Relative impacts of morphological alteration to shorelines and eutrophication on littoral macroinvertebrates in Mediterranean lakes

Development of effective methods for assessing the ecological status of lakes based on littoral benthic fauna has been hampered by the lack of quantitative data on the relative impacts of key pressures on the benthic community. We used variance partitioning at 126 sites belonging to 14 natural Mediterranean lakes to analyze the pure and shared effects of eutrophication, morphological alterations, microhabitat type, lake morphometry and geographic position on the littoral macroinvertebrate community. The spatial arrangement of the sampling sites was responsible for 9.1% of the total variance in littoral benthic community composition, lake morphometry accounted for 4.3% of variation, and microhabitat type accounted for 3.9%. Communities appeared to be affected primarily by morphological alterations to lake shorelines, and their impact was 2.5 times as important as that of eutrophication. The structure of littoral benthic communities was governed by processes acting at several spatial scales from region to lake scale. Thus, several pressures and the various spatial scales at which these act should be taken into account when implementing methods of assessing lake ecological condition based on littoral benthic invertebrates. Region-specific methods for subalpine and volcanic lakes might enhance the validity of assessment of results of morphological alterations and improve management of those water resources

Impacts of existing and planned hydropower dams on river fragmentation in the Balkan Region

The Balkan region has some of the best conserved rivers in Europe, but is also the location of ~3000 planned hydropower dams that are expected to help decarbonise energy production. A conflict between policies that promote renewable hydropower and those that prioritise river conservation has ensued, which can only be resolved with the help of reliable information. Using ground-truthed barrier data, we analysed the extent of current longitudinal river fragmentation in the Balkan region and simulated nine dam construction scenarios that varied depending on the number, location and size of the planned dams. Balkan rivers are currently fragmented by 83,017 barriers and have an average barrier density of 0.33 barriers/km after correcting for barrier underreporting; this is 2.2 times lower than the mean barrier density found across Europe and serves to highlight the relatively unfragmented nature of these rivers. However, our analysis shows that all simulated dam construction scenarios would result in a significant loss of connectivity compared to existing conditions. The largest loss of connectivity (−47 %), measured as reduction in barrier-free length, would occur if all planned dams were built, 20 % of which would impact on protected areas. The smallest loss of connectivity (−8 %) would result if only large dams (>10 MW) were built. In contrast, building only small dams (<10 MW) would cause a 45 % loss of connectivity while only contributing 32 % to future hydropower capacity. Hence, the construction of many small hydropower plants will cause a disproportionately large increase in fragmentation that will not be accompanied by a corresponding increase in hydropower. At present, hydropower development in the Balkan rivers does not require Strategic Environmental Assessment, and does not consider cumulative impacts. We encourage planners and policy makers to explicitly consider trade-offs between gains in hydropower and losses in river connectivity at the river basin scale.Impacts of existing and planned hydropower dams on river fragmentation in the Balkan RegionpublishedVersio

Macroinvertebrate community traits and nitrate removal in stream sediments

1. In-stream nitrate removal capacity may be used as a proxy for the ecosystem service of water quality regulation. It is well known that this natural function is driven by abiotic and biotic factors in running water environments. With regard to biotic drivers, most of the literature focuses on the microbial community influences, but there has been very little emphasis on the relationship with the benthic macroinvertebrate community. Since this community feeds on microbial assemblages (autotrophic and/or heterotrophic biofilms) that live on the streambed and in the hyporheic zone of the river, macroinvertebrates also have the potential to influence nitrate removal via its influences on microbiological processes.2. The objective of this study was to examine the potential relationship between the macroinvertebrate communities and nitrate removal. A dataset of in-stream nitrate removal rates measured in nine-third-order streams was analysed. The simultaneous influences of abiotic (hydromorphological, physical and chemical characteristics) and biotic (biofilm and macroinvertebrate) drivers were examined and together explained 56% of the in-stream nitrate removal variance. An analysis of the independent contributions of each driver showed that abiotic drivers (e.g. ammonium, dissolved organic carbon, temperature and transient zone) contributed 40% of this nitrate removal variance, whereas the macroinvertebrate community contributed 39%.3. The potential relationship between macroinvertebrates and nitrate removal was subsequently explored using trait-based approaches of the macroinvertebrate community. This method allows for the selection of trait modalities assuming a top-down control of microbial communities by macroinvertebrates, with in-stream abiotic conditions correlated with nitrate removal (assuming that environmental conditions affect macroinvertebrate community composition).4. The main trait modalities positively correlated with nitrate removal were scraper (feeding habit), flagstones/boulders/cobbles/pebbles (substrate preference), crawler and interstitial (locomotion) and detritus (food). The main modalities negatively correlated with nitrate removal were silt and mud with microphytes (as substrate preference), and with fine sediment with microorganisms, and dead animals (as food sources). These results agreed with the hypothesis of top-down control and enhanced understanding of the influence of hydromorphological factors on nitrate removal.5. This study highlights the involvement of the macroinvertebrate community in in-stream nitrate processing, and demonstrates the usefulness of applying a functional approach to explain relationships between biodiversity and ecosystem function

Simple large wood structures promote hydromorphological heterogeneity and benthic macroinvertebrate diversity in low-gradient rivers

This work has been carried out within the SMART Joint Doctorate Programme ‘Science for the MAnagement of Rivers and their Tidal systems’ funded by the Erasmus Mundus programme of the European Union

Assessing land use and flood management impacts on ecosystem services in a river landscape (Upper Danube, Germany)

Rivers and floodplains provide many regulating, provisioning and cultural ecosystem services (ES) such as flood risk regulation, crop production or recreation. Intensive use of resources such as hydropower production, construction of detention basins and intensive agriculture substantially change ecosystems and may affect their capacity to provide ES. Legal frameworks such as the European Water Framework Directive, Bird and Habitats Directive and Floods Directive already address various uses and interests. However, management is still sectoral and often potential synergies or trade‐offs between sectors are not considered. The ES concept could support a joint and holistic evaluation of impacts and proactively suggest advantageous options. The river ecosystem service index (RESI) method evaluates the capacity of floodplains to provide ES by using a standardized five‐point scale for 1 km‐floodplain segments based on available spatial data. This scaling allows consistent scoring of all ES and their integration into a single index. The aim of this article is to assess ES impacts of different flood prevention scenarios on a 75 km section of the Danube river corridor in Germany. The RESI method was applied to evaluate scenario effects on 13 ES with the standardized five‐point scale. Synergies and trade‐offs were identified as well as ES bundles and dependencies on land use and connectivity. The ratio of actual and former floodplain has the strongest influence on the total ES provision: the higher the percentage and area of an active floodplain, the higher the sum of ES. The RESI method proved useful to support decision‐making in regional planning.BMBF, 033W024A, ReWaM - Verbundprojekt RESI: River Ecosystem Service Index, Teilprojekt

The role of organisms in hyporheic processes : gaps in current knowledge, needs for future research and applications

Fifty years after the hyporheic zone was first defined (Orghidan, 1959), there are still gaps in the knowledge regarding the role of biodiversity in hyporheic processes. First, some methodological questions remained unanswered regarding the interactions between biodiversity and physical processes, both for the study of habitat characteristics and interactions at different scales. Furthermore, many questions remain to be addressed to help inform our understanding of invertebrate community dynamics, especially regarding the trophic niches of organisms, the functional groups present within sediment, and their temporal changes. Understanding microbial community dynamics would require investigations about their relationship with the physical characteristics of the sediment, their diversity, their relationship with metabolic pathways, their inter- actions with invertebrates, and their response to environmental stress. Another fundamental research question is that of the importance of the hyporheic zone in the global metabolism of the river, which must be explored in relation to organic matter recycling, the effects of disturbances, and the degradation of contaminants. Finally, the application of this knowledge requires the development of methods for the estimation of hydro- logical exchanges, especially for the management of sediment clogging, the optimization of self-purification, and the integration of climate change in environmental policies. The development of descriptors of hyporheic zone health and of new metrology is also crucial to include specific targets in water policies for the long-term management of the system and a clear evaluation of restoration strategies

Effects of Hydrographic Variability on the Spatial, Seasonal and Diel Diving Patterns of Southern Elephant Seals in the Eastern Weddell Sea

Weddell Sea hydrography and circulation is driven by influx of Circumpolar Deep Water (CDW) from the Antarctic Circumpolar Current (ACC) at its eastern margin. Entrainment and upwelling of this high-nutrient, oxygen-depleted water mass within the Weddell Gyre also supports the mesopelagic ecosystem within the gyre and the rich benthic community along the Antarctic shelf. We used Conductivity-Temperature-Depth Satellite Relay Data Loggers (CTD-SRDLs) to examine the importance of hydrographic variability, ice cover and season on the movements and diving behavior of southern elephant seals in the eastern Weddell Sea region during their overwinter feeding trips from Bouvetøya. We developed a model describing diving depth as a function of local time of day to account for diel variation in diving behavior. Seals feeding in pelagic ice-free waters during the summer months displayed clear diel variation, with daytime dives reaching 500-1500 m and night-time targeting of the subsurface temperature and salinity maxima characteristic of CDW around 150–300 meters. This pattern was especially clear in the Weddell Cold and Warm Regimes within the gyre, occurred in the ACC, but was absent at the Dronning Maud Land shelf region where seals fed benthically. Diel variation was almost absent in pelagic feeding areas covered by winter sea ice, where seals targeted deep layers around 500–700 meters. Thus, elephant seals appear to switch between feeding strategies when moving between oceanic regimes or in response to seasonal environmental conditions. While they are on the shelf, they exploit the locally-rich benthic ecosystem, while diel patterns in pelagic waters in summer are probably a response to strong vertical migration patterns within the copepod-based pelagic food web. Behavioral flexibility that permits such switching between different feeding strategies may have important consequences regarding the potential for southern elephant seals to adapt to variability or systematic changes in their environment resulting from climate change

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in $\textit{CHM}$ in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.This work was supported by The National Institute for Health Research England (NIHR) for the NIHR BioResource – Rare Diseases project (grant number RG65966). The Moorfields Eye Hospital cohort of patients and clinical and imaging data were ascertained and collected with the support of grants from the National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital, National Health Service Foundation Trust, and UCL Institute of Ophthalmology, Moorfields Eye Hospital Special Trustees, Moorfields Eye Charity, the Foundation Fighting Blindness (USA), and Retinitis Pigmentosa Fighting Blindness. M.M. is a recipient of an FFB Career Development Award. E.M. is supported by UCLH/UCL NIHR Biomedical Research Centre. F.L.R. and D.G. are supported by Cambridge NIHR Biomedical Research Centre

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe