Drivers and biological effects of mercury and organo-halogenated chemicals on Arctic predators

Pollutants have been identified as one of the major environmental threats to humankind, wildlife and ecosystems, including the Arctic. Organo-halogenated chemicals (OHCs) and mercury (Hg) are transported from anthropogenic sources via long-range transport to the Arctic, where many of these pollutants biomagnify within Arctic food chains, leaving in particular apex predators at the top of food chains vulnerable to potential health effects due to their hazardous properties. From a risk assessment perspective, top predators are valuable sentinels because they integrate chemical exposure across large areas and long time spans and, owing to their position at the top of food chains, reflect pollutant trends and ecosystem fluctuations. Thus, monitoring chemical exposure and understanding its impacts on Arctic predators is crucial for developing science-based recommendations for targeted conservation and management initiatives. The overall objective of the thesis was to assess the exposure of key Arctic marine and terrestrial mammal, bird and fish species to OHCs and Hg as well as their biological effects at the individual and population level. Specifically, we investigated dietary drivers of mercury exposure in two sentinel predator species inhabiting the circumpolar Arctic, namely the Arctic subspecies of the grey wolf (Canis lupus arctos) and the Arctic fox (Vulpes lagopus). In Chapter I, total mercury levels were analysed in the fur of 30 Arctic grey wolves sampled between 1869 – 1998 in Greenland and High Arctic Canada. Diet was evaluated with the help of stable isotope analysis by determining dietary carbon sources (as inferred by δ13C) and trophic level (as inferred by δ15N). As expected, we observed high dietary variation of marine and terrestrial food sources at various trophic positions. Variability in Hg burden in the wolves was significantly driven by biomagnification (δ15N) rather than by carbon source (δ13C) or study site. In Chapter II, various pathogens and Hg levels were evaluated as potential drivers of the Arctic fox population decline during 1970 – 1980 on the distinct, small Mednyi Island belonging to the Russian Commander Islands. We chose a study design that allowed the comparison of Hg fur levels from historical specimens from the Commander Islands representative for the population pre-crash period on Mednyi Island, contemporary Mednyi foxes sampled in 2011, and two unrelated and geographically remote ecotypes represented by inland and coastal Icelandic Arctic fox populations. As expected, Hg levels were significantly higher in foxes inhabiting coastal habitats regardless of geographic location than in those from inland sites and were highest during the pre-crash period in the Mednyi population. This was most likely because the Mednyi population depends solely on marine vertebrates that have been shown to be highly contaminated. Our large-scale health assessment using serological and DNA based pathogen screening techniques suggested a low prevalence of pathogens in contemporary foxes, although it does not allow a proper assessment of the health status of the Mednyi Arctic foxes during or before the crash period. Most likely a complex interplay of stressors explains the high cub mortality observed on Mednyi Island, including high mercury body burden, which renders particularly young foxes vulnerable to infectious diseases. Chapter III evaluates whether fur can be used as a minimally-invasive sampling matrix to reliably determine total Hg levels in soft tissues, specifically in liver and kidney of Arctic foxes. Associations between Hg levels in the fur, liver and kidney of 35 Arctic foxes sampled in 2011-2012 on Iceland were investigated. Observed total Hg concentrations varied considerably among tissues, with liver generally showing higher levels than fur and kidneys, and significant linear and sex-independent relationships based on regressions allowed to reliably extrapolate mercury liver and kidney concentrations from fur levels. Measurements in ecotoxicological studies frequently use different tissues (usually liver), which hinders cross-study comparison. Thus, the derived regression equations improve direct comparison of Hg levels among fur and soft tissues reported for Arctic canids. Chapters I-III show that Arctic wolves from Greenland and High Arctic Canada tend to have relatively low Hg concentrations (< 5 µg g-1 dry weight), whereas coastal Arctic fox populations from Iceland and the Commander Islands had up to 7-fold higher Hg fur levels, while coastal populations had 3-fold higher Hg levels than inland ones. While the health status of the Arctic wolves was most likely not affected, the mercury levels in some of the Arctic foxes exceed putative thresholds for Hg-mediated toxic health effects. Apart from trophic magnification as major driver, the observed inter-population and intra-population variability in Hg levels likely results from a combination of varying ecosystem conditions, changes in emission patterns and biological factors. Although the results of Chapter I-III are limited in terms of conclusive evidence because historic study material and/or sample sizes were scarce and relatively small, respectively, they do provide novel tools and information on temporal and spatial variation in Hg pollution in these understudied Arctic canids. In Chapter IV, exposure levels and health impacts of mercury and OHCs were evaluated in key Arctic marine and terrestrial mammals, birds and fish, using population-specific exposure data published between 2010 and 2019. Various pollutant induced health effects were summarized by each endpoint ranging from molecular to individual and population level effects. We identified quantifiable effects on vitamin metabolism, immune functioning, thyroid and steroid hormone balances, oxidative stress, tissue pathology, and reproduction. On this basis we calculated risk quotients in order to estimate critical body burdens specifically as regard to Hg and polychlorinated biphenyls (PCBs) shown to impair reproduction functions in vertebrates. The outcome was that most Arctic marine mammal species are at no or low risk in terms of health effects or reproductive impairments mediated by Hg or PCB exposure. However, for some species at high marine trophic levels, such as polar bear, narwhal and hooded seal, a segment of the population had body burden indicating a high or severe risk of suffering health effects and reproduction impairments. While bird Hg and PCB concentrations were also above toxicity benchmarks in many areas of the marine environment, terrestrial mammals were not at risk – with the exception of the Arctic foxes from Iceland and Commander Islands analysed in Chapter I – III. Overall, the thesis demonstrates the usefulness of fur samples for monitoring Hg and carbon and nitrogen stable isotopes in Arctic canids. It provides a practical tool for cross-study comparisons of Hg across different tissue types and fur, which will help with interpreting exposure risks of Arctic canids in future studies. It further suggests that absolute exposure to pollutants may be less important than indirect contamination via the feeding ecology and feeding opportunities of canid predators which may in turn affect population health and stability. Although the release of numerous, hazardous OHCs and Hg into the environment have been limited and regulated for a long time, the thesis emphasises that certain Arctic predator species are still highly exposed, which may pose a potential threat to their populations and the integrity of their ecosystems. Since our understanding and assessment methods of the specific risks and chronic impacts of pollutants on wildlife populations are still limited, chemical risk assessment should in future be up-scaled to population level effects. The results of the thesis will complement the existing data that form the basis for science-based recommendations for conservation management and policy measures and were already considered by the Arctic Monitoring and Assessment Program. Finally, to improve the effectiveness of the regulation of the release of pollutants into the environment and to support conservation initiatives for Arctic predators, particularly in view of climate change as a future stressor, further investigations are needed to improve our understanding of the mechanisms and interplay of drivers of pollution and its effects on Arctic wildlife populations and ecosystems

The role of natural science collections in the biomonitoring of environmental contaminants in apex predators in support of the EU's zero pollution ambition

The chemical industry is the leading sector in the EU in terms of added value. However, contaminants pose a major threat and significant costs to the environment and human health. While EU legislation and international conventions aim to reduce this threat, regulators struggle to assess and manage chemical risks, given the vast number of substances involved and the lack of data on exposure and hazards. The European Green Deal sets a ‘zero pollution ambition for a toxic free environment’ by 2050 and the EU Chemicals Strategy calls for increased monitoring of chemicals in the environment. Monitoring of contaminants in biota can, inter alia: provide regulators with early warning of bioaccumulation problems with chemicals of emerging concern; trigger risk assessment of persistent, bioaccumulative and toxic substances; enable risk assessment of chemical mixtures in biota; enable risk assessment of mixtures; and enable assessment of the effectiveness of risk management measures and of chemicals regulations overall. A number of these purposes are to be addressed under the recently launched European Partnership for Risk Assessment of Chemicals (PARC). Apex predators are of particular value to biomonitoring. Securing sufficient data at European scale implies large-scale, long-term monitoring and a steady supply of large numbers of fresh apex predator tissue samples from across Europe. Natural science collections are very well-placed to supply these. Pan-European monitoring requires effective coordination among field organisations, collections and analytical laboratories for the flow of required specimens, processing and storage of specimens and tissue samples, contaminant analyses delivering pan-European data sets, and provision of specimen and population contextual data. Collections are well-placed to coordinate this. The COST Action European Raptor Biomonitoring Facility provides a well-developed model showing how this can work, integrating a European Raptor Biomonitoring Scheme, Specimen Bank and Sampling Programme. Simultaneously, the EU-funded LIFE APEX has demonstrated a range of regulatory applications using cutting-edge analytical techniques. PARC plans to make best use of such sampling and biomonitoring programmes. Collections are poised to play a critical role in supporting PARC objectives and thereby contribute to delivery of the EU’s zero-pollution ambition

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes

BackgroundThe anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production.ResultsThe primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs.ConclusionsThis study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization

Milk microbial composition of Brazilian dairy cows entering the dry period and genomic comparison between Staphylococcus aureus strains susceptible to the bacteriophage vB_SauM-UFV_DC4

Brazil has the second-largest dairy cattle herd in the world, and bovine mastitis still can cause significant losses for dairy farmers. Despite this fact, little information is available about milk microbial composition of Brazilian dairy cows, as well as the potential use of bacteriophages in the control of S. aureus. Here, we investigated milk bacterial composition of 28 Holstein Fresian cows (109 teats), selected in the dry-off period, using 16S rRNA analysis. Furthermore, a representative S. aureus strain (UFV2030RH1) was obtained at drying-off for isolation of a bacteriophage (vB_SauM-UFV_DC4, UFV_DC4) and bacterial genomic comparison purposes. Our outcomes revealed that Staphylococcus was the third most prevalent genus and positively correlated with subclinical mastitis events. As a major finding, genomic analyses showed the presence of adhesive matrix molecules that recognize microbial surface components (MSCRAMM) in UFV2030RH1 and might indicate great biofilm formation capability. A minimum inhibitory concentration (MIC) assay showed that resistance to ampicillin was the highest among the antibiotic tested in S. aureus 3059 and UFV2030RH1, displaying values four and sixteen times greater than MIC resistance breakpoint, respectively. Together, our results suggest that Staphylococcus is highly prevalent in dairy cows at drying-off and the use of the phage UFV_DC4 as a biocontrol agent must be investigated in future studies

Genomic analysis and immune response in a murine mastitis model of vB_EcoM-UFV13, a potential biocontrol agent for use in dairy cows

Bovine mastitis remains the main cause of economic losses for dairy farmers. Mammary pathogenic Escherichia coli (MPEC) is related to an acute mastitis and its treatment is still based on the use of antibiotics. In the era of antimicrobial resistance (AMR), bacterial viruses (bacteriophages) present as an efficient treatment or prophylactic option. However, this makes it essential that its genetic structure, stability and interaction with the host immune system be thoroughly characterized. The present study analyzed a novel, broad host-range anti-mastitis agent, the T4virus vB-EcoM-UFV13 in genomic terms, and its activity against a MPEC strain in an experimental E. coli-induced mastitis mouse model. 4,975 Single Nucleotide Polymorphisms (SNPs) were assigned between vB-EcoM-UFV13 and E. coli phage T4 genomes with high impact on coding sequences (CDS) (37.60%) for virion proteins. Phylogenetic trees and genome analysis supported a recent infection mix between vB-EcoM-UFV13 and Shigella phage Shfl2. After a viral stability evaluation (e.g pH and temperature), intramammary administration (MOI 10) resulted in a 10-fold reduction in bacterial load. Furthermore, pro-inflammatory cytokines, such as IL-6 and TNF-\u3b1, were observed after viral treatment. This work brings the whole characterization and immune response to vB-EcoM-UFV13, a biocontrol candidate for bovine mastitis

Making use of apex predator sample collections: an integrated workflow for quality assured sample processing, analysis and digital sample freezing of archived samples

Using monitoring data from apex predators for chemicals risk assessment can provide important information on bioaccumulating as well as biomagnifying chemicals in food webs. A survey among European institutions involved in chemical risk assessment on their experiences with apex predator data in chemical risk assessment revealed great interest in using such data. However, the respondents indicated that constraints were related to expected high costs, lack of standardisation and harmonised quality criteria for exposure assessment, data access, and regulatory acceptance/application. During the Life APEX project, we demonstrated that European sample collections (i.e. environmental specimen banks (ESBs), research collection (RCs), natural history museums (NHMs)) archive a large variety of biological samples that can be readily used for chemical analysis once appropriate quality assurance/control (QA/QC) measures have been developed and implemented. We therefore issued a second survey on sampling, processing and archiving procedures in European sample collections to derive key quality QA/QC criteria for chemical analysis. The survey revealed great differences in QA/QC measures between ESBs, NHMs and RCs. Whereas basic information such as sampling location, date and biometric data were mostly available across institutions, protocols to accompany the sampling strategy with respect to chemical analysis were only available for ESBs. For RCs, the applied QA/QC measures vary with the respective research question, whereas NHMs are generally less aware of e.g. chemical cross-contamination issues. Based on the survey we derived key indicators for assessing the quality of biota samples that can be easily implemented in online databases. Furthermore, we provide a QA/QC workflow not only for sampling and processing but also for the chemical analysis of biota samples. We focussed on comprehensive analytical techniques such as non-target screening and provided insights into subsequent storage of high-resolution chromatograms in online databases (i.e. digital sample freezing platform) to ultimately support chemicals risk assessment

The importance of in-year seasonal fluctuations for biomonitoring of apex predators: a case study of 14 essential and non-essential elements in the liver of the common buzzard (Buteo buteo) in the United Kingdom

Trace elements are chemical contaminants spread in the environment by anthropogenic activities and threaten wildlife and human health. Many studies have investigated this contamination in apex raptors as sentinel birds. However, there is limited data for long-term biomonitoring of multiple trace elements in raptors. In the present study, we measured the concentrations of 14 essential and non-essential trace elements in the livers of the common buzzard (Buteo buteo) collected in the United Kingdom from 2001 to 2019 and investigated whether concentrations have changed during this period. In addition, we estimated the importance of selected variables for modelling element accumulations in tissues. •Except for cadmium, hepatic concentrations of harmful elements in most buzzards were lower than the biological significance level of each element. Hepatic concentrations of certain elements, including lead, cadmium, and arsenic, varied markedly seasonally within years. Their peak was in late winter and trough in late summer, except copper which showed an opposite seasonal pattern. In addition, lead in the liver consistently increased over time, whereas strontium showed a decreasing trend. Hepatic concentrations of cadmium, mercury, and chromium increased with age, whereas selenium and chromium were influenced by sex. Hepatic concentrations of arsenic and chromium also differed between different regions. •Overall, our samples showed a low risk of harmful effects of most elements compared to the thresholds reported in the literature. Seasonal fluctuation was an important descriptor of exposure, which might be related to the diet of the buzzard, the ecology of their prey, and human activities such as the use of lead shot for hunting. However, elucidating reasons for these observed trends needs further examination, and biomonitoring studies exploring the effects of variables such as age, sex, and seasonality are required

The role of natural science collections in the biomonitoring of environmental contaminants in apex predators in support of the EU's zero pollution ambition

The chemical industry is the leading sector in the EU in terms of added value. However, contaminants pose a major threat and significant costs to the environment and human health. While EU legislation and international conventions aim to reduce this threat, regulators struggle to assess and manage chemical risks, given the vast number of substances involved and the lack of data on exposure and hazards. The European Green Deal sets a 'zero pollution ambition for a toxic free environment' by 2050 and the EU Chemicals Strategy calls for increased monitoring of chemicals in the environment. Monitoring of contaminants in biota can, inter alia: provide regulators with early warning of bioaccumulation problems with chemicals of emerging concern; trigger risk assessment of persistent, bioaccumulative and toxic substances; enable risk assessment of chemical mixtures in biota; enable risk assessment of mixtures; and enable assessment of the effectiveness of risk management measures and of chemicals regulations overall. A number of these purposes are to be addressed under the recently launched European Partnership for Risk Assessment of Chemicals (PARC). Apex predators are of particular value to biomonitoring. Securing sufficient data at European scale implies large-scale, long-term monitoring and a steady supply of large numbers of fresh apex predator tissue samples from across Europe. Natural science collections are very well-placed to supply these. Pan-European monitoring requires effective coordination among field organisations, collections and analytical laboratories for the flow of required specimens, processing and storage of specimens and tissue samples, contaminant analyses delivering pan-European data sets, and provision of specimen and population contextual data. Collections are well-placed to coordinate this. The COST Action European Raptor Biomonitoring Facility provides a well-developed model showing how this can work, integrating a European Raptor Biomonitoring Scheme, Specimen Bank and Sampling Programme. Simultaneously, the EU-funded LIFE APEX has demonstrated a range of regulatory applications using cutting-edge analytical techniques. PARC plans to make best use of such sampling and biomonitoring programmes. Collections are poised to play a critical role in supporting PARC objectives and thereby contribute to delivery of the EU's zero-pollution ambition.Non peer reviewe

Linking landscape composition and biological factors with exposure levels of rodenticides and agrochemicals in avian apex predators from Germany

Intensification of agricultural practices has resulted in a substantial decline of Europe's farmland bird populations. Together with increasing urbanisation, chemical pollution arising from these land uses is a recognised threat to wildlife. Raptors are known to be particularly sensitive to pollutants that biomagnify and are thus frequently used sentinels for pollution in food webs. The current study focussed on anticoagulant rodenticides (ARs) but also considered selected medicinal products (MPs) and frequently used plant protection products (PPPs). We analysed livers of raptor species from agricultural and urban habitats in Germany, namely red kites (MIML; Milvus milvus), northern goshawks (ACGE; Accipiter gentilis) and Eurasian sparrowhawks (ACNI; Accipiter nisus) as well as white-tailed sea eagles (HAAL; Haliaeetus albicilla) and ospreys (PAHA; Pandion haliaetus) to account for potential aquatic exposures. Landscape composition was quantified using geographic information systems. The highest detection of ARs occurred in ACGE (81.3%; n = 48), closely followed by MIML (80.5%; n = 41), HAAL (38.3%; n = 60) and ACNI (13%; n = 23), whereas no ARs were found in PAHA (n = 13). Generalized linear models demonstrated (1) an increased probability for adults to be exposed to ARs with increasing urbanisation, and (2) that species-specific traits were responsible for the extent of exposure. For MPs, we found ibuprofen in 14.9% and fluoroquinolones in 2.3% in individuals that were found dead. Among 30 investigated PPPs, dimethoate (and its metabolite omethoate) and thiacloprid were detected in two MIML each. We assumed that the levels of dimethoate were a consequence of deliberate poisoning. AR and insecticide poisoning were considered to represent a threat to red kites and may ultimately contribute to reported decreased survival rates. Overall, our study suggests that urban raptors are at greatest risk for AR exposure and that exposures may not be limited to terrestrial food webs

Decipher syntrophies within C2-C4 organic acids-degrading anaerobic microbiomes: A multi-omic exploration

In methanogenic ecosystems, carboxylic acid degradation is a crucial process facilitated by specialized bacteria working in syntrophy with methanogens. This study explores the transcriptomic responses in 178 metagenome-assembled genomes upon changes in feeding composition, specifically lactate, butyrate, propionate, and acetate, in four lab-scale bioreactors. Methanothrix soehngenii and Methanoculleus sp. emerged as key biomethanation contributors. Through metatranscriptomics, machine learning-based functional annotation, and flux balance analysis the underlying microbial interactions and dynamics were deciphered. Syntrophomonadaceae and Mesotoga species maintained mutualistic metabolite exchanges with hydrogenotrophic methanogens, degrading primarily butyrate and lactate, respectively. Acetate was mainly consumed by Smithellaceae sp., in competition with M. soehngenii in all reactors. Furthermore, the acetoclastic archaeon exhibited a previously undocumented capability to metabolize lactate, thereby confirming the prevalence of acetotrophic pathway. Transcriptomic profiles revealed an additional layer of complexity, where propionate dismutation and beta-oxidation pathways are interconnected by the exchanges of butyrate between putative syntrophs, including Syntrophomonadaceae and Smithellaceae species. Integrating multi-omics data with genome-scale metabolic modeling enabled the accurate reconstruction of dynamics within the controlled ecosystem. This composite novel approach was applied to the AD system to unveil the intricate relationships operating within the microbiome to promote thriving. Results elucidated the still poorly explored organization of the so-called microbial dark matter