Testing the ecosystem service cascade framework for Atlantic salmon

Aligning nature protection with human well-being for the UN Sustainable Development Goals implies that conservation monitoring should indicate the sustainability of ecosystem services (ES). Here we test the value of the ES cascade framework using national, multi-decadal data for an iconic freshwater fish, the Atlantic salmon Salmo salar. For the first time, we assemble all long-term monitoring data for England and Wales along the ES cascade for this species from resource to benefit: juvenile density to measure the biological resource, returning adult numbers to measure potential ES use, and rod catches and angling effort as measures of actual ES use. We aimed to understand how the ES cascade framework reconciled conservation with ES sustainability targets. Only some linkages along the ES cascade could be evidenced: in catchments where juveniles declined, rod catches also generally decreased, but angling effort declined everywhere irrespective of the biological resource trends. We suggest that i) programmes focused on juvenile monitoring provide an early-warning system for ES provision as well as nature conservation, ii) the ES cascade framework can reconcile nature conservation and ES sustainability if monitoring efforts link biological resources fully to the ES, and ES monitoring explicitly relates biological resources to human use

Populations of high-value predators reflect the traits of their prey

The extent to which prey traits combine to influence the abundance of predators is still poorly understood, particularly for mixed predators in sympatry and in aquatic ecosystems. In this study, we characterise prey use and distribution in iconic bird (grey wagtails and Eurasian dippers) and fish species (brown trout and Atlantic salmon) to assess whether prey traits could predict populations of these four riverine predators. Specifically, we hypothesised that: 1) prey key traits would predict predator populations more effectively than 2) diversity of prey traits, 3) the taxonomic abundance or richness of prey (known as traditional or mass-effect types of biodiversity) or 4) the prevailing environmental conditions. Combined predator population sizes were predicted better by a few key traits – specifically those revealing prey habitat use, size and drifting behaviour – than by prey diversity or prey trait diversity or environmental conditions. Our findings demonstrate that the complex relationships between prey assemblages and multiple predator species can be represented mechanistically when the key prey traits that govern encounter and consumption rates are identified. Given their apparent potential to reveal trophic relationships, and to complement more traditional measures of prey abundance, we advocate further development of trait-based approaches in predator–prey research

Do contaminants originating from state-of-the-art treated wastewater impact the ecological quality of surface waters?

Since the 1980s, advances in wastewater treatment technology have led to considerably improved surface water quality in the urban areas of many high income countries. However, trace concentrations of organic wastewater-associated contaminants may still pose a key environmental hazard impairing the ecological quality of surface waters. To identify key impact factors, we analyzed the effects of a wide range of anthropogenic and environmental variables on the aquatic macroinvertebrate community. We assessed ecological water quality at 26 sampling sites in four urban German lowland river systems with a 0–100% load of state-of-the-art biological activated sludge treated wastewater. The chemical analysis suite comprised 12 organic contaminants (five phosphor organic flame retardants, two musk fragrances, bisphenol A, nonylphenol, octylphenol, diethyltoluamide, terbutryn), 16 polycyclic aromatic hydrocarbons, and 12 heavy metals. Non-metric multidimensional scaling identified organic contaminants that are mainly wastewater-associated (i.e., phosphor organic flame retardants, musk fragrances, and diethyltoluamide) as a major impact variable on macroinvertebrate species composition. The structural degradation of streams was also identified as a significant factor. Multiple linear regression models revealed a significant impact of organic contaminants on invertebrate populations, in particular on Ephemeroptera, Plecoptera, and Trichoptera species. Spearman rank correlation analyses confirmed wastewater-associated organic contaminants as the most significant variable negatively impacting the biodiversity of sensitive macroinvertebrate species. In addition to increased aquatic pollution with organic contaminants, a greater wastewater fraction was accompanied by a slight decrease in oxygen concentration and an increase in salinity. This study highlights the importance of reducing the wastewater-associated impact on surface waters. For aquatic ecosystems in urban areas this would lead to: (i) improvement of the ecological integrity, (ii) reduction of biodiversity loss, and (iii) faster achievement of objectives of legislative requirements, e.g., the European Water Framework Directive

A review of assessment methods for river hydromorphology

The work leading to this paper has received funding for the EU’s FP7 under Grant Agreement No. 282656 (REFORM

A unified framework for multi-locus association analysis of both common and rare variants

<p>Abstract</p> <p>Background</p> <p>Common, complex diseases are hypothesized to result from a combination of common and rare genetic variants. We developed a unified framework for the joint association testing of both types of variants. Within the framework, we developed a union-intersection test suitable for genome-wide analysis of single nucleotide polymorphisms (SNPs), candidate gene data, as well as medical sequencing data. The union-intersection test is a composite test of association of genotype frequencies and differential correlation among markers.</p> <p>Results</p> <p>We demonstrated by computer simulation that the false positive error rate was controlled at the expected level. We also demonstrated scenarios in which the multi-locus test was more powerful than traditional single marker analysis. To illustrate use of the union-intersection test with real data, we analyzed a publically available data set of 319,813 autosomal SNPs genotyped for 938 cases of Parkinson disease and 863 neurologically normal controls for which no genome-wide significant results were found by traditional single marker analysis. We also analyzed an independent follow-up sample of 183 cases and 248 controls for replication.</p> <p>Conclusions</p> <p>We identified a single risk haplotype with a directionally consistent effect in both samples in the gene <it>GAK</it>, which is involved in clathrin-mediated membrane trafficking. We also found suggestive evidence that directionally inconsistent marginal effects from single marker analysis appeared to result from risk being driven by different haplotypes in the two samples for the genes <it>SYN3 </it>and <it>NGLY1</it>, which are involved in neurotransmitter release and proteasomal degradation, respectively. These results illustrate the utility of our unified framework for genome-wide association analysis of common, complex diseases.</p

Classification of river morphology and hydrology to support management and restoration

The work leading to this paper has received funding from the European Union’s FP7 programme under Grant Agreement No. 282656 (REFORM

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

Background The control of Clostridium difficile infection is a major international healthcare priority, hindered by a limited understanding of transmission epidemiology for these bacteria. However, transmission studies of bacterial pathogens are rapidly being transformed by the advent of next generation sequencing. Results Here we sequence whole C. difficile genomes from 486 cases arising over four years in Oxfordshire. We show that we can estimate the times back to common ancestors of bacterial lineages with sufficient resolution to distinguish whether direct transmission is plausible or not. Time depths were inferred using a within-host evolutionary rate that we estimated at 1.4 mutations per genome per year based on serially isolated genomes. The subset of plausible transmissions was found to be highly associated with pairs of patients sharing time and space in hospital. Conversely, the large majority of pairs of genomes matched by conventional typing and isolated from patients within a month of each other were too distantly related to be direct transmissions. Conclusions Our results confirm that nosocomial transmission between symptomatic C. difficile cases contributes far less to current rates of infection than has been widely assumed, which clarifies the importance of future research into other transmission routes, such as from asymptomatic carriers. With the costs of DNA sequencing rapidly falling and its use becoming more and more widespread, genomics will revolutionize our understanding of the transmission of bacterial pathogens

Water velocity limits the temporal extent of herbivore effects on aquatic plants in a lowland river

The role of herbivores in regulating aquatic plant dynamics has received growing recognition from researchers and managers. However, the evidence for herbivore impacts on aquatic plants is largely based on short-term exclosure studies conducted within a single plant growing season. Thus, it is unclear how long herbivore impacts on aquatic plant abundance can persist for. We addressed this knowledge gap by testing whether mute swan (Cygnus olor) grazing on lowland river macrophytes could be detected in the following growing season. Furthermore, we investigated the role of seasonal changes in water current speed in limiting the temporal extent of grazing. We found no relationship between swan biomass density in 1 year and aquatic plant cover or biomass in the following spring. No such carry-over effects were detected despite observing high swan biomass densities in the previous year from which we inferred grazing impacts on macrophytes. Seasonal increases in water velocity were associated with reduced grazing pressure as swans abandoned river habitat. Furthermore, our study highlights the role of seasonal changes in water velocity in determining the length of the mute swan grazing season in shallow lowland rivers and thus in limiting the temporal extent of herbivore impacts on aquatic plant abundance

A large multi-country outbreak of monkeypox across 41 countries in the WHO European Region, 7 March to 23 August 2022

Following the report of a non-travel-associated cluster of monkeypox cases by the United Kingdom in May 2022, 41 countries across the WHO European Region have reported 21,098 cases and two deaths by 23 August 2022. Nowcasting suggests a plateauing in case notifications. Most cases (97%) are MSM, with atypical rash-illness presentation. Spread is mainly through close contact during sexual activities. Few cases are reported among women and children. Targeted interventions of at-risk groups are needed to stop further transmission. © 2022 European Centre for Disease Prevention and Control (ECDC). All rights reserved.The authors affiliated with the World Health Organization (WHO) are alone responsible for the views expressed in this publication and they do not necessarily represent the decisions or policies of the WHO. The co-author is a fellow of the ECDC Fellowship Programme, supported financially by the European Centre for Disease Prevention and Control (ECDC). The views and opinions expressed herein do not state or reflect those of ECDC. ECDC is not responsible for the data and information collation and analysis and cannot be held liable for conclusions or opinions drawn

Host Genes Related to Paneth Cells and Xenobiotic Metabolism Are Associated with Shifts in Human Ileum-Associated Microbial Composition

The aim of this study was to integrate human clinical, genotype, mRNA microarray and 16 S rRNA sequence data collected on 84 subjects with ileal Crohn’s disease, ulcerative colitis or control patients without inflammatory bowel diseases in order to interrogate how host-microbial interactions are perturbed in inflammatory bowel diseases (IBD). Ex-vivo ileal mucosal biopsies were collected from the disease unaffected proximal margin of the ileum resected from patients who were undergoing initial intestinal surgery. Both RNA and DNA were extracted from the mucosal biopsy samples. Patients were genotyped for the three major NOD2 variants (Leufs1007, R702W, and G908R) and the ATG16L1T300A variant. Whole human genome mRNA expression profiles were generated using Agilent microarrays. Microbial composition profiles were determined by 454 pyrosequencing of the V3–V5 hypervariable region of the bacterial 16 S rRNA gene. The results of permutation based multivariate analysis of variance and covariance (MANCOVA) support the hypothesis that host mucosal Paneth cell and xenobiotic metabolism genes play an important role in host microbial interactions