Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ...ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry.
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.
Although wetlands represent the largest natural source of atmospheric CH4, large uncertainties remain regarding the global wetland CH4 flux. Wetland hydrological oscillations contribute to this ...uncertainty, dramatically altering wetland area, water table height, soil redox potentials, and CH4 emissions. This study compares both terrestrial and aquatic CH4 fluxes in permanent and seasonal remediated freshwater wetlands in subtropical Australia over two field campaigns, representing differing hydrological and climatic conditions. We account for aquatic CH4 diffusion and ebullition rates and plant-mediated CH4 fluxes from three distinct vegetation communities, thereby examining diel and intra-habitat variability. CH4 emission rates were related to underlying sediment geochemistry. For example, distinct negative relationships between CH4 fluxes and both Fe(III) and SO42- were observed. Where sediment Fe(III) and SO42- were depleted, distinct positive trends occurred between CH4 emissions and Fe(II) ∕ acid volatile sulfur (AVS). Significantly higher CH4 emissions (p < 0.01) in the seasonal wetland were measured during flooded conditions and always during daylight hours, which is consistent with soil redox potential and temperature being important co-drivers of CH4 flux. The highest CH4 fluxes were consistently emitted from the permanent wetland (1.5 to 10.5 mmol m−2 d−1), followed by the Phragmites australis community within the seasonal wetland (0.8 to 2.3 mmol m−2 d−1), whilst the lowest CH4 fluxes came from a region of forested Juncus spp. (−0.01 to 0.1 mmol m−2 d−1), which also corresponded to the highest sedimentary Fe(III) and SO42-. We suggest that wetland remediation strategies should consider geochemical profiles to help to mitigate excessive and unwanted methane emissions, especially during early system remediation periods.
Seagrass ecosystems are significant carbon sinks, and their resident microbial communities ultimately determine the quantity and quality of carbon sequestered. However, environmental perturbations ...have been predicted to affect microbial-driven seagrass decomposition and subsequent carbon sequestration. Utilizing techniques including 16S-rDNA sequencing, solid-state NMR and microsensor profiling, we tested the hypothesis that elevated seawater temperatures and eutrophication enhance the microbial decomposition of seagrass leaf detritus and rhizome/root tissues. Nutrient additions had a negligible effect on seagrass decomposition, indicating an absence of nutrient limitation. Elevated temperatures caused a 19% higher biomass loss for aerobically decaying leaf detritus, coinciding with changes in bacterial community structure and enhanced lignocellulose degradation. Although, community shifts and lignocellulose degradation were also observed for rhizome/root decomposition, anaerobic decay was unaffected by temperature. These observations suggest that oxygen availability constrains the stimulatory effects of temperature increases on bacterial carbon remineralization, possibly through differential temperature effects on bacterial functional groups, including putative aerobic heterotrophs (e.g. Erythrobacteraceae, Hyphomicrobiaceae) and sulfate reducers (e.g. Desulfobacteraceae). Consequently, under elevated seawater temperatures, carbon accumulation rates may diminish due to higher remineralization rates at the sediment surface. Nonetheless, the anoxic conditions ubiquitous to seagrass sediments can provide a degree of carbon protection under warming seawater temperatures.
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•We review the impacts of contaminants of emerging concern (CECs) on coral reefs.•The sources, presence and potential effects of six CEC categories are discussed.•Known and likely ...sources are relatively well known and spatial represented.•Monitoring data and effect information for potential high risk CECs are scarce.•The findings are relevant to tropical marine ecosystems around the world.
Current policy and management for marine water quality in the Great Barrier Reef (GBR) in north-eastern Australia primarily focusses on sediment, nutrients and pesticides derived from diffuse source pollution related to agricultural land uses. In addition, contaminants of emerging concern (CECs) are known to be present in the marine environments of the GBR and the adjacent Torres Strait (TS). Current and projected agricultural, urban and industrial developments are likely to increase the sources and diversity of CECs being released into these marine ecosystems. In this review, we evaluate the sources, presence and potential effects of six different categories of CECs known to be present, or likely to be present, in the GBR and TS marine ecosystems. Specifically, we summarize available monitoring, source and effect information for antifouling paints; coal dust and particles; heavy/trace metals and metalloids; marine debris and microplastics; pharmaceuticals and personal care products (PPCPs); and petroleum hydrocarbons. Our study highlights the lack of (available) monitoring data for most of these CECs, and recommends: (i) the inclusion of all relevant environmental data into integrated databases for building marine baselines for the GBR and TS regions, and (ii) the implementation of local, targeted monitoring programs informed by predictive methods for risk prioritization. Further, our spatial representation of the known and likely sources of these CECs will contribute to future ecological risk assessments of CECs to the GBR and TS marine environments, including risks relative to those identified for sediment, nutrients and pesticides.
The Great Barrier Reef (GBR) is founded on reef-building corals. Corals build their exoskeleton with aragonite, but ocean acidification is lowering the aragonite saturation state of seawater (Ωa). ...The downscaling of ocean acidification projections from global to GBR scales requires the set of regional drivers controlling Ωa to be resolved. Here we use a regional coupled circulation-biogeochemical model and observations to estimate the Ωa experienced by the 3,581 reefs of the GBR, and to apportion the contributions of the hydrological cycle, regional hydrodynamics and metabolism on Ωa variability. We find more detail, and a greater range (1.43), than previously compiled coarse maps of Ωa of the region (0.4), or in observations (1.0). Most of the variability in Ωa is due to processes upstream of the reef in question. As a result, future decline in Ωa is likely to be steeper on the GBR than currently projected by the IPCC assessment report.
Since the mid-1990s, Australia's Commonwealth Science Industry and Research Organisation (CSIRO) has been developing a biogeochemical (BGC) model for coupling with a hydrodynamic and sediment model ...for application in estuaries, coastal waters and shelf seas. The suite of coupled models is referred to as the CSIRO Environmental Modelling Suite (EMS) and has been applied at tens of locations around the Australian continent. At a mature point in the BGC model's development, this paper presents a full mathematical description, as well as links to the freely available code and user guide. The mathematical description is structured into processes so that the details of new parameterisations can be easily identified, along with their derivation. In EMS, the underwater light field is simulated by a spectrally resolved optical model that calculates vertical light attenuation from the scattering and absorption of 20+ optically active constituents. The BGC model itself cycles carbon, nitrogen, phosphorous and oxygen through multiple phytoplankton, zooplankton, detritus and dissolved organic and inorganic forms in multiple water column and sediment layers. The water column is dynamically coupled to the sediment to resolve deposition, resuspension and benthic–pelagic biogeochemical fluxes. With a focus on shallow waters, the model also includes detailed representations of benthic plants such as seagrass, macroalgae and coral polyps. A second focus has been on, where possible, the use of geometric derivations of physical limits to constrain ecological rates. This geometric approach generally requires population-based rates to be derived from initially considering the size and shape of individuals. For example, zooplankton grazing considers encounter rates of one predator on a prey field based on summing relative motion of the predator with the prey individuals and the search area; chlorophyll synthesis includes a geometrically derived self-shading term; and the bottom coverage of benthic plants is calculated from their biomass using an exponential form derived from geometric arguments. This geometric approach has led to a more algebraically complicated set of equations when compared to empirical biogeochemical model formulations based on populations. But while being algebraically complicated, the model has fewer unconstrained parameters and is therefore simpler to move between applications than it would otherwise be. The version of EMS described here is implemented in the eReefs project that delivers a near-real-time coupled hydrodynamic, sediment and biogeochemical simulation of the Great Barrier Reef, northeast Australia, and its formulation provides an example of the application of geometric reasoning in the formulation of aquatic ecological processes.
Active restoration is becoming an increasingly important conservation intervention to counteract the degradation of marine coastal ecosystems. Understanding what has motivated the scientific ...community to research the restoration of marine coastal ecosystems and how restoration research projects are funded is essential if we want to scale-up restoration interventions to meaningful extents. Here, we systematically review and synthesize data to understand the motivations for research on the restoration of coral reefs, seagrass, mangroves, saltmarsh, and oyster reefs. We base this analysis off a published database of marine restoration studies, originally designed to estimate the cost and feasibility of marine coastal restoration, derived from mostly scientific studies published in peer-reviewed and some grey literature. For the present study, the database was updated with fields aimed at assessing the motivations, outcomes, and funding sources for each project. We classify restoration motivations into five categories: biotic, experimental, idealistic, legislative, and pragmatic. Moreover, we evaluate the variables measured and outcomes reported by the researchers and evaluate whether projects adhered to the Society for Ecological Restoration’s (SER) standards for the practice of ecological restoration. The most common motivation of the scientific community to study restoration in marine coastal ecosystems was experimental i.e. to seek experimental data to answer ecological research questions or improve restoration approach, as expected since mostly peer-reviewed literature was evaluated here. There were differences in motivations among the five coastal ecosystems. For instance, biodiversity enhancement was the most common case for a biotic motivation in mangrove restoration projects. The most common metrics evaluated were growth/productivity, survivorship, habitat function, physical attributes and reproduction. For most ecosystems, ecological outcomes were frequently reported, with socio-economic implications of the restoration rarely mentioned, except for mangroves. Projects were largely funded by governmental grants with some investment from private donations, non-governmental organizations, and the involvement of volunteers. Our findings and database provide critical data to align future research of the scientific community with the real social, economic and policy needs required to scale-up marine coastal restoration projects.
•Physics-based method estimating all components of surface solar irradiance (SSI).•Calibration removing requirement of any ancillary data during operation.•Time series based radiative transfer model ...to simultaneously retrieve properties of clouds, aerosols and surface.•Comprehensive validation showing consistently low bias and relatively small RMSE for all components.•For examples, <4 W/m2 bias for all components and time scales, and 58 W/m2 GHI hourly RMSE.
Surface Solar Irradiance (SSI) is required for solar energy planning and adoption, and is a fundamental parameter in modelling weather, climate, ecosystem and agricultural activities. Herein a time series based radiative transfer model was developed to simultaneously retrieve properties of clouds, aerosols and surface albedo, which were in turn used to calculate the components of SSI: i.e., global, direct and diffuse irradiance. The calculated results were calibrated across the Australian continent against in-situ measurements to account for minor factors (e.g., water vapor) not considered by the physics-based method. Detailed validation of the SSI components was performed against three years of in-situ measurements at 11 sites across Australia, at a range of time scales (i.e., instantaneous, hourly, daily and monthly) and under both all-sky and cloudy-sky conditions. The main advantage of the present method is the reliable separation of the direct and diffuse components with consistently low biases (~4 W/m2) at all four time scales, while still maintaining relatively low RMSE (root-mean-square-error) and MAE (mean-absolute-error). Once calibration has been performed the model does not require any ancillary data when implemented operationally: that is the model only requires geostationary satellite data. This model may be implemented across the globe using widely available next generation geostationary satellite data with a handful of ground-data for calibration.
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