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  • 1.
    Acuna, Lillian G.
    et al.
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Pablo Cardenas, Juan
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Covarrubias, Paulo C.
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Jose Haristoy, Juan
    Fundación Ciencia & Vida, Chile.
    Flores, Rodrigo
    Fundación Ciencia & Vida, Chile.
    Nuñez, Harold
    Fundación Ciencia & Vida, Chile.
    Riadi, Gonzalo
    Universidad de Talca, Chile.
    Shmaryahu, Amir
    Fundación Ciencia & Vida, Chile.
    Valdes, Jorge
    Center for Systems Biotechnology, Chile.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Rawlings, Douglas E.
    University of Stellenbosch, South Africa.
    Banfield, Jillian F.
    University of California, USA.
    Holmes, David S.
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Quatrini, Raquel
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 11, article id e78237Article in journal (Refereed)
    Abstract [en]

    Background: Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. Principal Findings: Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. Significance: For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.

  • 2.
    Akram, Neelam
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    From genes to ecological function in marine bacteria2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bacteria in the sea are constantly exposed to environmental challenges (e.g. variations in nutrient concentrations, temperature and light conditions), and therefore appropriate gene expression response strategies to cope with them efficiently are evolved. This thesis investigates some interconnected questions regarding such adaptive strategies employed by marine bacteria.

    The recently discovered ability of bacteria to use the membrane protein proteorhodopsin (PR) to harvest light energy for cell metabolism were investigated in Vibrio sp. AND4 and Dokdonia sp. MED134. PR phototrophy in AND4 promoted survival during starvation, the molecular basis for which were the upregulation of the PR gene by nutrient limitation rather than light. MED134, in contrast, uses PR phototrophy to grow better, and we discovered that the light-stimulated growth was stronger in seawater with the single carbon compound alanine compared to a mixture of complex organic matter. Thus, differences between bacteria in PR gene expression regulation in response to light, nutrients or organic matter quality critically determine the ecological role of PR phototrophy in the sea.

    Current observations that membrane transporters (including PR) are highly expressed in seawater inspired a comparative analysis of transporter distributions in marine bacteria. Totally, 192 transporter families were found in 290 genome-sequenced strains. Consistent differences, but also similarities, in the number of transporters were found between major bacterial groups. Interestingly, sodium transporters were found to be more abundant in PR-containing SAR11. These findings suggest that bacteria have inherently distinctive potentials to adapt to resource variations in the sea.

    To examine links between transcriptional responses and growth of bacteria under controlled environmental settings, a mesocosm phytoplankton bloom experiment was performed. Transcriptional analysis of the microbial community (i.e. metatranscriptomics) revealed 2800 categories of functional genes (SEED functions), of which around 10% were overrepresented in either the bloom mesocosms or the controls. Importantly, these functions indicated potential metabolic mechanisms (e.g. TonB mediated nutrient transport) by which bacteria took advantage of the bloom conditions.

    This thesis combines analyses of model organisms with community analysis and highlights the possibilities to identify important mechanisms that underlie the ecological success of different bacteria in the marine environment. 

  • 3. Alonso-Saez, L.
    et al.
    Vazquez-Dominguez, E.
    Cardelus, C.
    Pinhassi, Jarone
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Sala, M. M.
    Lekunberri, I.
    Balague, V.
    Vila-Costa, M.
    Unrein, F.
    Massana, R.
    Simo, R.
    Gasol, J. M.
    Factors controlling the year-round variability in carbon flux through bacteria in a coastal marine system2008In: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 11, no 3, p. 397-409Article in journal (Refereed)
    Abstract [en]

    Data from several years of monthly samplings are combined with a 1-year detailed study of carbon flux through bacteria at a NW Mediterranean coastal site to delineate the bacterial role in carbon use and to assess whether environmental factors or bacterial assemblage composition affected the in situ rates of bacterial carbon processing. Leucine (Leu) uptake rates [as an estimate of bacterial heterotrophic production (BHP)] showed high interannual variability but, on average, lower values were found in winter (around 50 pM Leu(-1) h(-1)) as compared to summer (around 150 pM Leu(-1) h(-1)). Leu-to-carbon conversion factors ranged from 0.9 to 3.6 kgC mol Leu(-1), with generally higher values in winter. Leu uptake was only weakly correlated to temperature, and over a full-year cycle (in 2003), Leu uptake peaked concomitantly with winter chlorophyll a (Chl a) maxima, and in periods of high ectoenzyme activities in spring and summer. This suggests that both low molecular weight dissolved organic matter (DOM) released by phytoplankton, and high molecular weight DOM in periods of low Chl a, can enhance BHP. Bacterial respiration (BR, range 7-48 mu g C l(-1) d(-1)) was not correlated to BHP or temperature, but was significantly correlated to DOC concentration. Total bacterial carbon demand (BHP plus BR) was only met by dissolved organic carbon produced by phytoplankton during the winter period. We measured bacterial growth efficiencies by the short-term and the long-term methods and they ranged from 3 to 42%, increasing during the phytoplankton blooms in winter (during the Chl a peaks), and in spring. Changes in bacterioplankton assemblage structure (as depicted by denaturing gradient gel electrophoresis fingerprinting) were not coupled to changes in ecosystem functioning, at least in bacterial carbon use.

  • 4. Alonso-Saéz, Laura
    et al.
    Waller, Allison S
    Mende, Daniel R
    Bakker, Kevin
    Farnelid, Hanna
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Yager, Patricia L
    Lovejoy, Connie
    Tremblay, Jean-Eric
    Potvin, Marianne
    Heinrich, Friederike
    Estrada, Marta
    Riemann, Lasse
    Marine Biological Section, University of Copenhagen, 3000 Helsingør, Denmark .
    Bork, Peer
    Pedros-Alio, Carlos
    Bertilsson, Stefan
    Role for urea in nitrification by polar marine Archaea2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 44, p. 17989-17994Article in journal (Refereed)
    Abstract [en]

    Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.

  • 5. Ammerman, J.W.
    et al.
    Fuhrman, J.A.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Azam, F.
    Bacterioplankton growth in seawater: I.Growth kinetics and cellular characteristics in seawater cultures1984In: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 18, p. 31-39Article in journal (Refereed)
  • 6. Andersson, A.
    et al.
    Falk, S.
    Samuelsson, G.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nutritional characteristics of a mixitropic nanoflagellate, Ochromonas sp.1989In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 17, p. 117-128Article in journal (Refereed)
  • 7.
    Andersson, Agneta
    et al.
    Department of Microbiology. University of Urnea. S-901 87 UMEA, Sweden.
    Lee, C.
    Azam, F.
    Hagström, Åke
    Department of Microbiology. University of Urnea. S-901 87 UMEA, Sweden.
    Release of aminoacids and inorganic nutrients by heterotrophic marine microflagellates1985In: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 23, p. 99-106Article in journal (Refereed)
    Abstract [en]

    Heterotrophic microflagellates isolated from the Baltic Sea and grown under laboratoryconditions were shown to release dissolved free amino acids (DFAA) when grazing bacteria. Flagellatesreleased 3H-amino acids when fed 3H-leucine-labelled bacteria, and concentrations of aminoacids increased in the experimental medium. Serine showed a strong positive correlation withflagellate feeding. Aspartic acid, glutamic acid and ornithine also increased more than other aminoacids. During consumption of bacteria, the flagellates released 13% of the ingested nitrogen asammonia, and 30 % of the ingested phosphorus as phosphate. In a field experiment off Scripps Pier, wemeasured bacterial production, flagellate abundance, and concentration of DFAA over a 28 h period.The concentration of DFAA showed a covariation with the flagellate numbers. Results from our fieldand laboratory experiments suggest that flagellates may be a source of DFAA in the sea. 

  • 8. Andersson, Anders F.
    et al.
    Riemann, Lasse
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Bertilsson, Stefan
    Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities2010In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, l, Vol. 4, p. 171-181Article in journal (Refereed)
    Abstract [en]

    Variation in traits causes bacterial populations to respond in contrasting ways to environmental drivers. Learning about this will help us understand the ecology of individual populations in complex ecosystems. We used 454 pyrosequencing of the hypervariable region V6 of the 16S rRNA gene to study seasonal dynamics in Baltic Sea bacterioplankton communities, and link community and population changes to biological and chemical factors. Surface samples were collected from May to October 2003 and in May 2004 at the Landsort Deep in the central Baltic Sea Proper. The analysis rendered, on average, 20 200 sequence reads for each of the eight samples analyzed, providing the first detailed description of Baltic Sea bacterial communities. Community composition varied dramatically over time, supporting the idea of strong temporal shifts in bacterioplankton assemblages, and clustered according to season (including two May samples from consecutive years), suggesting repeatable seasonal succession. Overall, community change was most highly correlated with change in phosphorus concentration and temperature. Individual bacterial populations were also identified that tightly co-varied with different Cyanobacteria populations. Comparing the abundance profiles of operational taxonomic units at different phylogenetic distances revealed a weak but significant negative correlation between abundance profile similarity and genetic distance, potentially reflecting habitat filtering of evolutionarily conserved functional traits in the studied bacterioplankton.

  • 9.
    Andersson, Martin O.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Chitimia-Dobler, Lidia
    Inst Diag & Anim Hlth, Romania ; German Ctr Infect Res DZIF Partner Munich, Germany.
    Detection of Cercopithifilaria bainae in western Romania2017In: Parasitology Research, ISSN 0932-0113, E-ISSN 1432-1955, Vol. 116, no 11, p. 3235-3238Article in journal (Refereed)
    Abstract [en]

    Cercopithifilaria species are tick-transmitted filarial parasites of mammals. In Europe, three Cercopithifilaria spp. are known to parasitize dogs, all occurring mainly in the Mediterranean countries. In Romania, Cercopithifilaria bainae has been reported in a single dog in eastern Romania but the occurrence in other parts of the country is not known. To further elucidate the geographic distribution of Cercopithifilaria spp. infection, 544 ticks were collected from dogs in several locations across Romania. The presence of Cercopithifilaria spp. was investigated with real-time PCR. A single Dermacentor reticulatus female tick was found to be infected with Cercopithifilaria bainae. The finding in the present study is geographically separated from the previous finding in Romania by 800 km, as well as by the Carpathian mountain range. Hence, C. bainae is more geographically widespread in Romania than previously recognized. However, the single detection does suggest that infection is rather uncommon in Romanian dogs. Nevertheless, further studies on Cercopithifilaria spp. distribution and prevalence are needed.

  • 10.
    Andersson, Martin O.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Radbea, Gabriel
    Sal Vet Private Vet Clin, Romania.
    Frangoulidis, Dimitrios
    Bundeswehr Inst Microbiol, Germany;German Ctr Infect Res DZIF Partner Munich.
    Tomaso, Herbert
    Friedrich Loeffler Inst, Germany.
    Rubel, Franz
    Univ Vet Med Vienna, Austria.
    Nava, Santiago
    Estn Expt Agr Rafaela, Argentina.
    Chitimia-Dobler, Lidia
    Bundeswehr Inst Microbiol, Germany;German Ctr Infect Res DZIF Partner Munich, Germany;Inst Diag & Anim Hlth, Romania.
    New records and host associations of the tick Ixodes apronophorus and the first detection of Ehrlichia sp HF in Romania2018In: Parasitology Research, ISSN 0932-0113, E-ISSN 1432-1955, Vol. 117, no 4, p. 1285-1289Article in journal (Refereed)
    Abstract [en]

    Ixodes (Ixodes) apronophorus is a neglected tick species and its geographical distribution, host associations, and role as a disease vector are not well known. We collected I. apronophorus from several locations in Romania. Morphological identification of ticks was confirmed by analysis of 16S rDNA and 12S rDNA gene sequences. We report new host associations of I. apronophorus, which was collected from dogs, foxes, and a hare-all new hosts for this tick species in Romania. Furthermore, we report for the first time occurrence of Ehrlichia sp. HF in I. apronophorus. Ehrlichia sp. HF was identified by sequencing a part of the 16S rDNA gene and was found in 16% (3/19) of the tested ticks. Ehrlichia sp. HF has not been previously reported in Eastern Europe and seems to have a much larger geographic distribution than previously known. Currently, it is unknown whether I. apronophorus is a competent vector for Ehrlichia sp. HF, or if the findings in this study represent infection in the hosts, namely dogs and fox.

  • 11.
    Andersson, Martin O.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Tolf, Conny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Tamba, Paula
    Inst Diag & Anim Hlth, Romania.
    Stefanache, Mircea
    PAUMI VET Private Vet Clin, Romania.
    Radbea, Gabriel
    Sal Vet Private Vet Clin, Romania.
    Frangoulidis, Dimitrios
    Bundeswehr Inst Microbiol, Germany.
    Tomaso, Herbert
    Friedrich Loeffler Inst, Germany.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dobler, Gerhard
    Bundeswehr Inst Microbiol, Germany;German Ctr Infect Res DZIF Partner Munich, Germany.
    Chitimia-Dobler, Lidia
    Inst Diag & Anim Hlth, Romania;Bundeswehr Inst Microbiol, Germany;German Ctr Infect Res DZIF Partner Munich, Germany.
    Molecular survey of neglected bacterial pathogens reveals an abundant diversity of species and genotypes in ticks collected from animal hosts across Romania2018In: Parasites & Vectors, ISSN 1756-3305, E-ISSN 1756-3305, Vol. 11, article id 144Article in journal (Refereed)
    Abstract [en]

    Background: Ticks are transmitting a wide range of bacterial pathogens that cause substantial morbidity and mortality in domestic animals. The full pathogen burden transmitted by tick vectors is incompletely studied in many geographical areas, and extensive studies are required to fully understand the diversity and distribution of pathogens transmitted by ticks. Results: We sampled 824 ticks of 11 species collected in 19 counties in Romania. Ticks were collected mainly from dogs, but also from other domestic and wild animals, and were subjected to molecular screening for pathogens. Rickettsia spp. was the most commonly detected pathogen, occurring in 10.6% (87/824) of ticks. Several species were detected: Rickettsia helvetica, R. raoultii, R. massiliae, R. monacensis, R. slovaca and R. aeschlimannii. A single occurrence of the zoonotic bacterium Bartonella vinsonii berkhoffii was detected in a tick collected from a dog. Anaplasma phagocytophilum occurred in four samples, and sequences similar to Anaplasma marginale/ovis were abundant in ticks from ruminants. In addition, molecular screening showed that ticks from dogs were carrying an Ehrlichia species identical to the HF strain as well as the enigmatic zoonotic pathogen "Candidatus Neoehrlichia mikurensis". An organism similar to E. chaffeensis or E. muris was detected in an Ixodes ricinus collected from a fox. Conclusions: We describe an abundant diversity of bacterial tick-borne pathogens in ticks collected from animal hosts in Romania, both on the level of species and genotypes/strains within these species. Several findings were novel for Romania, including Bartonella vinsonii subsp. berkhoffii that causes bacteremia and endocarditis in dogs. "Candidatus Neoehrlichia mikurensis" was detected in a tick collected from a dog. Previously, a single case of infection in a dog was diagnosed in Germany. The results warrant further studies on the consequences of tick-borne pathogens in domestic animals in Romania.

  • 12.
    Andersson, Martin O.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Tolf, Conny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Tamba, Paula
    Inst Diag & Anim Hlth, Romania.
    Stefanache, Mircea
    PAUMI VET Private Vet Clin, Romania.
    Radbea, Gabriel
    Sal Vet Private Vet Clin, Romania.
    Rubel, Franz
    Univ Vet Med Vienna, Austria.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dobler, Gerhard
    German Ctr Infect Res DZIF Partner Munich, Germany.
    Chitimia-Dobler, Lidia
    Inst Diag & Anim Hlth, Romania ; German Ctr Infect Res DZIF Partner Munich, Germany.
    Babesia, Theileria, and Hepatozoon species in ticks infesting animal hosts in Romania2017In: Parasitology Research, ISSN 0932-0113, E-ISSN 1432-1955, Vol. 116, no 8, p. 2291-2297Article in journal (Refereed)
    Abstract [en]

    Babesia spp., Theileria spp., and Hepatozoon spp. are tick-transmitted apicomplexan parasites that cause several important diseases in animals. To increase current knowledge about the diversity of tick-transmitted pathogens in Romania, we investigated the occurrence of Babesia spp., Theileria spp., and Hepatozoon spp. in a wide range of tick species infesting animal hosts. We collected 852 ticks from 10 different animal species from 20 counties in Romania. The assessment was based on detection of parasite DNA by PCR. Five different apicomplexan parasite species were detected; among them three different species of Babesia: B. canis, B. microti, and B. ovis. Hepatozoon canis was the most frequently detected parasite, found predominately in Ixodes ricinus ticks collected from domestic dogs. It was also detected in I. ricinus collected from goat, fox, and cat. Furthermore, H. canis was found in Haemaphysalis punctata and Haemaphysalis concinna ticks. In addition, Theileria buffeli was detected in Rhipicephalus bursa ticks collected from cattle.

  • 13.
    Andersson, Martin O.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vichova, Bronislava
    Slovak Acad Sci, Slovakia.
    Tolf, Conny
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Krzyzanowska, Sandra
    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.
    Karlsson, Maria E.
    Swedish University of Agricultural Sciences.
    Co-infection with Babesia divergens and Anaplasma phagocytophilum in cattle (Bos taurus), Sweden2017In: Ticks and Tick-borne Diseases, ISSN 1877-959X, E-ISSN 1877-9603, Vol. 8, no 6, p. 933-935Article in journal (Refereed)
    Abstract [en]

    Babesiosis is a severe disease in cattle worldwide. In Europe, the main causative agent of bovine babesiosis is Babesia divergens. In some areas, this species is reported to have declined or even disappeared, and its etiological role overtaken by other piroplasmid species. Moreover, co-infection with other tick-transmitted pathogens can be expected to complicate diagnosis in cattle. Hence, molecular identification of the causative agent of babesiosis should be a priority. Therefore, samples from 71 domestic cattle, 39 with clinical signs of babesiosis and 32 without, from southern Sweden were screened for Babesia spp. and Anaplasma spp. using molecular methods Babesia divergens was detected in 38 of the samples, and Anaplasma phagocytophilum in 17. Co-infections with both pathogens were frequent, occurring in 18% of the animals with a B. divergens infection. The possibility of co-infection should be considered in diagnosis and treatment of bovine babesiosis.

  • 14. Andersson, P
    et al.
    Edman, Kjell
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Lindberg, A. Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Molecular analysis of the echovirus 18 prototype2002In: Virus research, Vol. 85, p. 71-83Article in journal (Refereed)
  • 15.
    Arahal, David R.
    et al.
    Univ Valencia, Spain.
    Lucena, Teresa
    Univ Valencia, Spain.
    Carmen Macian, M.
    Univ Valencia, Spain.
    Ruvira, Maria A.
    Univ Valencia, Spain.
    Gonzalez, Jose M.
    Univ La Laguna, Spain.
    Lekumberri, Itziar
    Univ Girona, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pujalte, Maria J.
    Univ Valencia, Spain.
    Marinomonas blandensis sp nova, a novel marine gammaproteobacterium2016In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 66, p. 5544-5549Article in journal (Refereed)
    Abstract [en]

    A novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121(T), was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to Marinomonas dokdonensis and other Marinomonas species (96.3 and 93.3-95.7% sequence similarities, respectively), within the family Oceanospirillaceae. Strain MED121(T) was included into a whole-genome sequencing study and, subsequently, it was characterized using a polyphasic taxonomic approach. It was found to be oxidase and catalase positive, its cells are cocci to short rods, it does not ferment carbohydrates and does not reduce nitrate to nitrite or gas and it requires at least 2.5% (w/v) marine salts and tolerates up to 7% (w/v) salts. Its major cellular fatty acids in order of abundance are C-16:1 omega 7c/C-16:1 omega 6c,C-18:1 omega 7c(1), C-16:0 and C-10:0 3-OH. Its genome had an approximate length of 5.1 million bases and a DNA G+C content equal to 40.9 mol%. Analysis of the annotated genes reveals the capacity for the synthesis of ubiquinone 8 (O8) and the polar lipids phosphatidylglycerol and phosphatidylethanolannine, in agreement with other members of the genus. All the data collected supported the creation of a novel species to accommodate this bacterium, for which the name Marinomonas blandensis sp. nov. is proposed. The type strain is MED121(T) (=CECT 7076(T)=LMG 29722(T)).

  • 16.
    Ardiles-Villegas, Karen
    et al.
    Universidad de Concepción, Chile.
    González-Acuña, Daniel
    Universidad de Concepción, Chile.
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Olsen, Björn
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Uppsala University.
    Hernandez, Jorge
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Uppsala University.
    Antibiotic resistance patterns in fecal bacteria isolated from Christmas shearwater (Puffinus nativitatis) and masked booby (Sula dactylatra) at remote Easter Island2011In: Avian diseases, ISSN 0005-2086, E-ISSN 1938-4351, Vol. 55, no 3, p. 486-489Article in journal (Refereed)
    Abstract [en]

    Antibiotic use and its implications have been discussed extensively in the past decades. This situation has global consequences when antibiotic resistance becomes widespread in the intestinal bacterial flora of stationary and migratory birds. This study investigated the incidence of fecal bacteria and general antibiotic resistance, with special focus on extended spectrum beta-lactamase (ESBL) isolates, in two species of seabirds at remote Easter Island. We identified 11 species of bacteria from masked booby (Sula dactylatra) and Christmas shearwater (Puffinus nativitatis); five species of gram-negative bacilli, four species of Streptococcus (Enterococcus), and 2 species of Staphylococcus. In addition, 6 types of bacteria were determined barely to the genus level. General antibiotic susceptibility was measured in the 30 isolated Enterobacteriaceae to 11 antibiotics used in human and veterinary medicine. The 10 isolates that showed a phenotypic ESBL profile were verified by clavulanic acid inhibition in double mixture discs with cefpodoxime, and two ESBL strains were found, one strain in masked booby and one strain in Christmas shearwater. The two bacteria harboring the ESBL type were identified as Serratia odorifera biotype 1, which has zoonotic importance. Despite minimal human presence in the masked booby and Christmas shearwater habitats, and the extreme geographic isolation of Easter Island, we found several multiresistant bacteria and even two isolates with ESBL phenotypes. The finding of ESBLs has animal and public health significance and is of potential concern, especially because the investigation was limited in size and indicated that antibiotic-resistant bacteria now are distributed globally.

  • 17.
    Asplund-Samuelsson, Johannes
    et al.
    Stockholm University.
    Sundh, John
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dupont, Chris L.
    Craig Venter Institute, USA.
    Allen, Andrew E.
    Craig Venter Institute, USA.
    McCrow, John P.
    Craig Venter Institute, USA.
    Celepli, Narin A.
    Stockholm University.
    Bergman, Birgitta
    Stockholm University.
    Ininbergs, Karolina
    Stockholm University.
    Ekman, Martin
    Stockholm University.
    Diversity and expression of bacterial metacaspases in an aquatic ecosystem2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, p. 1-18, article id 1043Article in journal (Refereed)
    Abstract [en]

    Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response, and programmed cell death (PCD) in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and metatranscriptomic datasets from the brackish Baltic Sea, a water body characterized by pronounced environmental gradients and periods of massive cyanobacterial blooms. Metacaspase genes were restricted to ~4% of the bacteria, taxonomically affiliated mainly to Bacteroidetes, Alpha- and Betaproteobacteria and Cyanobacteria. The gene abundance was significantly higher in larger or particle-associated bacteria (<0.8 μm), and filamentous Cyanobacteria dominated metacaspase gene expression throughout the bloom season. Distinct seasonal expression patterns were detected for the three metacaspase genes in Nodularia spumigena, one of the main bloom-formers. Clustering of normalized gene expression in combination with analyses of genomic and assembly data suggest functional diversification of these genes, and possible roles of the metacaspase genes related to stress responses, i.e., sulfur metabolism in connection to oxidative stress, and nutrient stress induced cellular differentiation. Co-expression of genes encoding metacaspases and nodularin toxin synthesis enzymes was also observed in Nodularia spumigena. The study shows that metacaspases represent an adaptation of potentially high importance for several key organisms in the Baltic Sea, most prominently Cyanobacteria, and open up for further exploration of their physiological roles in microbes and assessment of their ecological impact in aquatic habitats.

  • 18.
    Atterby, Clara
    et al.
    Uppsala University.
    Mourkas, Evangelos
    Uppsala University;Univ Bath, UK.
    Meric, Guillaume
    Univ Bath, UK.
    Pascoe, Ben
    Univ Bath, UK;MRC CLIMB Consortium, UK.
    Wang, Helen
    Uppsala University.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sheppard, Samuel K.
    Univ Bath, UK;MRC CLIMB Consortium, UK.
    Olsen, Björn
    Uppsala University.
    Jarhult, Josef D.
    Uppsala University.
    Ellström, Patrik
    Uppsala University.
    The Potential of Isolation Source to Predict Colonization in Avian Hosts: A Case Study in Campylobacter jejuni Strains From Three Bird Species2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 591Article in journal (Refereed)
    Abstract [en]

    Campylobacter jejuni is the primary cause of bacterial gastroenteritis worldwide, infecting humans mostly through consumption of contaminated poultry. C. jejuni is common in the gut of wild birds, and shows distinct strain-specific association to particular bird species. This contrasts with farm animals, in which several genotypes co-exist. It is unclear if the barriers restricting transmission between host species of such specialist strains are related to environmental factors such as contact between host species, bacterial survival in the environment, etc., or rather to strain specific adaptation to the intestinal environment of specific hosts. We compared colonization dynamics in vivo between two host-specific C. jejuni from a song thrush (ST-1304 complex) and a mallard (ST-995), and a generalist strain from chicken (ST-21 complex) in a wild host, the mallard (Anas platyrhynchos). In 18-days infection experiments, the song thrush strain showed only weak colonization and was cleared from all birds after 10 days, whereas both mallard and chicken strains remained stable. When the chicken strain was given 4 days prior to co-infection of the same birds with a mallard strain, it was rapidly outcompeted by the latter. In contrast, when the mallard strain was given 4 days prior to co-infection with the chicken strain, the mallard strain remained and expansion of the chicken strain was delayed. Our results suggest strain-specific differences in the ability of C. jejuni to colonize mallards, likely associated with host origin. This difference might explain observed host association patterns in C. jejuni from wild birds.

  • 19.
    Axelsson Olsson, Diana
    Kalmar County Hospital.
    Acanthamoebae polyphaga – en trojansk häst vid campylobacter-infektion?2004Conference paper (Refereed)
  • 20.
    Axelsson Olsson, Diana
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Campylobacters and protozoans: the missing link in the epidemiology of campylobacteriosis?2006Conference paper (Refereed)
  • 21.
    Axelsson Olsson, Diana
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Interaktioner mellan bakterier och protozoer i vattenmiljö, ett dolt hot?2014Conference paper (Refereed)
  • 22.
    Axelsson Olsson, Diana
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Interaktioner mellan bakterier och protozoer i vattenmiljö, ett dolt hot?2012Conference paper (Refereed)
  • 23.
    Axelsson Olsson, Diana
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Ellström, Patrik
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Haemig, Paul D
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Brudin, Lars
    Olsen, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Acanthamoeba-Campylobacter coculture as a novel method for enrichment of Campylobacter species2007In: Applied and Environmental Microbiology, Vol. 73, no 21, p. 6864-6869Article in journal (Refereed)
    Abstract [en]

    In this study, we present a novel method to isolate and enrich low concentrations of Campylobacter pathogens. This method, Acanthamoeba-Campylobacter coculture (ACC), is based on the intracellular survival and multiplication of Campylobacter species in the free-living protozoan Acanthamoeba polyphaga. Four of the Campylobacter species relevant to humans and livestock, Campylobacter jejuni, C. coli, C. lari, and C. hyointestinalis, were effectively enriched by the coculture method, with growth rates comparable to those observed in other Campylobacter enrichment media. Studying six strains of C. jejuni isolated from different sources, we found that all of the strains could be enriched from an inoculum of fewer than 10 bacteria. The sensitivity of the ACC method was not negatively affected by the use of Campylobacter-selective antibiotics in the culture medium, but these were effective in suppressing the growth of seven different bacterial species added at a concentration of 10(4) CFU/ml of each species as deliberate contamination. The ACC method has advantages over other enrichment methods as it is not dependent on a microaerobic milieu and does not require the use of blood or other oxygen-quenching agents. Our study found the ACC method to be a promising tool for the enrichment of Campylobacter species, particularly from water samples with low bacterial concentrations.

  • 24.
    Axelsson Olsson, Diana
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Olofsson, J.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Svensson, L.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Ellström, P.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Olsen, B.
    Uppsala University Hospital.
    Campylobacter jejuni acid tolerance increases when co-incubated with amoebae2009Conference paper (Refereed)
    Abstract [en]

    Background: Although Campylobacter jejuni is a frequent cause of bacterial gastroenteritis, one of the enigmas is how thisfragile organism can survive the transit through the acid milieu of the stomach. C. jejuni is very sensitive to low pH, but cansurvive in moderately acid environment for short periods of time. We have previously shown that C. jejuni can colonize andeven replicate in different species of amoebas, thereby gaining protection from adverse environments.

    Objectives: We evaluated the effects of hydrochloric acid (HCl) on C. jejuni at various pH and time intervals, to study whetherco-cultivation with amoeba influenced C.jejuni acid tolerance. The setup was chosen to mimic the acidified milieu of the humangastrointestinal tract.

    Methods: Cultures of C. jejuni (CCUG 11284) were co-cultured with Acanthamoeba polyphaga in either PBS or tap wateracidified with HCl to pH 1, 2, 3 and 4. We also evaluated different treatments effect on campylobacter survival, by exposingsome bacterial samples to an acid shock and some to a slower acidification process.

    Results and conclusions: We show that C. jejuni can withstand pH below the normal range of survival, when co-cultured withA. polyphaga. C. jejuni co-cultured with amoebae survived acidified conditions at pH 3 for 20 hours and pH 2 for approximately5 hours. We also found a pH increase during the experiment, which correlated with campylobacter survival. These results pointto an unknown mechanism for C.jejuni to survive at low pH levels. This could be in the form of excretion of pH-increasingsubstances and simultaneous chemotaxic orientation towards a protective host. Our results could give one possible explanationto C. jejuni survival through the low pH of the gastrointestinal tract.

  • 25.
    Axelsson Olsson, Diana
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Olofsson, Jenny
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Ellström, Patrik
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Olsen, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    A simple method for long-term storage Acanthamoeba species2009In: Parasitology Research, ISSN 0932-0113, E-ISSN 1432-1955, Vol. 104, no 4, p. 935-937Article in journal (Refereed)
    Abstract [en]

    We present a novel and simple technique for storing live Acanthamoeba for long periods of time. The amoebae are maintained at refrigerator temperatures in a peptone-yeast extract-glucose (PYG) medium normally used for cultivation. Using this method, we obtained survival rates of at least 4 years for Acanthamoeba polyphaga and 3 years for Acanthamoeba castellanii and Acanthamoeba rhysodes. Advantages of this storage method are: (1) it is quick and simple, (2) inexpensive, (3) does not require encystment before storage, (4) resuscitation of cysts can be achieved within a week of culture in PYG medium at 27A degrees C, and does not require co-culture with bacteria or any special equipment.

  • 26.
    Axelsson Olsson, Diana
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Olofsson, Jenny
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Svensson, Lovisa
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Griekspoor, Petra
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Ellström, Patrik
    University of Kalmar, School of Pure and Applied Natural Sciences. Uppsala University ; Uppsala University Hospital.
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Olsen, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Protozoa as hosts for Campylobacter spp2009Conference paper (Refereed)
  • 27.
    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.

  • 28. Azam, F.
    et al.
    Ammerman, J.W.
    Fuhrman, J.A.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Role of bacteria in polluted marine ecosystems. ed R Colwell1983In: Proceedings of Workshop on meaningful measures of marine pollution effects NOAA, 1983Conference paper (Other academic)
  • 29.
    Baker-Austin, Craig
    et al.
    Savannah River Ecology Laboratory, University of Georgia, USA.
    Dopson, Mark
    Umeå University.
    Life in acid: pH homeostasis in acidophiles.2007In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 15, no 4, p. 165-171Article, review/survey (Refereed)
    Abstract [en]

    Microorganisms that have a pH optimum for growth of less than pH 3 are termed "acidophiles". To grow at low pH, acidophiles must maintain a pH gradient of several pH units across the cellular membrane while producing ATP by the influx of protons through the F(0)F(1) ATPase. Recent advances in the biochemical analysis of acidophiles coupled to sequencing of several genomes have shed new insights into acidophile pH homeostatic mechanisms. Acidophiles seem to share distinctive structural and functional characteristics including a reversed membrane potential, highly impermeable cell membranes and a predominance of secondary transporters. Also, once protons enter the cytoplasm, methods are required to alleviate effects of a lowered internal pH. This review highlights recent insights regarding how acidophiles are able to survive and grow in these extreme conditions.

  • 30.
    Baker-Austin, Craig
    et al.
    University of East Anglia, UK.
    Dopson, Mark
    University of East Anglia, UK.
    Wexler, Margaret
    University of East Anglia, UK.
    Sawers, R Gary
    John Innes Centre, Norwich, UK.
    Bond, Philip L
    University of East Anglia, UK ; .
    Molecular insight into extreme copper resistance in the extremophilic archaeon 'Ferroplasma acidarmanus' Fer1.2005In: Microbiology, ISSN 1350-0872, E-ISSN 1465-2080, Vol. 151, no 8, p. 2637-46Article in journal (Refereed)
    Abstract [en]

    'Ferroplasma acidarmanus' strain Fer1 is an extremely acidophilic archaeon involved in the genesis of acid mine drainage, and was isolated from copper-contaminated mine solutions at Iron Mountain, CA, USA. Here, the initial proteomic and molecular investigation of Cu(2+) resistance in this archaeon is presented. Analysis of Cu(2+) toxicity via batch growth experiments and inhibition of oxygen uptake in the presence of ferrous iron demonstrated that Fer1 can grow and respire in the presence of 20 g Cu(2+) l(-1). The Fer1 copper resistance (cop) loci [originally detected by Ettema, T. J. G., Huynen, M. A., de Vos, W. M. & van der Oost, J. Trends Biochem Sci 28, 170-173 (2003)] include genes encoding a putative transcriptional regulator (copY), a putative metal-binding chaperone (copZ) and a putative copper-transporting P-type ATPase (copB). Transcription analyses demonstrated that copZ and copB are co-transcribed, and transcript levels were increased significantly in response to exposure to high levels of Cu(2+), suggesting that the transport system is operating for copper efflux. Proteomic analysis of Fer1 cells exposed to Cu(2+) revealed the induction of stress proteins associated with protein folding and DNA repair (including RadA, thermosome and DnaK homologues), suggesting that 'Ferroplasma acidarmanus' Fer1 uses multiple mechanisms for resistance to high levels of copper.

  • 31.
    Baker-Austin, Craig
    et al.
    University of East Anglia, UK ; University of Georgia, USA.
    Dopson, Mark
    University of East Anglia, UK ; Umeå University.
    Wexler, Margaret
    University of East Anglia, UK.
    Sawers, R Gary
    John Innes Centre, Norwich, UK.
    Stemmler, Ann
    Wayne State University, School of Medicine, Detroit, USA.
    Rosen, Barry P
    Wayne State University, School of Medicine, Detroit, USA.
    Bond, Philip L
    University of East Anglia, UK ; University of Queensland, Brisbane, Australia.
    Extreme arsenic resistance by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.2007In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 11, no 3, p. 425-34Article in journal (Refereed)
    Abstract [en]

    'Ferroplasma acidarmanus' Fer1 is an arsenic-hypertolerant acidophilic archaeon isolated from the Iron Mountain mine, California; a site characterized by heavy metals contamination. The presence of up to 10 g arsenate per litre [As(V); 133 mM] did not significantly reduce growth yields, whereas between 5 and 10 g arsenite per litre [As(III); 67-133 mM] significantly reduced the yield. Previous bioinformatic analysis indicates that 'F. acidarmanus' Fer1 has only two predicted genes involved in arsenic resistance and lacks a recognizable gene for an arsenate reductase. Biochemical analysis suggests that 'F. acidarmanus' Fer1 does not reduce arsenate indicating that 'F. acidarmanus' Fer1 has an alternative resistance mechanism to arsenate other than reduction to arsenite and efflux. Primer extension analysis of the putative ars transcriptional regulator (arsR) and efflux pump (arsB) demonstrated that these genes are co-transcribed, and expressed in response to arsenite, but not arsenate. Two-dimensional polyacrylamide gel electrophoresis analysis of 'F. acidarmanus' Fer1 cells exposed to arsenite revealed enhanced expression of proteins associated with protein refolding, including the thermosome Group II HSP60 family chaperonin and HSP70 DnaK type heat shock proteins. This report represents the first molecular and proteomic study of arsenic resistance in an acidophilic archaeon.

  • 32.
    Baker-Austin, Craig
    et al.
    University of East Anglia, UK ; Cefas Weymouth Laboratory, Dorset, UK.
    Potrykus, Joanna
    Umeå University.
    Wexler, Margaret
    University of East Anglia, UK.
    Bond, Philip L
    University of East Anglia, UK ; University of Queensland, Brisbane, Australia.
    Dopson, Mark
    University of East Anglia, UK ; Umeå University.
    Biofilm development in the extremely acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.2010In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 14, no 6, p. 485-491Article in journal (Refereed)
    Abstract [en]

    'Ferroplasma acidarmanus' Fer1 is an iron-oxidizing extreme acidophile isolated from the Iron Mountain mine, California, USA. This archaeon is predominantly found in biofilm-associated structures in the environment, and produces two distinct biofilm morphologies. Bioinformatic analysis of the 'F. acidarmanus' Fer1 genome identified genes annotated as involved in attachment and biofilm formation. No putative quorum sensing signaling genes were identified and no N-acyl homoserine lactone-like compounds were found in 'F. acidarmanus' Fer1 biofilm supernatant. Scanning confocal microscopy analysis of biofilm development on the surface of pyrite demonstrated the temporal and spatial development of biofilm growth. Furthermore, two-dimensional polyacrylamide gel electrophoresis was used to examine differential protein expression patterns between biofilm and planktonic populations. Ten up-regulated proteins were identified that included six enzymes associated with anaerobic growth, suggesting that the dominating phenotype in the mature biofilm was associated with anaerobic modes of growth. This report increases our knowledge of the genetic and proteomic basis of biofilm formation in an extreme acidophilic archaeon.

  • 33.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Otago, New Zealand.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Palovaara, Joakim
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lekunberri, Itziar
    Univ Vienna, Austria ; Inst Catala Recerca Aigua, Spain.
    Reinthaler, Thomas
    Univ Vienna, Austria.
    Herndl, Gerhard J.
    Univ Vienna, Austria ; Univ Utrecht, Netherlands.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 1670Article in journal (Refereed)
    Abstract [en]

    To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.

  • 34.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Otago, New Zealand.
    Palovaara, Joakim
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vila-Costa, Maria
    Univ Barcelona, Spain.
    Salazar, Guillem
    CSIC, Spain.
    Calvo, Eva
    CSIC, Spain.
    Pelejero, Carles
    CSIC, Spain ; Inst Catalana Recerca & Estudis Avancats, Spain.
    Marrase, Celia
    CSIC, Spain.
    Gasol, Josep M.
    CSIC, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site2015In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 91, no 6, article id UNSP fiv058Article in journal (Refereed)
    Abstract [en]

    Bacterioplankton communities are made up of a small set of abundant taxa and a large number of low-abundant organisms (i.e. 'rare biosphere'). Despite the critical role played by bacteria in marine ecosystems, it remains unknown how this large diversity of organisms are affected by human-induced perturbations, or what controls the responsiveness of rare compared to abundant bacteria. We studied the response of a Mediterranean bacterioplankton community to two anthropogenic perturbations (i.e. nutrient enrichment and/or acidification) in two mesocosm experiments (in winter and summer). Nutrient enrichment increased the relative abundance of some operational taxonomic units (OTUs), e.g. Polaribacter, Tenacibaculum, Rhodobacteraceae and caused a relative decrease in others (e.g. Croceibacter). Interestingly, a synergistic effect of acidification and nutrient enrichment was observed on specific OTUs (e.g. SAR86). We analyzed the OTUs that became abundant at the end of the experiments and whether they belonged to the rare (<0.1% of relative abundance), the common (0.1-1.0% of relative abundance) or the abundant (>1% relative abundance) fractions. Most of the abundant OTUs at the end of the experiments were abundant, or at least common, in the original community of both experiments, suggesting that ecosystem alterations do not necessarily call for rare members to grow.

  • 35.
    Bentzon-Tilia, Mikkel
    et al.
    Univ Copenhagen.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Jürgens, Klaus
    Leibniz Inst Balt Sea Res IOW, Germany.
    Riemann, Lasse
    Univ Copenhagen.
    Cultivation and isolation of N2-fixing bacteria from suboxic waters in the Baltic Sea2014In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 88, no 2, p. 358-371Article in journal (Refereed)
    Abstract [en]

    Nitrogenase genes (nifH) from heterotrophic dinitrogen (N-2)-fixing bacteria appear ubiquitous in marine bacterioplankton, but the significance of these bacteria for N cycling is unknown. Quantitative data on the N-2-fixation potential of marine and estuarine heterotrophs are scarce, and the shortage of cultivated specimens currently precludes ecophysiological characterization of these bacteria. Through the cultivation of diazotrophs from suboxic (1.79molO(2)L(-1)) Baltic Sea water in an artificial seawater medium devoid of combined N, we report the cultivability of a considerable fraction of the diazotrophic community in the Gotland Deep. Two nifH clades were present both in situ and in enrichment cultures showing gene abundances of up to 4.6x10(5) and 5.8x10(5)nifH gene copies L-1 within two vertical profiles in the Baltic Sea. The distributions of the two clades suggested a relationship with the O-2 concentrations in the water column as abundances increased in the suboxic and anoxic waters. It was possible to cultivate and isolate representatives from one of these prevalent clades, and preliminary analysis of their ecophysiology demonstrated growth optima at 0.5-15molO(2)L(-1) and 186-194molO(2)L(-1) in the absence of combined N.

  • 36.
    Bertos-Fortis, Mireia
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Casini, Michele
    Swedish University of Agricultural Sciences.
    Andersson, Agneta
    Umeå University.
    Pinhassi, Jarone
    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.
    Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 625Article in journal (Refereed)
    Abstract [en]

    Future climate scenarios in the Baltic Sea project an increase of cyanobacterial bloom frequency and duration, attributed to eutrophication and climate change. Some cyanobacteria can be toxic and their impact on ecosystem services is relevant for a sustainable sea. Yet, there is limited understanding of the mechanisms regulating cyanobacterial diversity and biogeography. Here we unravel successional patterns and changes in cyanobacterial community structure using a 2-year monthly time series during the productive season in a 100 km coastal-offshore transect using microscopy and high-throughput sequencing of 16S rRNA gene fragments. A total of 565 cyanobacterial OTUs were found, of which 231 where filamentous/colonial and 334 picocyanobacterial. Spatial differences in community structure between coastal and offshore waters were minor. An "epidemic population structure" (dominance of a single cluster) was found for Aphanizomenon/Dolichospermum within the filamentous/colonial cyanobacterial community. In summer, this cluster simultaneously occurred with opportunistic clusters/OTUs, e.g., Nodulana spumigena and Pseudanabaena. Picocyanobacteria, Synechococcus/Cyanobium, formed a consistent but highly diverse group. Overall, the potential drivers structuring summer cyanobacterial communities were temperature and salinity. However, the different responses to environmental factors among and within genera suggest high niche specificity for individual OTUs. The recruitment and occurrence of potentially toxic filamentous/colonial clusters was likely related to disturbance such as mixing events and short-term shifts in salinity, and not solely dependent on increasing temperature and nitrogen-limiting conditions. Nutrients did not explain further the changes in cyanobacterial community composition. Novel occurrence patterns were identified as a strong seasonal succession revealing a tight coupling between the emergence of opportunistic picocyanobacteria and the bloom of filamentous/colonial clusters. These findings highlight that if environmental conditions can partially explain the presence of opportunistic picocyanobacteria, microbial and trophic interactions with filamentous/colonial cyanobacteria should also be considered as potential shaping factors for single-celled communities. Regional climate change scenarios in the Baltic Sea predict environmental shifts leading to higher temperature and lower salinity; conditions identified here as favorable for opportunistic filamentous/colonial cyanobacteria. Altogether, the diversity and complexity of cyanobacterial communities reported here is far greater than previously known, emphasizing the importance of microbial interactions between filamentous and picocyanobacteria in the context of environmental disturbances.

  • 37.
    Bijmans, Martijn F M
    et al.
    Wageningen University and Research Centre, Wageningen, The Netherlands.
    de Vries, Erik
    Wageningen University and Research Centre, Wageningen, The Netherlands.
    Yang, Chun-Hui
    Umeå University.
    N Buisman, Cees J
    Wageningen University and Research Centre, Wageningen, The Netherlands.
    Lens, Piet N L
    Wageningen University and Research Centre, Wageningen, The Netherlands.
    Dopson, Mark
    Umeå University.
    Sulfate reduction at pH 4.0 for treatment of process and wastewaters.2010In: Biotechnology progress (Print), ISSN 8756-7938, E-ISSN 1520-6033, Vol. 26, no 4, p. 1029-1037Article in journal (Refereed)
    Abstract [en]

    Acidic industrial process and wastewaters often contain high sulfate and metal concentrations and their direct biological treatment is thus far not possible as biological processes at pH < 5 have been neglected. Sulfate-reducing bacteria convert sulfate to sulfide that can subsequently be used to recover metals as metal-sulfides precipitate. This study reports on high-rate sulfate reduction with a mixed microbial community at pH 4.0 and 4.5 with hydrogen and/or formate as electron donors. The maximum sulfate reducing activity at pH 4.0 was sustained for over 40 days with a specific activity 500-fold greater than previously reported values: 151 mmol sulfate reduced/L reactor liquid per day with a maximum specific activity of 84 mmol sulfate per gram of volatile suspended solids per day. The biomass yield gradually decreased from 38 to 0.4 g volatile suspended solids per kilogram of sulfate when decreasing the reactor pH from pH 6 to 4. The microorganisms had a high maintenance requirement probably due maintaining pH homeostasis and the toxicity of sulfide at low pH. The microbial community diversity in the pH 4.0 membrane bioreactor decreased over time, while the diversity of the sulfate reducing community increased. Thus, a specialized microbial community containing a lower proportion of microorganisms capable of activity at pH 4 developed in the reactor compared with those present at the start of the experiment. The 16S rRNA genes identified from the pH 4.0 grown mixed culture were most similar to those of Desulfovibrio species and Desulfosporosinus sp. M1.

  • 38.
    Bijmans, Martijn F M
    et al.
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Dopson, Mark
    Umeå University.
    Ennin, Frederick
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Lens, Piet N L
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Buisman, Cees J N
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Effect of sulfide removal on sulfate reduction at pH 5 in a hydrogen fed gas-lift bioreactor.2008In: Journal of Microbiology and Biotechnology, ISSN 1017-7825, E-ISSN 1738-8872, Vol. 18, no 11, p. 1809-1818Article in journal (Refereed)
    Abstract [en]

    Biotechnological treatment of sulfate- and metal-ionscontaining acidic wastewaters from mining and metallurgical activities utilizes sulfate-reducing bacteria to produce sulfide that can subsequently precipitate metal ions. Reducing sulfate at a low pH has several advantages above neutrophilic sulfate reduction. This study describes the effect of sulfide removal on the reactor performance and microbial community in a high-rate sulfidogenic gas-lift bioreactor fed with hydrogen at a controlled internal pH of 5. Under sulfide removal conditions, 99% of the sulfate was converted at a hydraulic retention time of 24 h, reaching a volumetric activity as high as 51 mmol sulfate/l/d. Under nonsulfide removal conditions, <25% of the sulfate was converted at a hydraulic retention time of 24 h reaching volumetric activities of <13mmol sulfate/l/d. The absence of sulfide removal at a hydraulic retention time of 24 h resulted in an average H2S concentration of 18.2 mM (584 mg S/l). The incomplete sulfate removal was probably due to sulfide inhibition. Molecular phylogenetic analysis identified 11 separate 16S rRNA bands under sulfide stripping conditions, whereas under nonsulfide removal conditions only 4 separate 16S rRNA bands were found. This shows that a less diverse population was found in the presence of a high sulfide concentration.

  • 39.
    Bijmans, Martijn F M
    et al.
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Dopson, Mark
    Umeå University.
    Peeters, Tom W T
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Lens, Piet N L
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Buisman, Cees J N
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Sulfate reduction at pH 5 in a high-rate membrane bioreactor: reactor performance and microbial community analyses.2009In: Journal of Microbiology and Biotechnology, ISSN 1017-7825, E-ISSN 1738-8872, Vol. 19, no 7, p. 698-708Article in journal (Refereed)
    Abstract [en]

    High rate sulfate reduction under acidic conditions opens possibilities for new process flow sheets that allow the selective recovery of metals from mining and metallurgical waste and process water. However, knowledge about high-rate sulfate reduction under acidic conditions is limited. This paper investigates sulfate reduction in a membrane bioreactor at a controlled pH of 5. Sulfate and formate were dosed using a pH-auxostat system while formate was converted into hydrogen, which was used for sulfate reduction. Sulfide was removed from the gas phase to prevent sulfide inhibition. This study shows a high-rate sulfate-reducing bioreactor system for the first time at pH 5, with a volumetric activity of 188mmol SO(4)(2-)/I/d and a specific activity of 81mmol SO(4)(2-) volatile suspended. The microbial community at the end of the reactor run consisted of a diverse mixed population including sulfate-reducing bacteria.

  • 40.
    Bijmans, Martijn F M
    et al.
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    van Helvoort, Pieter-Jan
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    Dar, Shabir A
    Umeå University.
    Dopson, Mark
    Umeå University.
    Lens, Piet N L
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    Buisman, Cees J N
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    Selective recovery of nickel over iron from a nickel-iron solution using microbial sulfate reduction in a gas-lift bioreactor.2009In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 43, no 3, p. 853-861Article in journal (Refereed)
    Abstract [en]

    Process streams with high concentrations of metals and sulfate are characteristic for the mining and metallurgical industries. This study aims to selectively recover nickel from a nickel-iron-containing solution at pH 5.0 using a single stage bioreactor that simultaneously combines low pH sulfate reduction and metal-sulfide formation. The results show that nickel was selectively precipitated in the bioreactor at pH 5.0 and the precipitates consisted of >or=83% of the nickel content. The nickel-iron precipitates were partly crystalline and had a metal/sulfur ratio of 1, suggesting these precipitates were NiS and FeS. Experiments focusing on nickel recovery at pH 5.0 and 5.5 reached a recovery of >99.9%, resulting in a nickel effluent concentration<0.05 microM. The mixed microbial population included known sulfate reducers and acetogens. This study shows that selective metal precipitation in a single stage sulfate reducing bioreactor operated at low pH has the potential to produce metal-sulfides that can be used by the metallurgical industry as a resource for metal production.

  • 41.
    Blomqvist, Maria
    et al.
    Uppsala University.
    Christerson, Linus
    Uppsala University.
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Lindberg, Peter
    Swedish Museum of Natural History.
    Helander, Björn
    Gothenburg University.
    Gunnarsson, Gunnar
    Kristianstad University.
    Herrman, Björn
    Uppsala University.
    Olsen, Björn
    Uppsala University.
    Chlamydophila psittaci in birds of prey, Sweden2012In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 2, article id 8435Article in journal (Refereed)
    Abstract [en]

    Background: Chlamydia psittaci is an intracellular bacterium primarily causing respiratory diseases in birds but may also be transmitted to other animals, including humans. The prevalence of the pathogen in wild birds in Sweden is largely unknown.

    Methods: DNA was extracted from cloacae swabs and screened for C. psittaci by using a 23S rRNA gene PCR assay. Partial 16S rRNA and ompA gene fragments were sequence determined and phylogenies were analysed by the neighbour-joining method.

    Results and conclusion: The C. psittaci prevalence was 1.3% in 319 Peregrine Falcons and White-tailed Sea Eagles, vulnerable top-predators in Sweden. 16S rRNA and ompA gene analysis showed that novel Chlamydia species, as well as novel C. psittaci strains, are to be found among wild birds.

  • 42.
    Bonnedahl, Jonas
    et al.
    Uppsala University ; Kalmar County Hospital.
    Drobni, M
    Gauthier-Clerc, M
    Hernandez, Jorge
    Kalmar County Hospital.
    Granholm, S
    Kayser, Y
    Melhus, Å
    Kahlmeter, G
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Johansson, A
    Olsen, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Dissemination of Escherichia coli with CTX-M Type ESBL between Humans and Yellow-Legged Gulls in the South of France2009In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 4, no Article number: e5958Article in journal (Refereed)
    Abstract [en]

     Extended Spectrum beta-Lactamase (ESBL) producing Enterobacteriaceae started to appear in the 1980s, and have since emerged as some of the most significant hospital-acquired infections with Escherichia coli and Klebsiella being main players. More than 100 different ESBL types have been described, the most widespread being the CTX-M beta-lactamase enzymes (bla(CTX-M) genes). This study focuses on the zoonotic dissemination of ESBL bacteria, mainly CTX-M type, in the southern coastal region of France. We found that the level of general antibiotic resistance in single randomly selected E. coli isolates from wild Yellow-legged Gulls in France was high. Nearly half the isolates (47,1%) carried resistance to one or more antibiotics (in a panel of six antibiotics), and resistance to tetracycline, ampicillin and streptomycin was most widespread. In an ESBL selective screen, 9,4% of the gulls carried ESBL producing bacteria and notably, 6% of the gulls carried bacteria harboring CTX-M-1 group of ESBL enzymes, a recently introduced and yet the most common clinical CTX-M group in France. Multi locus sequence type and phylogenetic group designations were established for the ESBL isolates, revealing that birds and humans share E. coli populations. Several ESBL producing E. coli isolated from birds were identical to or clustered with isolates with human origin. Hence, wild birds pick up E. coli of human origin, and with human resistance traits, and may accordingly also act as an environmental reservoir and melting pot of bacterial resistance with a potential to re-infect human populations.

  • 43.
    Bonnedahl, Jonas
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Kalmar County Hospital.
    Stedt, Johan
    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.
    Svensson, Lovisa
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Drobni, Mirva
    Uppsala University.
    Olsen, Björn
    Uppsala University.
    Comparison of Extended-Spectrum beta-Lactamase (ESBL) CTX-M Genotypes in Franklin Gulls from Canada and Chile2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 10, article id e0141315Article in journal (Refereed)
    Abstract [en]

    Migratory birds have been suggested to contribute to long-distance dispersal of antimicrobial resistant bacteria, but tests of this hypothesis are lacking. In this study we determined resistance profiles and genotypes of ESBL-producing bacteria in randomly selected Escherichia coli from Franklin's gulls (Leucophaeus pipixcan) at breeding sites in Canada and compared with similar data from the gulls' wintering grounds in Chile. Resistant E. coli phenotypes were common, most notably to ampicillin (30.1%) and cefadroxil (15.1%). Furthermore, 17.0% of the gulls in Canada carried ESBL producing bacteria, which is higher than reported from human datasets from the same country. However, compared to gulls sampled in Chile (30.1%) the prevalence of ESBL was much lower. The dominant ESBL variants in Canada were bla(CTX-M-14) and bla(CTX-M-15) and differed in proportions to the data from Chile. We hypothesize that the observed differences in ESBL variants are more likely linked to recent exposure to bacteria from anthropogenic sources, suggesting high local dissemination of resistant bacteria both at breeding and non-breeding times rather than a significant trans-hemispheric exchange through migrating birds.

  • 44.
    Boström, Kjärstin H.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nitrogen fixation among marine bacterioplankton2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    While bacterioplankton indisputably control vital biogeochemical paths in the cycling of carbon and nutrients in the world’s oceans, our knowledge about the functional and genetic diversity of bacterioplankton communities is negligible. In this thesis, molecular and more traditional microbiological methods were used to study the specific function of N2-fixation and in a general sense diversity of marine bacterioplankton species.

    Most oceans are nitrogen limited and, therefore, adaptive to bacterioplankton capable of N2-fixation. Recent studies have found nifH genes (coding for the nitrogenase enzyme) related to diverse heterotrophic bacteria in oceanic seawater samples indicating that, along with cyanobacteria, also heterotrophic bacteria benefit from N2-fixation. Here, molecular and cultivation methods were used to examine diazotrophic bacterioplankton in the Baltic Sea. We successfully isolated heterotrophic N2-fixing bacteria belonging to the γ-proteobacterial class by means of low-nitrogen plates and semi-solid diazotrophic medium tubes. The isolates required low-O2 conditions for N2-fixation. Using Real-time PCR it was found that heterotrophic bacterioplankton carrying the nifH gene was abundant (3 x 104 nifH gene copies L seawater-1) at locations in the Southwest Baltic proper.

    With the aim to identify the main N2-fixing organisms in Baltic Proper surface waters, a clone library of nifH gene transcripts (RNA) was generated. Clone inserts were exclusively related to Aphanizomenon sp. and Nodularia sp. Using quantitative real-time PCR it was found that the nifH gene expression from Nodularia sp. was highly variable between stations in the Baltic Proper but was 10-fold higher during mid summer relative to early summer and fall. A diel study showed a 4-fold increase in Nodularia transcript concentrations at early to mid day relative to rest of the day. Real-time PCR was found to be a powerful and highly sensitive method for measuring gene expression.

    Since nucleic acids are a prerequisite for molecular analyses of bacterioplankton dynamics a protocol to extract DNA from seawater samples was developed with the aim to maximize the yield of high-quality DNA. Each step in the protocol was important for the efficiency of extraction. The obtained extraction efficiencies were up to 92% for seawater samples and up to 96% for isolates. The protocol provides a guideline for DNA extraction from seawater samples for other studies.

    In a global sampling campaign (9 locations from polar, tropical and temperate regions) we sampled DNA from surface water and constructed 16S rRNA gene libraries to investigate diversity and biogeography of bacterioplankton. Approx. 80% of the sequences found were similar to sequences already deposited in GenBank, indicating that a large fraction of the marine bacterioplankton already has been sampled, which in turn suggests a limited global bacterioplankton diversity.

    This thesis have improved our knowledge about the composition and nifH gene expression of the diazotrophic bacterioplankton community in the Baltic Sea and contribute significantly to the discussion on global marine bacterioplankton diversity and biogeography.

  • 45.
    Boström, Kjärstin H.
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Reimann, Lasse
    Kühl, Michael
    Hagström, Åke
    Isolation and gene quantification of heterotrophic N2-fixing bacterioplankton in the Baltic Sea2007In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 9, no 1, p. 152-164Article in journal (Refereed)
  • 46.
    Boström, Kjärstin H.
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Riemann, Lasse
    Zweifel, Ulla Li
    Hagström, Åke
    Nodularia sp. nifH gene transcripts in the Baltic Sea proper2007In: Journal of Plankton Research, ISSN 0142-7873, E-ISSN 1464-3774, Vol. 29, no 4, p. 391-399Article in journal (Refereed)
  • 47.
    Boström, Kjärstin
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Simu, Karin
    Hagström, Åke
    Riemann, Lasse
    Optimization of DNA extraction for quantitative marine bacterioplankton community analysis2004In: Limnology and oceanography: methods, Vol. 2, p. 365-373Article in journal (Refereed)
  • 48.
    Brindefalk, Bjorn
    et al.
    Stockholm University.
    Ekman, Martin
    Stockholm University.
    Ininbergs, Karolina
    Stockholm University.
    Dupont, Christopher L.
    J Craig Venter Inst, USA.
    Yooseph, Shibu
    J Craig Venter Inst, USA.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bergman, Birgitta
    Stockholm University.
    Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4442-4455Article in journal (Refereed)
    Abstract [en]

    Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from similar to 0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 mu m), relative to the medium (0.8-3.0 mu m) and large (> 3.0 mu m) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.

  • 49. Brojer, Caroline
    et al.
    Jarhult, Josef D.
    Muradrasoli, Shaman
    Soderstrom, Hanna
    Olsen, Björn
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gavier-Widen, Dolores
    Pathobiology and virus shedding of low-pathogenic avian influenza virus (A/H1N1) infection in mallards exposed to oseltamivir2013In: Journal of Wildlife Diseases, ISSN 0090-3558, E-ISSN 1943-3700, Vol. 49, no 1, p. 103-113Article in journal (Refereed)
    Abstract [en]

    Low-pathogenic avian influenza (LPAI) viruses in wild birds are important as they can constitute the basis for the development of highly pathogenic avian influenza viruses or form part of human-adapted strains with pandemic potential. However, the pathogenesis of LPAI viruses is not well characterized in dabbling ducks, one of the natural reservoirs of LPAI viruses. Between 21 September 2009 and 21 December 2009, we used real-time reverse transcriptase polymerase chain reaction (q-PCR), histopathology, and immunohistochemistry (IHC) to study Mallards (Anas platyrhynchos) infected with an influenza A/H1N1 virus isolated from a wild Mallard in Sweden. The ducks were either inoculated intraesophageally ("artificial infection") or infected by virus shed by other ducks in the experiment ("contact infection"). The ducks were subjected to three low concentrations (80 ng/L, 1 mu g/L, and 80 mu g/L) of the active metabolite of oseltamivir (Tamiflu (R)), oseltamivir carboxylate (OC), which resulted in the development of the viral resistance mutation H274Y at 1 and 80 mu g/L. The LPAI virus infection was localized to the intestinal tract and cloacal bursa except in one Mallard. The exception was a duck euthanized 1 day postinoculation, whose infection was located solely in the lung, possibly due to intratracheal deposition of virus. The intestinal infection was characterized by occasional degenerating cells in the lamina propria and presence of viral antigen as detected by IHC, as well as positive q-PCR performed on samples from feces and intestinal contents. Histopathologic changes, IHC positivity, and viral shedding all indicated that the infection peaked early, around 2 days postinfection. Furthermore, more viral antigen and viral RNA were detected with IHC and q-PCR in the proximal parts early in the infection. There was no obvious difference in the course of the infection in artificial versus contact infection, when the level of OC was increased from 80 ng/L to 1 mu g/L (based on IHC and q-PCR), when the level of OC was increased to 80 mu/L, or when the resistance mutation H274Y developed (based on q-PCR).

  • 50.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Abbtesaim, Jawad
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wu, Xiaofen
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Copenhagen, Denmark.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ni, Gaofeng
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lopez-Fernandez, Margarita
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sundkvist, Jan-Eric
    Boliden Mineral AB, Boliden, Sweden.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor2017In: Biodegradation, ISSN 0923-9820, E-ISSN 1572-9729, Vol. 28, no 4, p. 287-301Article in journal (Refereed)
    Abstract [en]

    Wastewaters generated during mining and processing of metal sulfide ores are often acidic (pH < 3) and can contain significant concentrations of nitrate, nitrite, and ammonium from nitrogen based explosives. In addition, wastewaters from sulfide ore treatment plants and tailings ponds typically contain large amounts of inorganic sulfur compounds, such as thiosulfate and tetrathionate. Release of these wastewaters can lead to environmental acidification as well as an increase in nutrients (eutrophication) and compounds that are potentially toxic to humans and animals. Waters from cyanidation plants for gold extraction will often conjointly include toxic, sulfur containing thiocyanate. More stringent regulatory limits on the release of mining wastes containing compounds such as inorganic sulfur compounds, nitrate, and thiocyanate, along the need to increase production from sulfide mineral mining calls for low cost techniques to remove these pollutants under ambient temperatures (approximately 8 °C). In this study, we used both aerobic and anaerobic continuous cultures to successfully couple inorganic sulfur compound (i.e. thiosulfate and thiocyanate) oxidation for the removal of nitrogenous compounds under neutral to acidic pH at the low temperatures typical for boreal climates. Furthermore, the development of the respective microbial communities was identified over time by DNA sequencing, and found to contain a consortium including populations aligning within Flavobacterium, Thiobacillus, and Comamonadaceae lineages. This is the first study to remediate mining waste waters by coupling autotrophic thiocyanate oxidation to nitrate reduction at low temperatures and acidic pH by means of an identified microbial community.

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