ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels

The ERSEM model is one of the most established ecosystem models for the lower trophic levels of the marine food-web in the scientific literature. Since its original development in the early nineties it has evolved significantly from a coastal ecosystem model for the North-Sea to a generic tool for ecosystem simulations from shelf seas to the global ocean. The current model release contains all essential elements for the pelagic and benthic part of the marine ecosystem, including the microbial food-web, the carbonate system and calcification. Its distribution is accompanied by a testing framework enabling the analysis of individual parts of the model. Here we provide a detailed mathematical description of all ERSEM components along with case-studies of mesocosm type simulations, water column implementations and a brief example of a full-scale application for the North-West European shelf. Validation against in situ data demonstrates the capability of the model to represent the marine ecosystem in contrasting environments.

Spatio-temporal Bayesian network models with latent variables for revealing trophic dynamics and functional networks in fisheries ecology

Ecosystems consist of complex dynamic interactions among species and the environment, the understanding of which has implications for predicting the environmental response to changes in climate and biodiversity. However, with the recent adoption of more explorative tools, like Bayesian networks, in predictive ecology, few assumptions can be made about the data and complex, spatially varying interactions can be recovered from collected field data. In this study, we compare Bayesian network modelling approaches accounting for latent effects to reveal species dynamics for 7 geographically and temporally varied areas within the North Sea. We also apply structure learning techniques to identify functional relationships such as prey–predator between trophic groups of species that vary across space and time. We examine if the use of a general hidden variable can reflect overall changes in the trophic dynamics of each spatial system and whether the inclusion of a specific hidden variable can model unmeasured group of species. The general hidden variable appears to capture changes in the variance of different groups of species biomass. Models that include both general and specific hidden variables resulted in identifying similarity with the underlying food web dynamics and modelling spatial unmeasured effect. We predict the biomass of the trophic groups and find that predictive accuracy varies with the models' features and across the different spatial areas thus proposing a model that allows for spatial autocorrelation and two hidden variables. Our proposed model was able to produce novel insights on this ecosystem's dynamics and ecological interactions mainly because we account for the heterogeneous nature of the driving factors within each area and their changes over time. Our findings demonstrate that accounting for additional sources of variation, by combining structure learning from data and experts' knowledge in the model architecture, has the potential for gaining deeper insights into the structure and stability of ecosystems. Finally, we were able to discover meaningful functional networks that were spatially and temporally differentiated with the particular mechanisms varying from trophic associations through interactions with climate and commercial fisheries.

Compound-specific isotope analysis of amino acids: A tool to unravel complex symbiotic trophic relationships

Carbon and nitrogen stable isotope ratios of amino acids (δ13CAA and δ15NAA) have been recently used to unravel trophic relationships in aquatic and terrestrial environments. However, none have studied the specific case of a symbiotic relationship. Here we use the stable isotope ratios of amino acids (AAs) to investigate the link between a scarab larva (Pericoptustruncatus) and its mite guest (Mumulaelaps, Mesostigmata: Laelapidae: Hypoaspidini). Five scenarios for the relationship between larva and mite were proposed and δ13CAA and δ15NAA respective data and patterns helped eliminate those that were inconsistent. The calculated gap of two trophic levels ruled out a parasitic trophic relationship scenario. The trophic relationship between P. truncatus was shown to most likely be commensalistic with the mites feeding on the larva's castings. Alongside this study, a comparison with the stable isotope bulk analysis method was made and demonstrated that the AA method brings a significant refinement to the results by providing a means of determining absolute tropic level without the need for prior knowledge of the isotopic composition of primary source material.

ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels

The European Regional Seas Ecosystem Model (ERSEM) is one of the most established ecosystem models for the lower trophic levels of the marine food web in the scientific literature. Since its original development in the early nineties it has evolved significantly from a coastal ecosystem model for the North Sea to a generic tool for ecosystem simulations from shelf seas to the global ocean. The current model release contains all essential elements for the pelagic and benthic parts of the marine ecosystem, including the microbial food web, the carbonate system, and calcification. Its distribution is accompanied by a testing framework enabling the analysis of individual parts of the model. Here we provide a detailed mathematical description of all ERSEM components along with case studies of mesocosm-type simulations, water column implementations, and a brief example of a full-scale application for the north-western European shelf. Validation against in situ data demonstrates the capability of the model to represent the marine ecosystem in contrasting environments.

Isotopic variation complicates analysis of trophic relations within the fish community of Plußsee: a small, deep, stratifying lake

Analysis of carbon and nitrogen stable isotopes has allowed freshwater ecologists to examine lake food webs in increasing detail. Many such studies have highlighted the existence of separate within-lake pelagic and benthic-littoral food webs but are typically conducted on large (> 10 km2) lakes, whereas the majority of lakes are actually relatively small. We used stable isotope analysis (δ13C & δ15N) to examine trophic interactions between fish and their prey in Plu�see, as an example of a small, stratifying lake, and to determine whether separate pelagic/benthic-littoral food webs could be distinguished in such systems. Our results indicate that the Plu�see food web was complicated, and due to extensive intra-annual isotopic variation in zooplankton (e.g. cladoceran δ13C annual range = 25.6�), it may be impossible to definitively assign consumers from small, eutrophic stratified lakes to pelagic or benthic-littoral food webs. We present evidence that some components of the Plu�see food web (large bream) may be subsidised by carbon of methanogenic origin.

Impairments of hippocampal synaptic plasticity induced by aggregated beta-amyloid (25-35) are dependent on stimulation-protocol and genetic background

The aggregation of beta-amyloid to plaques in the brain is one of the hallmarks of Alzheimer disease (AD). Numerous studies have tried to elucidate to what degree amyloid peptides play a role in the neurodegenerative developments seen in AD. While most studies report an effect of amyloid on neural activity and cognitive abilities of rodents, there have been many inconsistencies in the results. This study investigated to what degree the different genetic backgrounds affect the outcome of beta-amyloid fragment (25-35) on synaptic plasticity in vivo in the rat hippocampus. Two strains, Wistar and Lister hooded rats, were tested. In addition, the effects of a strong (600 stimuli) and a weak stimulation protocol (100 stimuli) on impairments of LTP were analysed. Furthermore, since the state of amyloid aggregation appears to play a role in the induction of toxic processes, it was tested by dual polarisation interferometry to what degree and at what speed beta-amyloid (25-35) can aggregate in vitro. It was found that 100 nmol beta-amyloid (25-35) injected icv did impair LTP in Wistar rats when using the weak but not the strong stimulation protocol (P <0.001). One-hundred nano mole of the reverse sequence amyloid (35-25) had no effect. LTP in Lister Hooded rats was not impaired by amyloid at any stimulation protocol. The aggregation studies showed that amyloid (25-35) aggregated within hours, while amyloid (35-25) did not. These results show that the genetic background and the stimulation protocol are important variables that greatly influence the experimental outcome. The fact that amyloid (25-35) aggregated quickly and showed neurophysiological effects, while amyloid (35-25) did not aggregate and did not show any effects indicates that the state of aggregation plays an important role in the physiological effects.

Recapitulation of embryological programmes in renal fibrosis - The importance of epithelial cell plasticity and developmental genes

Chronic fibrosis represents the final common pathway in progressive renal disease. Myofibroblasts deposit the constituents of renal scar, thus crippling renal function. It has recently emerged that an important source of these pivotal effector cells is the injured renal epithelium. This review concentrates on the process of epithelial-mesenchymal transition (EMT) and its regulation. The role of the developmental gene, gremlin, which is reactivated in adult renal disease, is the subject of particular focus. This member of the cysteine knot protein superfamily is critical to the process of nephrogenesis but quiescent in normal adult kidney. There is increasing evidence that gremlin expression reactivates in diabetic nephropathy, and in the diseased fibrotic kidney per se. Known to antagonize members of the bone morphogenic protein (BMP) family, gremlin may also act downstream of TGF-beta in induction of EMT. An increased understanding of the extracellular modulation of EMT and, in particular, of the gremlin-BMP axis may result in strategies that can halt or reverse the devastating progression of chronic renal fibrosis. Copyright (c) 2006 S. Karger AG, Basel.

Trophic interactions and consequent impacts of the invasive fish Pseudorasbora parva in a native aquatic foodweb: a field investigation in the UK

Introduction of the invasive Asian cyprinid fish Pseudorasbora parva into a 0.3 ha pond in England with a fish assemblage that included Cyprinus carpio, Rutilus rutilus and Scardinius erythrophthalmus resulted in their establishment of a numerically dominant population in only 2 years; density estimates exceeded 60 ind. m(-2) and they comprised > 99% of fish present. Stable isotope analysis (SIA) revealed significant trophic overlap between P. parva, R. rutilus and C. carpio, a shift associated with significantly depressed somatic growth in R. rutilus. Despite these changes, fish community composition remained similar between the ponds. Comparison with SIA values collected from an adjacent pond free of P. parva revealed a simplified food web in P. parva presence, but with an apparent trophic position shift for several fishes, including S. erythrophthalmus which appeared to assimilate energy at a higher trophic level, probably through P. parva consumption. The marked isotopic shifts shown in all taxa in the P. parva invaded pond (C-13-enriched, N-15 depleted) were indicative of a shift to a cyanobacteria-dominated phytoplankton community. These findings provide an increased understanding of the ecological consequences of the ongoing P. parva invasion of European freshwater ecosystems.

Behavioral plasticity allows short-term adjustment to a novel environment

Many species are currently experiencing anthropogenically driven environmental changes. Among these changes, increasing noise levels are specifically a problem for species relying on acoustic communication. Recent evidence suggests that some species adjust their acoustic signals to man-made noise. However, it is unknown whether these changes occur through short-term and reversible adjustments by behavioral plasticity or through long-term adaptations by evolutionary change. Using behavioral observations and playback experiments, we show that male reed buntings (Emberiza schoeniclus) adjusted their songs immediately, singing at a higher minimum frequency and at a lower rate when noise levels were high. Our data showed that these changes in singing behavior were short-term adjustments of signal characteristics resulting from behavioral plasticity, rather than a long-term adaptation. However, more males remained unpaired at a noisy location than at a quiet location throughout the breeding season. Thus, phenotypic plasticity enables individuals to respond to environmental changes, but whether these short-term adjustments are beneficial remains to be seen.