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  • 1. Christersson, Linus
    et al.
    Blomqvist, Maria
    Grannas, Karin
    Thollesson, Mikael
    Laroucau, Karine
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Eliasson, Ingvar
    Olsen, Björn
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Herrmann, Björn
    A novel Chlamydiaceae-like bacterium found in fecal specimens from sea birds from the Bering Sea.2010In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 2, no 4, p. 605-610Article in journal (Refereed)
    Abstract [en]

    The family Chlamydiaceae contains several bacterial pathogens of important human and veterinary medical concern, such as Chlamydia trachomatis and Chlamydophila psittaci. Within the order Chlamydiales there are also an increasing number of chlamydia-like bacteria whose biodiversity, host range and environmental spread seem to have been largely underestimated, and which are currently being investigated for their potential medical relevance. In this study we present 16S rRNA, rnpB and ompA gene sequence data congruently indicating a novel chlamydia-like bacterium found in faecal specimens from opportunistic fish-eating sea birds, belonging to the Laridae and Alcidae families, from the Bering Sea. This novel bacterium appears to be closer to the Chlamydiaceae than other chlamydia-like bacteria and is most likely a novel genus within the Chlamydiaceae family.

  • 2.
    Cody, Alison J.
    et al.
    Univ Oxford, UK.
    McCarthy, Noel D.
    Univ Oxford,UK;Hlth Protect Agcy, UK;Univ Warwick, UK;Univ Oxford, UK.
    Bray, James E.
    Univ Oxford, UK.
    Wimalarathna, Helen M. L.
    Univ Oxford, UK.
    Colles, Frances M.
    Univ Oxford, UK.
    van Rensburg, Melissa J. Jansen
    Univ Oxford, UK.
    Dingle, Kate E.
    Univ Oxford, UK.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Maiden, Martin C. J.
    Univ Oxford, UK.
    Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom2015In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 7, no 5, p. 782-788Article in journal (Refereed)
    Abstract [en]

    The contribution of wild birds as a source of human campylobacteriosis was investigated in Oxfordshire, United Kingdom (UK) over a 10 year period. The probable origin of human Campylobacter jejuni genotypes, as described by multilocus sequence typing, was estimated by comparison with reference populations of isolates from farm animals and five wild bird families, using the STRUCTURE algorithm. Wild bird-attributed isolates accounted for between 476 (2.1%) and 543 (3.5%) cases annually. This proportion did not vary significantly by study year (P=0.934) but varied seasonally, with wild bird-attributed genotypes comprising a greater proportion of isolates during warmer compared with cooler months (P=0.003). The highest proportion of wild bird-attributed illness occurred in August (P<0.001), with a significantly lower proportion in November (P=0.018). Among genotypes attributed to specific groups of wild birds, seasonality was most apparent for Turdidae-attributed isolates, which were absent during cooler, winter months. This study is consistent with some wild bird species representing a persistent source of campylobacteriosis, and contributing a distinctive seasonal pattern to disease burden. If Oxfordshire is representative of the UK as a whole in this respect, these data suggest that the national burden of wild bird-attributed isolates could be in the order of 10000 annually.

  • 3.
    Fahlgren, Camilla
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gómez-Consarnau, Laura
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Zabori, Julia
    Stockholm University.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Krejci, Radovan
    Stockholm University.
    Mårtensson, E. Monica
    Stockholm University;Uppsala University.
    Nilsson, Douglas
    Stockholm University.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Seawater mesocosm experiments in the Arctic uncover differential transfer of marine bacteria to aerosols2015In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 7, no 3, p. 460-470Article in journal (Refereed)
    Abstract [en]

    Biogenic aerosols critically control atmospheric processes. However, although bacteria constitute major portions of living matter in seawater, bacterial aerosolization from oceanic surface layers remains poorly understood. We analysed bacterial diversity in seawater and experimentally generated aerosols from three Kongsfjorden sites, Svalbard. Construction of 16S rRNA gene clone libraries from paired seawater and aerosol samples resulted in 1294 sequences clustering into 149 bacterial and 34 phytoplankton operational taxonomic units (OTUs). Bacterial communities in aerosols differed greatly from correspondingseawater communities in three out of four experiments. Dominant populations of both seawater and aerosols were Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria. Across the entire dataset, most OTUs from seawater could also be found in aerosols; in each experiment, however, several OTUs were either selectively enriched in aerosols or little aerosolized. Notably, a SAR11 clade OTU was consistently abundant in the seawater, but was recorded insignificantly lower proportions in aerosols. A strikingly high proportion of colony-forming bacteria were pigmented in aerosols compared with seawater, suggesting that selection during aerosolization contributes to explaining elevated proportions of pigmented bacteria frequently observed in atmospheric samples. Our findings imply that atmospheric processes could be considerably influenced by spatiotemporal variations in the aerosolization efficiency of different marine bacteria.

  • 4.
    Farnelid, Hanna
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Öberg, Tomas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Riemann, Lasse
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Identity and dynamics of putative N-2-fixing picoplankton in the Baltic Sea proper suggest complex patterns of regulation2009In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 1, p. 145-154Article in journal (Refereed)
    Abstract [en]

    Heterocystous filamentous cyanobacteria are regarded as the main N-2-fixing organisms (diazotrophs) in the Baltic Sea. However, some studies indicate that picoplankton may also be important. The aim of this study was to examine the composition of putative diazotrophs in the picoplankton (< 3 mu m) and to identify links to environmental factors. Nitrogenase (nifH) genes were amplified from community DNA by nested PCR, followed by cloning and sequencing. Clone libraries from nine environmental samples collected from the central Baltic Sea (April-October 2003, 3 m depth) and a negative control yielded a total of 433 sequences with an average clone library coverage of 92%. The sequences fell within nifH Clusters I, II and III and formed 15 distinct groups (> 96% amino acid similarity). Most of the sequences (77%) fell into nifH Cluster I (cyanobacteria and alpha-, beta- and gamma-Proteobacteria). However, only 26 sequences were related to cyanobacteria (e. g. Pseudanabaena) and among these no unicellular phylotypes were found. Sequences clustering with alternative nitrogenases (anfH) and Archaea were found in one sample while sequences related to anaerobic phylotypes were found in six samples distributed throughout the season. The identified phylogenetic groups showed covariance with several environmental factors but no strong links could be established. This suggests a variable and complex regulation of diazotrophic groups within Baltic Sea picoplankton.

  • 5.
    Lindh, Markus V.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Riemann, Lasse
    University of Copenhagen, Denmark.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Romero-Oliva, Claudia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Salomon, Paulo
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Granéli, Edna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Consequences of increased temperature and acidification on bacterioplankton community composition during a mesocosm spring bloom in the Baltic Sea2013In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 5, no 2, p. 252-262Article in journal (Refereed)
    Abstract [en]

    Despite the paramount importance of bacteria for biogeochemical cycling of carbon and nutrients, little is known about the potential effects of climate change on these key organisms. The consequences of the projected climate change on bacterioplankton community dynamics were investigated in a Baltic Sea spring phytoplankton bloom mesocosm experiment by increasing temperature with 3°C and decreasing pH by approximately 0.4 units via CO2 addition in a factorial design. Temperature was the major driver of differences in community composition during the experiment, as shown by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rRNA gene fragments. Several bacterial phylotypes belonging to Betaproteobacteria were predominant at 3°C but were replaced by members of the Bacteriodetes in the 6°C mesocosms. Acidification alone had a limited impact on phylogenetic composition, but when combined with increased temperature, resulted in the proliferation of specific microbial phylotypes. Our results suggest that although temperature is an important driver in structuring bacterioplankton composition, evaluation of the combined effects of temperature and acidification is necessary to fully understand consequences of climate change for marine bacterioplankton, their implications for future spring bloom dynamics, and their role in ecosystem functioning.

  • 6.
    Lundin, Daniel
    et al.
    KTH Royal Institute of Technology ; Vetenskapsrådet.
    Severin, Ina
    Uppsala University.
    Logue, Jürg Brendan
    Uppsala University.
    Östman, Örjan
    Uppsala University.
    Andersson, Anders F.
    KTH Royal Institute of Technology.
    Lindström, Eva S.
    Uppsala University.
    Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?2012In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 4, no 3, p. 367-372Article in journal (Refereed)
    Abstract [en]

    The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may therefore prevent appropriate study designs. However, for many questions in ecology it is not essential to know the actual diversity but rather the trends among samples thereof. It is, hence, important to know to what depth microbial communities need to be sampled to accurately measure trends in diversity. We used three data sets of freshwater and sediment bacteria, where diversity was explored using 454 pyrosequencing. Each data set contained 6–15 communities from which 15 000–20 000 16S rRNA gene sequences each were obtained. These data sets were subsampled repeatedly to 10 different depths down to 200 sequences per community. Diversity estimates varied with sequencing depth, yet, trends in diversity among samples were less sensitive. We found that 1000 denoised sequences per sample explained to 90% the trends in β-diversity (Bray-Curtis index) among samples observed for 15 000–20 000 sequences. Similarly, 5000 denoised sequences were sufficient to describe trends in α-diversity (Shannon index) with the same accuracy. Further, 5000 denoised sequences captured to more than 80% the trends in Chao1 richness and Pielou's evenness.

  • 7.
    Sandegren, Linus
    et al.
    Uppsala University.
    Stedt, Johan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lustig, Ulrika
    Uppsala University.
    Bonnedahl, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Kalmar County Hospital.
    Andersson, Dan I.
    Uppsala University.
    Jaerhult, Josef D.
    Uppsala University.
    Long-term carriage and rapid transmission of extended spectrum beta-lactamase-producing E-coli within a flock of Mallards in the absence of antibiotic selection2018In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, no 5, p. 576-582Article in journal (Refereed)
    Abstract [en]

    Wild birds have been suggested as transmitters and reservoirs for antibiotic resistant bacteria. We performed an experimental study investigating carriage time and interindividual transmission of extended spectrum beta-lactamase- (ESBL-)producing Escherichia coli in Mallards (Anas platyrhynchos) to assess if the birds carry the bacteria long enough to transfer them geographically during migration. Mallards were inoculated intraoesophageally with four different strains of ESBL-producing E. coli and kept together in a flock. The ESBL-strains belonged to sequence types previously shown to spread between birds and humans. Culturing from faecal samples showed presence of ESBL-producing E. coli the entire 29 day experimental period. An extensive and rapid transmission of the different ESBL-strains between individuals (including non-inoculated controls) was observed. In necropsy samples, we detected ESBL-strains in the cecum even in faeces-negative birds, indicating that this part of the intestine could function as a reservoir of resistant bacteria. We demonstrate that birds can carry ESBL-producing E. coli for long enough times to travel far during migration and the extensive interindividual transmission suggests spread between individuals in a dense bird population as a mechanism that allow persistence of resistant bacteria.

  • 8.
    Sjöstedt, Johanna
    et al.
    Uppsala University;Lund University.
    Langenheder, Silke
    Uppsala University.
    Kritzberg, Emma
    Lund University.
    Karlsson, Christofer M. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindström, Eva S.
    Uppsala University.
    Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community2018In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, no 4, p. 493-500Article in journal (Refereed)
    Abstract [en]

    Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.

  • 9.
    Sörenson, Eva
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bertos-Fortis, Mireia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Kremp, Anke
    Finnish Environment Institute, Finland;Leibniz Institute for Baltic Sea Research Warnemunde, Germany.
    Kruget, Karen
    Max Planck Institute for Marine Microbiology, Germany.
    Lindehoff, Elin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Finnish Environment Institute, Finland.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Consistency in microbiomes in cultures of Alexandrium species isolated from brackish and marine waters2019In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 11, no 3, p. 425-433Article in journal (Refereed)
    Abstract [en]

    Phytoplankton and bacteria interactions have a significant role in aquatic ecosystem functioning. Associations can range from mutualistic to parasitic, shaping biogeochemical cycles and having a direct influence on phytoplankton growth. How variations in phenotype and sampling location, affect the phytoplankton microbiome is largely unknown. A high‐resolution characterization of the bacterial community in cultures of the dinoflagellate Alexandrium was performed on strains isolated from different geographical locations and at varying anthropogenic impact levels. Microbiomes of Baltic Sea Alexandrium ostenfeldii isolates were dominated by Betaproteobacteria and were consistent over phenotypic and genotypic Alexandrium strain variation, resulting in identification of an A. ostenfeldii core microbiome. Comparisons with in situ bacterial communities showed that taxa found in this A. ostenfeldii core were specifically associated to dinoflagellate dynamics in the Baltic Sea. Microbiomes of Alexandrium tamarense and minutum, isolated from the Mediterranean Sea, differed from those of A. ostenfeldii in bacterial diversity and composition but displayed high consistency, and a core set of bacterial taxa was identified. This indicates that Alexandrium isolates with diverse phenotypes host predictable, species‐specific, core microbiomes reflecting the abiotic conditions from which they were isolated. These findings enable in‐depth studies of potential interactions occurring between Alexandrium and specific bacterial taxa.

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