A biophysical representation of seagrass growth for application in a complex shallow-water biogeochemical model

Reactive persistence, spatial management, and conservation of metapopulations: An application to seagrass restoration

Assessing the conditions for persistence of spatially structured populations, especially those that are exploited by humans or threatened by global change, is of critical importance to inform management and conservation efforts. Observations for entire metapopulations are usually incomplete and rarely, if ever, sufficiently long to deduce population persistence from spatial patterns of abundance. Instead, insights based on metapopulation theory are often used for interpreting the demographic trajectories of real populations and for informing management decisions. The classical theoretical tool used to assess conditions for metapopulation persistence is the "invasibility criterion," which characterizes the asymptotic, or long-term, stability of a small colonizing population. Essentially, when the linear operator governing the metapopulation dynamics of an invasion event has a positive eigenvalue, recovery and resistance to extinction (resilience) are implied. The converse, however, is not necessarily the case-an invasion may grow over multiple generations, even when the eigenvalues indicate that extinction will eventually occur, a situation referred to here as "reactive persistence." For the management, restoration, and conservation of real metapopulations subject to continual disturbance, this transient behavior is often more relevant than the asymptotic behavior over long time scales. We develop the theoretical tools for assessing reactive persistence, demonstrating how the conditions for asymptotic and reactive persistence differ in both the patch-occupancy models suited to many terrestrial populations and those where local patch extinctions can be disregarded in the dynamics, often suited to marine species. After presenting the mathematical basis for generalizing the invasibility criterion to include reactive persistence, we illustrate how these concepts and tools can be applied in practice, using as a case study the population ecology and restoration of the seagrass Zostera muelleri (Irmisch ex Ascherson, 1867) in the Port of Gladstone in the Great Barrier Reef World Heritage Area Australia. It is shown how the analysis of the transient dynamics of the Z. muelleri metapopulation can be used to guide restoration efforts. Moreover, it is demonstrated that these reactive persistence concepts provide a more appropriate basis for site prioritization for restoration interventions than traditional stability analysis.

Habitat suitability modelling to improve understanding of seagrass loss and recovery and to guide decisions in relation to coastal discharge

Habitat suitability modelling was used to test the relationship between coastal discharges and seagrass occurrence based on data from Adelaide (South Australia). Seven variables (benthic light including epiphyte shading, temperature, salinity, substrate, wave exposure, currents and tidal exposure) were simulated using a coupled hydrodynamic-biogeochemical model and interrogated against literature-derived thresholds for nine local seagrass species. Light availability was the most critical driver across the study area but wave exposure played a key role in shallow nearshore areas. Model validation against seagrass mapping data showed 86 % goodness-of-fit. Comparison against later mapping data suggested that modelling could predict ~745 ha of seagrass recovery in areas previously classified as 'false positives'. These results suggest that habitat suitability modelling is reliable to test scenarios and predict seagrass response to reduction of land-based loads, providing a useful tool to guide (investment) decisions to prevent loss and promote recovery of seagrasses.

Impact of catchment-derived nutrients and sediments on marine water quality on the Great Barrier Reef: An application of the eReefs marine modelling system

Water quality of the Great Barrier Reef (GBR) is determined by a range of natural and anthropogenic drivers that are resolved in the eReefs coupled hydrodynamic - biogeochemical marine model forced by a process-based catchment model, GBR Dynamic SedNet. Model simulations presented here quantify the impact of anthropogenic catchment loads of sediments and nutrients on a range of marine water quality variables. Simulations of 2011-2018 show that reduction of anthropogenic catchment loads results in improved water quality, especially within river plumes. Within the 16 resolved river plumes, anthropogenic loads increased chlorophyll concentration by 0.10 (0.02-0.25) mg Chl m^-3. Reductions of anthropogenic loads following proposed Reef 2050 Water Quality Improvement Plan targets reduced chlorophyll concentration in the plumes by 0.04 (0.01-0.10) mg Chl m^-3. Our simulations demonstrate the impact of anthropogenic loads on GBR water quality and quantify the benefits of improved catchment management.

A flood of information: Using Sentinel-3 water colour products to assure continuity in the monitoring of water quality trends in the Great Barrier Reef (Australia)

An operational method to assess trends in marine water composition and ecosystem health during flood periods has been developed for the Great Barrier Reef (GBR), Queensland, Australia. This method integrates satellite water colour data with field water quality and ecosystem monitoring data and involves the classification of Moderate-Resolution Imaging Spectroradiometer (MODIS satellite) pixels into six distinct water bodies using a "wet season" colour scale developed specifically for the GBR. Using this information, several monitoring and reporting products have been derived and are operationally implemented into a long-term water quality monitoring program for the GBR. However, MODIS sensors are aging and a long-term monitoring solution is needed. This study reviewed the water colour monitoring products currently used in the GBR. It tested the feasibility to transition these methods from historical MODIS satellite imagery to the new Sentinel-3 satellite of the European Space Agency and from the wet season colour scale to the historical Forel-Ule colour scale, using a freely-distributed Forel Ule (FU) Satellite Toolbox. Monitoring products derived from both satellites and colour scales showed very similar patterns across two case study regions of the GBR, the Wet Tropics and Burdekin marine regions, over the 2017-18 wet season. The results obtained in this study highlighted the potential of using FU Sentinel-3 imagery for the mapping of GBR marine water bodies, including flood conditions. Furthermore, the operational monitoring products and frameworks developed for the GBR are likely to provide valuable foundations for analysis of FU Sentinel-3 data in the future. Such satellite water colour datasets and frameworks will be instrumental to better understand the impact of floods and reduced water clarity on marine ecosystems, as well as to support water quality management and facilitate catchment management policy in the GBR and worldwide.

Fine sediment and particulate organic matter: A review and case study on ridge-to-reef transport, transformations, fates, and impacts on marine ecosystems

Studies documenting the effects of land-derived suspended particulate matter (SPM, i.e., particulate organic matter and mineral sediment) on marine ecosystems are typically disconnected from terrestrial studies that determine their origin, transport and fate. This study reviews sources, transport, transformations, fate and effects of SPM along the 'ridge-to-reef' continuum. We show that some of the SPM can be transported over long distances and transformed into large and easily resuspendible organic-rich sediment flocs. These flocs may lead to prolonged reductions in water clarity, impacting upon coral reef, seagrass and fish communities. Using the Great Barrier Reef (NE Australia) as a case study, we identify the latest research tools to determine thresholds of SPM exposure, allowing for an improved appreciation of marine risk. These tools are used to determine ecologically-relevant end-of-basin load targets and reliable marine water quality guidelines, thereby enabling enhanced prioritisation and management of SPM export from ridge-to-reef.

Expected limits on the ocean acidification buffering potential of a temperate seagrass meadow

Ocean acidification threatens many marine organisms, especially marine calcifiers. The only global-scale solution to ocean acidification remains rapid reduction in CO₂ emissions. Nevertheless, interest in localized mitigation strategies has grown rapidly because of the recognized threat ocean acidification imposes on natural communities, including ones important to humans. Protection of seagrass meadows has been considered as a possible approach for localized mitigation of ocean acidification due to their large standing stocks of organic carbon and high productivity. Yet much work remains to constrain the magnitudes and timescales of potential buffering effects from seagrasses. We developed a biogeochemical box model to better understand the potential for a temperate seagrass meadow to locally mitigate the effects of ocean acidification. Then we parameterized the model using data from Tomales Bay, an inlet on the coast of California, USA which supports a major oyster farming industry. We conducted a series of month-long model simulations to characterize processes that occur during summer and winter. We found that average pH in the seagrass meadows was typically within 0.04 units of the pH of the primary source waters into the meadow, although we did find occasional periods (hours) when seagrass metabolism may modify the pH by up to ±0.2 units. Tidal phasing relative to the diel cycle modulates localized pH buffering within the seagrass meadow such that maximum buffering occurs during periods of the year with midday low tides. Our model results suggest that seagrass metabolism in Tomales Bay would not provide long-term ocean acidification mitigation. However, we emphasize that our model results may not hold in meadows where assumptions about depth-averaged net production and seawater residence time within the seagrass meadow differ from our model assumptions. Our modeling approach provides a framework that is easily adaptable to other seagrass meadows in order to evaluate the extent of their individual buffering capacities. Regardless of their ability to buffer ocean acidification, seagrass meadows maintain many critically important ecosystem goods and services that will be increasingly important as humans increasingly affect coastal ecosystems.

Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance

Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.

Invasive Macrophytes Control the Spatial and Temporal Patterns of Temperature and Dissolved Oxygen in a Shallow Lake: A Proposed Feedback Mechanism of Macrophyte Loss

Submerged macrophytes can have a profound effect on shallow lake ecosystems through their ability to modify the thermal structure and dissolved oxygen levels within the lake. Invasive macrophytes, in particular, can grow rapidly and induce thermal gradients in lakes that may substantially change the ecosystem structure and challenge the survival of aquatic organisms. We performed fine-scale measurements and 3D numerical modeling at high spatiotemporal resolution to assess the effect of the seasonal growth of Potamogeton crispus L. on the spatial and temporal dynamics of temperature and dissolved oxygen in a shallow urban lake (Lake Monger, Perth, WA, Australia). Daytime stratification developed during the growing season and was clearly observed throughout the macrophyte bed. At all times measured, stratification was stronger at the center of the macrophyte bed compared to the bed edges. By fitting a logistic growth curve to changes in plant height over time (r² = 0.98), and comparing this curve to temperature data at the center of the macrophyte bed, we found that stratification began once the macrophytes occupied at least 50% of the water depth. This conclusion was strongly supported by a 3D hydrodynamic model fitted to weekly temperature profiles measured at four time periods throughout the growing season (r² > 0.78 at all times). As the macrophyte height increased and stratification developed, dissolved oxygen concentration profiles changed from vertically homogeneous oxic conditions during both the day and night to expression of night-time anoxic conditions close to the sediments. Spatially interpolated maps of dissolved oxygen and 3D numerical modeling results indicated that the plants also reduced horizontal exchange with surrounding unvegetated areas, preventing flushing of low dissolved oxygen water out of the center of the bed. Simultaneously, aerial imagery showed central dieback occurring toward the end of the growing season. Thus, we hypothesized that stratification-induced anoxia can lead to accelerated P. crispus dieback in this region, causing formation of a ring-shaped pattern in spatial macrophyte distribution. Overall, our study demonstrates that submerged macrophytes can alter the thermal characteristics and oxygen levels within shallow lakes and thus create challenging conditions for maximizing their spatial coverage.

Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species

When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluated twelve published empirical models for temperature-dependent tropical seagrass photosynthesis, based on two criteria: (1) goodness of fit, and (2) how easily biologically-meaningful parameters can be obtained. All models were formulated in terms of parameters characterising the thermal optimum (T_opt) for maximum photosynthetic rate (P_max). These parameters indicate the upper thermal limits of seagrass photosynthetic capacity, and hence can be used to assess the vulnerability of seagrass to temperature change. Our study exemplifies an approach to model selection which optimises the usefulness of empirical models for both modellers and ecologists alike.

Optimum Temperatures for Net Primary Productivity of Three Tropical Seagrass Species

Rising sea water temperature will play a significant role in responses of the world's seagrass meadows to climate change. In this study, we investigated seasonal and latitudinal variation (spanning more than 1,500 km) in seagrass productivity, and the optimum temperatures at which maximum photosynthesis and net productivity (for the leaf and the whole plant) occurs, for three seagrass species (Cymodocea serrulata, Halodule uninervis, and Zostera muelleri). To obtain whole plant net production, photosynthesis, and respiration rates of leaves and the root/rhizome complex were measured using oxygen-sensitive optodes in closed incubation chambers at temperatures ranging from 15 to 43°C. The temperature-dependence of photosynthesis and respiration was fitted to empirical models to obtain maximum metabolic rates and thermal optima. The thermal optimum (T_opt) for gross photosynthesis of Z. muelleri, which is more commonly distributed in sub-tropical to temperate regions, was 31°C. The T_opt for photosynthesis of the tropical species, H. uninervis and C. serrulata, was considerably higher (35°C on average). This suggests that seagrass species are adapted to water temperature within their distributional range; however, when comparing among latitudes and seasons, thermal optima within a species showed limited acclimation to ambient water temperature (T_opt varied by 1°C in C. serrulata and 2°C in H. uninervis, and the variation did not follow changes in ambient water temperature). The T_opt for gross photosynthesis were higher than T_opt calculated from plant net productivity, which includes above- and below-ground respiration for Z. muelleri (24°C) and H. uninervis (33°C), but remained unchanged at 35°C in C. serrulata. Both estimated plant net productivity and T_opt are sensitive to the proportion of below-ground biomass, highlighting the need for consideration of below- to above-ground biomass ratios when applying thermal optima to other meadows. The thermal optimum for plant net productivity was lower than ambient summer water temperature in Z. muelleri, indicating likely contemporary heat stress. In contrast, thermal optima of H. uninervis and C. serrulata exceeded ambient water temperature. This study found limited capacity to acclimate: thus the thermal optima can forewarn of both the present and future vulnerability to ocean warming during periods of elevated water temperature.