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Trace metal pollution is globally widespread, largely resulting from human activities. Due to the persistence and high toxicity of trace metals, these pollutants can have serious effects across ecosystems. However, few studies have directly assessed the presence and impact of trace metal pollution across ecosystems, specifically across multiple environmental sources and animal taxa. This study was designed to assess the environmental health impacts of trace metal pollution by assessing its extent and possible transfer into wildlife in the areas surrounding two abandoned metalliferous mine complexes in Wales in the UK. Water, sediment, and soil at the mine sites and in areas downstream had notably elevated concentrations of Pb, Zn, and, to a lesser extent, Cd and Cu, when compared to nearby control sites. These high trace metal concentrations were mirrored in the body burdens of aquatic invertebrates collected in the contaminated streams both at, and downstream of, the mines. Wood mice collected in contaminated areas appeared to be able to regulate their Zn and Cu tissue concentrations, but, when compared to wood mice from a nearby control site, they had significantly elevated concentrations of Cd and, particularly, Pb, detected in their kidney, liver, and bone samples. The Pb concentrations found in these tissues correlated strongly with local soil concentrations (kidney: ρ = 0.690; liver: ρ = 0.668, bone: ρ = 0.649), and were potentially indicative of Pb toxicity in between 10 % and 82 % of the rodents sampled at the mine sites and in areas downstream. The high trace metal concentrations found in the environment and in common prey species (invertebrates and rodents) indicates that trace metal pollution can have far-reaching, ecosystem-wide health impacts long after the polluting activity has ceased, and far beyond the originating site of the pollution.

The worldwide demand for vegetable oils is rising. Oilseed rape (Brassica napus) diversifies cereal dominated crop rotations but requires important nitrogen input. Yet, the root organ is offering an untapped opportunity to improve the nitrogen capture in soil. This study evaluates three culture systems in controlled environment, to observe root morphology and to identify root attributes for superior biomass production and nitrogen use. The phenotypic diversity in a panel of 55 modern winter oilseed rape cultivars was screened in response to two divergent nitrate supplies. Upon in vitro and hydroponic cultures, a large variability for root morphologies was observed. Root biomass and morphological traits positively correlated with shoot biomass or leaf area. The activities of high-affinity nitrate transport systems correlated negatively with the leaf area, while the combined high- and low-affinity systems positively with the total root length. The X-ray computed tomography permitted to visualize the root system in pipes filled with soil. The in vitro root phenotype at germination stage was indicative of lateral root deployment in soil-grown plants. This study highlights great genetic potential in oilseed rape, which could be manipulated to optimize crop root characteristics and nitrogen capture with substantial implications for agricultural production.

Abstract Bovine tuberculosis (bTB) is an important animal health and economic problem for the cattle industry and a potential zoonotic threat. Wild badgers (Meles meles) play a role on its epidemiology in some areas of high prevalence in cattle, particularly in the UK and Republic of Ireland and increasingly in parts of mainland Europe. However, little is known about the involvement of badgers in areas on the spatial edge of the cattle epidemic, where increasing prevalence in cattle is seen. Here we report the findings of a study of found-dead (mainly road-killed) badgers in six counties on the edge of the English epidemic of bTB in cattle. The overall prevalence of Mycobacterium tuberculosis complex (MTC) infection detected in the study area was 51/610 (8.3%, 95% CI 6.4–11%) with the county-level prevalence ranging from 15 to 4–5%. The MTC spoligotypes of recovered from badgers and cattle varied: in the northern part of the study area spoligotype SB0129 predominated in both cattle and badgers, but elsewhere there was a much wider range of spoligotypes found in badgers than in cattle, in which infection was mostly with the regional cattle spoligotype. The low prevalence of MTC in badgers in much of the study area, and, relative to in cattle, the lower density of sampling, make firm conclusions difficult to draw. However, with the exception of Cheshire (north-west of the study area), little evidence was found to link the expansion of the bTB epidemic in cattle in England to widespread badger infection.

Summary Here, we describe the development of a method that exploits bacteriophage D29 as a lysis agent for efficient DNA extraction from low numbers of mycobacterial cells. This method (Actiphage®) used in combination with PCR achieved rapid and sensitive (LOD ≤ 10 cell ml−1) detection and identification of viable, pathogenic mycobacteria in blood samples within 6 h. We demonstrate that mycobacteriophage D29 can be used to detect a range of mycobacteria from clinical blood samples including both Mycobacterium tuberculosis complex and Mycobacterium avium subsp. paratuberculosis without the need for culture and confirms our earlier observations that a low‐level bacteraemia is associated with these infections in cattle. In a study of M. bovis‐infected cattle (n = 41), the sensitivity of the Actiphage® method was 95 % (95 % CI; 0.84–0.99) and specificity was 100 % (95% CI; 0.92–1). We further used Actiphage® to demonstrate viable Mycobacterium avium subsp. paratuberculosis is present in the blood of Johne’s infected cattle. This method provides a revolutionary new tool for the study of infections caused by these difficult to grow pathogens.

Current recommendations for the elimination of canine-mediated human rabies focus on mass dog vaccination as the most feasible and cost-effective strategy. However, attempts to control rabies are often combined with canine surgical sterilisation programmes. The added value of sterilisation is widely debated. A systematic review was undertaken to compare the outcomes and impact of vaccination and sterilisation programmes with vaccination only programmes. A systematic search of three electronic databases (CAB Abstracts, Medline and Global Health) and grey literature was performed. From 8696 abstracts found, 5554 unique studies were identified, and 16 studies met the inclusion criteria. Eight described vaccination only programmes and eight described vaccination and sterilisation programmes. Indicators of impact measured were dog bites and/or doses of post-exposure prophylaxis administered; numbers of dog and/or human rabies cases; dog population demographic changes; changes in health and welfare of dogs, and indicators related to human behaviour change. The studies were contextually very diverse, programmes being implemented were complex, and there was variation in measurement and reporting of key indicators. Therefore, it was difficult to compare the two types of intervention, and impossible to make an evaluation of the role of sterilisation, using this evidence. Given the large number of vaccination and sterilisation programmes conducted globally, the lack of studies available for review highlights a gap in data collection or reporting, essential for impact assessment. There are several knowledge gaps concerning the impact of the sterilisation component alone, as well as subsequent effects on rabies transmission and control. Prospective studies comparing the outcomes and impact of the two interventions would be required in order to establish any additional contribution of sterilisation, as well as the underlying mechanisms driving any changes. In the absence of such evidence, the priority for rabies control objectives should be implementation of mass vaccination, as currently recommended by the World Health Organisation.

Parasites have the capacity to affect animal populations by modifying host survival, and it is increasingly recognized that infectious disease can negatively impact biodiversity. Populations of the house sparrow (Passer domesticus) have declined in many European towns and cities, but the causes of these declines remain unclear. We investigated associations between parasite infection and house sparrow demography across suburban London where sparrow abundance has declined by 71% since 1995. Plasmodium relictum infection was found at higher prevalences (averaging 74%) in suburban London house sparrows than previously recorded in any wild bird population in Northern Europe. Survival rates of juvenile and adult sparrows and population growth rate were negatively related to Plasmodium relictum infection intensity. Other parasites were much less prevalent and exhibited no relationship with sparrow survival and no negative relationship with population growth. Low rates of co-infection suggested sparrows were not immunocompromised. Our findings indicate that P. relictum infection may be influencing house sparrow population dynamics in suburban areas. The demographic sensitivity of the house sparrow to P. relictum infection in London might reflect a recent increase in exposure to this parasite.

Orthohantaviruses are globally distributed viruses, associated with rodents and other small mammals. However, data on the circulation of orthohantaviruses within the UK, particularly the UK-endemic Tatenale virus, is sparse. In this study, 531 animals from five rodent species were collected from two locations in northern and central England and screened using a degenerate, pan- orthohantavirus RT-PCR assay. Tatenale virus was detected in a single field vole (Microtus agrestis) from central England and twelve field voles from northern England. Unbiased high-throughput sequencing of the central English strain resulted in the recovery of the complete coding sequence of a novel strain of Tatenale virus, whilst PCR-primer walking of the northern English strain recovered almost complete coding sequence of a previously identified strain. These findings represented the detection of a third lineage of Tatenale virus in the United Kingdom and extended the known geographic distribution of these viruses from northern to central England. Furthermore, the recovery of the complete coding sequence revealed that Tatenale virus was sufficiently related to the recently identified Traemersee virus, to meet the accepted criteria for classification as a single species of orthohantavirus.

Arthropod-borne diseases (ABD) are of increasing interest in veterinary and public health. Eurasian badgers (Meles meles) are known to harbor a wide range of pathogens, but information on their role as ABD reservoirs and their potential epidemiological relevance is limited. This study aimed to investigate the occurrence of arthropod-borne pathogens, specifically piroplasmids and the bacteria Anaplasma phagocytophilum, Ehrlichia canis, Coxiella burnetii, Francisella tularensis and Bartonella spp., in badgers from Great Britain (GB). Blood and heart samples from 18 badgers were examined using PCR and sequencing. A neighbour-joining (NJ) phylogram was also produced. Nine animals tested positive for Babesia sp., while none of the samples was positive for the investigated bacteria. The sequences obtained clustered with other sequences of Babesia sp. from badgers from GB and elsewhere, including China, Hungary, Spain and Italy, showing a widespread distribution of this parasite in badgers. Badger-associated Babesia DNA was also found recently in a wild cat in Bosnia Herzegovina, in a wolf in Italy and in dogs in Hungary. Further investigations are needed to understand the epidemiology of this putative pathogen and its impact on the health of wild and domestic carnivores.

The advent of unbiased metagenomic virus discovery has revolutionized studies of virus biodiversity and evolution. Despite this, our knowledge of the virosphere, including in mammalian species, remains limited. We used unbiased metagenomic sequencing to identify RNA viruses in European field voles and rabbits. Accordingly, we identified a number of novel RNA viruses including astrovirus, rotavirus A, picorna-like virus and a narmovirus (paramyxovirus). In addition, we identified a sobemovirus and a novel luteovirus that likely originated from the rabbit diet. These newly discovered viruses were often divergent from those previously described. The novel astrovirus was most closely related to a virus sampled from the rodent-eating European roller bird (Coracias garrulous). PCR screening revealed that the novel narmovirus in the UK field vole had a prevalence of approximately 4%, and shared common ancestry with other rodent narmoviruses sampled globally. Two novel rotavirus A sequences were detected in a UK field vole and a French rabbit, the latter with a prevalence of 5%. Finally, a highly divergent picorna-like virus found in the gut of the French rabbit virus was only ~35% similar to an arilivirus at the amino acid level, suggesting the presence of a novel viral genus within the Picornaviridae.

Abstract The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex network of over 50 potentially interacting transcriptional activators and repressors, the auxin response factors (ARFs) and Aux/IAAs. Here, we perform a large‐scale analysis of the Aux/IAA‐ARF pathway in the shoot apex of Arabidopsis, where dynamic auxin‐based patterning controls organogenesis. A comprehensive expression map and full interactome uncovered an unexpectedly simple distribution and structure of this pathway in the shoot apex. A mathematical model of the Aux/IAA‐ARF network predicted a strong buffering capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predictions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunction with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin signalling network is essential to create robust patterns at the shoot apex.

Infectious bronchitis virus (IBV) causes a costly respiratory viral disease of chickens. The role of wild birds in the epidemiology of IBV is poorly understood. We detected diverse coronaviruses by PCR in wildfowl and wading birds in England. Sequence analysis showed some viruses to be related to IBV.

During a study to extend our knowledge of the host range and genetic diversity of arenaviruses in Great Britain, 66 of 1,147 rodent blood samples tested for antibody, and 127 of 482 tested by PCR, were found positive. All sequences most closely resembled those of previously identified lymphocytic choriomeningitis virus.

Non-destructive phenotyping of root system architecture can facilitate breeding for root traits that optimize resource acquisition. This protocol describes the construction of a low-cost, high-resolution root phenotyping platform, requiring no sophisticated equipment and adaptable to most laboratory and glasshouse environments. The phenotyping platform consists of germination paper abutting scanners and open-source image acquisition software which allows live imaging of root systems. The phenotyping platform is scalable, modular and inexpensive.

Reliable estimates are lacking of key epizootiologic parameters for plague caused by Yersinia pestis infection in its natural reservoirs. We report results of a 3-year longitudinal study of plague dynamics in populations of a maintenance host, the great gerbil (Rhombomys opimus), in 2 populations in Kazakhstan. Serologic results suggest a mid-summer peak in the abundance of infectious hosts and possible transmission from the reservoir to humans. Decrease in antibody titer to an undetectable level showed no seasonal pattern. Our findings did not support the use of the nitroblue-tetrazolium test characterization of plague-infected hosts. Y. pestis infection reduced survival of otherwise asymptomatic hosts.

Bartonella species are increasingly associated with a range of human and animal diseases. Despite this, we have a poor understanding of the ecology and epidemiology of many species, especially those circulating in wild populations. Previous studies have demonstrated that a diverse range of Bartonella species are abundant in wild rodent populations; little is known regarding their modes of transmission, although both direct and indirect routes have been suggested. In this study, with bank voles (Clethrionomys glareolus) as the host species, we demonstrate that the rodent flea Ctenophthalmus nobilis is a competent vector of at least two Bartonella species, B. grahamii, which has previously been associated with human infection, and B. taylorii. In contrast, no evidence of either horizontal or vertical transmission was seen in bank voles inoculated with B. taylorii maintained in an arthropod-free environment; this finding suggests that fleas may be essential for transmitting some Bartonella species.

We investigated the reservoir role of European wild rodents for Anaplasma phagocytophila using polymerase chain reaction (PCR) analysis of blood collected from individually tagged rodents captured monthly over 2 years. The only tick species observed in the woodland study site was Ixodes trianguliceps, and ruminant reservoir hosts were not known to occur. A. phagocytophila infections were detected in both bank voles and wood mice but were restricted to periods of peak nymphal and adult tick activity. Most PCR-positive rodents were positive only once, suggesting that rodent infections are generally short-lived and that ticks rather than rodents may maintain the infection over winter. Bank voles were more likely to be PCR positive than wood mice, possibly because detectable infections are longer lived in bank voles. This study confirms that woodland rodents can maintain A. phagocytophila in Great Britain in the absence of other reservoir hosts and suggests that I. trianguliceps is a competent vector.

Medicago truncatula contains a family of at least five genes related to AUX1 of Arabidopsis thaliana (termed MtLAX genes for Medicago truncatula-like AUX1 genes). The high sequence similarity between the encoded proteins and AUX1 implies that the MtLAX genes encode auxin import carriers. The MtLAX genes are expressed in roots and other organs, suggesting that they play pleiotropic roles related to auxin uptake. In primary roots, the MtLAX genes are expressed preferentially in the root tips, particularly in the provascular bundles and root caps. During lateral root and nodule development, the genes are expressed in the primordia, particularly in cells that were probably derived from the pericycle. At slightly later stages, the genes are expressed in the regions of the developing organs where the vasculature arises (central position for lateral roots and peripheral region for nodules). These results are consistent with MtLAX being involved in local auxin transport and suggest that auxin is required at two common stages of lateral root and nodule development: development of the primordia and differentiation of the vasculature.

Arcobacter butzleri is considered to be an emerging human foodborne pathogen. The completion of an A. butzleri genome sequence along with microarray analysis of 13 isolates in 2007 revealed a surprising amount of diversity amongst A. butzleri isolates from humans, animals and food. In order to further investigate Arcobacter diversity, 792 faecal samples were collected from cattle on beef and dairy farms in the North West of England. Arcobacter was isolated from 42.5% of the samples and the diversity of the isolates was investigated using multilocus sequence typing. An A. butzleri whole genome sequence, obtained by 454 shotgun sequencing of an isolate from a clinically-healthy dairy cow, showed a number of differences when compared to the genome of a human-derived A. butzleri isolate. PCR-based prevalence assays for variable genes suggested some tentative evidence for source-related distributions. We also found evidence for phenotypic differences relating to growth capabilities between our representative human and cattle isolates. Our genotypic and phenotypic observations suggest that some level of niche adaptation may have occurred in A. butzleri.

X-ray Computed Tomography (CT) is a non-destructive imaging technique originally designed for diagnostic medicine, which was adopted for rhizosphere and soil science applications in the early 1980s. X-ray CT enables researchers to simultaneously visualise and quantify the heterogeneous soil matrix of mineral grains, organic matter, air-filled pores and water-filled pores. Additionally, X-ray CT allows visualisation of plant roots in situ without the need for traditional invasive methods such as root washing. However, one routinely unreported aspect of X-ray CT is the potential effect of X-ray dose on the soil-borne microorganisms and plants in rhizosphere investigations. Here we aimed to i) highlight the need for more consistent reporting of X-ray CT parameters for dose to sample, ii) to provide an overview of previously reported impacts of X-rays on soil microorganisms and plant roots and iii) present new data investigating the response of plant roots and microbial communities to X-ray exposure. Fewer than 5% of the 126 publications included in the literature review contained sufficient information to calculate dose and only 2.4% of the publications explicitly state an estimate of dose received by each sample. We conducted a study involving rice roots growing in soil, observing no significant difference between the numbers of root tips, root volume and total root length in scanned versus unscanned samples. In parallel, a soil microbe experiment scanning samples over a total of 24 weeks observed no significant difference between the scanned and unscanned microbial biomass values. We conclude from the literature review and our own experiments that X-ray CT does not impact plant growth or soil microbial populations when employing a low level of dose (

A survey of fecal samples found enterococcal excretion in 82% of 388 bank voles (Clethrionomys glareolus), 92% of 131 woodmice (Apodemus sylvaticus), and 75% of 165 badgers (Meles meles). Vancomycin-resistant enterococci, all Enterococcus faecium of vanA genotype, were excreted by 4.6% of the woodmice and 1.2% of the badgers, but by none of the bank voles.

Studies of wild animals responding to their native parasites are essential if we are to understand how the immune system functions in the natural environment. While immune defence may bring increased survival, this may come at a resource cost to other physiological traits, including reproduction. Here, we tested the hypothesis that wild common shrews (Sorex araneus), which produce large numbers of offspring during the one breeding season of their short life span, forgo investment in immunity and immune system maintenance, as increased longevity is unlikely to bring further opportunities for mating. In particular, we predicted that adult shrews, with shorter expected lifespans, would not respond as effectively as young animals to infection.We examined haemolymphatic tissues from wild-caught common shrews using light and transmission electron microscopy, applied in conjunction with immunohistology. We compared composition and function of these tissues in shrews of different ages, and the extent and type of inflammatory reactions observed in response to natural parasitic infections. All ages seemed able to mount systemic, specific immune responses, but adult shrews showed some signs of lymphatic tissue exhaustion: lymphatic follicles in adults (n = 21) were both smaller than those in sub-adults (n = 18; Wald = 11.1, p

There have been virtually no studies of ‘who acquires infection from whom’ in wildlife populations, but patterns of transmission within and between different classes of host are likely to be reflected in the spatiotemporal distribution of infection among those host classes. Here, we use a modified form of K-function analysis to test for space–time interaction among bank voles and wood mice infectious with cowpox virus. There was no evidence for transmission between the two host species, supporting previous evidence that they act as separate reservoirs for cowpox. Among wood mice, results suggested that transmission took place primarily between individuals of the opposite sex, raising the possibility that cowpox is sexually transmitted in this species. Results for bank voles indicated that infected females might be a more important source of infection to either sex than are males. The suggestion of different modes of transmission in the two species is itself consistent with the apparent absence of transmission between species. [ABSTRACT FROM AUTHOR]

The possible role of pathogens in rodent population cycles has been largely neglected since Elton's 'epidemic hypothesis' of 1931. To revisit this question, 12 adjacent, cyclic but out-of-phase populations of field voles (Microtus agrestis) in North East England were studied and the initial results are presented here. The prevalences of antibodies to cowpox virus and of clinical signs of Mycobacterium microti infection (vole tuberculosis) showed delayed (not direct) density dependence (with a lag of three to six months). This did not result from changes in population structure, even though there were such changes associated with the different phases of the cycle. The prevalences rose as vole numbers rose, and peaked as numbers declined. The apparent lag in the numerical response of infection prevalence to changes in host abundance is consistent with the hypothesis that diseases, singly or in combination, play a hitherto underestimated role in the dynamics of cyclic populations. [ABSTRACT FROM AUTHOR]