PhyloPars: estimation of missing parameter values using phylogeny

A wealth of information on metabolic parameters of a species can be inferred from observations on species that are phylogenetically related. Phylogeny-based information can complement direct empirical evidence, and is particularly valuable if experiments on the species of interest are not feasible. The PhyloPars web server provides a statistically consistent method that combines an incomplete set of empirical observations with the species phylogeny to produce a complete set of parameter estimates for all species. It builds upon a state-of-the-art evolutionary model, extended with the ability to handle missing data. The resulting approach makes optimal use of all available information to produce estimates that can be an order of magnitude more accurate than ad-hoc alternatives. Uploading a phylogeny and incomplete feature matrix suffices to obtain estimates of all missing values, along with a measure of certainty. Real-time cross-validation provides further insight in the accuracy and bias expected for estimated values. The server allows for easy, efficient estimation of metabolic parameters, which can benefit a wide range of fields including systems biology and ecology. PhyloPars is available at: http://www.ibi.vu.nl/programs/phylopars/

Scoping report on the potential impact of on-board desulphurization on the water quality in SOx Emission Control Areas

The input of acid substances (like SO2) into the sea has been recognized as an environmental issue that needs to be considered in terms of ocean acidification; acid inputs and techniques to deal with them have implications for member states' obligations under the Water Framework Directive and Marine Strategy Framework Directive. This study provides an initial assessment on the potential impact of on-board desulphurisation equipment (open loop scrubbers) on the seawater quality with focus on SOx Emission Control Areas (SECAs). The study focuses on the potential impact of ship-borne SO2 on acidification (pH) of seawater in comparison to the impact from climate change. The report comprises a literature study and a dedicated modelling exercise covering the North Sea region. Most available studies and the peer reviewed literature found only a small additional impact from SO2 emissions on acidification in the various investigated parts of the world ocean. However these studies generally assessed spatially averaged effects and regional and coastal oriented studies are mostly lacking from the literature, which means that potential effects to vulnerable ecosystems in such areas have not previously been considered. A coupled hydrodynamic-chemistry model was employed to assess the impact of adding SO2 and CO2 on the complex carbonate system in sea water. The impact on the pH decrease in the open North Sea region from discharging the acid wash water into the seawater was found to be small, but not insignificant, and regionally varying. The calculated annual mean decrease of pH due to SO2 injection for the North Sea total water column is 0.00011; when considering only the change in the surface layer (0-20m), the annual decrease is 0.00024. The total annual impact from increasing atmospheric CO2 concentrations on the acidification of the North Sea surface area is about 8 times stronger (0.001) as the impact from wash water injection. However because of the pronounced spatial variations the mean impact does not reflect the overall situation well. Consequently we find critical regions with high ship traffic intensity, for example along the shipping lanes and in the larger Rotterdam port area. Here, the contribution from SO2 injection can be double the impact from increasing CO2 concentrations and 20 times larger than the North Sea mean value. These critical regions indicate potential problems related to the surface water quality in ports, estuaries and coastal waters that fall under regulation under the Water Framework Directive (WFD). The problem of decreasing pH caused by SO2 input from ship exhaust gases in regional seas (North Sea) is relevant to the obligation of the Member States to assess the environmental state of their marine areas and to establish a Good Environmental Status (GES) under the Marine Strategy Framework Directive (MFSD), as pH value is one of the GES criteria.JRC.H.1-Water Resource

Uncovering the environmental drivers of short-term temporal dynamics in an epibenthic community from the Western English Channel

Benthic communities, critical to the health and function of marine ecosystems, are under increasing pressure from anthropogenic impacts such as pollution, eutrophication and climate change. In order to refine predictions of likely future changes in benthic communities resulting from these impacts, we must first better constrain their responses to natural seasonality in environmental conditions. Epibenthic time series data (July 2008–May 2014) have been collected from Station L4, situated 7.25 nautical miles south of Plymouth in the Western English Channel. These data were analysed to establish patterns in community abundance, wet biomass and composition, and to link any observed patterns to environmental variables. A clear response to the input of organic material from phytoplankton blooms was detected, with sediment surface living deposit feeders showing an immediate increase in abundance, while predators and scavengers responded later, with an increase in biomass. We suggest that this response is a result of two factors. The low organic content of the L4 sediment results in food limitation of the community, and the mild winter/early spring bottom water temperatures allow the benthos to take immediate advantage of bloom sedimentation. An inter-annual change in community composition was also detected, as the community shifted from one dominated by the anomuran Anapagurus laevis to one dominated by the gastropod Turitella communis. This appeared to be related to a period of high larval recruitment for T. communis in 2013/2014, suggesting that changes in the recruitment success of one species can affect the structure of an entire community

Biological trait profiles discriminate between native and non-indigenous marine invertebrates

The increasing rate of marine invasions to Western Europe in recent decades highlights the importance of addressing the central questions of invasion biology: what allows an invader to be successful, and which species are likely to become invasive? Consensus is currently lacking regarding the key traits that determine invasiveness in marine species and the extent to which invasive and indigenous species differ in their trait compositions. This limits the ability to predict invasive potential. Here we propose a method based on trait profiles which can be used to predict non-indigenous species likely to cause the greatest impact and native species with a tendency for invasion. We compiled a database of 12 key biological and life history traits of 85 non-indigenous and 302 native marine invertebrate species from Western Europe. Using multivariate methods, we demonstrate that biological traits were able to discriminate between native and non-indigenous species with an accuracy of 78%. The main discriminant traits included body size, lifespan, fecundity, offspring protection, burrowing depth and, to a lesser extent, pelagic stage duration. Analysis revealed that the typical non-indigenous marine invertebrate is a mid-sized, long-lived, highly fecund suspension feeder which either broods its offspring or has a pelagic stage duration of 1–30 days, and is either attached-sessile or burrows to a depth of 5 cm. Biological traits were also able to predict native species classed as “potentially invasive” with an accuracy of 78%. Targeted surveillance and proactive management of invasive species requires accurate predictions of which species are likely to become invasive in the future. Our findings add to the growing evidence that non-indigenous species possess a greater affinity for certain traits. These traits are typically present in the profile of “potentially invasive” native species

Influence of suspended sediment front on nutrients and phytoplankton dynamics off the Changjiang Estuary: A FVCOM-ERSEM coupled model experiment

Under embargo until: 2021-12-27High-turbidity water is a common feature in the estuary and inner shelf. Sediment suspension functions as a modulator that directly influences the interactions among nutrients, phytoplankton and other related ecosystem variables. A physical-biological coupling model system was applied to examine the impact of sediment front on interactions among on suspended sediment, vertical mixing, nutrients and phytoplankton over the inner shelf off the high-turbidity, phosphate-limited Changjiang Estuary. The physical model was the Finite-Volume Community Ocean Model (FVCOM) and the biological model was the European Regional Seas Ecosystem Model (ERSEM). Results revealed that in the nearshore region the growth of phytoplankton over the spring-summer seasons was limited by suspended sediments and intensified vertical mixing during the autumn-winter seasons extended the sediment-induced suppression extended offshore to restrict the phytoplankton growth over the shelf. Nutrients were diluted by spreading of freshwater discharge and significantly decreased off the suspended sediment front due to the depletion by the offshore phytoplankton growth. The simulation results showed that although the diatom phytoplankton dominated the Chlorophyll a (Chl-a) concentration, the non-diatom group had a more contribution to the biomass. The relatively high phytoplankton biomass was found over the offshore deep underwater valley area as results of remote advection by the Taiwan Warm Current and weak turbulent mixing.acceptedVersio

Modelling mixotrophic functional diversity and implications for ecosystem function

Mixotrophy is widespread among protist plankton displaying diverse functional forms within a wide range of sizes. However, little is known about the niches of different mixotrophs and how they affect nutrient cycling and trophodynamics in marine ecosystems. Here we built a plankton food web model incorporating mixotrophic functional diversity. A distinction was made between mixotrophs with the innate capacity for photosynthesis (constitutive mixotrophs, CMs) and those which acquire phototrophy from their prey (non-constitutive mixotrophs, NCMs). We present the simulations of ecosystems limited by different light and nutrient regimes. Our simulations show that strict autotrophic and heterotrophic competitors increased in relative importance in the transition from nutrient to light limitation, consistent with observed oceanic biomass ratios. Among CMs, cells <20 μm dominate in nutrient-poor conditions while larger cells dominate in light-limited environments. The specificity of the prey from which NCMs acquire their phototrophic potential affects their success, with forms able to exploit diverse prey dominating under nutrient limitation. Overall, mixotrophy decreases the regeneration of inorganics and boosts the trophic transfer efficiency of carbon. Our results show that mixotrophic functional diversity has the potential to radically change our understanding of the ecosystem functioning in the lower trophic levels of food webs

The impact of ocean biogeochemistry on physics and its consequences for modelling shelf seas

We use modelling and assimilation tools to explore the impact of biogeochemistry on physics in the shelf sea environment, using North-West European Shelf (NWES) as a case study. We demonstrate that such impact is significant: the attenuation of light by biogeochemical substances heats up the upper 20 m of the ocean by up to 1 °C and by a similar margin cools down the ocean within the 20–200 m range of depths. We demonstrate that these changes to sea temperature influence mixing in the upper ocean and feed back into marine biology by influencing the timing of the phytoplankton bloom, as suggested by the critical turbulence hypothesis. We compare different light schemes representing the impact of biogeochemistry on physics, and show that the physics is sensitive to both the spectral resolution of radiances and the represented optically active constituents. We introduce a new development into the research version of the operational model for the NWES, in which we calculate the heat fluxes based on the spectrally resolved attenuation by the simulated biogeochemical tracers, establishing a two-way coupling between biogeochemistry and physics. We demonstrate that in the late spring-summer the two-way coupled model increases heating in the upper oceanic layer compared to the existing model and improves by 1–3 days the timing of the simulated phytoplankton bloom. This improvement is relatively small compared with the existing model bias in bloom timing, but is sufficient to have a visible impact on model skill in the free run. We also validate the skill of the two-way coupling in the context of the weakly coupled physical-biogeochemical assimilation currently used for operational forecasting of the NWES. We show that the change to the skill is negligible for analyses, but it remains to be seen how much it differs for the forecasts

Exploring, exploiting and evolving diversity of aquatic ecosystem models: A community perspective

Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5–10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary