Adaptive management in the context of barriers in European freshwater ecosystems

Many natural habitats have been modified to accommodate for the presence of humans and their needs. Infrastructures – such as hydroelectric dams, weirs, culverts and bridges – are now a common occurrence in streams and rivers across the world. As a result, freshwater ecosystems have been altered extensively, affecting both biological and geomorphological components of the habitats. Many fish species rely on these freshwater ecosystems to complete their lifecycles, and the presence of barriers has been shown to reduce their ability to migrate and sustain healthy populations. In the long run, barriers may have severe repercussions on population densities and dynamics of aquatic animal species. There is currently an urgent need to address these issues with adequate conservation approaches. Adaptive management provides a relevant approach to managing barriers in freshwater ecosystems as it addresses the uncertainties of dealing with natural systems, and accommodates for future unexpected events, though this approach may not be suitable in all instances. A literature search on this subject yielded virtually no output. Hence, we propose a step-by-step guide for implementing adaptive management, which could be used to manage freshwater barriers

Hydrographic features of anguillid spawning areas: potential signposts for migrating eels

Catadromous anguillid eels (genus Anguilla) migrate from their freshwater or estuarine habitats to marine spawning areas. Evidence from satellite tagging studies indicates that tropical and temperate eel species exhibit pronounced diel vertical migrations, from between 150-300 m nighttime depths to 600-800 m during the day. Collections of eggs and larvae of Japanese eels A. japonica suggest they may spawn at these upper nighttime migration depths. How anguillid eels navigate through the ocean and find their spawning areas remains unknown; thus, this study describes the salinity, temperature and geostrophic currents between 0 and 800 m depths within 2 confirmed and 3 hypothetical anguillid spawning areas during likely spawning seasons. Within the 4 ocean gyres in which these spawning areas are located, many eels would encounter subducted 'Subtropical Underwater' water masses during their nighttime ascents that could provide odor plumes as signposts. Four of the spawning areas are located near the western margins of where subducted water masses form cores of elevated salinities (similar to 35.0 to 36.8) around 150 m depths, and one is located near the center of subduction. Low salinity surface waters and fronts are present in some of the areas above the high-salinity cores. Spawning may occur at temperatures between 16 and 24 degrees C where the thermocline locally deepens. At spawning depths, weak westward currents (similar to 0 to 0.1 m s(-1)) prevail, and eastward surface countercurrents are present. Anguillid eels possess acute sensory capabilities to detect these hydrographic features as potential signposts, guiding them to their spawning areas

The emergence of nalidixic acid resistant, multiresistant S. typhimurium DT104 in Denmark. An outbreak in humans traced back to pork

Infection with the zoonotic Salmonella enterica serovar typhimurium DTI04 has been recognised since the beginning of the 90\u27s as a health problem in several industrialised countries. The present investigation demonstrates that results of surveillance of Salmonella infection in food animals, food production and among humans enabled identification of an outbreak of human salmonellosis caused by a nalidixic acid resistant strain of S. typhimurium DTJ 04. The source of infection was traced back to a single slaughterhouse and two pig herds

PP-235 Analysis of clinical features of 70 adult patients with varicella

Analysing the genomic data of pathogens with the help of next-generation sequencing (NGS) is an increasingly important part of disease outbreak investigations and helps guide responses. While this technology has already been successfully employed to elucidate and control disease outbreaks, wider implementation of NGS also depends on its cost-effectiveness. COMPARE - short for 'Collaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks' - is a major project, funded by the European Union, to develop a global platform for sharing and analysing NGS data and thereby improve the rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks. This article introduces the project and presents the results of a review of the literature, composed of previous relevant cost-benefit and cost-effectiveness analyses. The authors also outline the implications for a methodological framework to assess the cost- effectiveness of COMPARE and similar systems

Predation on migrating eels (Anguilla anguilla L.) from the Western Mediterranean

Nineteen female silver European eels (Anguilla anguilla L.) were tagged with satellite tags and released in the Gulf of Lion in the Mediterranean during the migration seasons 2013 and 2015. Sixteen tags transmitted data: five in the Atlantic Ocean, and eleven in the Mediterranean. Of those, 50% of migrating eels were consumed by marine mammals in each year, all in the Mediterranean. The diving behaviour recorded by the tags after the eels were consumed indicated that the most likely predators were deep diving toothed whales. Measurements of the acoustic target strength of the tag showed a negligible effect on the detectability by whale biosonar. Overall, the observed predation rate was similar to that reported for eels escaping into the Atlantic. However, unlike eels in the Atlantic, which are most vulnerable to predators in the first week of escapement as they traverse the continental shelf and before they reach the refuge of the deep ocean, eels escaping from the Mediterranean were predated in deep water, months after release, likely as a consequence of their migration within a relatively narrow and deep corridor in the Alboran Sea. This emphasises the challenge of accounting for natural mortality in management plans for the long-term recovery of the European eel

Oxidative stress and partial migration in brown trout (Salmo trutta)

During migration, animals are typically limited by their endogenous energetic resources that must be allocated to the physiological costs associated with locomotion, as well as avoiding and (or) compensating for oxidative stress. To date, there have been few attempts to understand the role of oxidative status in migration biology, particularly in fish. Semi-anadromous brown trout (Salmo trutta L., 1758) exhibit partial migration, where some individuals smoltify and migrate to sea, and others become stream residents, providing us with an excellent model to investigate the link between oxidative stress and migration. Using the brown trout, we obtained blood samples from juveniles from a coastal stream in Denmark in the fall prior to peak seaward migration that occurs in the spring, and assayed for antioxidant capacity (oxygen radical absorbance capacity) and oxidative stress levels (ratio of oxidized to reduced glutathione). We found that individuals that migrated had higher antioxidant capacity than residents and that future migration date was negatively correlated with both antioxidant capacity and body length in the fall. This study provides the first evidence that oxidative status is associated with migration strategy and timing, months in advance of the actual migration, and provides insight into the role of oxidative status in animal migration. </jats:p

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare in a stepwise approach a total of eight commercially available DNA extraction kits and 16 procedures based on these for three specimen types (human feces, pig feces, and hospital sewage). We assess DNA extraction using spike-in controls and different types of beads for bead beating, facilitating cell lysis. We evaluate DNA concentration, purity, and stability and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate than that in standard protocols. Based on this insight, we designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens. A standard operating procedure is available from https://dx.doi.org/10.6084/m9.figshare.3475406. IMPORTANCE Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an organism (pathogen)-independent language that can be used across sectors, space, and time. Harmonized standards, protocols, and workflows for sample processing and analysis can facilitate the generation of such actionable information. In this study, we assessed several procedures for the isolation of DNA for next-generation sequencing. Our study highlights several important aspects to consider in the design and conduct of sequence-based analysis of microbiomes. We provide a standard operating procedure for the isolation of DNA from a range of biological specimens particularly relevant in clinical diagnostics and epidemiology