a global shortfall in recovery of 35% below a predisturbed state. While efficient restoration methods boost recovery and minimize recovery shortfalls, the time to full recovery is yet to be quantified. Therefore, potential future coastal development should weigh up not only the instantaneous damage to ecosystem functions but also the potential for generational loss of services.

The potential of historical ecology to aid understanding of human-ocean interactions throughout the Anthropocene

Marine historical ecology emerged in the scholarly literature with the aim of understanding long-term dynamics in marine ecosystems and the outcomes of past human-ocean interactions. The use of historical sources, which differ in temporal scale and resolution to most scientific monitoring data, present both opportunities and challenges for informing our understanding of past marine ecosystems and the ways in which human communities made use of them. With an emphasis upon marine social-ecological changes over the past 200 years, I present an overview of the relevant historical ecology literature and summarise how this approach generates a richer understanding of human-ocean interactions and the legacies associated with human-induced ecosystem change. Marine historical ecology methodologies continue to be developed, whereas expanded inter- and multidisciplinary collaborations provide exciting avenues for future discoveries. Beyond scholarship, historical ecology presents opportunities to foster a more sustainable relationship with oceans going forward: by challenging ingrained perceptions of what is "normal" within marine ecosystems, reconnecting human communities to the oceans and providing cautionary lessons and exemplars of sustainable human-ocean interactions from the past. To leverage these opportunities, scholars must work alongside practitioners, managers and policy makers to foster mutual understanding, explore new opportunities to communicate historical findings and address the challenges of integrating historical data into modern-day frameworks.

The Use of Non-Plastic Materials for Oyster Reef and Shoreline Restoration: Understanding What Is Needed and Where the Field Is Headed

Oyster and shoreline restoration is occurring around the globe to recover lost ecosystem services. In the state of Florida, USA, dozens of estuarine habitat restoration projects are underway. These projects have traditionally relied on both natural and man-made materials, including plastics. As the impacts of plastics on marine ecosystems are better understood, practitioners are increasingly focused on plastic-free restoration. To better understand this transition, we surveyed Florida restoration practitioners in April 2021 to capture current non-plastic restoration project trends and their status. Our descriptive survey goals were to understand: (1) what non-plastic materials have been tested, (2) trade-offs between plastic and non-plastic materials (e.g., cost, sourcing, volunteer engagement), and (3) the performance of non-plastic materials. Responses indicated that a variety of non-plastic materials are currently being used, including rock, cement-infused jute structures, cement Reef Balls™ (Reef Ball Foundation, USA), BESE-elements®, and metal gabions. Overall, these materials are more expensive and equally or more difficult to install than previously popular plastic-based materials. No “best” non-plastic material emerged from our survey in part because many novel materials have been deployed for under three years. Long-term performance under a variety of abiotic and biotic conditions is thus a future research priority.

Indigenous oyster fisheries persisted for millennia and should inform future management

Historical ecology has revolutionized our understanding of fisheries and cultural landscapes, demonstrating the value of historical data for evaluating the past, present, and future of Earth’s ecosystems. Despite several important studies, Indigenous fisheries generally receive less attention from scholars and managers than the 17th–20th century capitalist commercial fisheries that decimated many keystone species, including oysters. We investigate Indigenous oyster harvest through time in North America and Australia, placing these data in the context of sea level histories and historical catch records. Indigenous oyster fisheries were pervasive across space and through time, persisting for 5000–10,000 years or more. Oysters were likely managed and sometimes “farmed,” and are woven into broader cultural, ritual, and social traditions. Effective stewardship of oyster reefs and other marine fisheries around the world must center Indigenous histories and include Indigenous community members to co-develop more inclusive, just, and successful strategies for restoration, harvest, and management.

‘Commercial fisheries have decimated keystone species, including oysters in the past 200 years. Here, the authors examine how Indigenous oyster harvest in North America and Australia was managed across 10,000 years, advocating for effective future stewardship of oyster reefs by centering Indigenous peoples.’

Estimation of Intertidal Oyster Reef Density Using Spectral and Structural Characteristics Derived from Unoccupied Aircraft Systems and Structure from Motion Photogrammetry

Eastern oysters (Crassostrea virginica) are an important component of the ecology and economy in coastal zones. Through the long-term consolidation of densely clustered shells, oyster reefs generate three-dimensional and complex structures that yield a suite of ecosystem services, such as nursery habitat, stabilizing shorelines, regulating nutrients, and increasing biological diversity. The decline of global oyster habitat has been well documented and can be attributed to factors, such as overharvesting, pollution, and disease. Monitoring oyster reefs is necessary to evaluate persistence and track changes in habitat conditions but can be time and labor intensive. In this present study, spectral and structural metrics of intertidal oyster reefs derived from Unoccupied Aircraft Systems (UAS) and Structure from Motion (SfM) outputs are used to estimate intertidal oyster density. This workflow provides a remote, rapid, nondestructive, and potentially standardizable method to assess large-scale intertidal oyster reef density that will significantly improve management strategies to protect this important coastal resource from habitat degradation.

Mapping oysters on the Pacific coast of North America: A coast-wide collaboration to inform enhanced conservation

To conserve coastal foundation species, it is essential to understand patterns of distribution and abundance and how they change over time. We synthesized oyster distribution data across the west coast of North America to develop conservation strategies for the native Olympia oyster (Ostrea lurida), and to characterize populations of the non-native Pacific oyster (Magallana gigas). We designed a user-friendly portal for data entry into ArcGIS Online and collected oyster records from unpublished data submitted by oyster experts and from the published literature. We used the resulting 2,000+ records to examine spatial and temporal patterns and made an interactive web-based map publicly available. Comparing records from pre-2000 vs. post-2000, we found that O. lurida significantly decreased in abundance and distribution, while M. gigas increased significantly. Currently the distribution and abundance of the two species are fairly similar, despite one species being endemic to this region since the Pleistocene, and the other a new introduction. We mapped the networks of sites occupied by oysters based on estimates of larval dispersal distance, and found that these networks were larger in Canada, Washington, and southern California than in other regions. We recommend restoration to enhance O. lurida, particularly within small networks, and to increase abundance where it declined. We also recommend restoring natural biogenic beds on mudflats and sandflats especially in the southern range, where native oysters are currently found most often on riprap and other anthropogenic structures. This project can serve as a model for collaborative mapping projects that inform conservation strategies for imperiled species or habitats.

Dynamics of Restored and Natural Oyster Reefs After a Hurricane

Restoration of shellfish reefs has increased exponentially over the past two decades, due in part to increased awareness of widespread oyster habitat loss. Large-scale, acute disturbances such as hurricanes have the potential to influence restoration outcomes, but because storm occurrence is unpredictable with respect to restoration timelines, the responses of restored habitats are not well understood. We quantified the ecological dynamics of a newly constructed Crassostrea virginica oyster reef and nearby reference reef in a Texas estuary immediately after Hurricane Harvey, a major category 4 storm. Biophysical structure (e.g., oyster density, shell height, sediment grain size), and community composition (abundance of reef-associated epifauna, and nearby infauna) were measured for 18 months. A sharp decrease in salinity and temporary deposition of fine sediments within the first 3 months corresponded with increases in oyster and epifaunal recruitment on the restored reef, although densities were generally below those measured on restored reefs without hurricanes. Criteria for oyster reef restoration success were met within 12–18 months post-storm. Infaunal densities decreased but returned to pre-storm densities within 2 months, but bivalves were delayed, returning to pre-storm levels after 9 months. A lack of historical baseline data on the newly restored reef limited our ability to assess the magnitude of reef recovery to pre-disturbance levels or separate the direct effects of the hurricane from the dynamics of early recruitment and growth. Results provide important information about restored and natural oyster reef dynamics after large-scale disturbance and can help inform effective management and conservation measures.

Negligible Greenhouse Gas Release from Sediments in Oyster Habitats

After centuries of decline, oyster populations are now on the rise in coastal systems globally following aquaculture development and restoration efforts. Oysters regulate the biogeochemistry of coastal systems in part by promoting sediment nutrient recycling and removing excess nitrogen via denitrification. Less clear is how oysters alter sediment greenhouse gas (GHG) fluxes-an important consideration as oyster populations grow. Here, we show that sediments in oyster habitats produce carbon dioxide (CO₂), with highest rates in spring (2396.91 ± 381.98 μmol CO₂ m^-2 h^-1) following deposition of seasonal diatom blooms and in summer (2795.20 ± 307.55 μmol CO₂ m^-2 h^-1) when temperatures are high. Sediments in oyster habitats also consistently released methane to the water column (725.94 ± 150.34 nmol CH₄ m^-2 h^-1) with no seasonal pattern. Generally, oyster habitat sediments were a sink for nitrous oxide (N₂O; -36.11 ± 7.24 nmol N₂O m^-2 h^-1), only occasionally releasing N₂O in spring. N₂O release corresponded to high organic matter and dissolved nitrogen availability, suggesting denitrification as the production pathway. Despite potential CO₂ production increases under aquaculture in some locations, we conclude that in temperate regions oysters have an overall negligible impact on sediment GHG cycling.

Medium-term monitoring reveals effects of El Niño Southern Oscillation climate variability on local salinity and faunal dynamics on a restored oyster reef

Human activities and regional-scale climate variability drive changes in the ecology of coastal and marine ecosystems. Ecological restoration has emerged as a best-management practice to combat habitat degradation and restore lost ecological functions. However, relatively short project monitoring timeframes have limited our understanding of the effects of interannual climate cycles on water quality and restoration dynamics. We collected measurements on a 23-ha oyster reef constructed in the Gulf of Mexico to determine the relationship between El Niño Southern Oscillation (ENSO)-driven climate variability and local salinity patterns, and to evaluate the effects of this climate variability and salinity on oyster population dynamics and faunal community composition over a medium-term (five-year) timeframe. The role of ENSO-driven climate variability on local salinity patterns (primarily from changes in precipitation and evaporation) and faunal dynamics was investigated using the Oceanic Niño Index (ONI). Salinity was negatively correlated with ONI with an approximately 4-month lag. Higher ONI values (El Niño periods) were followed by reductions in salinity, increases in oyster recruitment and density, and reductions in resident motile fauna density and species richness. Lower ONI values (La Niña periods) had higher and less variable salinities, and higher areal coverage of restoration substrates by large oysters. ENSO-driven salinity reductions in the second year after reef construction coincided with a shift in resident motile faunal community composition that was maintained despite a second strong salinity reduction in year 5. Our results indicate that it is important to expand the typical monitoring timeframes to at least five years so that resource managers and restoration practitioners can better understand how both short-term environmental variability and longer-term climate cycles can affect the outcomes of restoration actions.

Contemporary Oyster Reef Restoration: Responding to a Changing World

Globally, there is growing interest in restoring previously widespread oyster reefs to reinstate key ecosystem services such as shoreline protection, fisheries productivity and water filtration. Yet, since peak expiration of oysters in the 1800s, significant and ongoing environmental change has occurred. Estuaries and coasts are undergoing some of the highest rates of urbanization, warming and ocean acidification on the planet, necessitating novel approaches to restoration. Here, we review key design considerations for oyster reef restoration projects that maximize the probability that they will meet biological and socio-economic goals not only under present-day conditions, but into the future. This includes selection of sites, and where required, substrates and oyster species and genotypes for seeding, not only on the basis of their present and future suitability in supporting oyster survival, growth and reproduction, but also based on their match to specific goals of ecosystem service delivery. Based on this review, we provide a road map of design considerations to maximize the success of future restoration projects.

Recruitment enhancement varies by taxonomic group and oyster reef habitat characteristics

The rapid loss of coastal and estuarine biogenic habitats has reduced the delivery of valuable ecosystem services, resulting in calls for increased habitat restoration. Yet, a lack of information on how key habitat characteristics (e.g., area, vertical relief, age) influence the ability of restored habitats to deliver these ecosystem services hinders efforts to maximize the return on restoration investments. We conducted a meta-analysis to assess the influence of reef type (natural or restored), taxa, and restored reef size, vertical relief, age, and tidal zone on the presence and magnitude of recruitment enhancement for nekton (i.e., fish and swimming crabs). Both intertidal and subtidal reefs, as well as restored and natural reefs, enhanced nekton recruitment, though there was variation among taxonomic groups with reef types. Recruitment enhancement was more common across taxa on restored (six families) than on natural (one family) reefs. Resident nekton families were more consistently enhanced than transient families. Nekton enhancement varied with a number of restored reef characteristics. Recruitment enhancement increased with greater reef size across taxa, decreased with higher vertical relief for two families, showed maximum recruitment around a single intertidal reef age for one family, and showed minimum recruitment around a single subtidal reef age for three families. Understanding variation across species in response to key design elements will improve restoration success and enhance return on investment. Moving forward, we recommend studies that vary reef habitat characteristics independently and in combination to identify how variation in these characteristics interact to influence nekton recruitment enhancement by oyster reefs.

Conservation aquaculture as a tool for imperiled marine species: Evaluation of opportunities and risks for Olympia oysters, Ostrea lurida

Conservation aquaculture is becoming an important tool to support the recovery of declining marine species and meet human needs. However, this tool comes with risks as well as rewards, which must be assessed to guide aquaculture activities and recovery efforts. Olympia oysters (Ostrea lurida) provide key ecosystem functions and services along the west coast of North America, but populations have declined to the point of local extinction in some estuaries. Here, we present a species-level, range-wide approach to strategically planning the use of aquaculture to promote recovery of Olympia oysters. We identified 12 benefits of culturing Olympia oysters, including identifying climate-resilient phenotypes that add diversity to growers’ portfolios. We also identified 11 key risks, including potential negative ecological and genetic consequences associated with the transfer of hatchery-raised oysters into wild populations. Informed by these trade-offs, we identified ten priority estuaries where aquaculture is most likely to benefit Olympia oyster recovery. The two highest scoring estuaries have isolated populations with extreme recruitment limitation—issues that can be addressed via aquaculture if hatchery capacity is expanded in priority areas. By integrating social criteria, we evaluated which project types would likely meet the goals of local stakeholders in each estuary. Community restoration was most broadly suited to the priority areas, with limited commercial aquaculture and no current community harvest of the species, although this is a future stakeholder goal. The framework we developed to evaluate aquaculture as a tool to support species recovery is transferable to other systems and species globally; we provide a guide to prioritizing local knowledge and developing recommendations for implementation by using transparent criteria. Our collaborative process engaging diverse stakeholders including managers, scientists, Indigenous Tribal representatives, and shellfish growers can be used elsewhere to seek win-win opportunities to expand conservation aquaculture where benefits are maximized for both people and imperiled species.

Evaluating connections between nitrogen cycling and the macrofauna in native oyster beds in a New England estuary

Recent efforts to quantify biogeochemical and ecological processes in oyster habitats have focused on provision of habitat and regulation of the nitrogen cycle. However, it is unclear how these two processes may interact. In this study, seasonal patterns of habitat use and nitrogen removal from natural oyster beds were quantified for comparison with nearby bare sediment in Green Hill Pond, a temperate coastal lagoon in Rhode Island USA. Relationships were tested between benthic macrofaunal abundance and nitrogen removal via denitrification and burial in sediments. Nitrogen removal by oyster bio-assimilation was quantified and compared with nearby oyster aquaculture. Despite limited differences in habitat use by macrofauna, there were fewer non-oyster benthic organisms (e.g., filter-feeders, detritivores) where oysters were present, possibly due to competition for resources. Additionally, low rugosity of the native oyster beds provided little refuge value for prey. There was a shift from net N removal via denitrification in bare sediments to nitrogen fixation beneath oysters, though this change was not statistically significant (t₍₉₆₎ = 1.201; p = 0.233). Sediments contained low concentrations of N, however sediments beneath oysters contained almost twice as much N (0.07%) as bare sediments (0.04%; p < 0.001). There was no difference in tissue N content between wild oysters and those raised in aquaculture nearby, though caged oysters had more tissue per shell mass and length, and therefore removed more N on a shell length basis. These oyster beds lacked the complex structure of 3-dimensional oyster reefs which may have diminished their ability to provide habitat for refugia, foraging sites for macrofauna, and conditions known to stimulate denitrification.

Habitat benefits of restored oyster reefs and aquaculture to fish and invertebrates in a coastal pond in Rhode Island, US

Oyster habitat restoration seeks to recover lost ecosystem services including increased provisioning of refuge and foraging habitat for fish and invertebrate communities. The goal of this study was to quantify the ecosystem service benefit of habitat provisioning in Ninigret Pond, RI following oyster restoration. We measured four metrics, abundance, biomass, species richness and diversity, as well as isotopic composition in fish and invertebrates collected seasonally from restored oyster, aquaculture, and bare sediment sites, to examine whether the oyster habitat outperformed the bare sediment habitat. Sampling locations were chosen in Foster's Cove north and south, Grassy Point, South Sanctuary, and an Aquaculture lease; each had two restored oyster sites and one bare sediment site. Each site was sampled using a box trap, seine net, shrimp trap, and minnow trap. Oyster habitats had significantly greater metrics than did bare sediment habitats in some comparisons from the box trap and seine net samples. Restored oyster sites at South Sanctuary had lower metric values than the other oyster sites. Metrics from the Aquaculture sites were comparable to the Foster's Cove and Grassy Point restored oyster sites and often outperformed South Sanctuary restored oyster sites. Seasonally, spring and autumn samples tended to have higher abundance and biomass values than summer. Isotopic composition of five species occurring at both restored oyster and bare sediment sites demonstrated some differences in the trophic levels between species but not between habitat types. In Ninigret Pond, fish and invertebrate abundance, biomass, species richness, and diversity benefit from the use of oyster and bare sediment habitats. Coastal zone managers interested in restoring the ecological function of oyster reefs to support fish and invertebrate communities should consider strategically locating restoration projects within the mosaic of structured habitats and monitoring them for selected ecosystem services.

The Aichi Biodiversity Targets: achievements for marine conservation and priorities beyond 2020

In 2010 the Conference of the Parties (COP) for the Convention on Biological Diversity revised and updated a Strategic Plan for Biodiversity 2011–2020, which included the Aichi Biodiversity Targets. Here a group of early career researchers mentored by senior scientists, convened as part of the 4th World Conference on Marine Biodiversity, reflects on the accomplishments and shortfalls under four of the Aichi Targets considered highly relevant to marine conservation: target 6 (sustainable fisheries), 11 (protection measures), 15 (ecosystem restoration and resilience) and 19 (knowledge, science and technology). We conclude that although progress has been made towards the targets, these have not been fully achieved for the marine environment by the 2020 deadline. The progress made, however, lays the foundations for further work beyond 2020 to work towards the 2050 Vision for Biodiversity. We identify key priorities that must be addressed to better enable marine biodiversity conservation efforts moving forward.

Reference state and benchmark concepts for better biodiversity conservation in contemporary ecosystems

Measuring the status and trends of biodiversity is critical for making informed decisions about the conservation, management or restoration of species, habitats and ecosystems. Defining the reference state against which status and change are measured is essential. Typically, reference states describe historical conditions, yet historical conditions are challenging to quantify, may be difficult to falsify, and may no longer be an attainable target in a contemporary ecosystem. We have constructed a conceptual framework to help inform thinking and discussion around the philosophical underpinnings of reference states and guide their application. We characterize currently recognized historical reference states and describe them as Pre-Human, Indigenous Cultural, Pre-Intensification and Hybrid-Historical. We extend the conceptual framework to include contemporary reference states as an alternative theoretical perspective. The contemporary reference state framework is a major conceptual shift that focuses on current ecological patterns and identifies areas with higher biodiversity values relative to other locations within the same ecosystem, regardless of the disturbance history. We acknowledge that past processes play an essential role in driving contemporary patterns of diversity. The specific context for which we design the contemporary conceptual frame is underpinned by an overarching goal-to maximize biodiversity conservation and restoration outcomes in existing ecosystems. The contemporary reference state framework can account for the inherent differences in the diversity of biodiversity values (e.g. native species richness, habitat complexity) across spatial scales, communities and ecosystems. In contrast to historical reference states, contemporary references states are measurable and falsifiable. This 'road map of reference states' offers perspective needed to define and assess the status and trends in biodiversity and habitats. We demonstrate the contemporary reference state concept with an example from south-eastern Australia. Our framework provides a tractable way for policy-makers and practitioners to navigate biodiversity assessments to maximize conservation and restoration outcomes in contemporary ecosystems.

Mobilisation of data to stakeholder communities. Bridging the research-practice gap using a commercial shellfish species model

Knowledge mobilisation is required to “bridge the gap” between research, policy and practice. This activity is dependent on the amount, richness and quality of the data published. To understand the impact of a changing climate on commercial species, stakeholder communities require better knowledge of their past and current situations. The common cockle (Cerastoderma edule) is an excellent model species for this type of analysis, as it is well-studied due to its cultural, commercial and ecological significance in west Europe. Recently, C. edule harvests have decreased, coinciding with frequent mass mortalities, due to factors such as a changing climate and diseases. In this study, macro and micro level marine historical ecology techniques were used to create datasets on topics including: cockle abundance, spawning duration and harvest levels, as well as the ecological factors impacting those cockle populations. These data were correlated with changing climate and the Atlantic Multidecadal Oscillation (AMO) index to assess if they are drivers of cockle abundance and harvesting. The analyses identified the key stakeholder communities involved in cockle research and data acquisition. It highlighted that data collection was sporadic and lacking in cross-national/stakeholder community coordination. A major finding was that local variability in cockle populations is influenced by biotic (parasites) and abiotic (temperature, legislation and harvesting) factors, and at a global scale by climate (AMO Index). This comprehensive study provided an insight into the European cockle fishery but also highlights the need to identify the type of data required, the importance of standardised monitoring, and dissemination efforts, taking into account the knowledge, source, and audience. These factors are key elements that will be highly beneficial not only to the cockle stakeholder communities but to other commercial species.

Prehistoric baseline reveals substantial decline of oyster reef condition in a Gulf of Mexico conservation priority area

The Gulf of Mexico (GoM) is home to the world's largest remaining wild oyster fisheries, but baseline surveys needed to assess habitat condition are recent and may represent an already-shifted reference state. Here, we use prehistoric oysters from archaeological middens to show that oyster size, an indicator of habitat function and population resilience, declined prior to the earliest assessments of reef condition in an area of the GoM previously considered pristine. Stable isotope sclerochronlogy reveals extirpation of colossal oysters occurred through truncated life history and slowed growth. More broadly, our study suggests that management strategies affected by shifting baselines may overestimate resilience and perpetuate practices that risk irreversible decline.

A method to estimate pre-exploitation population size

Antarctic fur seals (Arctocephalus gazella) were commercially exploited on the subantarctic island of South Georgia for over 100 years and nearly driven to extinction. Since the cessation of harvesting, however, their populations have rebounded, and they are now often considered a nuisance species whose impact on the terrestrial landscape should be mitigated. Any evaluation of their current population requires the context provided by their historic, pre-exploitation abundance, lest ecologists fall prey to shifting baseline syndrome in which their perspective on current abundance is compared only with an altered state resulting from past anthropogenic disturbance. Estimating pre-exploitation abundance is critical to defining species recovery and setting recovery targets, both of which are needed for the International Union for the Conservation of Nature's recent efforts to develop a green list of recovering species. To address this issue, we reconstructed the South Georgia fur seal harvest from 1786 to 1908 from ship logbooks and other historical records and interpolated missing harvest data as necessary with a generalized linear model fit to the historical record. Using an approximate Bayesian computation framework, harvest data, and a stochastic age-structured population model, we estimated the pre-exploitation abundance of Antarctic fur seals on South Georgia was 2.5 million females (95% CI 1.5-3.5 million). This estimate is similar to recent abundance estimates, and suggests current populations, and the ecological consequences of so many fur seals on the island, may be similar to conditions prior to human harvest. Although the historic archive on the fur sealing era is unavoidably patchy, the use of archival records is essential for reconstructing the past and, correspondingly, to understanding the present. Article impact statement: Defining species recovery requires an understanding of baseline population state, which can be estimated through statistical methods.

Rapid and Accurate Monitoring of Intertidal Oyster Reef Habitat Using Unoccupied Aircraft Systems and Structure from Motion

Oysters support an economically important fishery in many locations in the United States and provide benefits to the surrounding environment by filtering water, providing habitat for fish, and stabilizing shorelines. Changes in oyster reef health reflect variations in factors such as recreational and commercial harvests, predation, disease, storms, and broader anthropogenic influences, such as climate change. Consistent measurements of reef area and morphology can help effectively monitor oyster habitat across locations. However, traditional approaches to acquiring these data are time-consuming and can be costly. Unoccupied aircraft systems (UAS) present a rapid and reliable method for assessing oyster habitat that may overcome these limitations, although little information on the accuracy of platforms and processing techniques is available. In the present study, oyster reefs ranging in size from 30 m2 to 300 m2 were surveyed using both fixed-wing and multirotor UAS and compared with ground-based surveys of each reef conducted with a real-time kinematic global positioning system (RTK-GPS). Survey images from UAS were processed using structure from motion (SfM) stereo photogrammetry techniques, with and without the use of ground control point (GCP) correction, to create reef-scale measures of area and morphology for comparison to ground-based measures. UAS-based estimates of both reef area and morphology were consistently lower than ground-based estimates, and the results of matched pairs analyses revealed that differences in reef area did not vary significantly by aircraft or the use of GCPs. However, the use of GCPs increased the accuracy of UAS-based reef morphology measurements, particularly in areas with the presence of water and/or homogeneous spectral characteristics. Our results indicate that both fixed-wing and multirotor UAS can be used to accurately monitor intertidal oyster reefs over time and that proper ground control techniques will improve measurements of reef morphology. These non-destructive methods help modernize oyster habitat monitoring by providing useful and accurate knowledge about the structure and health of oyster reefs ecosystems.

Effects of chronic pesticide exposure on an epibenthic oyster reef community

In recent decades, oyster reefs have been deteriorating throughout North America as a result of multiple interacting anthropogenic stressors, including pesticide pollution. Here we elucidated the potential chronic effects of the commonly utilized pesticide, carbaryl, on oyster reef communities in the Loxahatchee River Estuary in southeast Florida. Though carbaryl had a limited effect on total epifaunal community diversity, species richness and evenness, the results of this experiment indicate that carbaryl significantly shifted crustacean community composition, resulting in a substantial loss in total crustacean abundance. One crustacean in particular, Americorophium spp. (tube building amphipod), was significantly less abundant within the carbaryl treatment, driving the shift in crustacean community composition. Ultimately, our results signal that pesticide pollution in estuaries will negatively impact crustaceans. Over time, this may shift benthic community composition, potentially disrupting species interactions and threatening valuable economic and ecosystem services.

Microencapsulated diets to improve growth and survivorship in juvenile European flat oysters (Ostrea edulis)

Sustainable expansion of aquaculture is critical to global food security, and bivalve shellfish aquaculture represents a sustainable method to provide people with affordable nutritious food. Oysters represent 54% of the global bivalve market by value, with propagation of juveniles within hatcheries critical to allow the industry to grow. Growth and survival of juvenile oysters in hatchery systems is constrained by suboptimal feed. The live algal feed currently used is expensive, of variable quality, contamination prone, and the high level of skill and equipment required limits where hatcheries can be located. We demonstrate how a novel microencapsulated diet can increase the growth and survivorship of Ostrea edulis (European flat oyster) juveniles in both the laboratory and hatchery setting. The microcapsules are easily produced in large quantities, stable for long term storage, and can be customised to have exceptionally high levels of nutrients key for oyster growth. O. edulis larvae fed a combined diet of microcapsules and algae for 8 days had a 46% greater increase in maximum size, 171% greater increase in minimum size, and 5% higher survival than larvae fed algae alone. O. edulis spat of 4 mm fed the combined diet for 7 weeks also had significantly greater survivorship (16% greater in hatchery, 58% greater in laboratory) and growth comparable (hatchery) or better (laboratory experiments) than algae alone. Further tailoring of the nutritional composition of microcapsules to specific bivalve species or growth stages could allow microcapsules to replace a greater proportion of or even completely replace algal diets. There is potential for these diets to revolutionise bivalve shellfish farming globally.

ZooArchNet: Connecting zooarchaeological specimens to the biodiversity and archaeology data networks

Interdisciplinary collaborations and data sharing are essential to addressing the long history of human-environmental interactions underlying the modern biodiversity crisis. Such collaborations are increasingly facilitated by, and dependent upon, sharing open access data from a variety of disciplinary communities and data sources, including those within biology, paleontology, and archaeology. Significant advances in biodiversity open data sharing have focused on neontological and paleontological specimen records, making available over a billion records through the Global Biodiversity Information Facility. But to date, less effort has been placed on the integration of important archaeological sources of biodiversity, such as zooarchaeological specimens. Zooarchaeological specimens are rich with both biological and cultural heritage data documenting nearly all phases of human interaction with animals and the surrounding environment through time, filling a critical gap between paleontological and neontological sources of data within biodiversity networks. Here we describe technical advances for mobilizing zooarchaeological specimen-specific biological and cultural data. In particular, we demonstrate adaptations in the workflow used by biodiversity publisher VertNet to mobilize Darwin Core formatted zooarchaeological data to the GBIF network. We also show how a linked open data approach can be used to connect existing biodiversity publishing mechanisms with archaeoinformatics publishing mechanisms through collaboration with the Open Context platform. Examples of ZooArchNet published datasets are used to show the efficacy of creating this critically needed bridge between biological and archaeological sources of open access data. These technical advances and efforts to support data publication are placed in the larger context of ZooarchNet, a new project meant to build community around new approaches to interconnect zoorchaeological data and knowledge across disciplines.

A decline in molluscan carbonate production driven by the loss of vegetated habitats encoded in the Holocene sedimentary record of the Gulf of Trieste

Carbonate sediments in non-vegetated habitats on the north-east Adriatic shelf are dominated by shells of molluscs. However, the rate of carbonate molluscan production prior to the 20th century eutrophication and overfishing on this and other shelves remains unknown because: (i) monitoring of ecosystems prior to the 20th century was scarce; and (ii) ecosystem history inferred from cores is masked by condensation and mixing. Here, based on geochronological dating of four bivalve species, carbonate production during the Holocene is assessed in the Gulf of Trieste, where algal and seagrass habitats underwent a major decline during the 20th century. Assemblages of sand-dwelling Gouldia minima and opportunistic Corbula gibba are time-averaged to >1000 years and Corbula gibba shells are older by >2000 years than shells of co-occurring Gouldia minima. This age difference is driven by temporally disjunct production of two species coupled with decimetre-scale mixing. Stratigraphic unmixing shows that Corbula gibba declined in abundance during the highstand phase and increased again during the 20th century. In contrast, one of the major contributors to carbonate sands - Gouldia minima - increased in abundance during the highstand phase, but declined to almost zero abundance over the past two centuries. Gouldia minima and herbivorous gastropods associated with macroalgae or seagrasses are abundant in the top-core increments but are rarely alive. Although Gouldia minima is not limited to vegetated habitats, it is abundant in such habitats elsewhere in the Mediterranean Sea. This live-dead mismatch reflects the difference between highstand baseline communities (with soft-bottom vegetated zones and hard-bottom Arca beds) and present-day oligophotic communities with organic-loving species. Therefore, the decline in light penetration and the loss of vegetated habitats with high molluscan production traces back to the 19th century. More than 50% of the shells on the sea floor in the Gulf of Trieste reflect inactive production that was sourced by heterozoan carbonate factory in algal or seagrass habitats.

Ecosystem metabolism drives pH variability and modulates long-term ocean acidification in the Northeast Pacific coastal ocean

Ocean acidification poses serious threats to coastal ecosystem services, yet few empirical studies have investigated how local ecological processes may modulate global changes of pH from rising atmospheric CO₂. We quantified patterns of pH variability as a function of atmospheric CO₂ and local physical and biological processes at 83 sites over 25 years in the Salish Sea and two NE Pacific estuaries. Mean seawater pH decreased significantly at −0.009 ± 0.0005 pH yr⁻¹ (0.22 pH over 25 years), with spatially variable rates ranging up to 10 times greater than atmospheric CO₂-driven ocean acidification. Dissolved oxygen saturation (%DO) decreased by −0.24 ± 0.036% yr⁻¹, with site-specific trends similar to pH. Mean pH shifted from <7.6 in winter to >8.0 in summer concomitant to the seasonal shift from heterotrophy (%DO < 100) to autotrophy (%DO > 100) and dramatic shifts in aragonite saturation state critical to shell-forming organisms (probability of undersaturation was >80% in winter, but <20% in summer). %DO overwhelmed the influence of atmospheric CO₂, temperature and salinity on pH across scales. Collectively, these observations provide evidence that local ecosystem processes modulate ocean acidification, and support the adoption of an ecosystem perspective to ocean acidification and multiple stressors in productive aquatic habitats.

Successful recruitment, survival and long-term persistence of eastern oyster and hooked mussel on a subtidal, artificial restoration reef system in Chesapeake Bay

Restoration efforts with native eastern oyster, Crassostrea virginica, in Chesapeake Bay and elsewhere have been limited by shell availability, necessitating the use of alternative structures as subtidal reefs, yet these have rarely been evaluated quantitatively. We quantified population structure, density, abundance and biomass of eastern oyster and hooked mussel, Ischadium recurvum, on a concrete modular reef (75 m² surface area over 5 m² of river bottom) deployed subtidally at 7 m depth in the Rappahannock River, Virginia during October, 2000. After nearly 5 y (May 2005), we took 120 stratified random samples over the reef. The reef was heavily colonized by 28-168 oysters and 14-2177 mussels m^-2 surface area. These densities translate to 1085 oysters and 8617 mussels m^-2 river bottom, which are the highest recorded for artificial oyster reefs. Size structure of oysters reflected four year classes, with over half of oysters more than 1 y old and of reproductive age. Oyster biomass (1663 g dry mass m^-2 river bottom) and condition index were equally high, whereas parasite prevalence and intensity were low. Oyster density correlated positively in a sigmoid fashion with mussel density up to high densities, then declined. This modular reef is one of the most successful artificial reefs for eastern oyster and hooked mussel restoration, and details features that are conducive for successful settlement, growth and survival in subtidal habitats.

Restoration of eastern oyster populations with positive density dependence

Positive density dependence (i.e., Allee effects) can create a threshold of population states below which extinction of the population occurs. The existence of this threshold, which can often be a complex, multi-dimensional surface, rather than a single point, is of particular importance in degraded populations for which there is a desire for successful restoration. Here, we incorporated positive density dependence into a closed, size- and age-structured integral projection model parameterized with empirical data from an eastern oyster, Crassostrea virginica, population in Pamlico Sound, North Carolina, USA. To understand the properties of the threshold surface, and implications for restoration, we introduced a general method based on a linearization of the threshold surface at its unique, unstable equilibrium. We estimated the number of oysters of a particular age (i.e., stock enhancement), or the surface area of dead shell substrate required (i.e., habitat enhancement) to move a population from an extinction trajectory to a persistence trajectory. The location of the threshold surface was strongly affected by changes in the amount of local larval retention. Traditional stock enhancement with oysters <1 yr old (i.e., spat) required three times as many oysters relative to stock enhancement with oysters between ages 3 and 7 yr old, while the success of habitat enhancement depended upon the initial size distribution of the population. The methodology described here demonstrates the importance of considering positive density dependence in oyster populations, and also provides insights into effective management and restoration strategies when dealing with a high dimensional threshold separating extinction and persistence.

Australian shellfish ecosystems: Past distribution, current status and future direction

We review the status of marine shellfish ecosystems formed primarily by bivalves in Australia, including: identifying ecosystem-forming species, assessing their historical and current extent, causes for decline and past and present management. Fourteen species of bivalves were identified as developing complex, three-dimensional reef or bed ecosystems in intertidal and subtidal areas across tropical, subtropical and temperate Australia. A dramatic decline in the extent and condition of Australia’s two most common shellfish ecosystems, developed by Saccostrea glomerata and Ostrea angasi oysters, occurred during the mid-1800s to early 1900s in concurrence with extensive harvesting for food and lime production, ecosystem modification, disease outbreaks and a decline in water quality. Out of 118 historical locations containing O. angasi-developed ecosystems, only one location still contains the ecosystem whilst only six locations are known to still contain S. glomerata-developed ecosystems out of 60 historical locations. Ecosystems developed by the introduced oyster Crasostrea gigas are likely to be increasing in extent, whilst data on the remaining 11 ecosystem-forming species are limited, preventing a detailed assessment of their current ecosystem-forming status. Our analysis identifies that current knowledge on extent, physical characteristics, biodiversity and ecosystem services of Australian shellfish ecosystems is extremely limited. Despite the limited information on shellfish ecosystems, a number of restoration projects have recently been initiated across Australia and we propose a number of existing government policies and conservation mechanisms, if enacted, would readily serve to support the future conservation and recovery of Australia’s shellfish ecosystems.

Oyster reefs as carbon sources and sinks

Carbon burial is increasingly valued as a service provided by threatened vegetated coastal habitats. Similarly, shellfish reefs contain significant pools of carbon and are globally endangered, yet considerable uncertainty remains regarding shellfish reefs' role as sources (+) or sinks (-) of atmospheric CO₂ While CO₂ release is a by-product of carbonate shell production (then burial), shellfish also facilitate atmospheric-CO₂ drawdown via filtration and rapid biodeposition of carbon-fixing primary producers. We provide a framework to account for the dual burial of inorganic and organic carbon, and demonstrate that decade-old experimental reefs on intertidal sandflats were net sources of CO₂ (7.1 ± 1.2 MgC ha^-1 yr^-1 (µ ± s.e.)) resulting from predominantly carbonate deposition, whereas shallow subtidal reefs (-1.0 ± 0.4 MgC ha^-1 yr^-1) and saltmarsh-fringing reefs (-1.3 ± 0.4 MgC ha^-1 yr^-1) were dominated by organic-carbon-rich sediments and functioned as net carbon sinks (on par with vegetated coastal habitats). These landscape-level differences reflect gradients in shellfish growth, survivorship and shell bioerosion. Notably, down-core carbon concentrations in 100- to 4000-year-old reefs mirrored experimental-reef data, suggesting our results are relevant over centennial to millennial scales, although we note that these natural reefs appeared to function as slight carbon sources (0.5 ± 0.3 MgC ha^-1 yr^-1). Globally, the historical mining of the top metre of shellfish reefs may have reintroduced more than 400 000 000 Mg of organic carbon into estuaries. Importantly, reef formation and destruction do not have reciprocal, counterbalancing impacts on atmospheric CO₂ since excavated organic material may be remineralized while shell may experience continued preservation through reburial. Thus, protection of existing reefs could be considered as one component of climate mitigation programmes focused on the coastal zone.