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  • 401.
    Wille, Michelle
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Uppsala University.
    Latorre-Margalef, Neus
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Georgia, USA.
    Tolf, Conny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Stallknecht, D. E.
    University of Georgia, USA.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    No evidence for homosubtypic immunity of influenza H3 in Mallards following vaccination in a natural experimental system2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 5, p. 1420-1431Article in journal (Refereed)
    Abstract [en]

    The Mallard (Anas platyrhynchos) is an important reservoir species for influenza A viruses (IAV), and in this host, prevalence and virus diversity are high. Studies have demonstrated the presence of homosubtypic immunity, where individuals are unlikely to be reinfected with the same subtype within an autumn season. Further, evidence for heterosubtypic immunity exists, whereby immune responses specific for one subtype offer partial or complete protection against related HA subtypes. We utilized a natural experimental system to determine whether homo- or heterospecific immunity could be induced following experimental vaccination. Thirty Mallards were vaccinated with an inactivated H3, H6 or a sham vaccine and after seroconversion were exposed to naturally infected wild conspecifics. All ducks were infected within 2days and had both primary and secondary infections. Overall, there was no observable difference between groups; all individuals were infected with H3 and H10 IAV. At the cessation of the experiment, most individuals had anti-NP antibodies and neutralizing antibodies against H10. Not all individuals had H3 neutralizing antibodies. The isolated H3 IAVs revealed genetic dissimilarity to the H3 vaccine strain, specifically substitutions in the vicinity of the receptor-binding site. There was no evidence of vaccine-induced homosubtypic immunity to H3, a likely result of both a poor H3 immune response in the ducks and H3 immune escape. Likewise, there was no observed heterosubtypic protection related to H6 vaccination. This study highlights the need for experimental approaches to assess how exposure to pathogens and resulting immune processes translates to individual and population disease dynamics.

  • 402.
    Wille, Michelle
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Uppsala University.
    Muradrasoli, Shaman
    Uppsala University;Swedish University of Agricultural Sciences.
    Nilsson, Anna
    Uppsala University.
    Jarhult, Josef D.
    Uppsala University.
    High Prevalence and Putative Lineage Maintenance of Avian Coronaviruses in Scandinavian Waterfowl2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3, article id e0150198Article in journal (Refereed)
    Abstract [en]

    Coronaviruses (CoVs) are found in a wide variety of wild and domestic animals, and constitute a risk for zoonotic and emerging infectious disease. In poultry, the genetic diversity, evolution, distribution and taxonomy of some coronaviruses have been well described, but little is known about the features of CoVs in wild birds. In this study we screened 764 samples from 22 avian species of the orders Anseriformes and Charadriiformes in Sweden collected in 2006/2007 for CoV, with an overall CoV prevalence of 18.7%, which is higher than many other wild bird surveys. The highest prevalence was found in the diving duck-smainly Greater Scaup (Aythya marila; 51.5%)-and the dabbling duck Mallard (Anas platyrhynchos; 19.2%). Sequences from two of the Greater Scaup CoV fell into an infrequently detected lineage, shared only with a Tufted Duck (Aythya fuligula) CoV. Coronavirus sequences from Mallards in this study were highly similar to CoV sequences from the sample species and location in 2011, suggesting long-term maintenance in this population. A single Black-headed Gull represented the only positive sample from the order Charadriiformes. Globally, Anas species represent the largest fraction of avian CoV sequences, and there seems to be no host species, geographical or temporal structure. To better understand the eitiology, epidemiology and ecology of these viruses more systematic surveillance of wild birds and subsequent sequencing of detected CoV is imperative.

  • 403.
    Wille, Michelle
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Tolf, Conny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Avril, Alexis
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. CIRAD, Campusinternational de Baillarguet, Montpellier 34398, France.
    Latorre-Margalef, Neus
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wallerström, Sofie
    Karolinska institutet.
    Olsen, Björn
    Uppsala universitet.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Frequency and patterns of reassortment in natural influenza A virus infection in a reservoir host2013In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 443, no 15, p. 150-160Article in journal (Refereed)
    Abstract [en]

    Influenza A viruses (IAV) can dramatically alter both genotype and phenotype at a rapid rate as a product of co-infection and reassortment Avian IAV exhibit high levels of phylogenetic incongruence, suggesting high levels of reassortment in the virus reservoir. Using a natural-experimental system, we reconstructed relationships amongst 92 viruses across 15 subtypes from 10 Mallards in an autumn season. Phylogenetic analyses estimated that 56% of the isolated viruses were reassorted. Network analysis demonstrated different patterns of reassortment and limited exchange of segments between primary and secondary infections. No clear patterns of linkage between segments were found, and patterns within a season were likely the consequence of continued introduction ofnew constellations, high viral load and diversity in the wild bird reservoir, and co-infections. This is the first IAV study to implement multiple tools available for elucidating factors governing reassortment patterns in naturally infected Mallards.

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  • 404.
    Wille, Michelle
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    van Run, Peter
    Erasmus Medical Centre, The Netherlands.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Kuiken, Thijs
    Erasmus Medical Centre, The Netherlands.
    Infected or not: are PCR-positive oropharyngeal swabs indicative of low pathogenic influenza A virus infection in the respiratory tract of Mallard Anas platyrhynchos?2014In: Veterinary research (Print), ISSN 0928-4249, E-ISSN 1297-9716, Vol. 45, p. Article ID: 53-Article in journal (Refereed)
    Abstract [en]

    Detection of influenza virus in oropharyngeal swabs collected during wild bird surveillance is assumed to representrespiratory infection, although intestine is the main site of infection. We tested this assumption by histologicalexamination of the respiratory tract of wild Mallards with virus-positive oropharyngeal swabs. Thirty-two of 125Mallards tested had viral-RNA positive oropharyngeal swabs. The respiratory tracts of four Mallards with the mostvirus were examined in detail by immunohistochemistry. None had detectable virus antigen in the respiratory tract,suggesting it was not infected. An alternative explanation is that the oropharynx was contaminated with virusthrough feeding in surface water or through preening.

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    Wille_2014_VetRes_IHC
  • 405.
    Williams, C. M.
    et al.
    Univ Georgia, USA.
    Dupont, A. M.
    Univ Georgia, USA.
    Loevenich, J.
    Univ Georgia, USA.
    Post, A. F.
    URI, USA.
    Dinasquet, Julie
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Copenhagen, Denmark.
    Yager, P. L.
    Univ Georgia, USA.
    Pelagic microbial heterotrophy in response to a highly productive bloom of Phaeocystis antarctica in the Amundsen Sea Polynya, Antarctica2016In: Elementa: Science of the Anthropocene, E-ISSN 2325-1026, Vol. 4, p. 1-18, article id 000102Article in journal (Refereed)
    Abstract [en]

    Heterotrophic bacteria play a key role in marine carbon cycling, and understanding their activities in polar systems is important for considering climate change impacts there. One goal of the ASPIRE project was to examine the relationship between the phytoplankton bloom and bacterial heterotrophy in the Amundsen Sea Polynya (ASP). Bacterial abundance, production (BP), respiration, growth efficiency, and extracellular enzyme activity (EEA) were compared to nutrient and organic matter inventories, chlorophyll a (Chl a), viral and microzooplankton abundance, and net primary production (NPP). Bacterial production and respiration clearly responded (0.04-4.0 and 10-53 mu g C L-1 d(-1), respectively) to the buildup of a massive Phaeocystis antarctica bloom (Chl a: 0.2-22 mu g L-1), with highest rates observed in the central polynya where Chl a and particulate organic carbon (POC) were greatest. The highest BP rates exceeded those reported for the Ross Sea or any other Antarctic coastal system, yet the BP: NPP ratio (2.1-9.4%) was relatively low. Bacterial respiration was also high, and growth efficiency (2-27%; median = 10%) was similar to oligotrophic systems. Thus, the integrated bacterial carbon demand (0.8-2.8 g C m(-2) d(-1)) was a high fraction (25-128%; median = 43%) of NPP during bloom development. During peak bloom, activity was particle-associated: BP and EEA correlated well with POC, and size fractionation experiments showed that the larger size fraction (> 3 mu m) accounted for a majority (similar to 75%) of the BP. The community was psychrophilic, with a 5x reduction in BP when warmed to 20 degrees C. In deeper waters, respiration remained relatively high, likely fueled by the significant downward particle flux in the region. A highly active, particle-associated, heterotrophic microbial community clearly responded to the extraordinary phytoplankton bloom in the ASP, likely limiting biological pump efficiency during the early season.

  • 406.
    Woksepp, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Medicine and Optometry. Kalmar County Hospital.
    Individualized treatment and control of bacterial infections2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Infectious diseases cause substantial morbidity and mortality, exacerbated by increasing antibiotic resistance. In critically ill patients, recent studies indicate a substantial variability in β-lactam antibiotic levels when standardized dosing is applied. New methods for characterizing nosocomial outbreaks of bacterial infections are needed to limit transmission. The goals of this thesis were to investigate new strategies towards individualized treatment and control of bacterial infections. 

    In Paper I we confirmed high variability in β-lactam antibiotic levels among intensive care unit (ICU) patients from southeastern Sweden, where 45 % failed to reach treatment targets (100 % fT>MIC). Augmented renal clearance and establishing the minimum inhibitory concentration of the bacteria were important for evaluating the risk of not attaining adequate drug levels. In Paper II a rapid ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method for simultaneous quantification of 11 commonly used antibiotics was developed and tested in clinical samples. Performance goals (CV<15%) were reached. A microbiological method for quantification of β-lactam antibiotics in serum was developed in Paper III. The method could be important for hospitals without access to an LC-MS method. Paper IV and Paper V investigated ligation-mediated qPCR with high resolution melt analysis (LMqPCR HRMA), for transmission investigation of extended spectrum β-lactamase (ESBL)-producing E. coli and other common bacterial pathogens. Results comparable to the reference method (PFGE) could be achieved within one day in a closed system and confirmed a nosocomial outbreak in Kalmar County. In Paper VI whole genome sequencing followed by bioinformatic analysis resolved transmission links within a nosocomial outbreak due to improved discriminatory power compared to LMqPCR HRMA.

    The high proportion of ICU patients with insufficient β-lactam drug levels emphasizes the need for individualized treatment by therapeutic drug monitoring (TDM). TDM is enabled by a highly sensitive method, such as UPLC-MS/MS, but if unavailable, also by a microbial method. Molecular typing methods used for transmission investigation can detect nosocomial outbreaks. LMqPCR HRMA can be used for screening purposes. For enhanced resolution, whole genome sequencing should be used, but always together with a rigorous epidemiological investigation. 

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  • 407.
    Woksepp, Hanna
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Medicine and Optometry.
    Ryberg, Anna
    Linköping University.
    Billström, Hanna
    Publ Hlth Agcy Sweden, Solna, Sweden.
    Hallgren, Anita
    Linköping University.
    Nilsson, Lennart E.
    Linköping University.
    Marklund, Britt-Inger
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Olsson-Liljequist, Barbro
    Publ Hlth Agcy Sweden, Solna, Sweden.
    Schön, Thomas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Medicine and Optometry. Kalmar County Hospital ; Linköping university.
    Evaluation of High-Resolution Melting Curve Analysis of Ligation-Mediated Real-Time PCR, a Rapid Method for Epidemiological Typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) Pathogens2014In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 52, no 12, p. 4339-4342Article in journal (Refereed)
    Abstract [en]

    A single-tube method, ligation-mediated real-time PCR high-resolution melt analysis (LMqPCR HRMA), was modified for the rapid typing of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. A 97% agreement (60/62 isolates) was achieved in comparison to pulsed-field gel electrophoresis (PFGE) results, which indicates that LMqPCR HRMA is a rapid and accurate screening tool for monitoring nosocomial outbreaks.

  • 408.
    Wouters, Johanna
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Hetrocystous cyanobacteria living within symbiosomes: genetic and physiological aspects2005Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    The objective of the thesis was to get a deeper genetic and physiological insight into the two heterocystous cyanobacterial species known today to live within symbiosomes: the marine cyanobacterium Richelia and the terrestrial cyanobacterium Nostoc. Symbiosomes are organelle-like structures formed by algal and plant hosts that accommodate symbiotic microbes inside their cellular compartment. Both cyanobacterial species are contained in photosynthesizing hosts, however while Richelia forms a symbioses with unicellular diatoms (algae), Nostoc is hosted by multi-cellular higher plants, among them species of the angiosperm genus Gunnera. Special emphasis was on the Nostoc-angiosperm symbiosis as it can be reconstituted in vitro. Phylogenetic analysis using the hetR gene showed Richelia and Nostoc to be separate lineages in the cyanobacterial genetic radiation, hence, symbiosome structures in conjunction with heterocystous cyanobacteria have evolved at least twice. In contrast to the Nostoc-angiosperm symbiosis, the Richelia-diatom symbiosis has a distinct species to host specificity and is possibly evolving towards a permanent organelle. Similar to Richelia, Nostoc is known as epiphytic or endophytic on its host, Nostoc is in addition occurring as free-living, it is speculated that the epiphytic character is a key to how cyanobiont symbiosomes may have evolved. Although the genetic cyanobiont specificity is lower and the genetic diversity is higher in the Nostoc-angiosperm symbiosis, the isolation of the infection process expressed cgt gene shows that there are regions in the Nostoc genome that are, although not unique to symbiosis forming strain, regions that are typical for symbiosis forming strains. Hexoses are shown to be carbohydrates that induce cellular responses such as heterocyst differentiation and nitrogen fixation in the symbiotically competent Nostoc PCC 9229 when contained in darkness. The data suggest that a hexose-type compound is likely to be supplied by the angiosperm host to the cyanobiont living in darkness in return for the fixed nitrogen. Other carbohydrates were shown to support cell survival. Two key metabolic genes, coding for the enzymes, sucrose synthase and glutamine synthetase were isolaled from the host: Gunnera, neither gene showed an altered expression pattern by the presence of Nostoc inside the tissue. It is speculated that once the Nostoc symbiosome is established, Nostoc is perceived as a pseudo-plastid by its host and that nitrogen fixation and other cellular processes are intimately controlled by Gunnera. This is possible as Nostoc and plastids are genetically related and cyanobacterial genes and metabolic pathways are present in all plants.

  • 409.
    Wouters, Johanna
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Bergman, Birgitta
    Janson, Sven
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Cloning and expression of a putative cyclodextrine glycosyltransferase from the symbiotically competet cyanobacteruium Nostoc sp. PCC 92292003In: FEMS Microbioloy Letters, ISSN 0378-1097, Vol. 219, no 2, p. 181-185Article in journal (Refereed)
    Abstract [en]

    A polymerase chain reaction-based method was used to isolate a Nostoc sp. PCC 9229 cDNA from infected glands of Gunnera chilensis. The complete gene sequence was isolated from a genomic Nostoc sp. PCC 9229 library. Sequence analysis showed 84% amino acid similarity to a putative cyclodextrin glycosyltransferase from Nostoc sp. PCC 7120 and the gene was therefore termed cgt. Southern blot revealed that the cgt gene was present in symbiotically competent cyanobacteria. The cgt gene was expressed in free-living nitrogen-fixing cultures in light or in darkness when supplemented with fructose. This is the first expression analysis of a cgt gene from a cyanobacterium.

  • 410.
    Wu, Xiaofen
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Holmfeldt, Karin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hubalek, Valerie
    Uppsala University.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Åström, Mats E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bertilsson, Stefan
    Uppsala University.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 5, p. 1192-1203Article in journal (Refereed)
    Abstract [en]

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

  • 411.
    Wu, Xiaofen
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pedersen, Karsten
    Microbial Analytics Sweden.
    Edlund, Johanna
    Eriksson, Lena
    Åström, Mats E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Andersson, Anders
    Bertilsson, Stefan
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hydrogen fed chemolithoautotrophic and diazotrophic populations initiate biofilm formation in oligotrophic, deep terrestrial subsurface watersManuscript (preprint) (Other academic)
  • 412.
    Wu, Xiaofen
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sten, Pekka
    Vaasa University of Applied Sciences, Finland.
    Engblom, Sten
    Novia University of Applied Sciences, Finland.
    Nowak, Pawel
    Polish Academy of Sciences, Poland.
    Österholm, Peter
    Åbo Akademi University, Finland.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Impact of mitigation strategies on acid sulfate soil chemistry and microbial community2015In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 526, p. 215-221Article in journal (Refereed)
    Abstract [en]

    Potential acid sulfate soils contain reduced iron sulfides that if oxidized, can cause significant environmental damage by releasing large amounts of acid and metals. This study examines metal and acid release as well as the microbial community capable of catalyzing metal sulfide oxidation after treating acid sulfate soil with calcium carbonate (CaCO3) or calcium hydroxide (Ca(OH)2). Leaching tests of acid sulfate soil samples were carried out in the laboratory. The pH of the leachate during the initial flushing with water lay between 3.8 and 4.4 suggesting that the jarosite/schwertmannite equilibrium controls the solution chemistry. However, the pH increased to circa 6 after treatment with CaCO3 suspension and circa 12 after introducing Ca(OH)2 solution. 16S rRNA gene sequences amplified from community DNA extracted from the untreated and both CaCO3and Ca(OH)2 treated acid sulfate soils were most similar to bacteria (69.1% to 85.7%) and archaea (95.4% to 100%) previously identified from acid and metal contaminated environments. These species included a Thiomonas cuprina-like and an Acidocella-like bacteria as well as a Ferroplasma acidiphilum-like archeon. Although the CaCO3 and Ca(OH)2 treatments did not decrease the proportion of microorganisms capable of accelerating acid and metal release, the chemical effects of the treatments suggested their reduced activity.

  • 413.
    Wu, Xiaofen
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wong, Zhen Lim
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sten, Pekka
    Engblom, Sten
    Osterholm, Peter
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Microbial community potentially responsible for acid and metal release from an Ostrobothnian acid sulfate soil2013In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 84, no 3, p. 555-563Article in journal (Refereed)
    Abstract [en]

    Soils containing an approximately equal mixture of metastable iron sulfides and pyrite occur in the boreal Ostrobothnian coastal region of Finland, termed 'potential acid sulfate soil materials'. If the iron sulfides are exposed to air, oxidation reactions result in acid and metal release to the environment that can cause severe damage. Despite that acidophilic microorganisms catalyze acid and metal release from sulfide minerals, the microbiology of acid sulfate soil (ASS) materials has been neglected. The molecular phylogeny of a depth profile through the plough and oxidized ASS layers identified several known acidophilic microorganisms and environmental clones previously identified from acid- and metal-contaminated environments. In addition, several of the 16S rRNA gene sequences were more similar to sequences previously identified from cold environments. Leaching of the metastable iron sulfides and pyrite with an ASS microbial enrichment culture incubated at low pH accelerated metal release, suggesting microorganisms capable of catalyzing metal sulfide oxidation were present. The 16S rRNA gene analysis showed the presence of species similar to Acidocella sp. and other clones identified from acid mine environments. These data support that acid and metal release from ASSs was catalyzed by indigenous microorganisms adapted to low pH.

  • 414.
    Yin, Shenglai
    et al.
    Wageningen Univ & Res, Netherlands.
    Kleijn, David
    Wageningen Univ & Res, Netherlands.
    Muskens, Gerard J. D. M.
    Wageningen Univ & Res, Netherlands.
    Fouchier, Ron A. M.
    Erasmus MC, Netherlands.
    Verhagen, Josanne H.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Glazov, Petr M.
    Russian Acad Sci, Russia.
    Si, Yali
    Wageningen Univ & Res, Netherlands;Tsinghua Univ, Peoples Republic of China.
    Prins, Herbert H. T.
    Wageningen Univ & Res, Netherlands.
    de Boer, Willem Frederik
    Wageningen Univ & Res, Netherlands.
    No evidence that migratory geese disperse avian influenza viruses from breeding to wintering ground2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 5, article id e0177790Article in journal (Refereed)
    Abstract [en]

    Low pathogenic avian influenza virus can mutate to a highly pathogenic strain that causes severe clinical signs in birds and humans. Migratory waterfowl, especially ducks, are considered the main hosts of low pathogenic avian influenza virus, but the role of geese in dispersing the virus over long-distances is still unclear. We collected throat and cloaca samples from three goose species, Bean goose (Anser fabalis), Barnacle goose (Branta leucopsis) and Greater white-fronted goose (Anser albifrons), from their breeding grounds, spring stopover sites, and wintering grounds. We tested if the geese were infected with low pathogenic avian influenza virus outside of their wintering grounds, and analysed the spatial and temporal patterns of infection prevalence on their wintering grounds. Our results show that geese were not infected before their arrival on wintering grounds. Barnacle geese and Greater white-fronted geese had low prevalence of infection just after their arrival on wintering grounds in the Netherlands, but the prevalence increased in successive months, and peaked after December. This suggests that migratory geese are exposed to the virus after their arrival on wintering grounds, indicating that migratory geese might not disperse low pathogenic avian influenza virus during autumn migration.

  • 415. Yohannes, E.
    et al.
    Hansson, B.
    Lee, R.W.
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Åkesson, M.
    Hasselquist, D.
    Bensch, S
    Isotope signatures in winter moulted feathers predict malaria prevalence in a breeding avian host2008In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 158, no 2, p. 299-306Article in journal (Refereed)
    Abstract [en]

    It is widely accepted that animal distribution and migration strategy might have co-evolved in relation to selection pressures exerted by parasites. Here, we first determined the prevalence and types of malaria blood parasites in a breeding population of great reed warblers Acrocephalus arundinaceus using PCR. Secondly, we tested for differences in individual feather stable isotope signatures (δ 13C, δ 15N, δD and δ 34S) to investigate whether malaria infected and non-infected birds had occupied different areas in winter. We show that birds moulting in Afro-tropical habitats with significantly higher δ 13C and δ 15N but lower δD and δ34S values were more frequently infected with malaria parasites. Based on established patterns of isotopic distributions, our results indicate that moulting sites with higher incidence of malaria are generally drier and situated further to the north in West Africa than sites with lower incidence of malaria. Our findings are pertinent to the general hypothesis that animal distribution and particularly avian migration strategy might evolve in response to selection pressures exerted by parasites at different geographic scales. Tradeoffs between investment in energy demanding life history traits (e.g. migration and winter moult) and immune function are suggested to contribute to the particular choice of habitat during migration and at wintering sites.

  • 416. Zammit, Carla M
    et al.
    Mangold, Stefanie
    Jonna, Venkateswara rao
    Mutch, Lesley A
    Watling, Helen R
    Dopson, Mark
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Department of Molecular Biology, Umeå University, Umeå, Sweden .
    Watkin, Elizabeth L J
    Bioleaching in brackish waters--effect of chloride ions on the acidophile population and proteomes of model species.2012In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 93, no 1, p. 319-329Article in journal (Refereed)
    Abstract [en]

    High concentrations of chloride ions inhibit the growth of acidophilic microorganisms used in biomining, a problem particularly relevant to Western Australian and Chilean biomining operations. Despite this, little is known about the mechanisms acidophiles adopt in order to tolerate high chloride ion concentrations. This study aimed to investigate the impact of increasing concentrations of chloride ions on the population dynamics of a mixed culture during pyrite bioleaching and apply proteomics to elucidate how two species from this mixed culture alter their proteomes under chloride stress. A mixture consisting of well-known biomining microorganisms and an enrichment culture obtained from an acidic saline drain were tested for their ability to bioleach pyrite in the presence of 0, 3.5, 7, and 20 g L(-1) NaCl. Microorganisms from the enrichment culture were found to out-compete the known biomining microorganisms, independent of the chloride ion concentration. The proteomes of the Gram-positive acidophile Acidimicrobium ferrooxidans and the Gram-negative acidophile Acidithiobacillus caldus grown in the presence or absence of chloride ions were investigated. Analysis of differential expression showed that acidophilic microorganisms adopted several changes in their proteomes in the presence of chloride ions, suggesting the following strategies to combat the NaCl stress: adaptation of the cell membrane, the accumulation of amino acids possibly as a form of osmoprotectant, and the expression of a YceI family protein involved in acid and osmotic-related stress.

  • 417.
    Zell, R.
    et al.
    Friedrich Schiller Univ, Germany.
    Delwart, E.
    Univ Calif San Francisco, USA.
    Gorbalenya, A. E.
    Leiden Univ, Netherlands.
    Hovi, T.
    Natl Inst Hlth & Welf THL, Finland.
    King, A. M. Q.
    Pirbright Inst, UK.
    Knowles, N. J.
    Pirbright Inst, UK.
    Lindberg, A. Michael
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Pallansch, M. A.
    CDC, USA.
    Palmenberg, A. C.
    Inst Mol Virol, USA.
    Reuter, G.
    Univ Pecs, Hungary.
    Simmonds, P.
    Univ Oxford, UK.
    Skern, T.
    Med Univ Vienna, Austria.
    Stanway, G.
    Univ Essex, UK.
    Yamashita, T.
    Shubun Univ, Japan.
    ICTV Virus Taxonomy Profile: Picornaviridae2017In: Journal of General Virology, ISSN 0022-1317, E-ISSN 1465-2099, Vol. 98, no 10, p. 2421-2422Article in journal (Refereed)
    Abstract [en]

    The family Picornaviridae comprises small non-enveloped viruses with RNA genomes of 6.7 to 10.1 kb, and contains > 30 genera and > 75 species. Most of the known picornaviruses infect mammals and birds, but some have also been detected in reptiles, amphibians and fish. Many picornaviruses are important human and veterinary pathogens and may cause diseases of the central nervous system, heart, liver, skin, gastrointestinal tract or upper respiratory tract. Most picornaviruses are transmitted by the faecal-oral or respiratory routes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Picornaviridae, which is available at www. ictv. global/report/picornaviridae.

  • 418.
    Zhang, Hao
    et al.
    Chinese Univ Hong Kong, Peoples Republic of China.
    Yoshizawa, Susumu
    Univ Tokyo, Japan.
    Sun, Ying
    Chinese Univ Hong Kong, Peoples Republic of China.
    Huang, Yongjie
    Chinese Univ Hong Kong, Peoples Republic of China.
    Chu, Xiao
    Chinese Univ Hong Kong, Peoples Republic of China.
    Gonzalez, Jose M.
    Univ La Laguna, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Luo, Haiwei
    Chinese Univ Hong Kong, Peoples Republic of China.
    Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 2, p. 648-666Article in journal (Refereed)
    Abstract [en]

    The taxonomy of marine and non-marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean-to-land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non-marine adaptive genes. This included various Na+-dependent transporters, osmolyte transporters and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non-marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K+ scavenging ATPase was repeatedly gained whereas the corresponding low-affinity transporter repeatedly lost upon transitions, reflecting K+ ions are less available to non-marine bacteria. Strikingly, the central metabolism Na+-translocating NADH: quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H+-translocating counterpart was repeatedly gained in non-marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non-marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non-marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components.

  • 419.
    Zhu, Ling
    et al.
    University of Oxford, UK ; The Pirbright Institute, UK.
    Wang, Xiangxi
    Chinese Academy of Science, China.
    Ren, Jingshan
    University of Oxford, UK.
    Porta, Claudine
    University of Oxford, UK ; The Pirbright Institute, UK.
    Wenham, Hannah
    The Pirbright Institute, UK.
    Ekström, Jens-Ola
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Panjwani, Anusha
    The Pirbright Institute, UK.
    Knowles, Nick J.
    The Pirbright Institute, UK.
    Kotecha, Abhay
    University of Oxford, UK.
    Siebert, C. Alistair
    University of Oxford, UK.
    Lindberg, A. Michael
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Fry, Elizabeth E.
    University of Oxford, UK.
    Rao, Zihe
    Chinese Academy of Science, China ; Tsinghua University, China.
    Tuthill, Tobias J.
    The Pirbright Institute, UK.
    Stuart, David I.
    University of Oxford, UK ; Harwell Science and Innovation Campus, UK.
    Structure of Ljungan virus provides insight into genome packaging of this picornavirus2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 8316Article in journal (Refereed)
    Abstract [en]

    Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans. The 3.78-angstrom resolution cryo-electron microscopy structure shows remarkable features, including an extended VP1 C terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N terminus of VP3, binding to which orders some 12% of the viral genome. This apparently charge-driven RNA attachment suggests that this branch of the picornaviruses uses a different mechanism of genome encapsidation, perhaps explored early in the evolution of picornaviruses.

  • 420. Zohari, Siamak
    et al.
    Gyarmati, P.
    Ejdersund, A.
    Berglöf, U.
    Thorén, P.
    Ehrenberg, M.
    Czifra, G.
    Belak, S.
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Olsen, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Berg, M.
    Phylogenetic analysis of the non-structural (NS) gene of influenza A viruses isolated from mallards in Northern Europe in 20052008In: Virology Journal, ISSN 1743-422X, E-ISSN 1743-422X, Vol. 5, no Article ID: 147Article in journal (Refereed)
    Abstract [en]

    Background: Although the important role of the non-structural 1 (NS) gene of influenza A in virulence of the virus is well established, our knowledge about the extent of variation in the NS gene pool of influenza A viruses in their natural reservoirs in Europe is incomplete. In this study we determined the subtypes and prevalence of influenza A viruses present in mallards in Northern Europe and further analysed the NS gene of these isolates in order to obtain a more detailed knowledge about the genetic variation of NS gene of influenza A virus in their natural hosts. Results: A total number of 45 influenza A viruses of different subtypes were studied. Eleven haemagglutinin-and nine neuraminidase subtypes in twelve combinations were found among the isolated viruses. Each NS gene reported here consisted of 890 nucleotides; there were no deletions or insertions. Phylogenetic analysis clearly shows that two distinct gene pools, corresponding to both NS allele A and B, were present at the same time in the same geographic location in the mallard populations in Northern Europe. A comparison of nucleotide sequences of isolated viruses revealed a substantial number of silent mutations, which results in high degree of homology in amino acid sequences. The degree of variation within the alleles is very low. In our study allele A viruses displays a maximum of 5% amino acid divergence while allele B viruses display only 2% amino acid divergence. All the viruses isolated from mallards in Northern Europe possessed the typical avian ESEV amino acid sequence at the C-terminal end of the NSI protein. Conclusion: Our finding indicates the existence of a large reservoir of different influenza A viruses in mallards population in Northern Europe. Although our phylogenetic analysis clearly shows that two distinct gene pools, corresponding to both NS allele A and B, were present in the mallards populations in Northern Europe, allele B viruses appear to be less common in natural host species than allele A, comprising only about 13% of the isolates sequenced in this study.

  • 421. Zweifel, Ulla Li
    et al.
    Hagström, Åke
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Holmfeldt, Karin
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Thyrhaug, Runar
    Geels, Camilla
    Frohn, Lise Marie
    Skjoth, Carsten A.
    Karlson, Ulrich Gosewinkel
    High bacterial 16S rRNA gene diversity above the atmospheric boundary layer2012In: Aerobiologia, ISSN 0393-5965, E-ISSN 1573-3025, Vol. 28, no 4, p. 481-498Article in journal (Refereed)
    Abstract [en]

    The atmosphere is host to an omnipresent bacterial community that may influence fundamental atmospheric processes such as cloud formation and precipitation onset. Knowledge of this bacterial community is scarce, particularly in air masses relevant to cloud formation. Using a light aircraft, we sampled above the atmospheric boundary layer-that is, at heights at which cloud condensation occurs-over coastal areas of Sweden and Denmark in summer 2009. Enumeration indicated total bacterial numbers of 4 x 10(1) to 1.8 x 10(3) m(-3) air and colony-forming units of 0-6 bacteria m(-3) air. 16S rRNA gene libraries constructed from samples collected above the Baltic Sea coast revealed a highly diverse bacterial community dominated by species belonging to the genera Sphingomonas and Pseudomonas. Bacterial species known to carry ice-nucleating proteins were found in several samples. Modeled back trajectories suggested the potential sources of the sampled bacteria to be diverse geographic regions, including both marine and terrestrial environments in the northern hemisphere. Several samples contained 16S rRNA genes from plant chloroplasts, confirming a terrestrial contribution to these samples. Interestingly, the airborne bacterial community displayed an apparent seasonal succession that we tentatively ascribe to in situ succession in the atmosphere.

  • 422.
    Ålkärr, Linus
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Studies on skin microbiota and growth of Northern pike (Esox lucius) larvae from a translocation experiment in two Swedish wetlands2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Pike (Esox lucius) larvae from a translocation experiment conducted in two wetlands connected to Lerviksbäcken and Oknebäcken were used to study larval skin microbiomes and growth of individuals from two reproductively isolated populations of anadromous Baltic Sea pike. Microbial communities were investigated by amplifying and sequencing the 16S rRNA gene from DNA extracts of mucus swabs. The purpose of this study was to explore the larval skin associated microbiota to look for signs of divergence between populations and families in host mechanisms that influence microbial adhesion to skin mucosa. Principal coordinates analyses and PERMANOVA of microbiome data, as well as studies of alpha diversity and taxonomic composition, showed that the communities on larval skin were distinct from and more diverse than those in the surrounding water. However, the two populations did not exhibit any significant differences in microbiomes, and an apparent effect of genetic distance on microbiome characteristics could be due to cross contamination. Measurements of body length indicated that while the two populations did not differ in length at the end of the yolk sac stage, rearing site had an effect on body length as individuals reared in the Oknebäck wetland were significantly longer than those reared in the Lervik wetland.

  • 423. Öquist, G.
    et al.
    Hagström, Åke
    Department of Microbiology, University of Ume~i; S-90187 Umeh, Sweden.
    Alm, P.
    Samuelsson, G.
    Richardsson, K.
    Chlorophyll a fluorescence an alternative method for estimating primary production1982In: Marine Biology, ISSN 1230-7688, Vol. 68, no 1, p. 71-75Article in journal (Refereed)
    Abstract [en]

    The in vivo chlorophyll a fluorescence index (F+DcM u-F-DcMu/F+DcMU) of natural waters was compared to the 14C-determined primary production, and the fluorescence intensity in the presence of 3-(3,4-dichlorophenyl)-l,l-dimethylurea (F + DCM~) was studied as a function of extracted and spectrophotometrically determined chlorophyll concentrations. Samples were taken every second week from May through October, 1979, at the station "Systrarna" situated in a coastal area of the Bottnian Sea. In addition, samples from the Archipelago Sea of the Baltic were collected on board the Finnish research vessel R/S "Aranda" during the September cruise 1979. The correlations between the fluorescence index and the 14C-determined primary production and between F+DcMu and total chlorophyll concentration were good when samples taken over short time intervals were compared. The shortcomings of both the fluorescence and the 14C methods are discussed. It is concluded that the fluorescence method is useful if it is desirable to follow with high time resolution any changes in the potential for photosynthesis (or pirmary production) in a water mass over relatively short time periods; e.g. during an algal bloom. The fluorescence method can furthermore be technically developed for automatic monitoring with a high time resolution. Efforts are being made in our laboratory to develop the method further to give information about the in situ rates of photosynthesis rather than the potential for photosynthesis in a phytoplankton population.

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