Genomic signatures of climate adaptation in bank voles.

Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.

Interactions between common vole and winter rape.

Winter rape is a widespread crop in Europe that provides the common vole with a suitable diet and cover from autumn to late spring (approximately 8 months). This review shows the following: That common vole populations reach a high density in winter rape. Widespread rape fields (large size) provide better support for common vole populations compared to winter cereals. That a high-quality supply from winter rape enables the common vole to extend its reproductive season and successfully overwinter. That the diet of the common vole primarily comprises the green vegetative parts of winter rape. The percentage of weed species in the diet depends on weed coverage in the crop. That the impact of the common vole on winter rape correlates with vole density. That no-tillage farming enhances common vole infestation of winter rape fields, particularly in spring, and is related to damage to adjacent crops. © 2020 Society of Chemical Industry.

Molecular Epidemiology of Hantaviruses in the Czech Republic.

During 2008-2018, we collected samples from rodents and patients throughout the Czech Republic and characterized hantavirus isolates. We detected Dobrava-Belgrade and Puumala orthohantaviruses in patients and Dobrava-Belgrade, Tula, and Seewis orthohantaviruses in rodents. Increased knowledge of eco-epidemiology of hantaviruses will improve awareness among physicians and better outcomes of patients.

Highly prevalent bartonellae and other vector-borne pathogens in small mammal species from the Czech Republic and Germany.

BACKGROUND: Rodents are important reservoirs for zoonotic vector-borne agents. Thus, the distribution of rodents and their vicinity to humans and companion animals may have an important impact on human and animal health. However, the reservoir potential of some rodent genera, e.g. Microtus, has not yet been precisely examined concerning tick-borne pathogens in Central Europe. Therefore, we examined small mammals from Germany and the Czech Republic for the following vector-borne pathogens: Babesia spp., Bartonella spp., Anaplasma phagocytophilum, "Candidatus Neoehrlichia mikurensis" (CNM) and Coxiella burnetii. Spleen DNA from 321 small mammals belonging to four genera, Myodes (n = 78), Apodemus (n = 56), Microtus (n = 149), Sorex (n = 38), collected during 2014 in Germany and the Czech Republic were available for this study. DNA samples were examined for the presence of Babesia and Bartonella DNA by conventional PCR targeting the 18S rRNA gene and the 16S-23S rRNA intergenic spacer region, respectively. For the detection of CNM, A. phagocytophilum and C. burnetii real-time PCR assays were performed. RESULTS: Bartonella spp. DNA was detected in 216 specimens (67.3%) with 102/174 (58.6%) positive in Germany and 114/147 (77.6%) in the Czech Republic. The prevalence in each genus was 44.9% for Myodes, 63.2% for Sorex, 77.2% for Microtus and 75% for Apodemus. Four Bartonella species, i.e. Bartonella sp. N40, B. grahamii, B. taylorii and B. doshiae, as well as uncultured bartonellae, were detected. The Bartonella species diversity was higher in rodents than in shrews. In total, 27/321 (8.4%) small mammals were positive for CNM and 3/321 (0.9%) for A. phagocytophilum (S. coronatus and M. glareolus). All samples were negative for Babesia spp. and Coxiella spp. CONCLUSIONS: While the detected high prevalence for Bartonella in Apodemus and Myodes spp. is confirmatory with previous findings, the prevalence in Microtus spp. was unexpectedly high. This indicates that individuals belonging to this genus may be regarded as potential reservoirs. Interestingly, only Sorex spp. and M. glareolus were positive for A. phagocytophilum in the present study, suggesting a possible importance of the latter for the maintenance of certain A. phagocytophilum strains in nature.

Detection of Francisella tularensis in three vole species in Central Europe.

Francisella tularensis is a zoonotic, gram-negative bacterium that causes tularemia in humans. Depending on its subspecies and the route of transmission, mild to lethal courses have been reported. F. tularensis subsp. holarctica is the only subspecies found in Europe and affects a plenitude of vertebrates including lagomorphs and rodents. Population outbreaks of certain rodent species are likely to be involved in the transmission of this pathogen. This molecular survey aims to evaluate the presence of F. tularensis in small mammals from three Central European countries. Using a real-time polymerase chain reaction, F. tularensis DNA was detected in common voles (Microtus arvalis) from Switzerland and in field voles (Microtus agrestis) and a bank vole (Myodes glareolus) from Germany, but not in any other small mammal species. All common voles from the Czech Republic were negative for F. tularensis DNA. The prevalence in the three vole species varied between 1.3% and 3.0%. In conclusion, Francisella tularensis DNA was detected in three vole species in two of three countries investigated. The observed low prevalence raises questions on the role of voles for the transmission of Francisella tularensis in Central Europe.

Wild rodents and shrews are natural hosts of Staphylococcus aureus.

Laboratory mice are the most commonly used animal model for Staphylococcus aureus infection studies. We have previously shown that laboratory mice from global vendors are frequently colonized with S. aureus. Laboratory mice originate from wild house mice. Hence, we investigated whether wild rodents, including house mice, as well as shrews are naturally colonized with S. aureus and whether S. aureus adapts to the wild animal host. 295 animals of ten different species were caught in different locations over four years (2012-2015) in Germany, France and the Czech Republic. 45 animals were positive for S. aureus (15.3%). Three animals were co-colonized with two different isolates, resulting in 48 S. aureus isolates in total. Positive animals were found in Germany and the Czech Republic in each studied year. The S. aureus isolates belonged to ten different spa types, which grouped into six lineages (clonal complex (CC) 49, CC88, CC130, CC1956, sequence type (ST) 890, ST3033). CC49 isolates were most abundant (17/48, 35.4%), followed by CC1956 (14/48, 29.2%) and ST890 (9/48, 18.8%). The wild animal isolates lacked certain properties that are common among human isolates, e.g., a phage-encoded immune evasion cluster, superantigen genes on mobile genetic elements and antibiotic resistance genes, which suggests long-term adaptation to the wild animal host. One CC130 isolate contained the mecC gene, implying wild rodents might be both reservoir and vector for methicillin-resistant . In conclusion, we demonstrated that wild rodents and shrews are naturally colonized with S. aureus, and that those S. aureus isolates show signs of host adaptation.

Influence of no-tillage versus tillage system on common vole (Microtus arvalis) population density.

BACKGROUND: While the 'no-tillage' management system generally improves soil properties and helps to control arthropod pests, it may also intensify crop infestation by the common vole (Microtus arvalis Pallas). In this study, we evaluated the impact of soil management (no-tillage or tillage), crop and previous crop (winter wheat or winter rape), and season (spring or autumn) on common vole density using data from the Common Vole Monitoring Programme undertaken by the Plant Protection Service of the Czech Republic between 2000 and 2009. RESULTS: Models predicted low mean values of vole infestation across management types, crops, and seasons. The untilled fields hosted significantly more voles than the tilled fields in spring but not in autumn. More common voles were found in winter rape than in winter wheat during both seasons. CONCLUSION: Recent studies suggest that no-tillage management is more profitable than tillage management as a result of its positive impact on soil properties and pest control. During periods of high vole infestation, however, tillage may constitute an alternative strategy for reducing yield losses. © 2017 Society of Chemical Industry.

Phylogenetic analysis of Puumala virus strains from Central Europe highlights the need for a full-genome perspective on hantavirus evolution.

Puumala virus (PUUV), carried by bank voles (Myodes glareolus), is the medically most important hantavirus in Central and Western Europe. In this study, a total of 523 bank voles (408 from Germany, 72 from Slovakia, and 43 from Czech Republic) collected between the years 2007-2012 were analyzed for the presence of hantavirus RNA. Partial PUUV genome segment sequences were obtained from 51 voles. Phylogenetic analyses of all three genome segments showed that the newfound strains cluster with other Central and Western European PUUV strains. The new sequences from Sumava (Bohemian Forest), Czech Republic, are most closely related to the strains from the neighboring Bavarian Forest, a known hantavirus disease outbreak region. Interestingly, the Slovak strains clustered with the sequences from Bohemian and Bavarian Forests only in the M but not S segment analyses. This well-supported topological incongruence suggests a segment reassortment event or, as we analyzed only partial sequences, homologous recombination. Our data highlight the necessity of sequencing all three hantavirus genome segments and of a broader bank vole screening not only in recognized endemic foci but also in regions with no reported human hantavirus disease cases.

Detection of shrew-borne hantavirus in Eurasian pygmy shrew (Sorex minutus) in Central Europe.

Recently, it was found that not only rodents but also shrews are reservoir hosts of hantaviruses. In Central Europe, only Seewis virus, associated with the Eurasian common shrew (Sorex araneus), has been recognized until now. In the present report, tissue samples from shrews belonging to Crocidurinae and Soricinae subfamilies, trapped in Czech Republic, Germany, and Slovakia, were screened for the presence of novel hantaviruses. Three new hantavirus partial L-segment sequences were obtained from pygmy shrews (Sorex minutus) trapped in Czech Republic and Germany. Complete nucleocapsid protein- and glycoprotein precursor-coding S- and M-segment sequences were then determined for the newly recognized hantavirus strains, CZ/Beskydy/412/2010/Sm, CZ/Drahany/420/2010/Sm, and DE/Dürrbach/1912/2009/Sm. Phylogenetic analyses showed that they represent strains of Asikkala virus (ASIV), a novel hantavirus also found in pygmy shrews from Finland. Our study reveals a broad geographic distribution of ASIV across Europe and indicates pygmy shrew as the primary reservoir host. Future studies will have to determine the pathogenic relevance of ASIV.

Rodent damage to natural and replanted mountain forest regeneration.

Impact of small rodents on mountain forest regeneration was studied in National Nature Reserve in the Beskydy Mountains (Czech Republic). A considerable amount of bark damage was found on young trees (20%) in spring after the peak abundance of field voles (Microtus agrestis) in combination with long winter with heavy snowfall. In contrast, little damage to young trees was noted under high densities of bank voles (Myodes glareolus) with a lower snow cover the following winter. The bark of deciduous trees was more attractive to voles (22% damaged) than conifers (8%). Young trees growing in open and grassy localities suffered more damage from voles than those under canopy of forest stands (χ² = 44.04, P < 0.001). Natural regeneration in Nature Reserve was less damaged compared to planted trees (χ² = 55.89, P < 0.001). The main factors influencing the impact of rodent species on tree regeneration were open, grassy habitat conditions, higher abundance of vole species, tree species preferences- and snow-cover condition. Under these conditions, the impact of rodents on forest regeneration can be predicted. Foresters should prefer natural regeneration to the artificial plantings.

Broad geographical distribution and high genetic diversity of shrew-borne Seewis hantavirus in Central Europe.

For a long time hantaviruses were believed to be exclusively rodent-borne pathogens. Recent findings of numerous shrew- and mole-borne hantaviruses raise important questions on their phylogenetic origin. The objective of our study was to prove the presence and distribution of shrew-associated Seewis virus (SWSV) in different Sorex species in Central Europe. Therefore, a total of 353 Sorex araneus, 59 S. minutus, 27 S. coronatus, and one S. alpinus were collected in Germany, the Czech Republic, and Slovakia. Screening by hantavirus-specific L-segment RT-PCR revealed specific amplification products in tissues of 49 out of 353 S. araneus and four out of 59 S. minutus. S-segment sequences were obtained for 45 of the L-segment positive S. araneus and all four L-segment positive S. minutus. Phylogenetic investigation of these sequences from Germany, the Czech Republic, and Slovakia demonstrated their similarity to SWSV sequences from Hungary, Finland, Austria, and other sites in Germany. The low intra-cluster sequence variability and the high inter-cluster divergence suggest a long-term SWSV evolution in isolated Sorex populations. In 28 of the 49 SWSV S-segment sequences, an additional putative open reading frame (ORF) on the opposite strand to the nucleocapsid protein-encoding ORF was identified. This is the first comprehensive sequence analysis of SWSV strains from Germany, the Czech Republic, and Slovakia, indicating its broad geographical distribution and high genetic divergence. Future studies have to prove whether both S. araneus and S. minutus represent SWSV reservoir hosts or spillover infections are responsible for the parallel molecular detection of SWSV in both species.

Tula virus in populations of small terrestrial mammals in a rural landscape.

Over 5 years (2000-2004), populations of small mammals from a rural landscape in southern Moravia (Czech Republic) were investigated for the presence of Tula virus (TULV) antigen using the ELISA set Hantagnost. In total, 1566 individuals from 10 species were examined. The prevalence in the common vole (Microtus arvalis Pallas 1778), the main reservoir of TULV, was 10% (n = 871). The prevalence of TULV antigen increases with its population numbers. The highest number of TULV antigen-positive common voles was found in set-aside plots and winter crops, such as rape and winter wheat. All these habitats are important for common vole overwintering. Older and heavier individuals were more often hantavirus antigen positive. From the other small mammal species, 186 pygmy field mice (Apodemus uralensis Pallas, 1811) were examined, of which 3 were positive, which represents the first hantavirus antigen positive record for this species, and of 195 wood mice (Apodemus sylvaticus Linnaeus, 1758) only 1 was positive. The remaining five rodent species (Apodemus flavicollis Melchior, 1834, Mus musculus Linnaeus, 1758, Micromys minutus Pallas, 1771, Myodes glareolus Schreber, 1780, Microtus subterraneus de Sélys-Longchamps, 1836) and two Soricomorpha (Sorex araneus Linnaeus, 1758, Sorex minutus Linnaeus, 1766) were hantavirus antigen negative.

Age variation in a fluctuating population of the common vole.

We analysed variation in age in a fluctuating population of the common vole ( Microtus arvalis) in southern Moravia, Czech Republic, to test the assumption of the senescence hypothesis that the age of voles increases with increasing population density. Between 1996 and 1998, we monitored the demographic changes by snap-trapping and live-trapping in a field population passing through the increase, peak and decline phase of the population cycle. We used the eye lens mass method to determine the age of snap-trapped animals and those that died in live-traps. The average age of winter males was clearly higher after the peak phase breeding season than before it. No such phase-dependent shift in age, however, was observed in the female component. Male age continued to increase from autumn to spring over the pre-peak winter, and the highest age was in spring of the peak phase year. However, after the peak phase breeding season the highest age was achieved in winter, with the decline phase males during the next spring tending to be younger. The average age of females in spring populations was always lower than in winter populations. The average age of voles from live-traps was always higher than voles from snap-traps, particularly in winter and spring populations, suggesting the presence of senescent animals. Although the density-dependent changes in age are consistent with those observed for other voles, they provide only weak evidence that population cycles in the common vole are accompanied by pronounced shifts in individual age, particularly in female voles.