The Vistula river and its riparian zones

Vistula, the main Polish river, runs from the very south to the very north of Poland, draining 54% of its area. It serves as a source of water and at the same time as recipient of sewage. The pollution of the river is high in its upper reaches, where the country is heavily populated and industrialized. The pollution along the river fluctuates with the distribution of urban agglomerations and industry, but decreases towards the Baltic Sea, due to dilution and selfpurification. However, the load of nitrogen and phosphorus to the sea about 20% of the load from all Baltic countries is very high. Up to 50% of this load comes from dispersed sources. Despite of the heavy pollution, life in the river and its valley is thriving. The river, the many old river beds and rich vegetation in this valley are an ecological corridor along the whole country which is important for nature protection (including migrations of birds) and for recreation. A landscape park should be organized in the mist valuable middle course and upper part of low course of the Vistula. The river urgently needs measures to improve its purity: sewage purification plants, protective zones along most tributaries (such a zone along the Vistula itself is essentially sufficient), and improvement of the landscape management (especially agrotechnics) to decrease the load of substances to the Vistula and the Baltic Sea.     

Nitrogen transformations in microenvironments of river beds and riparian zones

The soil of flooded riparian zones, the rhizosphere of riparian plants, biofilms at solid surfaces in the river, and the surface layer of sediments all constitute important environments for the oxidative or reductive transformations of inorganic nitrogen compounds. The exact microzonation and coupling of the processes have recently been studied intensively with ¹⁵N enrichment methods and microsensors for NH₄⁺, NO₂⁻, NO₃⁻, and N₂O. Microsensor analyses of gradients in sediments and biofilms have shown that nitrate production takes place in an aerobic surface zone that has a maximum thickness of a few millimeters in most shallow-water sediments and may be as thin as 100 μm in biofilms from very eutrophic environments. In the anoxic zone, denitrification is also concentrated in a zone of maximum a few millimeters, and typically half of the nitrate produced by nitrification is denitrified while the other half escapes to the water. The supply of nitrate from above is primarily controlled by the oxic layer acting as a diffusion barrier, and therefore denitrification is generally a linear function of the nitrate concentration in the water. The overlying water is thus a much more important source of nitrate for denitrification if the concentration is high. The rate and location of denitrification are also affected by bioturbating animals, benthic microphytes, plants, and bacteria performing dissimilatory nitrate reduction to ammonium (DNRA).     

Managing the natural capital of papyrus within riparian zones of Lake Victoria,Kenya

The harvesting of natural products such as papyrus (Cyperus papyrus L.), whether for subsistence value or for the production of commodities intended for sale at local markets, contributes to the well-being of riparian peoples around Lake Victoria, Kenya. Serious losses of papyrus wetlands across East Africa have been reported, most of which are attributed to increasing anthropogenic stressors. Recent studies have called for restoration of these wetlands, emphasizing the need for sustainable harvesting strategies to be put in place, although few have provided suggestions as to how this might happen in practical terms and, crucially, with the consent and active participation of local communities as key stakeholders. Here we explore the socioeconomic characteristics of livelihoods based on papyrus, presenting data generated from surveys, interviews and group discussions collected at multiple sites within the Nyando river basin, Kenya. Conceptualizing papyrus stands as living stocks of natural capital, we then outline our proposal for maintaining the provisioning services of this species, without compromising the critical ecohydrological functions of these swamps as land–water buffer zones. Finally we suggest how this approach might be adapted for wider dissemination around Lake Victoria and beyond, motivated by what we believe to be the first reported case of successful papyrus restoration by a local community.     

LiDAR derived ecological integrity indicators for riparian zones: Application to the Houille river in Southern Belgium/Northern France

Riparian zones are central landscape features providing several ecosystem services and are exceptionally rich in biodiversity. Despite their relatively low area coverage, riparian zones consequently represent a major concern for land and water resource managers confirmed within several European directives. These directives involve effective multi-scale monitoring to assess their conditions and their ability to carry out their functions. The objective of this research was to develop automated tools to provide from a single aerial LiDAR dataset new mapping tools and keystone riparian zone attributes assessing the ecological integrity of the riparian zone at a network scale (24 km).Different metrics were extracted from the original LiDAR point cloud, notably the Digital Terrain Model and Canopy Height Model rasters, allowing the extraction of riparian zones attributes such as the wetted channel (0.89 m; mean residual) and floodplain extents (6.02 m; mean residual). Different riparian forest characteristics were directly extracted from these layers (patch extent, overhanging character, longitudinal continuity, relative water level, mean and relative standard deviation of tree height). Within the riparian forest, the coniferous stands were distinguished from deciduous and isolated trees, with high accuracy (87.3%, Kappa index).Going further the mapping of the indicators, our study proposed an original approach to study the riparian zone attributes within different buffer width, from local scale (50 m long channel axis reach) to a network scale (ca. 2 km long reaches), using a disaggregation/re-agraggation process. This novel approach, combined to graphical presentations of the results allow natural resource managers to visualise the variation of upstream–downstream attributes and to identify priority action areas.In the case study, results showed a general decrease of the riparian forests when the river crosses built-up areas. They also highlighted the lower flooding frequency of riparian forest patches in habitats areas.Those results showed that LiDAR data can be used to extract indicators of ecological integrity of riparian zones in temperate climate zone. They will enable the assessment of the ecological integrity of riparian zones to be undertaken at the regional scale (13,000 km, completely covered by an aerial LIDAR survey in 2014).     

PredCSF: an integrated feature-based approach for predicting conotoxin superfamily

Conotoxins are small disulfide-rich peptides that are invaluable channel-targeted peptides and target neuronal receptors. They show prospects for being potent pharmaceuticals in the treatment of Alzheimer's disease, Parkinson's disease, and epilepsy. Accurate and fast prediction of conotoxin superfamily is very helpful towards the understanding of its biological and pharmacological functions especially in the post-genomic era. In the present study, we have developed a novel approach called PredCSF for predicting the conotoxin superfamily from the amino acid sequence directly based on fusing different kinds of sequential features by using modified one-versus-rest SVMs. The input features to the PredCSF classifiers are composed of physicochemical properties, evolutionary information, predicted second structure and amino acid composition, where the most important features are further screened by random forest feature selection to improve the prediction performance. The prediction results show that PredCSF can obtain an overall accuracy of 90.65% based on a benchmark dataset constructed from the most recent database, which consists of 4 main conotoxin superfamilies and 1 class of non-conotoxin class. Systematic experiments also show that combing different features is helpful for enhancing the prediction power when dealing with complex biological problems. PredCSF is expected to be a powerful tool for in silico identification of novel conotonxins and is freely available for academic use at http://www.csbio.sjtu.edu.cn/bioinf/PredCSF.     

Ecosystem measures of river health and their response to riparian and catchment degradation

1. Measurements of ecological patterns are often used as primary biological indicators of river health. However, these patterns provide little information about important stream ecosystem processes (e.g. the sources and fate of energy and nutrients). The direct measurement of these processes is considered fundamental to the determination of the health of stream and river ecosystems. 2. In this paper we used two basic approaches to assess stream ecosystem response to catchment disturbance and, particularly, to the loss of riparian vegetation in different forested biomes across Australia. Benthic gross primary production (GPP) and respiration (R₂₄) provided measures of the amounts of organic carbon produced and consumed within the system, respectively. Stable isotope analysis was used to trace the fate of terrestrial and instream sources of organic matter in the aquatic food web. In a focal catchment in SE Queensland, additional measurements were taken of riparian attributes, catchment features and water quality. 3. Baseline measurements of GPP and R₂₄ from undisturbed forest streams provided reference values for healthy streams for comparison with sites where the catchment or riparian vegetation had been disturbed. These values of metabolism were low by world standards in all biomes examined. Preliminary data from the Mary River catchment in SE Queensland indicated that these parameters were sensitive to variations in riparian canopy cover and, to a lesser extent, catchment clearing, and predictive models were developed. The ratio P : R (GPP : R₂₄) was used to determine whether sites were net consumers (P < R) or producers (P > R) of carbon but this was not considered a reliable indicator of stream health on its own. 4. Although forest streams were typically net consumers of carbon (P < < R), stable isotope analysis of metazoan food webs indicated a high dependence on inconspicuous epilithic algae in some biomes. 5. A dramatic decline in the health of forest streams was observed when GPP substantially exceeded R₂₄, especially when instream primary producers shifted from palatable unicellular algae to prolific filamentous green algae and macrophytes. These sources of instream production do not appear to enter aquatic food webs, either directly through grazing or indirectly through a detrital loop. Accumulation of these plants has led to changes in channel morphology, loss of aquatic habitat and often a major decline in water quality in some of the streams studied.     

Mechanism of arsenic carcinogenesis: an integrated approach

Epidemiological evidence shows an association between inorganic arsenic in drinking water and increased risk of skin, lung and bladder cancers. The lack of animal models has hindered mechanistic studies of arsenic carcinogenesis in the past, but some promising new models for these cancers are now available. The various forms of arsenic to which humans are exposed, either directly or via metabolism of inorganic arsenic to various methylated forms, further complicate the issue of mechanism, since these compounds can have different effects, both genotoxic and non-genotoxic. This review will try to integrate all of these issues, with a strong bias toward effects that are produced by environmentally relevant arsenic concentrations.     

Rationale for an integrated approach to genetic epidemiology

Conclusion: Genetic knowledge is now in the public domain and its interpretation by the media and the citizens brings the issues into the public forum of discussion for the necessary ethical, legal and socio-cultural evaluation of its application. Science is being perceived by some as dangerous and as requiring international regulation. Others feel that genetic knowledge will be the breakthrough that will permit medical progress and individual autonomy with regards to personal health and lifestyle choices. The mapping of the human genome has already yielded valuable information on an increasing number of diseases and their variants. Prevailing popular and journalistic archetypes ("imaginaires") used in the media are perceived by the producers as slowing down the possible application of genetic knowledge. The answers to these dilemmas are not readily apparent nor are they prescribed by classical philosophy of medicine. Since genetic knowledge eventually resides with the individual who carries the genes of disease and/or susceptibility, a logical approach to integration of this knowledge at a societal level would seem to reside with individual education and decision-making. The politics of the ensuing social debate could transform the current social contract since an individual's interests need to be balanced against those of his or her immediate family in the sharing of information. The ethical foundations of such a contract requires the genetic education of "Everyone" as a matter of urgent priority. Genetic education should not serve ideological power struggles between the medical establishment and the ethical-legal alliance. Instead, it should ensure the transfer of knowledge to physicians, to patients, to users, to planners, to social science and humanities researchers and to politicians, so that they may make "informed" and free decisions....     

Dynamics of mycorrhizae during development of riparian forests along an unregulated river

In this study, we explore two mycorrhizal groups during development of riparian soils along a freely-flowing river. We provide the first documentation of a shift in abundance between arbuscular mycorrhizae and ectomycorrhizae during floodplain succession. We used a chronosequence spanning 0–70 yr along a river in northwestern Montana, USA, to test the hypothesis that abundance of arbuscular mycorrhizal fungi (AMF) is greatest in early stages of soil development, and abundance of ectomycorrhizal fungi (ECMF) is greatest later in floodplain succession. We also measured the AMF-mediated process of formation of soil aggregates during site development. AMF colonization of the dominant tree (black cottonwood, Populus trichocarpa ) remained low (<5%), while AMF colonization of understory species was high (45–90%), across the chronosequence. Mycorrhizal inoculum potential (MIP) and hyphal length of AMF in soil peaked within the first 13 yr of succession and then declined. No single variable significantly correlated with AMF abundance, but AMF tended to decline as litter and soil organic matter increased. Density of ectomycorrhizal root tips in soil increased linearly throughout the chronosequence, and ectomycorrhizal colonization of cottonwood roots increased rapidly in early stages of succession. These patterns suggest that ECMF are not limited by dispersal, but rather influenced by abundance of host plants. Formation of water stable aggregates increased rapidly during the first third of the chronosequence, which was the period of greatest AMF abundance in the soil. The peak in AMF infectivity and hyphal length during early succession suggests that regular flooding and establishment of new sites promotes AMF abundance in this ecosystem. Regulation of rivers that eliminates creation of new sites may reduce contributions of AMF to riparian areas.     

Managing mosquitoes without destroying wetlands: an eastern Australian approach

Recognising both the importance of intertidal wetlands and their role in mosquito-borne disease we discuss wise management to conserve wetland values and to reduce vector borne disease health risks. First we summarise the mosquito-borne diseases associated with intertidal wetlands in sub-tropical and tropical Australia. We consider the Ramsar Strategic Plan, its reflection in some key Australian statutes and the relationship between environment-focussed legislation and health legislation. This is followed by a brief overview of mosquito control and its impact on human health. Using a salt marsh example of an integrated process, we describe the development of what was, in the 1980s in Australia, a novel method of habitat modification (runnelling) for mosquito control. Runnelling modifies the tidal water flow on salt marshes, reducing mosquito larval numbers and minimising environmental impacts. The approach is related to two of the Ramsar goals (wise use and institutional capacity and effectiveness). We then describe the extension of its rationale to a complex mangrove system. Finally, with a concept model, we consider the convergence between minimal habitat modification for wetland conservation and human health protection using an interdisicplinary approach involving multiple stakeholders.     

Hydrologic effects on riparian vegetation in a boreal river: an experiment testing climate change predictions

Climate change is expected to alter the magnitude and variation of flow in streams and rivers, hence providing new conditions for riverine communities. We evaluated plant ecological responses to climate change by transplanting turfs of riparian vegetation to new elevations in the riparian zone, thus simulating expected changes in water‐level variation, and monitored the results over 6 years. Turfs moved to higher elevations decreased in biomass and increased in species richness, whereas turfs transplanted to lower elevations gained biomass but lost species. Transplanted plant communities responded slowly to the new hydrologic conditions. After 6 years, biomass of transplanted turfs was statistically indistinguishable from target level controls, but species richness and species composition of transplants were intermediate between original and target levels. By using projections of future stream flow according to IPCC climate change scenarios, we predict likely changes to riparian vegetation in boreal rivers. Climate‐driven hydrologic changes are predicted to result in narrower riparian zones along the studied Vindel River in northern Sweden towards the end of the 21st century. Present riparian plant communities are projected to be replaced by terrestrial communities at high elevations as a result of lower‐magnitude spring floods, and by amphibious or aquatic communities at low elevations as a result of higher autumn and winter flows. Changes to riparian vegetation may be larger in other boreal climate regions: snow melt fed spring floods are predicted to disappear in southern parts of the boreal zone, which would result in considerable loss of riparian habitat. Our study emphasizes the importance of long‐term ecological field experiments given that plant communities often respond slowly and in a nonlinear fashion to external pressures.     

Opinion: an integrated approach to classifying neuronal phenotypes

Characterizing the functional phenotypes of neurons is essential for understanding how genotypes can be related to the neural basis of behaviour. Traditional classifications of neurons by single features (such as morphology or firing behaviour) are increasingly inadequate for reflecting functional phenotypes, as they do not integrate functions across different neuronal types. Here, we describe a set of rules for identifying and predicting functional phenotypes that combine morphology, intrinsic ion channel species and their distributions in dendrites, and functional properties. This more comprehensive neuronal classification should be an improvement on traditional classifications for relating genotype to functional phenotype.     

Entangling ancient allotetraploidization in Asian Mitella: an integrated approach for multilocus combinations

The reconstruction of an ancient polyploidization history is often challenging, although it is a crucial step in clarifying the mechanisms underlying the contemporary success and diversity of polyploids. Phylogenetic relationships of duplicated gene pairs of polyploids, with respect to their orthologs in related diploids, have been used to address this problem, but they often result in conflicting topologies among different genes. Asimitellaria is an East Asian endemic tetraploid lineage of perennials (genus Mitella; Saxifragaceae) that has diversified in riparian habitats. Phylogenetic analyses of four nuclear-encoded, single-copy (per haploid) genes GBSSI-A, GBSSI-B, GS-II, and PepCK all supported a single allopolyploid origin of Asimitellaria, but they did not lead to a consensus about which diploid lineage gave rise to each of the Asimitellaria subgenomes. To address this issue, we used an integrated approach, whereby the four gene data sets and an additional nuclear ribosomal external transcribed spacer and internal transcribed spacer (including a 5.8S ribosomal DNA) data set were concatenated in all possible combinations, and the most probable data combination was determined together with the phylogenetic inference. This resulted in relatively robust support for the two closely related North American diploid species as the ancestral lineages of the Asimitellaria subgenomes, suggesting ancient intercontinental migration of the diploid or tetraploid lineages and subsequent tetraploid diversification in the Japanese Archipelago. The present approach enabled sorting out the duplicated genes into their original combinations in their preduplication ancestors under a maximum-likelihood framework, and its extension toward genome sequencing data may help in the reconstruction of ancestral, preduplicated, whole-genome structures.     

Tangled webs: reciprocal flows of invertebrate prey link streams and riparian zones

1. Streams and their adjacent riparian zones are closely linked by reciprocal flows of invertebrate prey. We review characteristics of these prey subsidies and their strong direct and indirect effects on consumers and recipient food webs. 2. Fluxes of terrestrial invertebrates to streams can provide up to half the annual energy budget for drift‐feeding fishes such as salmonids, despite the fact that input occurs principally in summer. Inputs appear highest from closed‐canopy riparian zones with deciduous vegetation and vary markedly with invertebrate phenology and weather. Two field experiments that manipulated this prey subsidy showed that it affected both foraging and local abundance of stream fishes. 3. Emergence of adult insects from streams can constitute a substantial export of benthic production to riparian consumers such as birds, bats, lizards, and spiders, and contributes 25–100% of the energy or carbon to such species. Emergence typically peaks in early summer in the temperate zone, but also provides a low‐level flux from autumn to spring in ice‐free streams. This flux varies with in‐stream productivity, and declines exponentially with distance from the stream edge. Some predators aggregate near streams and forage on these prey during periods of peak emergence, whereas others rely on the lower subsidy from autumn through spring when terrestrial prey are scarce. Several field experiments that manipulated this subsidy showed that it affected the short‐term behaviour, growth, and abundance of terrestrial consumers. 4. Reciprocal prey subsidies also have important indirect effects on both stream and riparian food webs. Theory predicts that allochthonous prey should increase density of subsidised predators, thereby increasing predation on in situ prey and causing a negative indirect effect via apparent competition. However, short‐term experiments have produced either positive or negative indirect effects. These contrasting results may be due to characteristics of the subsidies and individual consumers, but could also result from differences in experimental designs. 5. New study approaches are needed to better determine the direct and indirect effects of reciprocal prey subsidies. Experiments coupled with comparative research will be required to measure their effects on individual consumer fitness and population demographics. Future work should investigate whether reciprocal prey fluxes stabilise linked stream–riparian ecosystems, explore how landscape context affects the magnitude and importance of subsidies, and determine how impacts of human disturbance can propagate between streams and riparian zones via these trophic linkages. Study of these reciprocal connections is helping to define a more holistic perspective of catchments, and has the potential to shape new directions for ecology in general.