A review of the processes and effects of droughts and summer floods in rivers and threats due to climate change on current adaptive strategies

Europe is expected to experience a greater frequency of floods and droughts as precipitation and evapotranspiration patterns are modified by climate change in future. Several large scale drought and flooding events have occurred in Europe since 2000. Studies of drought are rare but indicate important impacts on freshwater habitats, water quality, plants and animals, which may have wider consequences for ecosystem functioning. The main factors determining the impacts of droughts and floods are event duration and seasonality of the event. A diverse habitat distribution and the presence of refugia at the reach scale confer the most resilience against droughts and floods. Management measures will also be impacted particularly with regard to riparian zones, channel morphology, flow and floodplain connectivity. However there is a conflict between management actions that target the effects of drought, and those that target floods. This report reviews information on droughts and aseasonal floods (summer floods) published since 2000 with a principal focus on small lowland rivers. Using several recent (post 2000) reviews on these topics, we describe abiotic and biotic effects of droughts and floods, providing recent European examples where possible. We explain the current status of droughts and summer floods in Europe, and where the main sources of data can be found. We highlight the threats posed by these phenomena to some of the most common current adaptive management strategies in place in the EU. To this end we use measures already described within REFRESH under Deliverables 1.1 and 1.2, and we focused solely on adaptive measures relating to riparian zones, channel morphology, flow and floodplain connectivity

Agricultural productivity in past societies: toward an empirically informed model for testing cultural evolutionary hypotheses

Agricultural productivity, and its variation in space and time, plays a fundamental role in many theories of human social evolution. However, we often lack systematic information about the productivity of past agricultural systems on a scale large enough to test these theories properly. The effect of climate on crop yields has received a great deal of attention resulting in a range of empirical and process-based models, yet the focus has primarily been on current or future conditions. In this paper, we argue for a “bottom-up” approach that estimates potential productivity based on information about the agricultural practices and technologies used in past societies. Of key theoretical interest is using this information to estimate the carrying high quality historical and archaeological information about past societies in order to infer the temporal and geographic patterns of change in agricultural productivity and potential. We discuss information we need to collect about past agricultural techniques and practices, and introduce a new databank initiative that we have developed for collating the best available historical and archaeological evidence. A key benefit of our approach lies in making explicit the steps in the estimation of past productivities and carrying capacities, and in being able to assess the effects of different modelling assumptions. This is undoubtedly an ambitious task, yet promises to provide important insights into fundamental aspects of past societies, enabling us to test more rigorously key hypotheses about human socio-cultural evolution

Phosphorus and nitrogen limitation and impairment of headwater streams relative to rivers in Great Britain: a national perspective on eutrophication

This study provides a first national-scale assessment of the nutrient status of British headwater streams within the wider river network, by joint analysis of the national Countryside Survey Headwater Stream and Harmonised River Monitoring Scheme datasets. We apply a novel Nutrient Limitation Assessment methodology to explore the extent to which nutrients may potentially limit primary production in headwater streams and rivers, by coupling ternary assessment of nitrogen (N), phosphorus (P), and carbon (C) depletion, with N:P stoichiometry, and threshold P and N concentrations. P limitation was more commonly seen in the rivers, with greater prevalence of N limitation in the headwater streams. High levels of potential P and N co-limitation were found in the headwater streams, especially the Upland-Low-Alkalinity streams. This suggests that managing both P and N inputs may be needed to minimise risks of degradation of these sensitive headwater stream environments. Although localised nutrient impairment of headwater streams can occur, there were markedly lower rates of P and N impairment of headwater streams relative to downstream rivers at the national scale. Nutrient source contributions, relative to hydrological dilution, increased with catchment scale, corresponding with increases in the extent of agricultural and urban land-use. The estimated nutrient reductions needed to achieve compliance with Water Framework Directive standards, and to reach limiting concentrations, were greatest for the Lowland-High-Alkalinity rivers and streams. Preliminary assessments suggest that reducing P concentrations in the Lowland-High-Alkalinity headwater streams, and N concentrations in the Upland-Low-Alkalinity rivers, might offer greater overall benefits for water-quality remediation at the national scale, relative to the magnitude of nutrient reductions required. This approach could help inform the prioritisation of nutrient remediation, as part of a directional approach to water quality management based on closing the gaps between current and target nutrient concentrations

Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms

Accurate quantification of biodiversity is fundamental to understanding ecosystem function and for environmental assessment. Molecular methods using environmental DNA (eDNA) offer a non-invasive, rapid, and cost-effective alternative to traditional biodiversity assessments, which require high levels of expertise. While eDNA analyses are increasingly being utilized, there remains considerable uncertainty regarding the dynamics of multispecies eDNA, especially in variable systems such as rivers. Here, we utilize four sets of upland stream mesocosms, across an acid–base gradient, to assess the temporal and environmental degradation of multispecies eDNA. Sampling included water column and biofilm sampling over time with eDNA quantified using qPCR. Our findings show that the persistence of lotic multispecies eDNA, sampled from water and biofilm, decays to non-detectable levels within 2 days and that acidic environments accelerate the degradation process. Collectively, the results provide the basis for a predictive framework for the relationship between lotic eDNA degradation dynamics in spatio-temporally dynamic river ecosystems

What works? The influence of changing wastewater treatment type, including tertiary granular activated charcoal, on downstream macroinvertebrate biodiversity over time

This study reviewed the impacts of wastewater on macroinvertebrates over four decades in a UK lowland river. This involved examining changes in chemicals, temperature, flow and macroinvertebrate diversity from the 1970s until 2017 for a wastewater‐dominated river downstream of Swindon in the UK (population about 220,000). When the wastewater treatment process changed from trickling filter to activated sludge in 1991, biological oxygen demand was nearly halved (90%ile 8.1 to 4.6 mg/L), ammonia peaks dropped more than 7‐fold (90%ile 3.9 to 0.53 mg/L) whilst dissolved oxygen climbed consistently above 60% saturation (10%ile went from 49% to 64%) at a sampling point 2 km downstream of the wastewater treatment plant. A sustained increase in the number of macroinvertebrate species was evident from that point. River flow did not change, temperature rose slightly, whilst the major metal concentrations declined steadily over most of the monitoring period. Neither the introduction of phosphate stripping in 1999, nor the use of tertiary granular activated charcoal from 2008 to 2014 had strong positive effects on subsequent macroinvertebrate diversity. That the diversity still had not reached the ideal status by 2016 may be related to the modest habitat quality, agricultural pesticides and the limited recolonization potential in the catchment. The results indicate that urban wastewaters, with their chemical pollutants, are today probably not the biggest threat to the macroinvertebrate diversity of multiple‐stressed lowland rivers in the UK

Protection of Macaques with Diverse MHC Genotypes against a Heterologous SIV by Vaccination with a Deglycosylated Live-Attenuated SIV

HIV vaccine development has been hampered by issues such as undefined correlates of protection and extensive diversity of HIV. We addressed these issues using a previously established SIV-macaque model in which SIV mutants with deletions of multiple gp120 N-glycans function as potent live attenuated vaccines to induce near-sterile immunity against the parental pathogenic SIVmac239. In this study, we investigated the protective efficacy of these mutants against a highly pathogenic heterologous SIVsmE543-3 delivered intravenously to rhesus macaques with diverse MHC genotypes. All 11 vaccinated macaques contained the acute-phase infection with blood viral loads below the level of detection between 4 and 10 weeks postchallenge (pc), following a transient but marginal peak of viral replication at 2 weeks in only half of the challenged animals. In the chronic phase, seven vaccinees contained viral replication for over 80 weeks pc, while four did not. Neutralizing antibodies against challenge virus were not detected. Although overall levels of SIV specific T cell responses did not correlate with containment of acute and chronic viral replication, a critical role of cellular responses in the containment of viral replication was suggested. Emergence of viruses with altered fitness due to recombination between the vaccine and challenge viruses and increased gp120 glycosylation was linked to the failure to control SIV. These results demonstrate the induction of effective protective immune responses in a significant number of animals against heterologous virus by infection with deglycosylated attenuated SIV mutants in macaques with highly diverse MHC background. These findings suggest that broad HIV cross clade protection is possible, even in hosts with diverse genetic backgrounds. In summary, results of this study indicate that deglycosylated live-attenuated vaccines may provide a platform for the elucidation of correlates of protection needed for a successful HIV vaccine against diverse isolates

Taxonomy of prokaryotic viruses : 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Peer reviewe

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale

A Functional Genomic Screen Combined with Time-Lapse Microscopy Uncovers a Novel Set of Genes Involved in Dorsal Closure of Drosophila Embryos

Morphogenesis, the establishment of the animal body, requires the coordinated rearrangement of cells and tissues regulated by a very strictly-determined genetic program. Dorsal closure of the epithelium in the Drosophila melanogaster embryo is one of the best models for such a complex morphogenetic event. To explore the genetic regulation of dorsal closure, we carried out a large-scale RNA interference-based screen in combination with in vivo time-lapse microscopy and identified several genes essential for the closure or affecting its dynamics. One of the novel dorsal closure genes, the small GTPase activator pebble (pbl), was selected for detailed analysis. We show that pbl regulates actin accumulation and protrusion dynamics in the leading edge of the migrating epithelial cells. In addition, pbl affects dorsal closure dynamics by regulating head involution, a morphogenetic process mechanically coupled with dorsal closure. Finally, we provide evidence that pbl is involved in closure of the adult thorax, suggesting its general requirement in epithelial closure processes