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  • 1.
    Axelsson Olsson, Diana
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Svensson, Lovisa
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Olofsson, Jenny
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Salomon, Paulo
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Ellström, Patrik
    Olsen, Björn
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Increase in Acid Tolerance of Campylobacter jejuni through Coincubation with Amoebae2010In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 76, no 13, p. 4194-4200Article in journal (Refereed)
    Abstract [en]

    Campylobacter jejuni is a recognized and common gastrointestinal pathogen in most parts of the world. Human infections are often food borne, and the bacterium is frequent among poultry and other food animals. However, much less is known about the epidemiology of C. jejuni in the environment and what mechanisms the bacterium depends on to tolerate low pH. The sensitive nature of C. jejuni stands in contrast to the fact that it is difficult to eradicate from poultry production, and even more contradictory is the fact that the bacterium is able to survive the acidic passage through the human stomach. Here we expand the knowledge on C. jejuni acid tolerance by looking at protozoa as a potential epidemiological pathway of infection. Our results showed that when C. jejuni cells were coincubated with Acanthamoeba polyphaga in acidified phosphate-buffered saline (PBS) or tap water, the bacteria could tolerate pHs far below those in their normal range, even surviving at pH 4 for 20 h and at pH 2 for 5 h. Interestingly, moderately acidic conditions (pH 4 and 5) were shown to trigger C. jejuni motility as well as to increase adhesion/internalization of bacteria into A. polyphaga. Taken together, the results suggest that protozoa may act as protective hosts against harsh conditions and might be a potential risk factor for C. jejuni infections. These findings may be important for our understanding of C. jejuni passage through the gastrointestinal tract and for hygiene practices used in poultry settings.

  • 2.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Arístegui, Javier
    Gasol, Josep M
    Herndl, Gerhard J
    Microbial functioning and community structure variability in the mesopelagic and epipelagic waters of the subtropical Northeast Atlantic Ocean.2012In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 78, no 9, p. 3309-3316Article in journal (Refereed)
    Abstract [en]

    We analyzed the regional distribution of bulk heterotrophic prokaryotic activity (leucine incorporation) and selected single-cell parameters (cell viability and nucleic acid content) as parameters for microbial functioning, as well as bacterial and archaeal community structure in the epipelagic (0-200 m) and mesopelagic (200-1000 m) subtropical Northeast Atlantic Ocean. We selectively sampled three contrasting regions covering a wide range of surface productivity and oceanographic properties within the same basin: (i) the eddy field south of the Canary Islands, (ii) the open-ocean Subtropical Gyre and (iii) the upwelling filament off Cape Blanc. In the epipelagic waters, a high regional variation in hydrographic parameters and bacterial community structure was detected accompanied, however, by a low variability in microbial functioning. In contrast, mesopelagic microbial functioning was highly variable between the studied regions despite the homogeneous abiotic conditions found therein. More microbial functioning parameters indicated differences among the three regions within the mesopelagic (i.e., viability of cells, nucleic acid content, cell-specific heterotrophic activity, nanoflagellate abundance, prokaryotic to nanoflagellate abundance ratio) than in the epipelagic (i.e., bulk activity, nucleic acid content and nanoflagellate abundance) waters. Our results show that the mesopelagic realm in the NE Atlantic is, in terms of microbial activity, more heterogeneous than its epipelagic counterpart, probably linked to mesoscale hydrographical variations.

  • 3. Blackburn, N.
    et al.
    Wikner, J.
    Cuadros Hanson, R.
    Bjørnsen, K.P.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Rapid determination of bacterial abundance, biovolume, morpology and growth by neural network based image analysis.1998In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 64, p. 3246-3255Article in journal (Refereed)
  • 4.
    Christel, Stephan
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Herold, Malte
    University of Luxembourg, Luxembourg.
    Bellenberg, Sören
    Universität Duisburg-Essen, Germany.
    El Hajjami, Mohamed
    Ruhr Universität Bochum, Germany.
    Buetti-Dinh, Antoine
    Università della Svizzera Italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Pivkine, Igor V.
    Università della Svizzera Italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Sand, Wolfgang
    Universität Duisburg-Essen, Germany;Donghua UniversityMining Academy and Technical University Freiberg, Germany, PR China;.
    Wilmes, Paul
    University of Luxembourg, Luxembourg.
    Poetsch, Ansgar
    Ruhr Universität Bochum, Germany;Plymouth University, UK.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilumT2018In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 4, no 3, article id UNSP e02091-17Article in journal (Refereed)
    Abstract [en]

    Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilumT applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilumT DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as substrate and bioleaching cultures containing chalcopyrite (CuFeS2). Leptospirillum ferriphilumT adaptations to growth on chalcopyrite included a possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, expression and translation of genes responsible for chemotaxis and motility were enhanced.

  • 5.
    Dopson, Mark
    et al.
    University of East Anglia, Norwich, United Kingdom.
    Baker-Austin, Craig
    University of East Anglia, Norwich, United Kingdom.
    Hind, Andrew
    University of East Anglia, Norwich, United Kingdom.
    Bowman, John P
    University of Tasmania, Hobart, Tasmania, Australia.
    Bond, Philip L
    University of East Anglia, Norwich, United Kingdom.
    Characterization of Ferroplasma isolates and Ferroplasma acidarmanus sp. nov., extreme acidophiles from acid mine drainage and industrial bioleaching environments.2004In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 70, no 4, p. 2079-2088Article in journal (Refereed)
    Abstract [en]

    Three recently isolated extremely acidophilic archaeal strains have been shown to be phylogenetically similar to Ferroplasma acidiphilum Y(T) by 16S rRNA gene sequencing. All four Ferroplasma isolates were capable of growing chemoorganotrophically on yeast extract or a range of sugars and chemomixotrophically on ferrous iron and yeast extract or sugars, and isolate "Ferroplasma acidarmanus" Fer1(T) required much higher levels of organic carbon. All four isolates were facultative anaerobes, coupling chemoorganotrophic growth on yeast extract to the reduction of ferric iron. The temperature optima for the four isolates were between 35 and 42 degrees C and the pH optima were 1.0 to 1.7, and "F. acidarmanus" Fer1(T) was capable of growing at pH 0. The optimum yeast extract concentration for "F. acidarmanus" Fer1(T) was higher than that for the other three isolates. Phenotypic results suggested that isolate "F. acidarmanus" Fer1(T) is of a different species than the other three strains, and 16S rRNA sequence data, DNA-DNA similarity values, and two-dimensional polyacrylamide gel electrophoresis protein profiles clearly showed that strains DR1, MT17, and Y(T) group as a single species. "F. acidarmanus" Fer1(T) groups separately, and we propose the new species "F. acidarmanus" Fer1(T) sp. nov.

  • 6.
    Dopson, Mark
    et al.
    Umeå University.
    Lindstrom, Börje
    Umeå University.
    Potential role of thiobacillus caldus in arsenopyrite bioleaching1999In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 65, no 1, p. 36-40Article in journal (Refereed)
    Abstract [en]

    We investigated the potential role of the three strains of Thiobacillus caldus (KU, BC13, and C-SH12) in arsenopyrite leaching in combination with a moderately thermophilic iron oxidizer, Sulfobacillus thermosulfidooxidans. Pure cultures of T. caldus and S. thermosulfidooxidans were used as well as defined mixed cultures. By measuring released iron, tetrathionate, and sulfur concentrations, we found that the presence of T. caldus KU and BC13 in the defined mixed culture lowered the concentration of sulfur, and levels of tetrathionate were comparable to or lower than those in the presence of S. thermosulfidooxidans. This suggests that T. caldus grows on the sulfur compounds that build up during leaching, increasing the arsenopyrite-leaching efficiency. This result was similar to leaching arsenopyrite with a pure culture of S. thermosulfidooxidans in the presence of yeast extract. Therefore, three possible roles of T. caldus in the leaching environment can be hypothesized: to remove the buildup of solid sulfur that can cause an inhibitory layer on the surface of the mineral, to aid heterotrophic and mixotrophic growth by the release of organic chemicals, and to solubilize solid sulfur by the production of surface-active agents. The results showed that T. caldus KU was the most efficient at leaching arsenopyrite under the conditions tested, followed by BC13, and finally C-SH12.

  • 7. Fuhrman, J.A.
    et al.
    Comeau, D.E.
    Hagström, Åke
    Department of Microbiology, University of Umeå.
    Chan, A.M.
    Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies1988In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 54, no 6, p. 1426-1429Article in journal (Refereed)
    Abstract [en]

    We developed a simple technique for the high-yield extraction of purified DNA from mixed populations ofnatural planktonic marine microbes (primarily bacteria). This is a necessary step for several molecularbiological approaches to the study of microbial communities in nature. The microorganisms from near-shoremarine and brackish water samples, ranging in volume from 8 to 40 liters, were collected on 0.22-,um-pore-sizefluorocarbon-based filters, after prefiltration through glass fiber filters, to remove most of the eucaryotes. DNAwas extracted directly from the filters in 1% sodium dodecyl sulfate that was heated to 95 to 100°C for 1.5 to2 min. This procedure lysed essentially all the bacteria and did not significantly denature the DNA. The DNAwas purified by phenol extraction, and precautions were taken to minimize shearing. Agarose gel electrophoresisshowed that most of the final preparation had a large molecular size (>23 kilobase pairs). The DNA wassufficiently pure to allow complete digestion by the restriction endonuclease Sau3AI and ligation to vector DNA.In a sample in which the extracted DNA was quantified by binding to the dye Hoechst H33258, DNA wasquantitatively extracted, and 45% of the initially extracted DNA was recovered after purification. Final yieldswere a few micrograms of DNA per liter of seawater and were roughly 25 to 50% of the total bacterial DNAin the sample. Alternatives to the initial harvest by filtration method, including continuous-flow centrifugationand thin-channel or hollow-fiber concentration followed by centrifugation, were less efficient than filtration interms of both time and yield, largely because of the difficulty of centrifuging the very small bacteria typical ofmarine plankton. These methods were judged to be less appropriate for studies of natural populations as theyimpose a strong selection for the larger bacteria. 

  • 8. Gasol, J.M.
    et al.
    Zweifel, Ulla Li
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Peters, F.
    Fuhrman, J.A.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Significance of size and nucleic acid content heterogeneity as measured by flow cytometry in natural planktonic bacteria.1999In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 65, p. 4475-4483Article in journal (Refereed)
  • 9.
    Gillman, Anna
    et al.
    Uppsala University.
    Muradrasoli, Shaman
    Uppsala University ; Swedish University of Agricultural Sciences.
    Söderström, Hanna
    Umeå University.
    Holmberg, Fredrik
    Uppsala University.
    Latorre-Margalef, Neus
    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.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gunnarsson, Gunnar
    Kristianstad University.
    Olsen, Björn
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Uppsala University.
    Jarhult, Josef D.
    Uppsala University.
    Oseltamivir-Resistant Influenza A (H1N1) Virus Strain with an H274Y Mutation in Neuraminidase Persists without Drug Pressure in Infected Mallards2015In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 81, no 7, p. 2378-2383Article in journal (Refereed)
    Abstract [en]

    Influenza A virus (IAV) has its natural reservoir in wild waterfowl, and emerging human IAVs often contain gene segments from avian viruses. The active drug metabolite of oseltamivir (oseltamivir carboxylate [OC]), stockpiled as Tamiflu for influenza pandemic preparedness, is not removed by conventional sewage treatment and has been detected in river water. There, it may exert evolutionary pressure on avian IAV in waterfowl, resulting in the development of resistant viral variants. A resistant avian IAV can circulate among wild birds only if resistance does not restrict viral fitness and if the resistant virus can persist without continuous drug pressure. In this in vivo mallard (Anas platyrhynchos) study, we tested whether an OC-resistant avian IAV (H1N1) strain with an H274Y mutation in the neuraminidase (NA-H274Y) could retain resistance while drug pressure was gradually removed. Successively infected mallards were exposed to decreasing levels of OC, and fecal samples were analyzed for the neuraminidase sequence and phenotypic resistance. No reversion to wild-type virus was observed during the experiment, which included 17 days of viral transmission among 10 ducks exposed to OC concentrations below resistance induction levels. We conclude that resistance in avian IAV that is induced by exposure of the natural host to OC can persist in the absence of the drug. Thus, there is a risk that human-pathogenic IAVs that evolve from IAVs circulating among wild birds may contain resistance mutations. An oseltamivir-resistant pandemic IAV would pose a substantial public health threat. Therefore, our observations underscore the need for prudent oseltamivir use, upgraded sewage treatment, and surveillance for resistant IAVs in wild birds.

  • 10. González, J. M.
    et al.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Fernández-Gómez, B.
    Coll-Lladó, M.
    González-Velázquez, M.
    Puigbò, P.
    Jaenicke, S.
    Gómez-Consarnau, Laura
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089.
    Fernàndez-Guerra, A.
    Goesmann, A.
    Pedrós-Alió, C.
    Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED1342011In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 77, no 24, p. 8676-8686Article in journal (Refereed)
    Abstract [en]

    Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO2 fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.

  • 11.
    Griekspoor, Petra
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Olofsson, Jenny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Axelsson Olsson, Diana
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Olsen, Björn
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Multilocus Sequence Typing and FlaA Sequencing Reveal the Genetic Stability of Campylobacter jejuni Enrichment during Coculture with Acanthamoeba polyphaga2013In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 79, no 7, p. 2477-2479Article in journal (Refereed)
    Abstract [en]

    Low concentrations of Campylobacter jejuni cells in environmental samples make them difficult to study with conventional culture methods. Here, we show that enrichment by amoeba cocultures works well with low-concentration samples and that this method can be combined with molecular techniques without loss of genetic specificity.

  • 12.
    Hagström, Åke
    et al.
    The National Environmental Protection Board, Brackish Water Toxicology Laboratory, Studsvik, S-611 01 Nyköping.
    Larsson, U.
    Hörstedt, P.
    Normark, S.
    Frequency of dividing cells a new approach to the determination of bacterial growth rates in aquatic environments1979In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 37, no 5, p. 805-812Article in journal (Refereed)
    Abstract [en]

    Frequency of dividing cells is suggested to be an indirect measureof the mean growth rate of an aquatic bacterial community. Seasonalchanges in frequency of dividing cells were found which covariatedwith the bacterial uptake of 14C-labeled phytoplankton exudates.Batch and continuous culture growth experiments, using brackishwater bacteria in pure and mixed enrichment cultures, were performedto establish a relationship between frequency of dividing cellsand growth rate. An improved technique for bacterial directcounts, using fluorescent staining and epifluorescence microscopy,is presented. Based on a 6-month survey in a coastal area ofthe Baltic Sea, the bacterial production in the photic zoneis estimated. Compared to the total primary production in thearea, the bacterial population during this period utilized approximately25% of the amount of carbon originally fixed by the primaryproducers.

  • 13.
    Hagström, Åke
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Pommier, Thomas
    Dembinska, D.
    Rohwer, F.
    Simu, Karin
    Zweifel, Ulla Li
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Use of 16S rDNA for species delineation of marine bacterioplankton.2002In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 68, p. 3628-3633Article in journal (Refereed)
  • 14.
    Hernandez, Jorge
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Stedt, Johan
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Bonnedahl, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Kalmar County Hospital.
    Molin, Y.
    Drobni, M.
    Calisto-Ulloa, N.
    Gomez-Fuentes, C.
    Astorga-Espana, M. S.
    Gonzalez-Acuna, D.
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Blomqvist, Maria
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Olsen, Björn
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Human-Associated Extended-Spectrum beta-Lactamase in the Antarctic2012In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 78, no 6, p. 2056-2058Article in journal (Refereed)
    Abstract [en]

    Escherichia coli bacteria with extended-spectrum beta-lactamase (ESBL) type CTX-M resistance were isolated from water samples collected close to research stations in Antarctica. The isolates had bla(CTX-M-1) and bla(CTX-M-15) genotypes and sequence types (ST) indicative of a human-associated origin. This is the first record of ESBL-producing enterobacteria from Antarctica.

  • 15.
    Holmfeldt, Karin
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Middelboe, Mathias
    Nybroe, Ole
    Riemann, Lasse
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts2007In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 73, p. 6730-6739Article in journal (Refereed)
  • 16.
    Holmfeldt, Karin
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Odić, Duško
    Sullivan, Matthew B
    Middelboe, Mathias
    Riemann, Lasse
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Cultivated single-stranded DNA phages that infect marine Bacteroidetes prove difficult to detect with DNA-binding stains.2012In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 78, no 3, p. 892-894Article in journal (Refereed)
    Abstract [en]

    This is the first description of cultivated icosahedral single-stranded DNA (ssDNA) phages isolated on heterotrophic marine bacterioplankton and with Bacteroidetes hosts. None of the 8 phages stained well with DNA-binding stains, suggesting that in situ abundances of ssDNA phages are drastically underestimated using conventional methods for enumeration.

  • 17.
    Larsson, Per
    et al.
    Department of Ecology, University of Lund.
    Okla, L
    Tranvik, Lars
    Microbial degradation of xenobiotic, aromatic pollutants in humic water1988In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 54, no 7, p. 1864-1867Article in journal (Refereed)
    Abstract [en]

    The microbial degradation of a number of 14C-labeled, recalcitrant,aromatic pollutants, including trichloroguaiacol and di-, tri-,and pentachlorophenol, was investigated in aquatic model systemsin the laboratory. Natural, mixed cultures of microorganismsin the water from a brown-water lake with a high content ofhumic compounds mineralized all of the tested substances toa higher degree than did microorganisms in the water from aclear-water lake. Dichlorophenol was the most rapidly degradedpollutant. 

  • 18.
    Latorre-Margalef, Neus
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Georgia, USA.
    Avril, Alexis
    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.
    Olsen, Björn
    Uppsala University.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?2016In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 82, no 4, p. 1147-1153Article in journal (Refereed)
    Abstract [en]

    Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data.

  • 19. Liljeqvist, Maria
    et al.
    Rzhepishevska, Olena I.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gene Identification and Substrate Regulation Provide Insights into Sulfur Accumulation during Bioleaching with the Psychrotolerant Acidophile Acidithiobacillus ferrivorans2013In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 79, no 3, p. 951-957Article in journal (Refereed)
    Abstract [en]

    The psychrotolerant acidophile Acidithiobacillus ferrivorans has been identified from cold environments and has been shown to use ferrous iron and inorganic sulfur compounds as its energy sources. A bioinformatic evaluation presented in this study suggested that Acidithiobacillus ferrivorans utilized a ferrous iron oxidation pathway similar to that of the related species Acidithiobacillus ferrooxidans. However, the inorganic sulfur oxidation pathway was less clear, since the Acidithiobacillus ferrivorans genome contained genes from both Acidithiobacillus ferrooxidans and Acidithiobacillus caldus encoding enzymes whose assigned functions are redundant. Transcriptional analysis revealed that the petA1 and petB1 genes (implicated in ferrous iron oxidation) were downregulated upon growth on the inorganic sulfur compound tetrathionate but were on average 10.5-fold upregulated in the presence of ferrous iron. In contrast, expression of cyoB1 (involved in inorganic sulfur compound oxidation) was decreased 6.6-fold upon growth on ferrous iron alone. Competition assays between ferrous iron and tetrathionate with Acidithiobacillus ferrivorans SS3 precultured on chalcopyrite mineral showed a preference for ferrous iron oxidation over tetrathionate oxidation. Also, pure and mixed cultures of psychrotolerant acidophiles were utilized for the bioleaching of metal sulfide minerals in stirred tank reactors at 5 and 25 degrees C in order to investigate the fate of ferrous iron and inorganic sulfur compounds. Solid sulfur accumulated in bioleaching cultures growing on a chalcopyrite concentrate. Sulfur accumulation halted mineral solubilization, but sulfur was oxidized after metal release had ceased. The data indicated that ferrous iron was preferentially oxidized during growth on chalcopyrite, a finding with important implications for biomining in cold environments.

  • 20.
    Muthusamy, Sarala Devi
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    González, José M.
    Univ La Laguna, Dept Microbiol, Tenerife, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dynamics of metabolic activities and gene expression in the Roseobacter clade bacterium Phaeobacter sp. MED193 during growth with thiosulfate2014In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 80, no 22, p. 6933-6942Article in journal (Refereed)
    Abstract [en]

    Metagenomic analyses of surface seawater reveal that genes for sulfur oxidation are widespread in bacterioplankton communities. However, little is known about the metabolic processes used to exploit the energy potentially gained from inorganic sulfur oxidation in oxic seawater. We therefore studied the sox gene system containing Roseobacter clade isolate Phaeobacter sp. strain MED193 in acetate minimal medium with and without thiosulfate. The addition of thiosulfate enhanced the bacterial growth yields up to 40% in this strain. Concomitantly, soxB and soxY gene expression increased about 8-fold with thiosulfate and remained 11-fold higher than that in controls through stationary phase. At stationary phase, thiosulfate stimulated protein synthesis and anaplerotic CO2 fixation rates up to 5- and 35-fold, respectively. Several genes involved in anaplerotic CO2 fixation (i.e., pyruvate carboxylase, propionyl coenzyme A [CoA], and crotonyl-CoA carboxylase) were highly expressed during active growth, coinciding with high CO2 fixation rates. The high expression of key genes in the ethylmalonyl-CoA pathway suggests that this is an important pathway for the utilization of two-carbon compounds in Phaeobacter sp. MED193. Overall, our findings imply that Roseobacter clade bacteria carrying sox genes can use their lithotrophic potential to gain additional energy from sulfur oxidation for both increasing their growth capacity and improving their long-term survival.

  • 21. Norquist, A.
    et al.
    Hagström, Åke
    Department of Microbiology, University of Umeå.
    Wolf-Watz, H.
    Protection against vibriosis and furunculosis by the use of attenuated strains of Vibrio anguillarum.1989In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 55, no 6, p. 1400-1405Article in journal (Refereed)
    Abstract [en]

    The fish pathogen Vibrio anguillarum causes a lethal infectionin rainbow trout (Salmo gairdneri). Three different avirulentmutants, constructed by transposon insertion mutagenesis (VAN20and VAN70) or as antibiotic-resistant mutants (VAN1000), wereisolated by screening 200 individual isolated mutants for avirulence.When used as live vaccines, all three avirulent mutants wereable to induce protective immunity against the homologous aswell as a heterologous strain of V. anguillarum. When VAN1000was used, protective immunity could be recorded 1 week afterbath vaccination with 10(7) bacteria per ml of water for 30min. A single-dose immunization was effective for at least 12weeks. Western immunoblotting showed that strains of V. anguillarumhave antigenic determinants in common with Aeromonas strains.Therefore, we tested and confirmed that VAN1000 also was ableto induce protective immunity against challenge with Aeromonassalmonicida. 

  • 22. Osorio, Hector
    et al.
    Mangold, Stefanie
    Denis, Yann
    Nancucheo, Ivan
    Esparza, Mario
    Johnson, D. Barrie
    Bonnefoy, Violaine
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Holmes, David S.
    Anaerobic Sulfur Metabolism Coupled to Dissimilatory Iron Reduction in the Extremophile Acidithiobacillus ferrooxidans2013In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 79, no 7, p. 2172-2181Article in journal (Refereed)
    Abstract [en]

    Gene transcription (microarrays) and protein levels (proteomics) were compared in cultures of the acidophilic chemolithotroph Acidithiobacillus ferrooxidans grown on elemental sulfur as the electron donor under aerobic and anaerobic conditions, using either molecular oxygen or ferric iron as the electron acceptor, respectively. No evidence supporting the role of either tetrathionate hydrolase or arsenic reductase in mediating the transfer of electrons to ferric iron (as suggested by previous studies) was obtained. In addition, no novel ferric iron reductase was identified. However, data suggested that sulfur was disproportionated under anaerobic conditions, forming hydrogen sulfide via sulfur reductase and sulfate via heterodisulfide reductase and ATP sulfurylase. Supporting physiological evidence for H2S production came from the observation that soluble Cu2+ included in anaerobically incubated cultures was precipitated (seemingly as CuS). Since H2S reduces ferric iron to ferrous in acidic medium, its production under anaerobic conditions indicates that anaerobic iron reduction is mediated, at least in part, by an indirect mechanism. Evidence was obtained for an alternative model implicating the transfer of electrons from S-0 to Fe3+ via a respiratory chain that includes a bc(1) complex and a cytochrome c. Central carbon pathways were upregulated under aerobic conditions, correlating with higher growth rates, while many Calvin-Benson-Bassham cycle components were upregulated during anaerobic growth, probably as a result of more limited access to carbon dioxide. These results are important for understanding the role of A. ferrooxidans in environmental biogeochemical metal cycling and in industrial bioleaching operations.

  • 23.
    Pinhassi, Jarone
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Zweifel, Ulla Li
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Dominant Marine Bacterioplankton Species Found Among Colony Forming Bacteria.1997In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 63, p. 3359-3366Article in journal (Refereed)
  • 24. Rehnstam, A.-S.
    et al.
    Norquist, A.
    Wolf-Watz, H.
    Hagström, Åke
    Department of Microbiology, University of Umeå.
    Identification of Vibrio anguillarum in fish using partial 16S rRNA sequences and a specific 16S rRNA oligonucleotide probe.1989In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 55, no 8, p. 1907-1910Article in journal (Refereed)
    Abstract [en]

    16S rRNA from seven different Vibrio anguillarum strains waspartially sequenced and compared. From this sequence informationwe could design a 25-base-long oligonucleotide and use it asa specific probe for identification of V. anguillarum. Thiswas determined by RNA-DNA colony hybridization and slot-blothybridization. Strong, specific hybridization to the probe wasobserved for all V. anguillarum strains tested. Furthermore,no cross-hybridization could be seen against five other bacterialspecies. The detection limit was 5 x 10(3) bacteria per ml.It was even possible to detect V. anguillarum, by slot-blothybridization, directly in a homogenized kidney from a fishthat had died of vibriosis. The partial sequence informationrevealed small but significant differences between strains ofthe same species. These sequence differences are sufficientlysignificant to allow serotyping on the RNA level. Comparingstrains of different serotypes revealed a 10-base and an 11-basedifference in V. anguillarum serotypes O8 and O9, respectively,in a 122-base partial sequence. 

  • 25.
    Riemann, Lasse
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Azam, F.
    Widespread N-acetyl-D-glucosamine uptake among pelagic marine bacteria and its ecological implications2002In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 68, 11, p. 5554-5562Article in journal (Refereed)
  • 26.
    Riemann, Lasse
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Leitet, C.
    Pommier, T.
    Simu, K.
    Holmfeldt, Karin
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Larsson, U.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    The Native Bacterioplankton Community in the Central Baltic Sea is Influenced by Freshwater Bacterial Species2008In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 74, p. 503-515Article in journal (Refereed)
  • 27.
    Riemann, Lasse
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Steward, G.F.
    Azam, F.
    Dynamics of bacterial community composition and activity during a mesocosm diatom bloom2000In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 66, p. 578-587Article in journal (Refereed)
  • 28.
    Rzhepishevska, Olena I
    et al.
    Umeå University.
    Valdés, Jorge
    Center for Bioinformatics and Genome Biology, Life Science Foundation, MIFAB and Andrés Bello University, Santiago, Chile.
    Marcinkeviciene, Liucija
    Institute of Biochemistry, Vilnius, Lithuania.
    Gallardo, Camelia Algora
    Umeå University.
    Meskys, Rolandas
    Institute of Biochemistry, Vilnius, Lithuania.
    Bonnefoy, Violaine
    CNRS, IBSM, Laboratoire de Chimie Bactérienne, France.
    Holmes, David S
    Center for Bioinformatics and Genome Biology, Life Science Foundation, MIFAB and Andrés Bello University, Santiago, Chile.
    Dopson, Mark
    Umeå University.
    Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds.2007In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 73, no 22, p. 7367-7372Article in journal (Refereed)
    Abstract [en]

    Acidithiobacillus caldus has been proposed to play a role in the oxidation of reduced inorganic sulfur compounds (RISCs) produced in industrial biomining of sulfidic minerals. Here, we describe the regulation of a new cluster containing the gene encoding tetrathionate hydrolase (tetH), a key enzyme in the RISC metabolism of this bacterium. The cluster contains five cotranscribed genes, ISac1, rsrR, rsrS, tetH, and doxD, coding for a transposase, a two-component response regulator (RsrR and RsrS), tetrathionate hydrolase, and DoxD, respectively. As shown by quantitative PCR, rsrR, tetH, and doxD are upregulated to different degrees in the presence of tetrathionate. Western blot analysis also indicates upregulation of TetH in the presence of tetrathionate, thiosulfate, and pyrite. The tetH cluster is predicted to have two promoters, both of which are functional in Escherichia coli and one of which was mapped by primer extension. A pyrrolo-quinoline quinone binding domain in TetH was predicted by bioinformatic analysis, and the presence of an o-quinone moiety was experimentally verified, suggesting a mechanism for tetrathionate oxidation.

  • 29. Simu, Karin
    et al.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Oligotrophic bacterioplankton with a novel single-cell life strategy.2004In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 70, p. 2445-2451Article in journal (Refereed)
  • 30. Simu, Karin
    et al.
    Holmfeldt, Karin
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Zweifel, Ulla Li
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Culturability and coexistence of colony forming and single cell marine bacterioplankton.2005In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, p. 4793-4800Article in journal (Refereed)
  • 31.
    Sjöstedt, Johanna
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Koch-Schmidt, Per
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Pontarp, Mikael
    Canbäck, Björn
    Tunlid, Anders
    Lundberg, Per
    Hagström, Åke
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Riemann, Lasse
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance.2012In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 78, no 5, p. 1361-1369Article in journal (Refereed)
    Abstract [en]

    A bacterial community may be resistant to environmental disturbances if some of its species show metabolic flexibility and physiological tolerance to the changing conditions. Alternatively, disturbances can change the composition of the community and thereby potentially affect ecosystem processes. The impact of disturbance on the composition of bacterioplankton communities was examined in continuous seawater cultures. Bacterial assemblages from geographically closely connected areas, the Baltic Sea (salinity 7 and high dissolved organic carbon [DOC]) and Skagerrak (salinity 28 and low DOC), were exposed to gradual opposing changes in salinity and DOC over a 3-week period such that the Baltic community was exposed to Skagerrak salinity and DOC and vice versa. Denaturing gradient gel electrophoresis and clone libraries of PCR-amplified 16S rRNA genes showed that the composition of the transplanted communities differed significantly from those held at constant salinity. Despite this, the growth yields (number of cells ml(-1)) were similar, which suggests similar levels of substrate utilization. Deep 454 pyrosequencing of 16S rRNA genes showed that the composition of the disturbed communities had changed due to the recruitment of phylotypes present in the rare biosphere of the original community. The study shows that members of the rare biosphere can become abundant in a bacterioplankton community after disturbance and that those bacteria can have important roles in maintaining ecosystem processes.

  • 32.
    Sjöstedt, Johanna
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Martiny, Jennifer B. H.
    Univ Calif Irvine.
    Munk, Peter
    Tech Univ Denmark.
    Riemann, Lasse
    Univ Copenhagen, Denmark.
    Abundance of Broad Bacterial Taxa in the Sargasso Sea Explained by Environmental Conditions but Not Water Mass2014In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 80, no 9, p. 2786-2795Article in journal (Refereed)
    Abstract [en]

    To explore the potential linkage between distribution of marine bacterioplankton groups, environmental conditions, and water mass, we investigated the factors determining the abundance of bacterial taxa across the hydrographically complex Subtropical Convergence Zone in the Sargasso Sea. Based on information from 16S rRNA gene clone libraries from various locations and two depths, abundances of the predominant taxa (eubacteria, Archaea, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and the Roseobacter, SAR11, and SAR86 clades) were quantified by real-time PCR. In addition, the abundances of Synechococcus, Prochlorococcus, and picoalgae were determined by flow cytometry. Linear multiple-regression models determining the relative effects of eight environmental variables and of water mass explained 35 to 86% of the variation in abundance of the quantified taxa, even though only one to three variables were significantly related to any particular taxon's abundance. Most of the variation in abundance was explained by depth and chlorophyll a. The predominant phototrophs, Prochlorococcus and picoalgae, were negatively correlated with phosphate, whereas eubacteria, heterotrophic bacteria, and SAR86 were negatively correlated with nitrite. Water mass showed limited importance for explaining the abundance of the taxonomical groups (significant only for Roseobacter, explaining 14% of the variation). The results suggest the potential for predicting the abundance of broad bacterioplankton groups throughout the Sargasso Sea using only a few environmental parameters.

  • 33. Turk, V.
    et al.
    Rehnstam, A.-S.
    Lundberg, E.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Release of Bacterial DNA by Marine Nanoflagellates, an Intermediate Step in Phosphorus Regeneration.1992In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 58, p. 3744-3750Article in journal (Refereed)
  • 34. Wikner, J.
    et al.
    Andersson, A.
    Normark, S.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Use of genetically marked minicells as a probe in measurement of predation on bacteria in aquatic environments.1986In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 52, p. 4-8Article in journal (Refereed)
  • 35.
    Zweifel, Ulla Li
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Total counts of marine bacteria include a large fraction of non-DNA containing ghosts.1995In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 61, p. 2180-2185Article in journal (Refereed)
1 - 35 of 35
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