Mixoplankton and mixotrophy: future research priorities

Phago-mixotrophy, the combination of photoautotrophy and phagotrophy in mixoplankton, organisms that can combine both trophic strategies, have gained increasing attention over the past decade. It is now recognized that a substantial number of protistan plankton species engage in phago-mixotrophy to obtain nutrients for growth and reproduction under a range of environmental conditions. Unfortunately, our current understanding of mixoplankton in aquatic systems significantly lags behind our understanding of zooplankton and phytoplankton, limiting our ability to fully comprehend the role of mixoplankton (and phago-mixotrophy) in the plankton food web and biogeochemical cycling. Here, we put forward five research directions that we believe will lead to major advancement in the field: (i) evolution: understanding mixotrophy in the context of the evolutionary transition from phagotrophy to photoautotrophy; (ii) traits and trade-offs: identifying the key traits and trade-offs constraining mixotrophic metabolisms; (iii) biogeography: large-scale patterns of mixoplankton distribution; (iv) biogeochemistry and trophic transfer: understanding mixoplankton as conduits of nutrients and energy; and (v) in situ methods: improving the identification of in situ mixoplankton and their phago-mixotrophic activity.

The performance of neutron diffractometers at long and short pulse spallation sources: Comparison between ESS and J-PARC

The general performance of diffractometers at the first long pulse spallation source ESS, is compared with their counterparts at J-PARC, a short pulse spallation source. The difference in the inherent pulse structure of these neutron sources presents opportunities for new concepts for instrumentation, where performance does not scale simply with source power. The article describes advantages and disadvantages of those diffractometers, adapting to the very different source characteristics. We find that the two sources offer comparable performance in flux and resolution when operating in high-resolution mode. ESS offers significant advantages in tunability and flexibility, notably in the ability to relax resolution in order to increase flux for a given experiment. The slow repetition rate of ESS favors long instruments. On the other hand, J-PARC instruments perform very well in spite of the lower source power and allow better access to epithermal neutrons, of particular interest for PDF analysis of diffraction data.

Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles

Nitrogen ([Formula: see text]) fixation by heterotrophic bacteria associated with sinking particles contributes to marine N cycling, but a mechanistic understanding of its regulation and significance are not available. Here we develop a mathematical model for unicellular heterotrophic bacteria growing on sinking marine particles. These bacteria can fix [Formula: see text] under suitable environmental conditions. We find that the interactive effects of polysaccharide and polypeptide concentrations, sinking speed of particles, and surrounding [Formula: see text] and [Formula: see text] concentrations determine the [Formula: see text] fixation rate inside particles. [Formula: see text] fixation inside sinking particles is mainly fueled by [Formula: see text] respiration rather than [Formula: see text] respiration. Our model suggests that anaerobic processes, including heterotrophic [Formula: see text] fixation, can take place in anoxic microenvironments inside sinking particles even in fully oxygenated marine waters. The modelled [Formula: see text] fixation rates are similar to bulk rates measured in the aphotic ocean, and our study consequently suggests that particle-associated heterotrophic [Formula: see text] fixation contributes significantly to oceanic [Formula: see text] fixation.

Spatial drivers of instability in marine size-spectrum ecosystems

Size-spectrum models are a recent class of models describing the dynamics of a whole community based on a description of individual organisms. The models are motivated by marine ecosystems where they cover the size range from multicellular plankton to the largest fish. We propose to extend the size-spectrum model with spatial components. The spatial dynamics is governed by a random motion and a directed movement in the direction of increased fitness, which we call 'fitness-taxis'. We use the model to explore whether spatial irregularities of marine communities can occur due to the internal dynamics of predator-prey interactions and spatial movements. This corresponds to a pattern-formation analysis generalized to an entire ecosystem but is not limited to one prey and one predator population. The analyses take the form of Fourier analysis and numerical experiments. Results show that diffusion always stabilizes the equilibrium but fitness-taxis destabilizes it, leading to non-stationary spatially inhomogeneous population densities, which are travelling in size. However, there is a strong asymmetry between fitness-induced destabilizing effects and diffusion-induced stabilizing effects with the latter dominating over the former. These findings reveal that fitness taxis acts as a possible mechanism behind pattern formations in ecosystems with high diversity of organism sizes, which can drive the emergence of spatial heterogeneity even in a spatially homogeneous environment.

Trait-based food web model reveals the underlying mechanisms of biodiversity-ecosystem functioning relationships

The concept of biodiversity-ecosystem functioning (BEF) has been studied over the last three decades using experiments, theoretical models and more recently observational data. While theoretical models revealed that species richness is the best metric summarizing ecosystem functioning, it is clear that ecosystem function is explained by other variables besides species richness. Additionally, theoretical models rarely focus on more than one ecosystem function, limiting ecosystem functioning to biomass or production. There is a lack of theoretical background to verify how other components of biodiversity and species interactions support ecosystem functioning. Here, using simulations from a food web model based on a community assembly process and a trait-based approach, we test how species biodiversity, food web structure and predator-prey interactions determine several ecosystem functions (biomass, metabolism, production and productivity). Our results demonstrate that the relationship between species richness and ecosystem functioning depends on the type of ecosystem function considered and the importance of diversity and food web structure differs across functions. Particularly, we show that dominance plays a major role in determining the level of biomass, and it is at least as important as the number of species. We find that dominance occurs in the food web when species do not experience strong predation. By manipulating the structure of the food web, we show that species using a wider trait space (generalist communities) result in more connected food webs and generally reach the same level of functioning with less species. The model shows the importance of generalist versus specialist communities on BEF relationships, and as such, empirical studies should focus on quantifying the importance of diet/habitat use on ecosystem functioning. Our study provides a better understanding of BEF underlying mechanisms and generates research hypotheses that can be considered and tested in observational studies. We recommend that studies investigating links between biodiversity and ecosystem functions should include metrics of dominance, species composition, trophic structure and possibly environmental trait space. We also advise that more effort should be made into calculating several ecosystem functions and properties with data from natural multitrophic systems.

Body Size, Light Intensity, and Nutrient Supply Determine Plankton Stoichiometry in Mixotrophic Plankton Food Webs

Trophic strategy determines stoichiometry of plankton. In general, heterotrophic zooplankton have lower and more stable C∶N and C∶P ratios than photoautotrophic phytoplankton, whereas mixotrophic protists, which consume prey and photosynthesize, have stoichiometry between zooplankton and phytoplankton. As trophic strategies change with cell size, body size may be a key trait influencing eukaryotic plankton stoichiometry. However, the relationship between body size and stoichiometry remains unclear. Here we measured plankton size-fractionated C∶N ratios under different intensities of light and nutrient supply in subtropical freshwater and marine systems. We found a unimodal body size-C∶N ratio pattern, with a maximum C∶N ratio at ∼50 μm diameter in marine and freshwater systems. Moreover, the variation in C∶N ratios is explained mainly by body size, followed by light intensity and nutrient concentration. To investigate the mechanisms behind this unimodal pattern, we constructed a size-based plankton food web model in which the trophic strategy and C∶N ratio are an emerging result. Our model simulations reproduce the unimodal pattern with a C∶N ratio of photoautotrophs ≤50 μm increasing with body size due to increase of photosynthetic carbon, whereas C∶N ratios of organisms >50 μm decrease with size due to decreasing photoautotrophic but increasing heterotrophic uptake. Based on our field observations and simulation, we extend the classic "light-nutrient" theory that determines plankton C∶N ratio to include body size and trophic strategy dependency. We conclude that body size and size-dependent uptake of resources (light, nutrients, and prey) determine plankton stoichiometry at various light and nutrient supplies.

Population variability under stressors is dependent on body mass growth and asymptotic body size

The recruitment and biomass of a fish stock are influenced by their environmental conditions and anthropogenic pressures such as fishing. The variability in the environment often translates into fluctuations in recruitment, which then propagate throughout the stock biomass. In order to manage fish stocks sustainably, it is necessary to understand their dynamics. Here, we systematically explore the dynamics and sensitivity of fish stock recruitment and biomass to environmental noise. Using an age-structured and trait-based model, we explore random noise (white noise) and autocorrelated noise (red noise) in combination with low to high levels of harvesting. We determine the vital rates of stocks covering a wide range of possible body mass (size) growth rates and asymptotic size parameter combinations. Our study indicates that the variability of stock recruitment and biomass are probably correlated with the stock's asymptotic size and growth rate. We find that fast-growing and large-sized fish stocks are likely to be less vulnerable to disturbances than slow-growing and small-sized fish stocks. We show how the natural variability in fish stocks is amplified by fishing, not just for one stock but for a broad range of fish life histories.

Interacting Temperature, Nutrients and Zooplankton Grazing Control Phytoplankton Size-Abundance Relationships in Eight Swiss Lakes

Biomass distribution among size classes follows a power law where the Log-abundance of taxa scales to Log-size with a slope that responds to environmental abiotic and biotic conditions. The interactions between ecological mechanisms controlling the slope of locally realized size-abundance relationships (SAR) are however not well understood. Here we tested how warming, nutrient levels, and grazing affect the slope of phytoplankton community SARs in decadal time-series from eight Swiss lakes of the peri-alpine region, which underwent environmental forcing due to climate change and oligotrophication. We expected rising temperature to have a negative effect on slope (favoring small phytoplankton), and increasing nutrient levels and grazing pressure to have a positive effect (benefiting large phytoplankton). Using a random forest approach to extract robust patterns from the noisy data, we found that the effects of temperature (direct and indirect through water column stability), nutrient availability (phosphorus and total biomass), and large herbivore (copepods and daphnids) grazing and selectivity on slope were non-linear and interactive. Increasing water temperature or total grazing pressure, and decreasing phosphorus levels, had a positive effect on slope (favoring large phytoplankton, which are predominantly mixotrophic in the lake dataset). Our results therefore showed patterns that were opposite to the expected long-term effects of temperature and nutrient levels, and support a paradigm in which (i) small phototrophic phytoplankton appear to be favored under high nutrients levels, low temperature and low grazing, and (ii) large mixotrophic algae are favored under oligotrophic conditions when temperature and grazing pressure are high. The effects of temperature were stronger under nutrient limitation, and the effects of nutrients and grazing were stronger at high temperature. Our study shows that the phytoplankton local SARs in lakes respond to both the independent and the interactive effects of resources, grazing and water temperature in a complex, unexpected way, and observations from long-term studies can deviate significantly from general theoretical expectations.

Disentangling time-focusing from beam divergence: A novel approach for high-flux thermal neutron spectroscopy at continuous and long-pulse sources

We present the concept of a novel time-focusing technique for neutron spectrometers, which allows us to disentangle time-focusing from beam divergence. The core of this approach is a double rotating-crystal monochromator that can be used to extract a larger wavelength band from a white beam, thus providing a higher flux at the sample compared to standard time-of-flight instruments, yet preserving energy resolution and beam collimation. The performances of a spectrometer based on this approach are quantitatively discussed in terms of possible incident wavelengths, flux at the sample, and (Q, E)-resolution. Analytical estimates suggest flux gains of about one order of magnitude at comparable resolutions in comparison to conventional time-of-flight spectrometers. Moreover, the double monochromator configuration natively shifts the sample away from the source line-of-sight, thus significantly improving the signal-to-noise ratio. The latter, in combination with a system that does not increase the beam divergence, brings the further advantage of a cleaner access to the low-Q region, which is recognized to be of fundamental interest for magnetism and for disordered materials, from glasses to biological systems.

Thermal performance of fish is explained by an interplay between physiology, behaviour and ecology

Increasing temperatures under climate change are thought to affect individual physiology of fish and other ectotherms through increases in metabolic demands, leading to changes in species performance with concomitant effects on species ecology. Although intuitively appealing, the driving mechanism behind thermal performance is contested; thermal performance (e.g. growth) appears correlated with metabolic scope (i.e. oxygen availability for activity) for a number of species, but a substantial number of datasets do not support oxygen limitation of long-term performance. Whether or not oxygen limitations via the metabolic scope, or a lack thereof, have major ecological consequences remains a highly contested question. size and trait-based model of energy and oxygen budgets to determine the relative influence of metabolic rates, oxygen limitation and environmental conditions on ectotherm performance. We show that oxygen limitation is not necessary to explain performance variation with temperature. Oxygen can drastically limit performance and fitness, especially at temperature extremes, but changes in thermal performance are primarily driven by the interplay between changing metabolic rates and species ecology. Furthermore, our model reveals that fitness trends with temperature can oppose trends in growth, suggesting a potential explanation for the paradox that species often occur at lower temperatures than their growth optimum. Our model provides a mechanistic underpinning that can provide general and realistic predictions about temperature impacts on the performance of fish and other ectotherms and function as a null model for contrasting temperature impacts on species with different metabolic and ecological traits.

Nutrient affinity, half-saturation constants and the cost of toxin production in dinoflagellates

The two parameters of the Michaelis-Menten model, the maximum uptake rate and the half-saturation constant, are not stochastically independent, and the half-saturation constant is not a measure of nutrient affinity, as commonly assumed. Failure to realise their interdependence and mechanistic interpretation may lead to the emergence of false trade-offs.

The cost of toxin production in phytoplankton: the case of PST producing dinoflagellates

Many species of phytoplankton produce toxins that may provide protection from grazing. In that case one would expect toxin production to be costly; else all species would evolve toxicity. However, experiments have consistently failed to show any costs. Here, we show that costs of toxin production are environment dependent but can be high. We develop a fitness optimization model to estimate rate, costs, and benefits of toxin production, using PST (paralytic shellfish toxin) producing dinoflagellates as an example. Costs include energy and material (nitrogen) costs estimated from well-established biochemistry of PSTs, and benefits are estimated from relationship between toxin content and grazing mortality. The model reproduces all known features of PST production: inducibility in the presence of grazer cues, low toxicity of nitrogen-starved cells, but high toxicity of P-limited and light-limited cells. The model predicts negligible reduction in cell division rate in nitrogen replete cells, consistent with observations, but >20% reduction when nitrogen is limiting and abundance of grazers high. Such situation is characteristic of coastal and oceanic waters during summer when blooms of toxic algae typically develop. The investment in defense is warranted, since the net growth rate is always higher in defended than in undefended cells.

A smartphone application supporting patients with psoriasis improves adherence to topical treatment: a randomized controlled trial

BACKGROUND

Adherence to topical psoriasis treatments is low, which leads to unsatisfactory treatment results. Smartphone applications (apps) for patient support exist but their potential to improve adherence has not been systematically evaluated.

OBJECTIVES

To evaluate whether a study-specific app improves adherence and reduces psoriasis symptoms compared with standard treatment.

METHODS

We conducted a randomized controlled trial (RCT, clinicaltrials.gov registration: NCT02858713). Patients received once-daily medication [calcipotriol/betamethasone dipropionate (Cal/BD) cutaneous foam] and were randomized to no app (n = 66) or app intervention (n = 68) groups. In total, 122 patients (91%) completed the 22-week follow-up. The primary outcome was adherence, which was defined as medication applied ≥ 80% of days during the treatment period and assessed by a chip integrated into the medication dispenser. Secondary outcomes were psoriasis severity measured by the Lattice System Physician's Global Assessment (LS-PGA) and quality of life, measured using the Dermatology Life Quality Index (DLQI) at all visits.

RESULTS

Intention-to-treat analyses using regression was performed. More patients in the intervention group were adherent to Cal/BD cutaneous foam than those in the nonintervention group at week 4 (65% vs. 38%, P = 0·004). The intervention group showed a greater LS-PGA reduction than the nonintervention group at week 4 (mean 1·86 vs. 1·46, P = 0·047). A similar effect was seen at weeks 8 and 26, although it did not reach statistical significance.

CONCLUSIONS

This RCT demonstrates that the app improved short-term adherence to Cal/BD cutaneous foam treatment and psoriasis severity.

Food-web dynamics under climate change

Climate change affects ecological communities through its impact on the physiological performance of individuals. However, the population dynamic of species well inside their thermal niche is also determined by competitors, prey and predators, in addition to being influenced by temperature changes. We use a trait-based food-web model to examine how the interplay between the direct physiological effects from temperature and the indirect effects due to changing interactions between populations shapes the ecological consequences of climate change for populations and for entire communities. Our simulations illustrate how isolated communities deteriorate as populations go extinct when the environment moves outside the species' thermal niches. High-trophic-level species are most vulnerable, while the ecosystem function of lower trophic levels is less impacted. Open communities can compensate for the loss of ecosystem function by invasions of new species. Individual populations show complex responses largely uncorrelated with the direct impact of temperature change on physiology. Such complex responses are particularly evident during extinction and invasion events of other species, where climatically well-adapted species may be brought to extinction by the changed food-web topology. Our results highlight that the impact of climate change on specific populations is largely unpredictable, and apparently well-adapted species may be severely impacted.

A smartphone application supporting patients with psoriasis improves adherence to topical treatment: a randomized controlled trial

BACKGROUND

Adherence to topical psoriasis treatments is low, which leads to unsatisfactory treatment results. Smartphone applications (apps) for patient support exist but their potential to improve adherence has not been systematically evaluated.

OBJECTIVES

To evaluate whether a study-specific app improves adherence and reduces psoriasis symptoms compared with standard treatment.

METHODS

We conducted a randomized controlled trial (RCT, clinicaltrials.gov registration: NCT02858713). Patients received once-daily medication [calcipotriol/betamethasone dipropionate (Cal/BD) cutaneous foam] and were randomized to no app (n = 66) or app intervention (n = 68) groups. In total, 122 patients (91%) completed the 22-week follow-up. The primary outcome was adherence, which was defined as medication applied ≥ 80% of days during the treatment period and assessed by a chip integrated into the medication dispenser. Secondary outcomes were psoriasis severity measured by the Lattice System Physician's Global Assessment (LS-PGA) and quality of life, measured using the Dermatology Life Quality Index (DLQI) at all visits.

RESULTS

Intention-to-treat analyses using regression was performed. More patients in the intervention group were adherent to Cal/BD cutaneous foam than those in the nonintervention group at week 4 (65% vs. 38%, P = 0·004). The intervention group showed a greater LS-PGA reduction than the nonintervention group at week 4 (mean 1·86 vs. 1·46, P = 0·047). A similar effect was seen at weeks 8 and 26, although it did not reach statistical significance.

CONCLUSIONS

This RCT demonstrates that the app improved short-term adherence to Cal/BD cutaneous foam treatment and psoriasis severity.

Recent upgrades of the neutron reflectometer D17 at ILL

The vertical sample-plane reflectometer D17 at the Institut Laue–Langevin in Grenoble, France, has undergone several major upgrades since its commissioning, which are summarized in this article. The three major improvements are (i) a new focusing guide, increasing the usable flux on the sample by a factor of 2.5; (ii) a new beam polarizer and new spin flippers, allowing for the use of polarized neutrons in time-of-flight mode; and (iii) a new detector with a particularly uniform response under homogeneous exposure, improved stability and state-of-the-art detector electronics. The combination of these factors has paved the road to new possibilities in fast kinetic measurements, magnetism and off-specular scattering. Examples and scientific references for the new capabilities are presented.

Size structures sensory hierarchy in ocean life

Survival in aquatic environments requires organisms to have effective means of collecting information from their surroundings through various sensing strategies. In this study, we explore how sensing mode and range depend on body size. We find a hierarchy of sensing modes determined by body size. With increasing body size, a larger battery of modes becomes available (chemosensing, mechanosensing, vision, hearing and echolocation, in that order) while the sensing range also increases. This size-dependent hierarchy and the transitions between primary sensory modes are explained on the grounds of limiting factors set by physiology and the physical laws governing signal generation, transmission and reception. We theoretically predict the body size limits for various sensory modes, which align well with size ranges found in literature. The treatise of all ocean life, from unicellular organisms to whales, demonstrates how body size determines available sensing modes, and thereby acts as a major structuring factor of aquatic life.

Modeling succession of key resource-harvesting traits of mixotrophic plankton

Unicellular eukaryotes make up the base of the ocean food web and exist as a continuum in trophic strategy from pure heterotrophy (phagotrophic zooplankton) to pure photoautotrophy (‘phytoplankton'), with a dominance of mixotrophic organisms combining both strategies. Here we formulate a trait-based model for mixotrophy with three key resource-harvesting traits: photosynthesis, phagotrophy and inorganic nutrient uptake, which predicts the trophic strategy of species throughout the seasonal cycle. Assuming that simple carbohydrates from photosynthesis fuel respiration, and feeding primarily provides building blocks for growth, the model reproduces the observed light-dependent ingestion rates and species-specific growth rates with and without prey from the laboratory. The combination of traits yielding the highest growth rate suggests high investments in photosynthesis, and inorganic nutrient uptake in the spring and increased phagotrophy during the summer, reflecting general seasonal succession patterns of temperate waters. Our trait-based model presents a simple and general approach for the inclusion of mixotrophy, succession and evolution in ecosystem models.

Adult and offspring size in the ocean: a database of size metrics and conversion factors

The purpose of this dataset was to compile adult and offspring size estimates for marine organisms. Adult and offspring size estimates of 408 species were compiled from the literature covering >17 orders of magnitude in body mass and including Cephalopoda (ink fish), Cnidaria ("jelly" fish), Crustaceans, Ctenophora (comb jellies), Elasmobranchii (cartilaginous fish), Mammalia (mammals), Sagittoidea (arrow worms) and Teleost (i.e., Actinopterygii, bony fish). Individual size estimates were converted to standardized size estimates (carbon weight, g) to allow for among-group comparisons. This required a number of size estimates to be converted and a compilation of conversion factors obtained from the literature are also presented.

Correction: Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source

Correction for 'Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source' by Mark T. F. Telling et al., Phys. Chem. Chem. Phys., 2005, 7, 1255-1261.

Characteristic Sizes of Life in the Oceans, from Bacteria to Whales

The size of an individual organism is a key trait to characterize its physiology and feeding ecology. Size-based scaling laws may have a limited size range of validity or undergo a transition from one scaling exponent to another at some characteristic size. We collate and review data on size-based scaling laws for resource acquisition, mobility, sensory range, and progeny size for all pelagic marine life, from bacteria to whales. Further, we review and develop simple theoretical arguments for observed scaling laws and the characteristic sizes of a change or breakdown of power laws. We divide life in the ocean into seven major realms based on trophic strategy, physiology, and life history strategy. Such a categorization represents a move away from a taxonomically oriented description toward a trait-based description of life in the oceans. Finally, we discuss life forms that transgress the simple size-based rules and identify unanswered questions.

Trade-offs between objectives for ecosystem management of fisheries

The strategic objectives for fisheries, which are enshrined in international conventions, are to maintain or restore stocks to produce maximum sustainable yield (MSY) and to implement the ecosystem approach, requiring that interactions between species be taken into account and conservation constraints be respected. While the yield and conservation aims are, to some extent, compatible when a fishery for a single species is considered, species interactions entail that MSY for a species depends on the species with which it interacts, and the yield and conservation objectives therefore conflict when an ecosystem approach to fisheries management is required. We applied a conceptual size- and trait-based model to clarify and resolve these issues by determining the fishing pattern that maximizes the total yield of an entire fish community in terms of catch biomass or economic rent under acceptable conservation constraints. Our results indicate that the eradication of large, predatory fish species results in a potential maximum catch at least twice as high as if conservation constraints are imposed. However, such a large catch could only be achieved at a cost of forgone rent; maximum rent extracts less than half of the potential maximum catch mass. When a conservation constraint is applied, catch can be maximized at negligible cost in forgone rent, compared with maximizing rent. Maximization of rent is the objective that comes closest to respecting conservation concerns.

Four types of interference competition and their impacts on the ecology and evolution of size-structured populations and communities

We investigate how four types of interference competition - which alternatively affect foraging, metabolism, survival, and reproduction - impact the ecology and evolution of size-structured populations. Even though all four types of interference competition reduce population biomass, interference competition at intermediate intensity sometimes significantly increases the abundance of adult individuals and the population׳s reproduction rate. We find that foraging and metabolic interference evolutionarily favor smaller maturation size when interference is weak and larger maturation size when interference is strong. The evolutionary response to survival interference and reproductive interference is always larger maturation size. We also investigate how the four types of interference competition impact the evolutionary dynamics and resultant diversity and trophic structure of size-structured communities. Like other types of trait-mediated competition, all four types of interference competition can induce disruptive selection and thus promote initial diversification. Even though foraging interference and reproductive interference are more potent in promoting initial diversification, they catalyze the formation of diverse communities with complex trophic structure only at high levels of interference intensity. By contrast, survival interference does so already at intermediate levels, while reproductive interference can only support relatively smaller communities with simpler trophic structure. Taken together, our results show how the type and intensity of interference competition jointly affect coexistence patterns in structured population models.

mizer: an R package for multispecies, trait-based and community size spectrum ecological modelling

Size spectrum ecological models are representations of a community of individuals which grow and change trophic level. A key emergent feature of these models is the size spectrum; the total abundance of all individuals that scales negatively with size. The models we focus on are designed to capture fish community dynamics useful for assessing the community impacts of fishing.We present mizer, an R package for implementing dynamic size spectrum ecological models of an entire aquatic community subject to fishing. Multiple fishing gears can be defined and fishing mortality can change through time making it possible to simulate a range of exploitation strategies and management options.mizer implements three versions of the size spectrum modelling framework: the community model, where individuals are only characterized by their size; the trait-based model, where individuals are further characterized by their asymptotic size; and the multispecies model where additional trait differences are resolved.A range of plot, community indicator and summary methods are available to inspect the results of the simulations.

A metacommunity perspective on source–sink dynamics and management: the Baltic Sea as a case study

The degree to which metapopulation processes influence fish stock dynamics is a largely unresolved issue in marine science and management, especially for highly mobile species such as Atlantic cod (Gadus morhua) and herring (Clupea harengus). The Baltic Sea comprises a heterogeneous oceanographic environment that structures the spatial and temporal distribution of the dominant species cod, herring, and sprat (Sprattus sprattus). Despite local differences, the stocks are traditionally managed as homogeneous units. Here, we present a metacommunity-perspective on source–sink dynamics of Baltic Sea fish stocks by using a spatially disaggregated statistical food web model. The model is fitted to area-specific time series of multiple abiotic and biotic variables using state-space methods. Our analysis reveals pronounced net fluxes between areas, indicative of source–sink dynamics, as well as area-specific differences in species interactions (i.e., density dependence, competition, and predator–prey) and the degree of fishing and climate impact on survival and recruitment. Furthermore, model simulations show that decreasing exploitation pressure in the source area for cod (without reallocating fishing effort) produces an increase in neighboring sink habitats, but a decline of prey species in response to increased predation. Our approach provides valuable insight concerning metacommunity-structuring of marine fish and may serve as an important tool for implementing sustainable management strategies under the ecosystem approach to marine and fisheries management.

The consequences of balanced harvesting of fish communities

Balanced harvesting, where species or individuals are exploited in accordance with their productivity, has been proposed as a way to minimize the effects of fishing on marine fish communities and ecosystems. This calls for a thorough examination of the consequences balanced harvesting has on fish community structure and yield. We use a size- and trait-based model that resolves individual interactions through competition and predation to compare balanced harvesting with traditional selective harvesting, which protects juvenile fish from fishing. Four different exploitation patterns, generated by combining selective or unselective harvesting with balanced or unbalanced fishing, are compared. We find that unselective balanced fishing, where individuals are exploited in proportion to their productivity, produces a slightly larger total maximum sustainable yield than the other exploitation patterns and, for a given yield, the least change in the relative biomass composition of the fish community. Because fishing reduces competition, predation and cannibalism within the community, the total maximum sustainable yield is achieved at high exploitation rates. The yield from unselective balanced fishing is dominated by small individuals, whereas selective fishing produces a much higher proportion of large individuals in the yield. Although unselective balanced fishing is predicted to produce the highest total maximum sustainable yield and the lowest impact on trophic structure, it is effectively a fishery predominantly targeting small forage fish.

Emerging asymmetric interactions between forage and predator fisheries impose management trade-offs

A size and trait-based marine community model was used to investigate interactions, with potential implications for yields, when a fishery targeting forage fish species (whose main adult diet is zooplankton) co-occurs with a fishery targeting larger-sized predator species. Predicted effects on the size structure of the fish community, growth and recruitment of fishes, and yield from the fisheries were used to identify management trade-offs among the different fisheries. Results showed that moderate fishing on forage fishes imposed only small effects on predator fisheries, whereas predator fisheries could enhance yield from forage fisheries under some circumstances.

A novel small-angle neutron scattering detector geometry. Corrigendum

Errors in the paper by Kanaki, Jackson, Hall-Wilton, Piscitelli, Kirstein & Andersen [J. Appl. Cryst. (2013), 46, 1031–1037] are corrected.

Errors in the paper by Kanaki, Jackson, Hall-Wilton, Piscitelli, Kirstein & Andersen [J. Appl. Cryst. (2013), 46, 1031–1037] are corrected.

Generalization of the classical xyz-polarization analysis technique to out-of-plane and inelastic scattering

The technique of longitudinal ("xyz") polarization analysis has been used successfully for many years to study disordered magnetic materials in thermal and cold neutron diffraction experiments. The technique allows the simultaneous and unambiguous separation of the nuclear, magnetic, and nuclear spin-incoherent contributions to the scattering. The technical advances seen in recent years, such as the availability of polarized (3)He analyzer cells to cover a large detector solid angle, the ability to detect out-of-plane scattering in a multi-detector, and a significant increase of the usable beam divergence, call for a generalization of the method. A general treatment of the formalism for carrying out neutron polarization analysis will be given in this paper, which describes a possible method of usage at a future, modern diffractometer or inelastic spectrometer with large area multi-detector coverage.

A novel small-angle neutron scattering detector geometry

A novel 2π detector geometry for small-angle neutron scattering (SANS) applications is presented and its theoretical performance evaluated. The shape of the detector is inspired by an optimization process based on the properties of the conversion material. Advantages over the detector geometry traditionally used on SANS instruments are discussed.

A novel 2π detector geometry for small-angle neutron scattering (SANS) applications is presented and its theoretical performance evaluated. Such a novel geometry is ideally suited for a SANS instrument at the European Spallation Source (ESS). Motivated by the low availability and high price of ³He, the new concept utilizes gaseous detectors with ¹⁰B as the neutron converter. The shape of the detector is inspired by an optimization process based on the properties of the conversion material. Advantages over the detector geometry traditionally used on SANS instruments are discussed. The angular and time resolutions of the proposed detector concept are shown to satisfy the requirements of the particular SANS instrument.

Simulation of a suite of generic long-pulse neutron instruments to optimize the time structure of the European Spallation Source

We here describe the result of simulations of 15 generic neutron instruments for the long-pulsed European Spallation Source. All instruments have been simulated for 20 different settings of the source time structure, corresponding to pulse lengths between 1 ms and 2 ms; and repetition frequencies between 10 Hz and 25 Hz. The relative change in performance with time structure is given for each instrument, and an unweighted average is calculated. The performance of the instrument suite is proportional to (a) the peak flux and (b) the duty cycle to a power of approximately 0.3. This information is an important input to determining the best accelerator parameters. In addition, we find that in our simple guide systems, most neutrons reaching the sample originate from the central 3-5 cm of the moderator. This result can be used as an input in later optimization of the moderator design. We discuss the relevance and validity of defining a single figure-of-merit for a full facility and compare with evaluations of the individual instrument classes.

Analysing migrations of Atlantic cod Gadus morhua in the north-east Atlantic Ocean: then, now and the future

The application of data storage tags bears the potential for a quantum leap in the research on fish migrations, because not only first-capture and recapture positions are known, but at least theoretically, the migration path during the period at large can be reconstructed. Position, however, cannot be measured directly but has to be estimated using the available data on light, temperature, pressure and salinity. The reconstructed locations based on advanced estimation techniques have been termed geolocations. Examples are discussed which illustrate the applicability of geolocations in individual path descriptions, separation of reproductively isolated populations, timing and areas of spawning, tidal transport and use of protected areas. The examples are based on archival tag data from the North Sea, the Baltic Sea, the Barents Sea and Faroese and Icelandic Waters. Besides presenting the state-of-the-art geolocations for cod Gadus morhua in the north-east Atlantic Ocean, the major aim of this review is to raise awareness of gaps in knowledge and to identify ideas for new research.

Global optimization of an entire neutron guide hall

This paper describes the optimization of an entire neutron guide system, from the moderator to the sample position for several instruments simultaneously, using no more than a desktop computer and a few days of CPU time. This is made possible by merging two relatively advanced computational techniques. Neutron acceptance diagram shading is a fast new method for modelling neutron beams, using an approach based on polygons similar to those featuring in computer games. Optimization algorithms based on swarm intelligence are efficient and reliable ways to maximize numerically calculable figures of merit with many strongly coupled geometry parameters. Recent developments in these methods are described, as well as their combination to optimize the geometry of the H5 beamlines at the Institut Laue–Langevin. The optimization was such that all instruments simultaneously gain as much on-sample flux as possible by taking unused phase space from their neighbours, whilst no instrument suffers any losses in its useful flux.

Food web framework for size-structured populations

We synthesise traditional unstructured food webs, allometric body size scaling, trait-based modelling, and physiologically structured modelling to provide a novel and ecologically relevant tool for size-structured food webs. The framework allows food web models to include ontogenetic growth and life-history omnivory at the individual level by resolving the population structure of each species as a size-spectrum. Each species is characterised by the trait 'size at maturation', and all model parameters are made species independent through scaling with individual body size and size at maturation. Parameter values are determined from cross-species analysis of fish communities as life-history omnivory is widespread in aquatic systems, but may be reparameterised for other systems. An ensemble of food webs is generated and the resulting communities are analysed at four levels of organisation: community level, species level, trait level, and individual level. The model may be solved analytically by assuming that the community spectrum follows a power law. The analytical solution provides a baseline expectation of the results of complex food web simulations, and agrees well with the predictions of the full model on biomass distribution as a function of individual size, biomass distribution as a function of size at maturation, and relation between predator-prey mass ratio of preferred and eaten food. The full model additionally predicts the diversity distribution as a function of size at maturation.

Polarized ³He as a probe for short-range spin-dependent interactions

We have studied the relaxation of a spin-polarized gas in a magnetic field, in the presence of short-range spin-dependent interactions. As a main result we have established a link between the specific properties of the interaction and the dependence of the spin-relaxation rate on the magnitude of the holding magnetic field. This allows us to formulate a new, extremely sensitive method to study (pseudo) magnetic properties at the submillimeter scale, which are difficult to access by other means. The method has been used as a probe for nucleon-nucleon axionlike P, T violating interactions which yields a two-order-of-magnitude improved constraint on the coupling strength (g(s)g(p)) as a function of the force range (λ): g(s)g(p)λ² < 3×10⁻²⁷ m².

Damped trophic cascades driven by fishing in model marine ecosystems

The largest perturbation on upper trophic levels of many marine ecosystems stems from fishing. The reaction of the ecosystem goes beyond the trophic levels directly targeted by the fishery. This reaction has been described either as a change in slope of the overall size spectrum or as a trophic cascade triggered by the removal of top predators. Here we use a novel size- and trait-based model to explore how marine ecosystems might react to perturbations from different types of fishing pressure. The model explicitly resolves the whole life history of fish, from larvae to adults. The results show that fishing does not change the overall slope of the size spectrum, but depletes the largest individuals and induces trophic cascades. A trophic cascade can propagate both up and down in trophic levels driven by a combination of changes in predation mortality and food limitation. The cascade is damped as it comes further away from the perturbed trophic level. Fishing on several trophic levels leads to a disappearance of the signature of the trophic cascade. Differences in fishing patterns among ecosystems might influence whether a trophic cascade is observed.

Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source

The OSIRIS neutron instrument on the ISIS pulsed source now affords the option of high-resolution quasi-elastic and inelastic neutron spectroscopy. In this paper, the performance of OSIRIS is presented, with the spectroscopic characteristics of the instrument being discussed in terms of energy resolution, signal to background ratio and neutron count rate. Recent improvements to the spectrometer are described, in particular the effect of cooling the crystal analysers close to liquid helium temperature to enhance the sensitivity of the instrument. The performance of OSIRIS is also likened to back-scattering, crystal analyser spectrometers at other neutron sources.

Design challenges and performance of nested neutron mirrors for microfocusing on SNAP

Kirkpatrick–Baez (KB) neutron supermirrors can efficiently focus polychromatic neutron beams to micrometre dimensions. The ultimate size is determined mainly by the perfection of the mirrors and by the size of the beam needed to have sufficient experimental signal. Nested or Montel KB mirrors can collect ∼2.6 times more beam than standard sequential KB optics, but require good figure perfection at the edge of one mirror. This paper describes the characterization of the figure errors over the important reflective portions of the two mirrors needed for a Montel focusing pair. The measurements are placed in context with theoretical predictions and are used to predict mirror focusing performance. Strategies to improve on the focusing of this class of optics are suggested and early results from these mirrors installed on the Spallation Neutrons at Pressure (SNAP) Beamline 3 at the Spallation Neutron Source (SNS) at Oak Ridge are presented.

Design and experimental tests of a novel neutron spin analyzer for wide angle spin echo spectrometers

This paper describes the design and experimental tests of a novel neutron spin analyzer optimized for wide angle spin echo spectrometers. The new design is based on nonremanent magnetic supermirrors, which are magnetized by vertical magnetic fields created by NdFeB high field permanent magnets. The solution presented here gives stable performance at moderate costs in contrast to designs invoking remanent supermirrors. In the experimental part of this paper we demonstrate that the new design performs well in terms of polarization, transmission, and that high quality neutron spin echo spectra can be measured.

Species competition: coexistence, exclusion and clustering

We present properties of Lotka-Volterra equations describing ecological competition among a large number of interacting species. First we extend previous stability conditions to the case of a non-homogeneous niche space, i.e. that of a carrying capacity depending on the species trait. Second, we discuss mechanisms leading to species clustering and obtain an analytical solution for a state with a lumped species distribution for a specific instance of the system. We also discuss how realistic ecological interactions may result in different types of competition coefficients.

Some Atlantic cod Gadus morhua in the Baltic Sea visit hypoxic water briefly but often

Individual behaviour of Atlantic cod Gadus morhua in the presence of hypoxic water was measured in situ in the vertically stratified Bornholm Basin of the Baltic Sea. Considering all recaptured individuals, the use of hypoxic habitat was comparable to data derived by traditional survey data, but some G. morhua had migrated towards the centre of the c.100 m deep basin and spent about a third of their time at oxygen saturation <50%, possibly to forage on zoobenthos. Maximal residence time per visit in such hypoxic water was limited to a few hours, allowing for the digestion of consumed prey items in waters with sufficient dissolved oxygen.

Trophic and individual efficiencies of size-structured communities

Individual and trophic efficiencies of size-structured communities are derived from mechanistically based principles at the individual level. The derivations are relevant for communities with a size-based trophic structure, i.e. where trophic level is strongly correlated with individual size as in many aquatic systems. The derivations are used to link Lindeman's trophic theory and trophic theory based on average individuals with explicit individual-level size spectrum theory. The trophic efficiency based on the transfer of mass between trophic levels through predator-prey interactions is demonstrated to be valid only when somatic growth can be ignored. Taking somatic growth into account yields an average individual growth efficiency that is smaller than the trophic efficiency.