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  • 301.
    Nicomrat, Duongruitai
    et al.
    The Ohio State University, Columbus, USA.
    Dick, Warren A.
    The Ohio State University, Columbus, USA.
    Dopson, Mark
    Umeå University.
    Tuovinen, Olli H.
    The Ohio State University, Columbus, USA.
    Bacterial phylogenetic diversity in a constructed wetland system treating acid coal mine drainage2007In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 40, no 2, p. 312-321Article in journal (Refereed)
    Abstract [en]

    Microorganisms in acid mine drainage are typically acidophiles that mediate the oxidation of reduced compounds of iron and sulfur. However, microbial populations in wetland systems constructed to treat acid mine drainage are not well characterized. The purpose of this study was to analyze bacterial diversity, using cultivation-independent molecular ecological techniques, in a constructed wetland that received acid drainage from an abandoned underground coal mine. DNA was purified from Fe(III)-precipitates from the oxidized surface zone of wetland sediments and 16S rRNA gene sequences were amplified and cloned. A total of 200 clones were analyzed by restriction fragment length polymorphism (RFLP) and 77 unique RFLP patterns were obtained with four restriction enzymes. Of these patterns, 30 most dominant unique clones were selected for sequencing of their 16S rRNA genes. Half of these 30 clones could be matched with autotrophic iron- and sulfur-oxidizing bacteria (Acidithiohacillus ferrooxidans and Acidithiobacillus thiooxidans). Several clones also formed a clade with heterotrophic iron-oxidizing bacteria (TRA2-10, TRA3-20, and TRA5-3) and heterotrophic bacteria (Stenotrophomas maltophilia, Bordetella spp., Alcalgenes sp., Alcaligenesfaecalis, and Alcaligenes xylosoxidans). Approximately 40% and 35% of the analyzed RFLP restriction patterns were consistent with A. ferrooxidans and A. thiooxidans, respectively. The relatively high frequency of acidithiobacilli is consistent with the chemical and physical characteristics of this site-i.e., continuous, abundant supply of reduced iron and sulfur compounds, pH 3-4, ambient temperature, and limited organics originating from the coal seam and from vegetation or soil surrounding the inlet channel to the wetland. The RFLP results were consistent with our previous culture-independent PCR-DGGE and FISH study, showing relatively low bacterial diversity and predominance of mesophilic acidithiobacilli in oxic wetland sediments.

  • 302.
    Niklasson, B
    et al.
    Uppsala University, Sweden.
    Johansson, S
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Elfström, T
    Lindberg, Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Ljunganvirus, a previously unrecognized picornavirus and its presence in humans1999In: XIth International Congress of Virology, Sydney Convention Center, Australia, 9-13 August 1999: Abstracts, 1999Conference paper (Refereed)
  • 303.
    Nilsson, A
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Echovirus 5: sequence analysis of the complete genome and phylogenetic relationship to other enteroviruses1997Conference paper (Refereed)
  • 304.
    Nilsson, Emelie
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bayfield, Oliver W.
    University of York, UK.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Antson, Alfred A.
    University of York, UK.
    Holmfeldt, Karin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Diversity and host interactions among virulent and temperate Baltic Sea Flavobacterium phages2020In: Viruses, ISSN 1999-4915, E-ISSN 1999-4915, Vol. 12, no 2, p. 1-21, article id 158Article in journal (Refereed)
    Abstract [en]

    Viruses in aquatic environments play a key role in microbial population dynamics and nutrient cycling. In particular, bacteria of the phylum Bacteriodetes are known to participate in recycling algal blooms. Studies of phage-host interactions involving this phylum are hence important to understand the processes shaping bacterial and viral communities in the ocean as well as nutrient cycling. In this study, we isolated and sequenced three strains of flavobacteria-LMO6, LMO9, LMO8-and 38 virulent phages infecting them. These phages represent 15 species, occupying three novel genera. Additionally, one temperate phage was induced from LMO6 and was found to be competent at infecting LMO9. Functions could be predicted for a limited number of phage genes, mainly representing roles in DNA replication and virus particle formation. No metabolic genes were detected. While the phages isolated on LMO8 could infect all three bacterial strains, the LMO6 and LMO9 phages could not infect LMO8. Of the phages isolated on LMO9, several showed a host-derived reduced efficiency of plating on LMO6, potentially due to differences in DNA methyltransferase genes. Overall, these phage-host systems contribute novel genetic information to our sequence databases and present valuable tools for the study of both virulent and temperate phages.

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  • 305.
    Nilsson, Emelie
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Li, K.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fridlund, Jimmy
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sulcius, S.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Nat Res Ctr, Lithuania.
    Bunse, Carina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Helmholtz Zentrum Polar & Meeresforsch, Germany;Carl von Ossietzky Univ Oldenburg, Germany.
    Karlsson, Christofer M. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Swedish Meteorological and Hydrological Institute, Sweden.
    Lundin, Daniel
    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.
    Holmfeldt, Karin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL3412019In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 85, no 18, p. 1-19, article id e01003-19Article in journal (Refereed)
    Abstract [en]

    Knowledge in aquatic virology has been greatly improved by culture-independent methods, yet there is still a critical need for isolating novel phages to identify the large proportion of "unknowns" that dominate metagenomes and for detailed analyses of phage-host interactions. Here, 54 phages infecting Rheinheimem sp. strain BAL341 (Gammaproteobacteria) were isolated from Baltic Sea seawater and characterized through genome content analysis and comparative genomics. The phages showed a myovirus-like morphology and belonged to a novel genus, for which we propose the name Barbavirus. All phages had similar genome sizes and numbers of genes (80 to 84 kb; 134 to 145 genes), and based on average nucleotide identity and genome BLAST distance phylogeny, the phages were divided into five species. The phages possessed several genes involved in metabolic processes and host signaling, such as genes encoding ribonucleotide reductase and thymidylate synthase, phoH, and rnazG. One species had additional metabolic genes involved in pyridine nucleotide salvage, possibly providing a fitness advantage by further increasing the phages' replication efficiency. Recruitment of viral metagenomic reads (25 Baltic Sea viral metagenomes from 2012 to 2015) to the phage genomes showed pronounced seasonal variations, with increased relative abundances of barba phages in August and September synchronized with peaks in host abundances, as shown by 16S rRNA gene amplicon sequencing. Overall, this study provides detailed information regarding genetic diversity, phage-host interactions, and temporal dynamics of an ecologically important aquatic phage-host system. IMPORTANCE Phages are important in aquatic ecosystems as they influence their microbial hosts through lysis, gene transfer, transcriptional regulation, and expression of phage metabolic genes. Still, there is limited knowledge of how phages interact with their hosts, especially at fine scales. Here, a Rheinheimera phage-host system constituting highly similar phages infecting one host strain is presented. This relatively limited diversity has previously been seen only when smaller numbers of phages have been isolated and points toward ecological constraints affecting the Rheinheimera phage diversity. The variation of metabolic genes among the species points toward various fitness advantages, opening up possibilities for future hypothesis testing. Phage-host dynamics monitored over several years point toward recurring "kill-the-winner" oscillations and an ecological niche fulfilled by this system in the Baltic Sea. Identifying and quantifying ecological dynamics of such phage-host model systems in situ allow us to understand and study the influence of phages on aquatic ecosystems.

  • 306. Nordberg, A
    et al.
    Hansson, M
    Sundh, I
    Nordkvist, E
    Carlsson Juhlin, Helena
    Institutionen för mikrobiologi, SLU.
    Mathisen, B
    Monitoring of a biogas process using electronic gas sensors and near-infrared spectroscopy (NIR)2000In: Water Science and Technology, ISSN 0273-1223, E-ISSN 1996-9732, Vol. 41, no 3, p. 1-8Article in journal (Refereed)
    Abstract [en]

    The use of electronic gas sensors and near-infrared spectroscopy (NIR) to monitor the dynamics in a biogas process was evaluated using multivariate data analysis. The digester, a completely stirred 81 tank reactor fed with a mixture of cellulose, albumin and minerals, was exposed to an overload of glucose after which monitoring of electronic gas sensor responses, NIR spectra as well as traditional chemical variables and analysis of microbial community structure were done. The responses from an array of electronic gas sensors consisting of MOS and MOSFET-sensors were correlated against volatile compounds in the headspace using partial least square (PLS) regressions. The root mean square error of prediction (RMSEP) was 0.15 g/l for acetate in the range of 0.14-1.72 g/l and the RMSEP for methane was 2.3% in the range of 27-73%. Selected wavelengths from the second derivative of the original NIR spectra (400-2500 nm) resulted in a PLS-model for predicting microbial biomass, measured as total phospholipid fatty acids, with a RMSEP of 9 nmol/ml in the range of 163-293 nmol/ml. The NIR model developed for acetate had a RMSEP of 0.20 g/l within the range of 0.14-1.72 g/l. The results clearly show that both NIR and an array of electronic gas sensors can provide simultaneous non-invasive in situ monitoring of important process variables in anaerobic digesters.

  • 307. 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. 

  • 308. Notini, M.
    et al.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Effects of oils on Baltic littoral community, as studied in an outdoor model test system. U.S1974In: Government printing office Washington, p. 251-254Article in journal (Other (popular science, discussion, etc.))
  • 309.
    Notini, M.
    et al.
    IVL Baltic Sea Laboratory, Studsvik, Fack, S-611 01 Nyköping, Sweden.
    Nagell, B.
    IVL, Box 21060, S-100 31 Stockholm, Sweden.
    Hagström, Åke
    Dept of Zoology, Box 6801, S-113 86 Stockholm, Sweden..
    Grahn, O.
    IVL, Box 5207, S-402 24 Gothenburg, Sweden..
    An outdoor model simulating a Baltic Sea littoral ecosystem1977In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 28, p. 2-9Article in journal (Refereed)
  • 310.
    Nuy, Julia K.
    et al.
    Univ Duisburg Essen, Germany.
    Hötzinger, Matthias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hahn, Martin W.
    Univ Innsbruck, Austria.
    Beisser, Daniela
    Univ Duisburg Essen, Germany.
    Boenigk, Jens
    Univ Duisburg Essen, Germany.
    Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients2020In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 11, p. 1-16, article id 154Article in journal (Refereed)
    Abstract [en]

    Polynucleobacter (Burkholderiaceae, Betaproteobacteria) and Limnohabitans (Comamonadaceae, Betaproteobacteria) are abundant freshwater bacteria comprising large genetic and taxonomic diversities, with species adapted to physico-chemically distinct types of freshwater systems. The relative importance of environmental drivers, i.e., physico-chemistry, presence of microeukaryotes and geographic position for the diversity and prevalence has not been investigated for both taxa before. Here, we present the first pan-European study on this topic, comprising 255 freshwater lakes. We investigated Limnohabitans and Polynucleobacter using an amplicon sequencing approach of partial 16S rRNA genes along environmental gradients. We show that physico-chemical factors had the greatest impact on both genera. Analyses on environmental gradients revealed an exceptionally broad ecological spectrum of operational taxonomic units (OTUs). Despite the coarse resolution of the genetic marker, we found OTUs with contrasting environmental preferences within Polynucleobacter and Limnohabitans subclusters. Such an ecological differentiation has been characterized for PnecC and LimC before but was so far unknown for less well studied subclusters such as PnecA and PnecB. Richness and abundance of OTUs are geographically clustered, suggesting that geographic diversity patterns are attributable to region-specific physico-chemical characteristics (e.g., pH and temperature) rather than latitudinal gradients or lake sizes.

  • 311.
    Nykvist, Marie
    et al.
    Uppsala University.
    Gillman, Anna
    Uppsala University.
    Söderström Lindström, Hanna
    Umeå University.
    Tang, Chaojun
    Umeå University.
    Fedorova, Ganna
    University of South Bohemia in Ceske Budejovice, Czech Republic.
    Lundkvist, Åke
    Uppsala University.
    Latorre-Margalef, Neus
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wille, Michelle
    Uppsala University.
    Järhult, Josef D.
    Uppsala University.
    In vivo mallard experiments indicate that zanamivir has less potential for environmental influenza A virus resistance development than oseltamivir2017In: Journal of General Virology, ISSN 0022-1317, E-ISSN 1465-2099, Vol. 98, no 12, p. 2937-2949Article in journal (Refereed)
    Abstract [en]

    Neuraminidase inhibitors are a cornerstone of influenza pandemic preparedness before vaccines can be mass-produced and thus a neuraminidase inhibitor-resistant pandemic is a serious threat to public health. Earlier work has demonstrated the potential for development and persistence of oseltamivir resistance in influenza A viruses exposed to environmentally relevant water concentrations of the drug when infecting mallards, the natural influenza reservoir that serves as the genetic base for human pandemics. As zanamivir is the major second-line neuraminidase inhibitor treatment, this study aimed to assess the potential for development and persistence of zanamivir resistance in an in vivo mallard model; especially important as zanamivir will probably be increasingly used. Our results indicate less potential for development and persistence of resistance due to zanamivir than oseltamivir in an environmental setting. This conclusion is based on: (1) the lower increase in zanamivir IC50 conferred by the mutations caused by zanamivir exposure (2–17-fold); (2) the higher zanamivir water concentration needed to induce resistance (at least 10 µg l−1); (3) the lack of zanamivir resistance persistence without drug pressure; and (4) the multiple resistance-related substitutions seen during zanamivir exposure (V116A, A138V, R152K, T157I and D199G) suggesting lack of one straight-forward evolutionary path to resistance. Our study also adds further evidence regarding the stability of the oseltamivir-induced substitution H275Y without drug pressure, and demonstrates the ability of a H275Y-carrying virus to acquire secondary mutations, further boosting oseltamivir resistance when exposed to zanamivir. Similar studies using influenza A viruses of the N2-phylogenetic group of neuraminidases are recommended.

  • 312.
    Olofsson, Jenny
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Uppsala University.
    Axelsson Olsson, Diana
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Brudin, Lars
    Kalmar County Hospital ; Linköping University.
    Olsen, Björn
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Uppsala University.
    Ellström, Patrik
    Uppsala University.
    Campylobacter jejuni Actively Invades the Amoeba Acanthamoeba polyphaga and Survives within Non Digestive Vacuoles2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 11, article id e78873Article in journal (Refereed)
    Abstract [en]

    The Gram-negative bacterium Campylobacter jejuni is able to enter, survive and multiply within the free living amoeba Acanthamoeba polyphaga, but the molecular mechanisms behind these events are still unclear. We have studied the uptake and intracellular trafficking of viable and heat killed bacterial cells of the C. jejuni strain 81-176 in A. polyphaga. We found that viable bacteria associated with a substantially higher proportion of Acanthamoeba trophozoites than heat killed bacteria. Furthermore, the kinetics of internalization, the total number of internalized bacteria as well as the intracellular localization of internalized C. jejuni were dramatically influenced by bacterial viability. Viable bacteria were internalized at a high rate already after 1 h of co-incubation and were observed in small vacuoles tightly surrounding the bacteria. In contrast, internalization of heat killed C. jejuni was low at early time points and did not peak until 96 h. These cells were gathered in large spacious vacuoles that were part of the degradative pathway as determined by the uptake of fluorescently labeled dextran. The amount of heat killed bacteria internalized by A. polyphaga did never reach the maximal amount of internalized viable bacteria. These results suggest that the uptake and intracellular survival of C. jejuni in A. polyphaga is bacterially induced.

  • 313.
    Olofsson, Martin
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lamela, Teresa
    Necton SA, Olhao, Portugal.
    Nilsson, Emmelie
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bergé, Jean-Pascal
    IFREMER, Nantes, France.
    del Pino, Victória
    Necton SA, Olhao, Portugal.
    Uronen, Pauliina
    Neste Oil, Ctr Technol, Porvoo, Finland.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Combined Effects of Nitrogen Concentration and Seasonal Changes on the Production of Lipids in Nannochloropsis oculata 2014In: Marine Drugs, ISSN 1660-3397, E-ISSN 1660-3397, Vol. 12, no 4, p. 1891-1910Article in journal (Refereed)
    Abstract [en]

    Instead of sole nutrient starvation to boost algal lipid production, we addressed nutrient limitation at two different seasons (autumn and spring) during outdoor cultivation in flat panel photobioreactors. Lipid accumulation, biomass and lipid productivity and changes in fatty acid composition of Nannochloropsis oculata were investigated under nitrogen (N) limitation (nitrate:phosphate N:P 5, N:P 2.5 molar ratio). N. oculata was able to maintain a high biomass productivity under N-limitation compared to N-sufficiency (N:P 20) at both seasons, which in spring resulted in nearly double lipid productivity under N-limited conditions (0.21 g L−1 day−1) compared to N-sufficiency (0.11 g L−1 day−1). Saturated and monounsaturated fatty acids increased from 76% to nearly 90% of total fatty acids in N-limited cultures. Higher biomass and lipid productivity in spring could, partly, be explained by higher irradiance, partly by greater harvesting rate (~30%). Our results indicate the potential for the production of algal high value products (i.e., polyunsaturated fatty acids) during both N-sufficiency and N-limitation. To meet the sustainability challenges of algal biomass production, we propose a dual-system process: Closed photobioreactors producing biomass for high value products and inoculum for larger raceway ponds recycling waste/exhaust streams to produce bulk chemicals for fuel, feed and industrial material.

  • 314.
    Olofsson, Martin
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindehoff, Elin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Frick, Brage
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Svensson, Fredrik
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltic Sea microalgae transform cement flue gas into valuable biomass2015In: Algal Research, ISSN 2211-9264, Vol. 11, p. 227-233Article in journal (Refereed)
    Abstract [en]

    We show high feasibility of using cement industrial flue gas as CO2 source for microalgal cultivation. The toxicity of cement flue gas (12-15% CO2) on algal biomass production and composition (lipids, proteins, carbohydrates) was tested using monocultures (Tetraselmis sp., green algae, Skeletonema marinoi, diatom) and natural brackish communities. The performance of a natural microalgal community dominated by spring diatoms was compared to a highly productive diatom monoculture S. marinoi fed with flue gas or air-CO2 mixture. Flue gas was not toxic to any of the microalgae tested. Instead we show high quality of microalgal biomass (lipids 20-30% DW, proteins 20-28% DW, carbohydrates 15-30% DW) and high production when cultivated with flue gas addition compared to CO2-air. Brackish Baltic Sea microalgal communities performed equally or better in terms of biomass quality and production than documented monocultures of diatom and green algae, often used in algal research and development. Hence, we conclude that microalgae should be included in biological solutions to transform waste into renewable resources in coastal waters. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

  • 315.
    Olsen, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Efterord2006In: Ett monster vid vår dörr: fågelinfluensan som globalt hot, Stockholm: Karneval , 2006, p. 207-216Chapter in book (Other academic)
  • 316.
    Olson, Sarah H.
    et al.
    Wildlife Conservation Society, USA.
    Parmley, Jane
    University of Guelph, Canada.
    Soos, Catherine
    Environment Canada, Canada.
    Gilbert, Martin
    Wildlife Conservation Society, USA.
    Latorre-Margalef, Neus
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Georgia, USA.
    Hall, Jeffrey S.
    National Wildlife Health Center, USA.
    Hansbro, Phillip M.
    University of Newcastle, Australia ; Hunter Medical Research Institute, Australia.
    Leighton, Frederick
    University of Saskatchewan, Canada.
    Munster, Vincent
    National Institutes of Health, USA.
    Joly, Damien
    Metabiota, Canada.
    Sampling Strategies and Biodiversity of Influenza A Subtypes in Wild Birds2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 3, article id e90826Article in journal (Refereed)
    Abstract [en]

    Wild aquatic birds are recognized as the natural reservoir of avian influenza A viruses (AIV), but across high and low pathogenic AIV strains, scientists have yet to rigorously identify most competent hosts for the various subtypes. We examined 11,870 GenBank records to provide a baseline inventory and insight into patterns of global AIV subtype diversity and richness. Further, we conducted an extensive literature review and communicated directly with scientists to accumulate data from 50 non-overlapping studies and over 250,000 birds to assess the status of historic sampling effort. We then built virus subtype sample-based accumulation curves to better estimate sample size targets that capture a specific percentage of virus subtype richness at seven sampling locations. Our study identifies a sampling methodology that will detect an estimated 75% of circulating virus subtypes from a targeted bird population and outlines future surveillance and research priorities that are needed to explore the influence of host and virus biodiversity on emergence and transmission.

  • 317. 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.

  • 318.
    Osorio, Hector
    et al.
    Fdn Ciencia & Vida, Chile;Pontificia Univ Catolica Chile, Chile.
    Mettert, Erin
    Univ Wisconsin, USA.
    Kiley, Patricia
    Univ Wisconsin, USA.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Jedlicki, Eugenia
    Fdn Ciencia & Vida, Chile.
    Holmes, David S.
    Fdn Ciencia & Vida, Chile;Univ San Sebastian, Chile;Univ Mayor, Chile.
    Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans2019In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, p. 1-14, article id 1642Article in journal (Refereed)
    Abstract [en]

    The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S](2+) iron-sulfur cluster. Under O-2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S](2+) center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O-2 stability could allow At. ferrooxidans to survive in environments with fluctuating O-2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.

  • 319.
    Paul, Carsten
    et al.
    Department for Bioorganic Analytics, Friedrich Schiller University Jena, 07743 Jena, Germany.
    Reunamo, Anna
    Department of Biology, Division of Genetics and Physiology, University of Turku, Finland.
    Lindehoff, Elin
    Umeå Marine Sciences Centre, Umeå University, 91020 Hörnefors, Sweden / Department of Ecology and Environmental Sciences, Umeå University, 901 87 Umeå, Sweden.
    Bergkvist, Johanna
    Department of Biological and Environmental Sciences, University of Gothenburg, Sweden.
    Mausz, Michaela A.
    Larsson, Henrik
    Richter, Hannes
    Wängberg, Sten-Åke
    Leskinen, Piia
    Båmstedt, Ulf
    Pohnert, Georg
    Diatom derived polyunsaturated aldehydes do not structure the planktonic microbial community in a mesocosm study2012In: Marine Drugs, ISSN 1660-3397, E-ISSN 1660-3397, Vol. 10, p. 775-792Article in journal (Refereed)
    Abstract [en]

    Several marine and freshwater diatoms produce polyunsaturated aldehydes (PUA) in wound-activated processes. These metabolites are also released by intact diatom cells during algal blooms. Due to their activity in laboratory experiments, PUA are considered as potential mediators of diatom-bacteria interactions. Here, we tested the hypothesis that PUA mediate such processes in a close-to-field mesocosm experiment. Natural plankton communities enriched with Skeletonema marinoi strains that differ in their PUA production, a plankton control, and a plankton control supplemented with PUA at natural and elevated concentrations were observed. We monitored bacterial and viral abundance as well as bacterial community composition and did not observe any influence of PUA on these parameters even at elevated concentrations. We rather detected an alternation of the bacterial diversity over time and differences between the two S. marinoi strains, indicating unique dynamic bacterial communities in these algal blooms. These results suggest that factors other than PUA are of significance for interactions between diatoms and bacteria. 

  • 320.
    Persson, Olof
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Pinhassi, Jarone
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Riemann, Lasse
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Marklund, Britt-Inger
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Rhen, M.
    Normark, S.
    Gonzalez, J.M.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    High abundance of virulence gene homologues in marine bacteria2009In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 11, no 6, p. 1348-1357Article in journal (Refereed)
    Abstract [en]

    Marine bacteria can cause harm to single-celled and multicellular eukaryotes. However, relatively little is known about the underlying genetic basis for marine bacterial interactions with higher organisms. We examined whole-genome sequences from a large number of marine bacteria for the prevalence of homologues to virulence genes and pathogenicity islands known from bacteria that are pathogenic to terrestrial animals and plants. As many as 60 out of 119 genomes of marine bacteria, with no known association to infectious disease, harboured genes of virulence-associated types III, IV, V and VI protein secretion systems. Type III secretion was relatively uncommon, while type IV was widespread among alphaproteobacteria (particularly among roseobacters) and type VI was primarily found among gammaproteobacteria. Other examples included homologues of the Yersinia murine toxin and a phage-related 'antifeeding' island. Analysis of the Global Ocean Sampling metagenomic data indicated that virulence genes were present in up to 8% of the planktonic bacteria, with highest values in productive waters. From a marine ecology perspective, expression of these widely distributed genes would indicate that some bacteria infect or even consume live cells, that is, generate a previously unrecognized flow of organic matter and nutrients directly from eukaryotes to bacteria.

  • 321.
    Pinhassi, Jarone
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    DeLong, Edward F.
    Univ Hawaii, USA ; MIT, USA.
    Béjà, Oded
    Technion Israel Inst Technol, Israel.
    González, José M.
    Univ La Laguna, Spain.
    Pedrós-Alió, Carlos
    CSIC, Spain.
    Marine bacterial and archaeal ion-pumping rhodopsins: genetic diversity, physiology, and ecology2016In: Microbiology and molecular biology reviews, ISSN 1092-2172, E-ISSN 1098-5557, Vol. 80, no 4, p. 929-954Article in journal (Refereed)
    Abstract [en]

    The recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of "heterotrophic" bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support lightdependent fitness strategies somewhere between these two extremes.

  • 322.
    Pinhassi, Jarone
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nedashkovskaya, O. I.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Vancanneyt, M.
    Winogradskyella rapida, sp. nov., isolated from protein-enriched seawater2009In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 59, p. 2180-2184Article in journal (Refereed)
    Abstract [en]

    Flavobacteria are emerging as an important group of organisms associated with the degradation of complex organic matter in aquatic environments. A novel Gram-reaction-negative, heterotrophic, rod-shaped, aerobic, yellow-pigmented and gliding bacterium, strain SCB36(T), was isolated from a protein-enriched seawater sample, collected at Scripps Pier, Southern California Bight (Eastern Pacific). Analysis of the 16S rRNA gene sequence showed that the bacterium was related to members of the genus Winogradskyella within the family Flavobacteriaceae, phylum Bacteroidetes. 16S rRNA gene sequence similarity to the other Winogradskyella species was 94.5-97.1%. DNA-DNA relatedness between strain SCB36(T) and Winogradskyella thalassocola KMM 3907(T), its closest relative in terms of 16S rRNA gene sequence similarity, was 20%. On the basis of the phylogenetic and phenotypic data, strain SCB36(T) represents a novel species of the genus Winogradskyella, for which the name Winogradskyella rapida sp. nov. is proposed. The type strain is SCB36(T) (=CECT 7392(T) =CCUG 56098(T)).

  • 323.
    Pinhassi, Jarone
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Pujalte, M. J.
    Pascual, J.
    Gonzalez, J. M.
    Lekunberri, I.
    Pedros-Alio, C.
    Arahal, D. R.
    Bermanella marisrubri gen. nov., sp. nov., a genome-sequenced gammaproteobacterium from the Red Sea2009In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 59, p. 373-377Article in journal (Refereed)
    Abstract [en]

    A novel heterotrophic, marine, strictly aerobic, motile bacterium was isolated from the Red Sea at a depth of 1 m. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to the genera Oleispira, Oceanobacter and Thalassolituus, each of which contains a single species, within the class Gammaproteobacteria. Phenotypic, genotypic and phylogenetic analyses supported the creation of a novel genus and species to accommodate this bacterium, for which the name Bermanella marisrubri gen. nov., sp. nov. is proposed. The type strain of Bermanella marisrubri is RED65(T) (-CECT 7074(T) =CCUG 52064(T)).

  • 324.
    Polacek, C
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Andersson, A
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Genetic analysis of the prototype strain of coxsackievirus B2 Ohio-11998In: EUROPIC 98: Jena, Germany, 1998Conference paper (Refereed)
  • 325.
    Polacek, C
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Johansson, S
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nilsson, A
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Ohlson, Sten
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, A. Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Reverse transcription and long distance enterovirus specific polymerase chain reaction (LDE-PCR) generates complete and infectious enterovirus cDNA genomes1996Conference paper (Refereed)
  • 326.
    Polacek, C
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Generation of wild type-like revertants upon transfection with a 3' end deletion mutant of coxsackievirusw B2 Ohio-12000In: EUROPIC 2000: XIth Meeting, Baia delle Zagare, Italy, 2000Conference paper (Refereed)
  • 327. Polacek, C
    et al.
    Lundgren, A
    Andersson, A.
    Lindberg, A. Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Genomic and phylogenetic characterization of coxsackievirus B2 prototype strain Ohio-11999In: Virus research, Vol. 59, p. 229-238Article in journal (Refereed)
  • 328.
    Polacek, Charlotta
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nilsson, Anne
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, A Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Study of tissue tropism using a cloned infectious full length cDNA derived from coxsackievirus B2 strain Ohio-11996Conference paper (Refereed)
  • 329.
    Polacel, C
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nilsson, A
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Characterization of the structural genes of the prototype strain of coxsackievirus B2 and a variant adapted to growth in rhabdomyosarcoma cells1997Conference paper (Refereed)
  • 330. Pontarp, Mikael
    et al.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundberg, Per
    Experimentally induced habitat filtering in marine bacterial communities2013In: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 477, p. 77-U406Article in journal (Refereed)
    Abstract [en]

    We tested the habitat filtering hypothesis by measuring the phylogenetic structure in marine bacterial communities before and after experimentally induced stress. The habitat filtering hypothesis predicts that phylogenetic clustering (mean relatedness) should increase as the environment becomes suitable for only a subset of the original community. We show that community composition and phylogenetic structure were considerably changed with changes in salinity and dissolved organic carbon. Community composition showed no consistent patterns, while the phylogenetic relatedness between species consistently increased with treatment. We have no information about species interactions in our system, but the phylogenetic signal is strong enough to suggest that habitat filtering is the dominant assembly process. Our results support the hypothesis that habitat characteristics and environmental stress can 'filter' a community so that only closely related species can persist. This non-random phylogenetic signal also implies a relationship between ecologically relevant characteristics and species relatedness.

  • 331.
    Poole, Anthony M.
    et al.
    University of Canterbury, New Zealand.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University.
    Rytkoenen, Kalle T.
    Yale University, USA.
    The evolution of early cellular systems viewed through the lens of biological interactions2015In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, article id 1144Article in journal (Refereed)
    Abstract [en]

    The minimal cell concept represents a pragmatic approach to the question of how few genes are required to run a cell. This is a helpful way to build a parts-list, and has been more successful than attempts to deduce a minimal gene set for life by inferring the gene repertoire of the last universal common ancestor, as few genes trace back to this hypothetical ancestral state. However, the study of minimal cellular systems is the study of biological outliers where, by practical necessity, coevolutionary interactions are minimized or ignored. In this paper, we consider the biological context from which minimal genomes have been removed. For instance, some of the most reduced genomes are from endosymbionts and are the result of coevolutionary interactions with a host; few such organisms are "free-living." As few, if any, biological systems exist in complete isolation, we expect that, as with modern life, early biological systems were part of an ecosystem, replete with organismal interactions. We favor refocusing discussions of the evolution of cellular systems on processes rather than gene counts. We therefore draw a distinction between a pragmatic minimal cell (an interesting engineering problem), a distributed genome (a system resulting from an evolutionary transition involving more than one cell) and the looser coevolutionary interactions that are ubiquitous in ecosystems. Finally, we consider the distributed genome and coevolutionary interactions between genomic entities in the context of early evolution.

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  • 332.
    Potrykus, Joanna
    et al.
    Umeå University.
    Jonna, Venkateswara Rao
    Umeå University.
    Dopson, Mark
    Umeå University.
    Iron homeostasis and responses to iron limitation in extreme acidophiles from the Ferroplasma genus.2011In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 11, no 1, p. 52-63Article in journal (Refereed)
    Abstract [en]

    Extremely acidophilic archaea from the genus Ferroplasma inhabit iron-rich biomining environments and are important constituents of naturally occurring microbial consortia that catalyze the production of acid mine drainage. A combined bioinformatic, transcript profiling, and proteomic approach was used to elucidate iron homeostasis mechanisms in "F. acidarmanus" Fer1 and F. acidiphilum Y(T) . Bioinformatic analysis of the "F. acidarmanus" Fer1 genome sequence revealed genes encoding proteins hypothesized to be involved in iron-dependent gene regulation and siderophore biosynthesis; the Fhu and NRAMP cation acquisition systems; iron storage proteins; and the SUF machinery for the biogenesis of Fe-S clusters. A subset of homologous genes was identified on the F. acidiphilum Y(T) chromosome by direct PCR probing. In both strains, some of the genes appeared to be regulated in a ferrous/ferric iron-dependent manner, as indicated by RT-PCR. A detailed gel-based proteomics analysis of responses to iron depletion showed that a putative isochorismatase, presumably involved in siderophore biosynthesis, and the SufBCD system were upregulated under iron-limiting conditions. No evidence was obtained for iron sparing response during iron limitation. This study constitutes the first detailed investigation of iron homeostasis in extremely acidophilic archaea.

  • 333.
    Raberg, L.
    et al.
    Lund University.
    Hagstrom, A.
    Lund University;Lab Med Clin Genet & Biobank, Lund.
    Andersson, Martin O.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University.
    Bartkova, S.
    Lund University.
    Scherman, K.
    Lund University.
    Strandh, M.
    Lund University.
    Tschirren, B.
    Lund University;Univ Exeter, UK.
    Evolution of antigenic diversity in the tick-transmitted bacterium Borrelia afzelii: a role for host specialization?2017In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, no 5, p. 1034-1041Article in journal (Refereed)
    Abstract [en]

    Antigenic diversity in pathogenic microbes can be a result of at least three different processes: diversifying selection by acquired immunity, host-pathogen coevolution and/or host specialization. Here, we investigate whether host specialization drives diversity at ospC (which encodes an immunodominant surface protein) in the tick-transmitted bacterium Borrelia afzelii. We determined prevalence and infection intensity of ospC strains in naturally infected wild mammals (rodents and shrews) by 454 amplicon sequencing in combination with qPCR. Neither prevalence nor infection intensity of specific ospC strains varied in a species-specific manner (i.e. there were no significant ospCxhost species interactions). Rankings of ospC prevalences were strongly positively correlated across host species. Rankings of ospC infection intensities were correlated more weakly, but only in one case significantly <1. ospC prevalences in the studied mammals were similar to those in ticks sampled at the study site, indicating that we did not miss any mammal species that are important hosts for specific ospC strains. Based on this, we conclude that there is at best limited host specialization in B.afzelii and that other processes are likely the main drivers of ospC diversity.

  • 334.
    Ramey, Andrew M.
    et al.
    U.S. Geological Survey, USA.
    Hernandez, Jorge
    Kalmar County Hospital.
    Tyrlöv, Veronica
    Uppsala University.
    Uher-Koch, Brian D.
    U.S. Geological Survey, USA.
    Schmutz, Joel A.
    U.S. Geological Survey, USA.
    Atterby, Clara
    Uppsala University.
    Järhult, Josef D.
    Uppsala Universit.
    Bonnedahl, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Kalmar County Hospital.
    Antibiotic-Resistant Escherichia coli in Migratory Birds Inhabiting Remote Alaska2018In: EcoHealth, ISSN 1612-9202, E-ISSN 1612-9210, Vol. 15, no 1, p. 72-81Article in journal (Refereed)
    Abstract [en]

    We explored the abundance of antibiotic-resistant Escherichia coli among migratory birds at remote sites in Alaska and used a comparative approach to speculate on plausible explanations for differences in detection among species. At a remote island site, we detected antibiotic-resistant E. coli phenotypes in samples collected from glaucous-winged gulls (Larus glaucescens), a species often associated with foraging at landfills, but not in samples collected from black-legged kittiwakes (Rissa tridactyla), a more pelagic gull that typically inhabits remote areas year-round. We did not find evidence for antibiotic-resistant E. coli among 347 samples collected primarily from waterfowl at a second remote site in western Alaska. Our results provide evidence that glaucous-winged gulls may be more likely to be infected with antibiotic-resistant E. coli at remote breeding sites as compared to sympatric black-legged kittiwakes. This could be a function of the tendency of glaucous-winged gulls to forage at landfills where antibiotic-resistant bacterial infections may be acquired and subsequently dispersed. The low overall detection of antibiotic-resistant E. coli in migratory birds sampled at remote sites in Alaska is consistent with the premise that anthropogenic inputs into the local environment or the relative lack thereof influences the prevalence of antibiotic-resistant bacteria among birds inhabiting the area.

  • 335. 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. 

  • 336.
    Retamal, Patricio
    et al.
    Univ Chile, Chile.
    Llanos-Soto, Sebastian
    Univ Concepcion, Chile.
    Moreno Salas, Lucila
    Univ Concepcion, Chile.
    Lopez, Juana
    Univ Concepcion, Chile.
    Vianna, Juliana
    Pontificia Univ Catolica Chile, Chile.
    Hernandez, Jorge
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Medina-Vogel, Gonzalo
    Univ Andres Bello, Chile.
    Castaneda, Francisco
    Univ Chile, Chile.
    Fresno, Marcela
    Univ Chile, Chile.
    Gonzalez-Acuna, Daniel
    Univ Concepcion, Chile.
    Isolation of drug-resistant Salmonella enterica serovar enteritidis strains in gentoo penguins from Antarctica2017In: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056, Vol. 40, no 12, p. 2531-2536Article in journal (Refereed)
    Abstract [en]

    Anthropogenic activity in Antarctica constitutes a continuous risk for the introduction of infectious diseases into indigenous wildlife populations. Penguin colonies living close to human settlements or inhabiting in areas considered for tourism could be facing a greater threat of infection. Fecal samples from Pygoscelis penguins (Pygoscelis spp.) were collected from different sites within Antarctic Peninsula and South Shetlands Islands in order to assess the presence of Salmonella enterica. Bacterial identification and characterization was performed applying biochemical and molecular techniques. Isolates were tested for antimicrobial resistance by the disk diffusion method, and PCR analyses were used for detection of resistance and virulence-associated genes. Four samples (1.74%) from P. papua were found to be positive to S. enterica serovar Enteritidis strains. All of them showed phenotypic antimicrobial resistance to at least three antimicrobials, and shared a similar gene profile through PCR. Results in this study urgently call for improvements in sanitary standards for waste disposal and sewage treatment in Antarctica. To our knowledge, this is the first study to report antimicrobial resistance in S. enterica isolated from Antarctic wild species.

  • 337.
    Riemann, Lasse
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Farnelid, Hanna
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Steward, Grieg F.
    Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity and regulation in marine waters2010In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 61, p. 225-237Article in journal (Refereed)
    Abstract [en]

    Marine waters are generally considered to be nitrogen (N) limited and are therefore favourable environments for diazotrophs, i.e. organisms converting atmospheric N-2 into ammonium or nitrogen oxides available for growth. In some regions, this import of N supports up to half of the primary productivity. Diazotrophic Cyanobacteria appear to be the major contributors to marine N-2 fixation in surface waters, whereas the contribution of heterotrophic or chemoautotrophic diazotrophs to this process is usually regarded inconsequential. Culture-independent studies reveal that non-cyanobacterial diazotrophs are diverse, widely distributed, and actively expressing the nitrogenase gene in marine and estuarine environments. The detection of nifH genes and nifH transcripts, even in N-replete marine waters, suggests that N-2 fixation is an ecologically important process throughout the oceans. Because this process is highly sensitive to and inhibited by molecular oxygen (O-2), diazotrophy requires efficient scavenging of intracellular O-2 or growth in environments with low ambient O-2 concentration. Particles with interior low-O-2 micro-zones and oceanic oxygen minimum zones are just 2 potential habitats suitable for N-2 fixation by non-cyanobacterial diazotrophs. Our ignorance about the regulation of N-2 fixation by non-Cyanobacteria in their natural marine environments currently prevents an evaluation of their importance in marine N cycling and budgets. A review of the molecular data on distribution and expression of nifH genes in non-Cyanobacteria suggests that further study of the role of these Bacteria in N cycling at local, regional and global scales is needed.

  • 338.
    Riemann, Lasse
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Holmfeldt, Karin
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Titelman, Josefin
    Importance of viral lysis and dissolved DNA for bacterioplankton activity in a P-limited estuary, northern Baltic Sea2009In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 57, no 2, p. 286-294Article in journal (Refereed)
    Abstract [en]

    Through lysis of bacterioplankton cells, viruses mediate an important, but poorly understood, pathway of carbon and nutrients from the particulate to the dissolved form. Via this activity, nutrient-rich cell lysates may become available to noninfected cells and support significant growth. However, the nutritional value of lysates for noninfected bacteria presumably depends on the prevailing nutrient limitation. In the present study, we examined dynamics of dissolved DNA (D-DNA) and viruses along a transect in the phosphorus (P)-limited A-re Estuary, northern Baltic Sea. We found that viruses were an important mortality factor for bacterioplankton and that their activity mediated a significant recycling of carbon and especially of P. Uptake of dissolved DNA accounted for up to 70% of the bacterioplankton P demand, and about a quarter of the D-DNA pool was supplied through viral lysis of bacterial cells. Generally, the importance of viral lysates and uptake of D-DNA was highest at the estuarine and offshore stations and was positively correlated with P limitation measured as alkaline phosphatase activity. Our results highlight the importance of viral activity for the internal recycling of principal nutrients and pinpoints D-DNA as a particularly relevant compound in microbial P dynamics.

  • 339.
    Roman, Pawel
    et al.
    Wageningen Univ, Netherlands;Wetsus, Netherlands.
    Klok, Johannes B. M.
    Wetsus, Netherlands;Paqell, Netherlands.
    Sousa, João A. B.
    Wageningen Univ, Netherlands;Wetsus, Netherlands.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Zessen, Erik Van
    Paques BV, Netherlands.
    Bijmans, Martijn F. M.
    Wetsus, Netherlands.
    Sorokin, Dimitry Y.
    Russian Acad Sci, Russia;Delft Univ Technol, Netherlands.
    Janssen, Albert J. H.
    Wageningen Univ, Netherlands;Shell Technol Ctr Bangalore, India.
    Selection and Application of Sulfide Oxidizing Microorganisms Able to Withstand Thiols in Gas Biodesulfurization Systems2016In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 50, no 23, p. 12808-12815Article in journal (Refereed)
    Abstract [en]

    After the first commercial applications of a new biological process for the removal of hydrogen sulfide (H2S) from low pressure biogas, the need arose to broaden the operating window to also enable the removal of organosulfur compounds from high pressure sour gases. In this study we have selected microorganisms from a full-scale biodesulfurization system that are capable of withstanding the presence of thiols. This full-scale unit has been in stable operation for more than 10 years. We investigated the microbial community by using high-throughput sequencing of 16S rRNA gene amplicons which showed that methanethiol gave a competitive advantage to bacteria belonging to the genera Thioalkalibacter (Halothiobacillaceae family) and Alkalilimnicola (Ectothiorhosdospiraceae family). The sulfide-oxidizing potential of the acclimatized population was investigated under elevated thiol loading rates (4.5–9.1 mM d–1), consisting of a mix of methanethiol, ethanethiol, and propanethiol. With this biomass, it was possible to achieve a stable bioreactor operation at which 80% of the supplied H2S (61 mM d–1) was biologically oxidized to elemental sulfur. The remainder was chemically produced thiosulfate. Moreover, we found that a conventionally applied method for controlling the oxygen supply to the bioreactor, that is, by maintaining a redox potential set-point value, appeared to be ineffective in the presence of thiols.

  • 340. Rosenberg, R.
    et al.
    Dahl, E.
    Edler, L.
    Fyrberg, L.
    Granéli, Edna
    Department of Marine Ecology, University of Lund .
    Granéli, W.
    Hagström, Åke
    Department of Microbiology, University of Umeå .
    Lindahl, O.
    Matos, M.O.
    Pettersson, K.
    Sahlsten, E.
    Tiselius, P.
    Turk, V.
    Wikner, J.
    Pelagic nutrient and energy transfer during spring in the open and coastal Skagerrak.1990In: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 61, no 3, p. 215-231Article in journal (Refereed)
  • 341.
    Rosengren, Johan
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    McManus, Ailsa
    Craik, David
    The structural and functional diversity of naturally occurring antimicrobial peptides2002In: Current Medicinal Chemistry - Anti Infective Agents, Vol. 1, no 4, p. 319-341Article, review/survey (Other academic)
    Abstract [en]

    Antimicrobial peptides occur in a diverse range of organisms from microorganisms to insects, plants and animals. Although they all have the common function of inhibiting or killing invading microorganisms they achieve this function using an extremely diverse range of structural motifs. Their sizes range from approximately 10-90 amino acids. Most carry an overall positive charge, reflecting a preferred mode of electrostatic interaction with negatively charged microbial membranes. This article describes the structural diversity of a representative set of antimicrobial peptides divided into five structural classes: those with -helical structure, those with -sheet structure, those with mixed helical / - sheet structure, those with irregular structure, and those incorporating a macrocyclic structure. There is a significant diversity in both the size and charge of molecules within each of these classes and between the classes. The common feature of their three-dimensional structures is, however, that they have a degree of amphipathic character in which there is separate localisation of hydrophobic regions and positively charged regions. An emerging trend amongst antimicrobial proteins is the discovery of more macrocyclic analogues. Cyclisation appears to impart an additional degree of stability on these molecules and minimizes proteolytic cleavage. In conclusion, there appear to be a number of promising opportunities for the development of novel clinically useful antimicrobial peptides based on knowledge of the structures of naturally occurring antimicrobial molecules.

  • 342.
    Rupar-Gadd, Katarina
    et al.
    Växjö University, Faculty of Mathematics/Science/Technology, School of Technology and Design. Avdelningen för Bioenergiteknik.
    Strandmark, Gunnar
    Växjö University, Faculty of Mathematics/Science/Technology, School of Technology and Design. Kemi.
    Welander, Ulrika
    Växjö University, Faculty of Mathematics/Science/Technology, School of Technology and Design. Avdelningen för Bioenergiteknik.
    Biological treatment of air polluted with alpha-pinene2008In: 16 th European Biomass Conference&Exhibition, Eta-Florence Renewable Energies , 2008Conference paper (Refereed)
    Abstract [en]

    A study was performed in order to evaluate if a more hydrophobic biofilter surface could facilitate the removal of hydrophobic pollutants from air. Alpha-pinene was used as a model compound since it is released from wood handling industries e.g. sawmills. Two biofilters were used during the study. One of the filter was filled with perlite soaked with silicone oil while the other was filled with untreated perlite. The removal efficiency was approximately the same for both filters except for the start up period when the oil soaked filter was more efficient.

  • 343.
    Rupar-Gadd, Katarina
    et al.
    Växjö University, Faculty of Mathematics/Science/Technology, School of Technology and Design. Avdelningen för Bioenergiteknik.
    Welander, Ulrika
    Växjö University, Faculty of Mathematics/Science/Technology, School of Technology and Design. Avdelningen för Bioenergiteknik.
    Emissions from stored biofuels for house-hold use, risks and health effects2008In: 16th European Biomass Conference&Exhibition, 2-6 June 2008, Valencia, Spain, ETA-Florence Renewable Energies , 2008Conference paper (Refereed)
    Abstract [en]

    By varying the storage conditions for lab-scale samples of different biomasses, the mircrobial growth in the samples varied. The microbial acitvity caused heat release and organic emissions were sampled. By measuring the heat release with isothermal calorimetry and organic emissions with solid phase microextraction (SPME) and gas chromatorgraphy with mass spectrometry (GC-MS), it may be posssible to predict the deterioriation in fuel quality, substance losses and health effects for a special fuel storage. The biofuels investigated were pellets made from peat/wood, bark/wood and wood pellets.

  • 344.
    Rzhepishevska, Olena I
    et al.
    Umeå University.
    Lindström, E Börje
    Umeå University.
    Tuovinen, Olli H
    Ohio State University, USA.
    Dopson, Mark
    Umeå University.
    Bioleaching of sulfidic tailing samples with a novel, vacuum-positive pressure driven bioreactor.2005In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 92, no 5, p. 559-567Article in journal (Refereed)
    Abstract [en]

    This study presents a design for a novel bioreactor that uses alternating vacuum and positive pressure cycles to transfer acidic leach solution in and out of contact with finely ground sulfidic mine tailings. These tailings constitute an environmental problem that needs experimental data to support the development of management and control strategies. A conventional stirred tank bioreactor was used as a reference system. Both bioreactors were inoculated with mixed cultures of acidophilic iron and sulfur oxidizers. The rate of the bioleaching of tailings was 0.50 +/- 0.14 g Fe/L . day in the stirred tank bioreactor and 0.17 +/- 0.05 g Fe/L . day in the novel bioreactor. Microbial populations were identified in the two-bioreactor systems by analysis of 16S rRNA genes involving amplification, denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The inoculum contained sulfur-oxidizing Acidithiobacillus caldus and Acidithiobacillus thiooxidans, iron oxidizers from the genera Leptospirillum and Ferroplasma, and a chemoorganotrophic Alicyclobacillus sp. During bioleaching of the tailings, the microbial populations in both bioreactors were similar to the inoculum culture, except that At. thiooxidans outgrew At. caldus. Sequences consistent with a Sulfobacillus sp. were amplified from both bioreactor samples although this bacterium was initially below the level of detection in the inoculum. After prolonged operation, Ferroplasma acidiphilum and an uncultured bacterium related to the CFB group were also detected in the novel bioreactor, whereas Sulfobacillus sp. was no longer detected. The novel bioreactor has potential uses in other areas of environmental biotechnology that involves periodic contact of liquids with solid substrates.

  • 345.
    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.

  • 346.
    Sabin, Charles
    et al.
    Masaryk Univ, Czech Republic.
    Fuzik, Tibor
    Masaryk Univ, Czech Republic.
    Skubnik, Karel
    Masaryk Univ, Czech Republic.
    Palkova, Lenka
    Masaryk Univ, Czech Republic.
    Lindberg, A. Michael
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Plevka, Pavel
    Masaryk Univ, Czech Republic.
    Structure of Aichi Virus 1 and Its Empty Particle: Clues to Kobuvirus Genome Release Mechanism2016In: Journal of Virology, ISSN 0022-538X, E-ISSN 1098-5514, Vol. 90, no 23, p. 10800-10810Article in journal (Refereed)
    Abstract [en]

    Aichi virus 1 (AiV-1) is a human pathogen from the Kobuvirus genus of the Picornaviridae family. Worldwide, 80 to 95% of adults have antibodies against the virus. AiV-1 infections are associated with nausea, gastroenteritis, and fever. Unlike most picornaviruses, kobuvirus capsids are composed of only three types of subunits: VP0, VP1, and VP3. We present here the structure of the AiV-1 virion determined to a resolution of 2.1 angstrom using X-ray crystallography. The surface loop puff of VP0 and knob of VP3 in AiV-1 are shorter than those in other picornaviruses. Instead, the 42-residue BC loop of VP0 forms the most prominent surface feature of the AiV-1 virion. We determined the structure of AiV-1 empty particle to a resolution of 4.2 angstrom using cryo-electron microscopy. The empty capsids are expanded relative to the native virus. The N-terminal arms of capsid proteins VP0, which mediate contacts between the pentamers of capsid protein protomers in the native AiV-1 virion, are disordered in the empty capsid. Nevertheless, the empty particles are stable, at least in vitro, and do not contain pores that might serve as channels for genome release. Therefore, extensive and probably reversible local reorganization of AiV-1 capsid is required for its genome release. IMPORTANCE Aichi virus 1 (AiV-1) is a human pathogen that can cause diarrhea, abdominal pain, nausea, vomiting, and fever. AiV-1 is identified in environmental screening studies with higher frequency and greater abundance than other human enteric viruses. Accordingly, 80 to 95% of adults worldwide have suffered from AiV-1 infections. We determined the structure of the AiV-1 virion. Based on the structure, we show that antiviral compounds that were developed against related enteroviruses are unlikely to be effective against AiV-1. The surface of the AiV-1 virion has a unique topology distinct from other related viruses from the Picornaviridae family. We also determined that AiV-1 capsids form compact shells even after genome release. Therefore, AiV-1 genome release requires large localized and probably reversible reorganization of the capsid.

  • 347.
    Sallstedt, Therese
    et al.
    Swedish Museum of Natural History, Sweden.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Sweden;Univ Southern Denmark, Denmark.
    Drake, Henrik
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Skogby, Henrik
    Swedish Museum of Natural History, Sweden.
    Instant Attraction: Clay Authigenesis in Fossil Fungal Biofilms2019In: Geosciences, E-ISSN 2076-3263, Vol. 9, no 9, p. 1-21, article id 369Article, review/survey (Refereed)
    Abstract [en]

    Clay authigenesis associated with the activity of microorganisms is an important process for biofilm preservation and may provide clues to the formation of biominerals on the ancient Earth. Fossilization of fungal biofilms attached to vesicles or cracks in igneous rock, is characterized by fungal-induced clay mineralization and can be tracked in deep rock and deep time, from late Paleoproterozoic (2.4 Ga), to the present. Here we briefly review the current data on clay mineralization by fossil fungal biofilms from oceanic and continental subsurface igneous rock. The aim of this study was to compare the nature of subsurface fungal clays from different igneous settings to evaluate the importance of host rock and ambient redox conditions for clay speciation related to fossil microorganisms. Our study suggests that the most common type of authigenic clay associated with pristine fossil fungal biofilms in both oxic (basaltic) and anoxic (granitic) settings are montmorillonite-like smectites and confirms a significant role of fungal biofilms in the cycling of elements between host rock, ocean and secondary precipitates. The presence of life in the deep subsurface may thus prove more significant than host rock geochemistry in directing the precipitation of authigenic clays in the igneous crust, the extent of which remains to be fully understood.

  • 348.
    Sanchez-Castro, Ivan
    et al.
    Univ Granada, Spain.
    Angel Ruiz-Fresneda, Miguel
    Univ Granada, Spain.
    Bakkali, Mohammed
    Univ Granada, Spain.
    Kaempfer, Peter
    Justus Liebig Univ Giessen, Germany.
    Glaeser, Stefanie P.
    Justus Liebig Univ Giessen, Germany.
    Busse, Hans Juergen
    Vet Med Univ Wien, Austria.
    Lopez-Fernandez, Margarita
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Granada, Spain.
    Martinez-Rodriguez, Pablo
    Univ Granada, Spain.
    Larbi Merroun, Mohamed
    Univ Granada, Spain.
    Stenotrophomonas bentonitica sp nov., isolated from bentonite formations2017In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 67, no 8, p. 2779-2786Article in journal (Refereed)
    Abstract [en]

    A Gram-stain negative, rod-shaped, aerobic bacterial strain, BII-R7(T), was isolated during a study targeting the culture-dependent microbial diversity occurring in bentonite formations from southern Spain. Comparative 16S rRNA gene sequence analysis showed that BII-R7T represented a member of the genus Stenotrophomonas (class Gammaproteobacteria), and was related most closely to Stenotrophomonas rhizophila e-p10(T) (99.2% sequence similarity), followed by Stenotrophomonas pavanii ICB 89(T) (98.5 %), Stenotrophomonas maltophilia IAM 12423(T), Stenotrophomonas chelatiphaga LPM-5(T) and Stenotrophomonas tumulicola T5916-2-1b(T) (all 98.3 %). Pairwise sequence similarities to all other type strains of species of the genus Stenotrophomonas were below 98 %. Genome- based calculations (orthologous average nucleotide identity, original average nucleotide identity, genome-to-genome distance and DNA G+C percentage) indicated clearly that the isolate represents a novel species within this genus. Different phenotypic analyses, such as the detection of a quinone system composed of the major compound ubiquinone Q-8 and a fatty acid profile with iso-C-15:0 and anteiso-C-15:0 as major components, supported this finding at the same time as contributing to a comprehensive characterization of BII-R7(T). Based on this polyphasic approach comprising phenotypic and genotypic/molecular characterization, BII-R7(T) can be differentiated clearly from its phylogenetic neighbours, establishing a novel species for which the name Stenotrophomonas bentonitica sp. nov.is proposed with BII-R7(T) as the type strain (= LMG 29893(T) = CECT 9180(T) = DSM 103927(T)).

  • 349. Sandaa, R.-A.
    et al.
    Gómez-Consarnau, Laura
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Pinhassi, Jarone
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Riemann, Lasse
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Malits, A.
    Weinbauer, M.G.
    Gasol, J.M.
    Thingstad, T.F.
    Viral control of bacterial biodiversity – Evidence from a nutrient enriched marine mesocosm experiment2009In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 11, no 10, p. 2585-2597Article in journal (Refereed)
    Abstract [en]

    We demonstrate here results showing that bottom-up and top-down control mechanisms can operate simultaneously and in concert in marine microbial food webs, controlling prokaryote diversity by a combination of viral lysis and substrate limitation. Models in microbial ecology predict that a shift in the type of bacterial growth rate limitation is expected to have a major effect on species composition within the community of bacterial hosts, with a subsequent shift in the composition of the viral community. Only moderate effects would, however, be expected in the absolute number of coexisting virus-host pairs. We investigated these relationships in nutrient-manipulated systems, under simulated in situ conditions. There was a strong correlation in the clustering of the viral and bacterial community data supporting the existence of an important link between the bacterial and viral communities. As predicted, the total number of viral populations was the same in all treatments, while the composition of the viral community varied. Our results support the theoretical prediction that there is one control mechanism for the number of niches for coexisting virus-host pairs (top-down control), and another mechanism that controls which virus-host pairs occupy these niches (bottom-up control).

  • 350. Sarmento, Hugo
    et al.
    Romera-Castillo, Cristina
    Lindh, Markus V.
    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.
    Sala, M. Montserrat
    Gasol, Josep M.
    Marrase, Celia
    Taylor, Gordon T.
    Phytoplankton species-specific release of dissolved free amino acids and their selective consumption by bacteria2013In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 58, no 3, p. 1123-1135Article in journal (Refereed)
    Abstract [en]

    Despite representing only a small fraction of the ocean's dissolved organic matter pool, dissolved free amino acids (DFAA) have high turnover rates and are major nitrogen and carbon sources for bacterioplankton. Both phytoplankton and bacterioplankton assimilate and release DFAA, but their consumption and production are difficult to quantify in nature due to their short residence times (min) as dissolved monomers. We segregated DFAA production by phytoplankton and bacterial consumption by measuring individual DFAA concentrations in four axenic phytoplankton cultures during the exponential growth phase, and also after 4 d incubations in the presence of a natural bacterioplankton community. The amounts and composition of the DFAA pool varied widely among phytoplankton species. The proportion of dissolved organic carbon attributed to DFAA varied among cultures. The picoeukaryotic prasinophyte, Micromonas pusilla, released higher amounts of DFAA than the other species tested (diatoms and dinoflagellate), especially alanine, which has been reported as the dominant individual DFAA in some oligotrophic environments. Community structure of heterotrophic prokaryotes responded to differences in the quality of organic matter released among microalgal species, with Roseobacter-related bacteria responding strongly to exudate composition. Our results demonstrate the specificity of DFAA extracellular release among several algal species and their preferential uptake by members of bacterial communities.

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