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

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

  • 252.
    Liljeqvist, Maria
    et al.
    Umeå University.
    Sundkvist, Jan-Eric
    Boliden Mineral AB, Boliden, Sweden.
    Saleh, Amang
    Boliden Mineral AB, Boliden, Sweden.
    Dopson, Mark
    Umeå University.
    Low temperature removal of inorganic sulfur compounds from mining process waters2011In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 108, no 6, p. 1251-1259Article in journal (Refereed)
    Abstract [en]

    Process water and effluents from mining operations treating sulfide rich ores often contain considerable concentrations of metastable inorganic sulfur compounds such as thiosulfate and tetrathionate. These species may cause environmental problems if released to downstream recipients due to oxidation to sulfuric acid catalyzed by acidophilic microorganisms. Molecular phylogenic analysis of the tailings pond and recipient streams identified psychrotolerant and mesophilic inorganic sulfur compound oxidizing microorganisms. This suggested year round thiosalt oxidation occurs. Mining process waters may also contain inhibiting substances such as thiocyanate from cyanidation plants. However, toxicity experiments suggested their expected concentrations would not inhibit thiosalt oxidation by Acidithiobacillus ferrivorans SS3. A mixed culture from a permanently cold (4-6 degrees C) low pH environment was tested for thiosalt removal in a reactor design including a biogenerator and a main reactor containing a biofilm carrier. The biogenerator and main reactors were successively reduced in temperature to 5-6 degrees C when 43.8% of the chemical oxidation demand was removed. However, it was found that the oxidation of thiosulfate was not fully completed to sulfate since low residual concentrations of tetrathionate and trithionate were found in the discharge. This study has demonstrated the potential of using biotechnological solutions to remove inorganic sulfur compounds at 6 degrees C and thus, reduce the impact of mining on the environment.

  • 253. Liljeqvist, Maria
    et al.
    Valdes, Jorge
    Holmes, David S
    Dopson, Mark
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Department of Molecular Biology, Umeå University.
    Draft genome of the psychrotolerant acidophile Acidithiobacillus ferrivorans SS3.2011In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 193, no 16, p. 4304-4305Article in journal (Refereed)
    Abstract [en]

    Acidithiobacillus ferrivorans SS3 is a psychrotolerant acidophile capable of growth in the range of 5° to 30°C (optimum, ≈25°C). It gains energy from the oxidation of ferrous iron and inorganic sulfur compounds and obtains organic carbon from carbon dioxide. Here, we present the draft genome sequence of A. ferrivorans SS3 that will permit investigation of genes involved in growth in acidic environments at low temperatures.

  • 254.
    Lim, S. M.
    et al.
    Artemis One Hlth Res Fdn, Netherlands.
    Geervliet, M.
    Artemis One Hlth Res Fdn, Netherlands;Wageningen Univ, Netherlands.
    Verhagen, Josanne H.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Erasmus MC, Netherlands.
    Muskens, G. J. D. M.
    Wageningen Environm Res Alterra, Netherlands.
    Majoor, F. A.
    Sovon Dutch Ctr Field Ornithol, Netherlands.
    Osterhaus, A. D. M. E.
    Artemis One Hlth Res Fdn, Netherlands;Univ Vet Med Hannover, Germany.
    Martina, B. E. E.
    Artemis One Hlth Res Fdn, Netherlands;Erasmus MC, Netherlands.
    Serologic evidence of West Nile virus and Usutu virus infections in Eurasian coots in the Netherlands2018In: Zoonoses and Public Health, ISSN 1863-1959, E-ISSN 1863-2378, Vol. 65, no 1, p. 96-102Article in journal (Refereed)
    Abstract [en]

    West Nile virus (WNV) and Usutu virus (USUV) are arboviruses that are maintained in enzootic transmission cycles between mosquitoes and birds and are occasionally transmitted to mammals. As arboviruses are currently expanding their geographic range and emerging in often unpredictable locations, surveillance is considered an important element of preparedness. To determine whether sera collected from resident and migratory birds in the Netherlands as part of avian influenza surveillance would also represent an effective source for proactive arbovirus surveillance, a random selection of such sera was screened for WNV antibodies using a commercial ELISA. In addition, sera of jackdaws and carrion crows captured for previous experimental infection studies were added to the selection. Of the 265 screened serum samples, 27 were found to be WNV-antibody-positive, and subsequent cross-neutralization experiments using WNV and USUV confirmed that five serum samples were positive for only WNV-neutralizing antibodies and seven for only USUV. The positive birds consisted of four Eurasian coots (Fulica atra) and one carrion crow (Corvus corone) for WNV, of which the latter may suggest local presence of the virus, and only Eurasian coots for USUV. As a result, the screening of a small selection of serum samples originally collected for avian influenza surveillance demonstrated a seroprevalence of 1.6% for WNV and 2.8% for USUV, suggesting that this sustained infrastructure could serve as a useful source for future surveillance of arboviruses such as WNV and USUV in the Netherlands.

  • 255.
    Lindberg, A Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Generation of full-length single stranded cDNAs from various types of enteroviruses1994In: EUROPIC 94: VIIIth Meeting, Korpilampi, Finland, 1994Conference paper (Refereed)
  • 256.
    Lindberg, A. Michael
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Andersson, A.
    Purification of full-length enterovirus cDNA by solid phase hybridization capture facilitates amplification of complete genomes1999In: Journal of virological methods, Vol. 77, p. 131-137Article in journal (Refereed)
  • 257.
    Lindberg, A. Michael
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Andersson, P
    Savolainen, C
    Mulders, M N
    Hovi, T
    Evolution of Human Enterovirus B genomes: incongruence between phylogenies of the VP1 and 3CD regions indicates frequent recombination within the species2003In: Journal of general virology, Vol. 84, p. 1223-1235Article in journal (Refereed)
  • 258.
    Lindberg, A. Michael
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nilsson, Anne
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Complete amplification of enterovirus genomes by long distance enterovirus-specific PCR (LDE-PCR) and the "Kalmar Collection" of infectious cDNA clones1996Conference paper (Refereed)
  • 259.
    Lindberg, A. Michael
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Polacel, Charlotta
    University of Kalmar, School of Pure and Applied Natural Sciences.
    An efficient strategy for RT-PCR cloning of complete enterovirus sequences1995Conference paper (Refereed)
  • 260.
    Lindberg, A Michael
    et al.
    Department of Medical Genetics and Microbiology, Biomedical Center, University of Uppsala.
    Stålhanske, POK
    Pettersson, U.
    Genome of Coxsackievirus B31987In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 156, no 1, p. 50-63Article in journal (Refereed)
    Abstract [en]

    The entire nucleotide sequence of the coxsackievirus B3 strain Nancy (CB3) genome has been determined from cDNA. The genome is 7396 nucleotides long, and encodes a 2185 amino acid long polyprotein. It exhibits the same gene organization as other enterovirus genomes. A detailed comparison was carried out between the proteins encoded by the CB3 and poliovirus type 1 strain Mahoney (PVI) genomes. The genes encoding the VPg polypeptide and the viral polymerase are the most conserved regions. The structural polypeptides VP1, VP2, and VP3 are less well conserved although proline and tryptophan residues frequently are found in identical positions. The VP1 protein of CB3 shows a particularly limited homology in those regions which have been found to induce neutralizing antibodies against PV1. The 5′ noncoding region of CB3 is closely related to that of PV1, with regard to both length and sequence organization, whereas the 3′ noncoding region of CB3 exhibits some unique features. 

  • 261.
    Lindberg, Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Molecular analysis of picornaviruses and their receptors1999In: PCR User Forum, Stockholm, Sweden, 1999Conference paper (Refereed)
  • 262.
    Lindberg, Michael
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Andersson, P
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Interserotypic recombination and the chimeric nature of coxsackievirus B4 strain E22001In: 6th International Symposium on Positive Strand RNA Viruses, Paris, France, 2001Conference paper (Refereed)
  • 263.
    Lindblom, Pontus
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Investigation of the Effect of Oxidation/Reduction Potential on Chalcopyrite Bioleaching2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The increasing metal demand in today’s society is a major factor behind the drive to develop the field of bioleaching, a cheap and effective technology which extracts metals from low grade ores. The world’s most abundant copper source, chalcopyrite (CuFeS2), is very difficult to process with bioleaching due to a phenomena called passivation. Many researchers across the globe work to improve the bioleaching of chalcopyrite for this very reason. One factor that has in previous studies been shown to increase the effect of the bioleaching mechanisms is the oxidation/reduction potential, or redox potential. In this study six different mineral-oxidizing bacterial cultures was tested and their pH, development of redox potential, Fe2+ concentration and the total concentrations of copper and iron leached by the cultures throughout the duration of the experiments was measured. The duration of the experiments varied for the cultures based on the time it took for their redox potentials to stabilize. The results indicate that the more efficient chalcopyrite bioleaching bacteria cultures were those which maintains a redox potential of >400 but <500 mV. Acidimicrobium ferrooxidans, Sulfobacillus acidophilus and Sulfobacillus thermosulfidooxidans was the most efficient bacterial strains used and kept their redox potential within the 400 to 500 mV range while Acidithiobacillus ferridurans and Acidithiobacillus ferriphilus were less efficient and their redox potential was kept at above 500 mV. These results also suggests a need for methods of managing the microbial populations in bioleaching heaps.

  • 264.
    Lindh, Markus
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Role of Different Carbon Sources for Growth, Production and Community Composition of Bacterioplankton2008Independent thesis Advanced level (degree of Magister), 20 poäng / 30 hpStudent thesis
    Abstract [en]

    It has been suggested that growth, production and community structure of bacterioplankton are dependent on resource availability. However, previous studies have only investigated the effect of either organic substrate mixtures or a few single organic substrates on the bacterioplankton community. The aims of this study were to investigate the impact of five different relevant carbon sources on the bacterioplankton community. This impact was evaluated comparing treatments on samples taken from Skagerrak and the Baltic Sea, in whole seawater cultures. Analysis of bacterial abundance, bacterial production (as leucine incorporation), bacterioplankton DNA community structure and colony-forming bacteria growing on agar plates were evaluated. Differences between carbon sources in terms of bacterial numbers were relatively small, with strong growth responses for L-amino acids, glucose, acetate and pyruvate with the only exception of glycolate where growth was lower. Bacterial production, on the other hand, presented marked differences, different patterns for each carbon source, especially in the Baltic Seawater. Furthermore, differences in colony size and number of colony forming bacteria in the different treatments were important. The analysis of DNA community from each experiment, by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rDNA, allowed a visualization of the microbial community structure. Sequencing of the stronger bands on the gel revealed the identity of the dominant bacterial species. In terms of bacterioplankton community structure, differences between carbon sources and between environments were important. One unknown species belonging to gamma-proteobacteria was both unique and dominant for glucose treatment in the Baltic experiment. Another gamma-proteobacteria , a Vibrio was found to specialize in glucose in the Skagerrak experiment. One uncultured bacterium belonging to a alpha-proteobacteria, both unique and dominant was found in glycolate, also this in Skagerrak, another uncultured alpha-proteobacteria was clearly dominant for glucose treatment in Skagerrak. Some bands were also present in most treatments, e.g. uncultured species belonging to bacteroidetes in Skagerrak and beta-proteobacteria in Baltic, suggesting that those species are not specialized in consuming a single carbon source. As a conclusion different carbon sources clearly had an individual but important role for bacterioplankton properties. The properties also showed to be dependent on the environment.

    Nr:6355

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  • 265.
    Lindh, Markus V.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Figueroa, Daniela
    Umeå University.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Otago, New Zealand.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Andersson, Agneta
    Umeå University.
    Legrand, Catherine
    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.
    Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities2015In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, article id 223Article in journal (Refereed)
    Abstract [en]

    Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates.

  • 266.
    Lindh, Markus V.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Swedish Meteorological and Hydrological Institute.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sensitivity of Bacterioplankton to Environmental Disturbance: A Review of Baltic Sea Field Studies and Experiments2018In: Frontiers in Marine Science, E-ISSN 2296-7745, Vol. 5, p. 1-17, article id UNSP 361Article, review/survey (Refereed)
    Abstract [en]

    Bacterioplankton communities regulate energy and matter fluxes fundamental to all aquatic life. The Baltic Sea offers an outstanding ecosystem for interpreting causes and consequences of bacterioplankton community composition shifts resulting from environmental disturbance. Yet, a systematic synthesis of the composition of Baltic Sea bacterioplankton and their responses to natural or human-induced environmental perturbations is lacking. We review current research on Baltic Sea bacterioplankton dynamics in situ (48 articles) and in laboratory experiments (38 articles) carried out at a variety of spatiotemporal scales. In situ studies indicate that the salinity gradient sets the boundaries for bacterioplankton composition, whereas, regional environmental conditions at a within-basin scale, including the level of hypoxia and phytoplankton succession stages, may significantly tune the composition of bacterial communities. Also the experiments show that Baltic Sea bacteria are highly responsive to environmental conditions, with general influences of e.g. salinity, temperature and nutrients. Importantly, nine out of ten experiments that measured both bacterial community composition and some metabolic activities showed empirical support for the sensitivity scenario of bacteria - i.e., that environmental disturbance caused concomitant change in both community composition and community functioning. The lack of studies empirically testing the resilience scenario, i.e., experimental studies that incorporate the long-term temporal dimension, precludes conclusions about the potential prevalence of resilience of Baltic Sea bacterioplankton. We also outline outstanding questions emphasizing promising applications in incorporating bacterioplankton community dynamics into biogeochemical and food-web models and the lack of knowledge for deep-sea assemblages, particularly bacterioplankton structure-function relationships. This review emphasizes that bacterioplankton communities rapidly respond to natural and predicted human-induced environmental disturbance by altering their composition and metabolic activity. Unless bacterioplankton are resilient, such changes could have severe consequences for the regulation of microbial ecosystem services.

  • 267.
    Lindh, Markus V.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University;Tech Univ Denmark, Denmark.
    Casini, Michele
    Swedish University of Agricultural Sciences.
    Andersson, Agneta
    Umeå University.
    Legrand, Catherine
    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.
    Local Environmental Conditions Shape Generalist But Not Specialist Components of Microbial Metacommunities in the Baltic Sea2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, p. 1-10, article id 2078Article in journal (Refereed)
    Abstract [en]

    Marine microbes exhibit biogeographical patterns linked with fluxes of matter and energy. Yet, knowledge of the mechanisms shaping bacterioplankton community assembly across temporal scales remains poor. We examined bacterioplankton 16S rRNA gene fragments obtained from Baltic Sea transects to determine phylogenetic relatedness and assembly processes coupled with niche breadth. Communities were phylogenetically more related over time than expected by chance, albeit with considerable temporal variation. Hence, habitat filtering, i.e., local environmental conditions, rather than competition structured bacterioplankton communities in summer but not in spring or autumn. Species sorting (SS) was the dominant assembly process, but temporal and taxonomical variation in mechanisms was observed. For May communities, Cyanobacteria, Actinobacteria, Alpha- and Betaproteobacteria exhibited SS while Bacteroidetes and Verrucomicrobia were assembled by SS and mass effect. Concomitantly, Gammaproteobacteria were assembled by the neutral model and patch dynamics. Temporal variation in habitat filtering and dispersal highlights the impact of seasonally driven reorganization of microbial communities. Typically abundant Baltic Sea populations such as the NS3a marine group (Bacteroidetes) and the SAR86 and SAR11 clade had the highest niche breadth. The verrucomicrobial Spartobacteria population also exhibited high niche breadth. Surprisingly, variation in bacterioplankton community composition was regulated by environmental factors for generalist taxa but not specialists. Our results suggest that generalists such as NS3a, SAR86, and SAR11 are reorganized to a greater extent by changes in the environment compared to specialists and contribute more strongly to determining overall biogeographical patterns of marine bacterial communities.

  • 268.
    Lindh, Markus V.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University ; Technical University of Denmark, Denmark.
    Ekstam, Börje
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Casini, Michele
    Swedish University of Agricultural Sciences.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hugerth, Luisa
    KTH Royal Institute of Technology.
    Hu, Yue
    KTH Royal Institute of Technology.
    Andersson, Anders
    KTH Royal Institute of Technology.
    Andersson, Agneta
    Umeå University.
    Legrand, Catherine
    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.
    Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 3, p. 1222-1236Article in journal (Refereed)
    Abstract [en]

    Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.

  • 269.
    Lisovski, Simeon
    et al.
    Deakin Univ, Australia;Swiss Ornithol Inst, Switzerland.
    van Dijk, Jacintha G. B.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Netherlands Inst Ecol NIOO KNAW, Netherlands.
    Klinkenberg, Don
    Univ Utrecht, Netherlands;Natl Inst Publ Hlth & Environm, Netherlands.
    Nolet, Bart A.
    Netherlands Inst Ecol NIOO KNAW, Netherlands;Univ Amsterdam, Netherlands.
    Fouchier, Ron A. M.
    Erasmus MC, Netherlands.
    Klaassen, Marcel
    Deakin Univ, Australia.
    The roles of migratory and resident birds in local avian influenza infection dynamics2018In: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 55, no 6, p. 2963-2975Article in journal (Refereed)
    Abstract [en]

    1. Migratory birds are an increasing focus of interest when it comes to infection dynamics and the spread of avian influenza viruses (AIV). However, we lack detailed understanding of migratory birds' contribution to local AIV prevalence levels and their downstream socio-economic costs and threats. 2. To explain the potential differential roles of migratory and resident birds in local AIV infection dynamics, we used a susceptible-infectious-recovered (SIR) model. We investigated five (mutually non- exclusive) mechanisms potentially driving observed prevalence patterns: (1) a pronounced birth pulse (e.g. the synchronised annual influx of immunologically naive individuals), (2) short-term immunity, (3) increase in susceptible migrants, (4) differential susceptibility to infection (i.e. transmission rate) for migrants and residents, and (5) replacement of migrants during peak migration. 3. SIR models describing all possible combinations of the five mechanisms were fitted to individual AIV infection data from a detailed longitudinal surveillance study in the partially migratory mallard duck (Anas platyrhynchos). During autumn and winter, the local resident mallard community also held migratory mallards that exhibited distinct AIV infection dynamics. 4. Replacement of migratory birds during peak migration in autumn was found to be the most important mechanism driving the variation in local AIV infection patterns. This suggests that a constant influx of migratory birds, likely immunological naive to locally circulating AIV strains, is required to predict the observed temporal prevalence patterns and the distinct differences in prevalence between residents and migrants. 5. Synthesis and applications. Our analysis reveals a key mechanism that could explain the amplifying role of migratory birds in local avian influenza virus infection dynamics; the constant flow and replacement of migratory birds during peak migration. Apart from monitoring efforts, in order to achieve adequate disease management and control in wildlife-with knock-on effects for livestock and humans,-we conclude that it is crucial, in future surveillance studies, to record host demographical parameters such as population density, timing of birth and turnover of migrants.

  • 270.
    Loderer, Christoph
    et al.
    Tech Univ Dresden, Germany.
    Holmfeldt, Karin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University, Sweden.
    Non-host class II ribonucleotide reductase in Thermus viruses: sequence adaptation and host interaction2019In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, p. 1-17, article id e6700Article in journal (Refereed)
    Abstract [en]

    Ribonucleotide reductases (RNR) are essential enzymes for all known life forms. Their current taxonomic distribution suggests extensive horizontal gene transfer e.g., by processes involving viruses. To improve our understanding of the underlying processes, we characterized a monomeric class II RNR (NrdJm) enzyme from a Thermus virus, a subclass not present in any sequenced Thermus spp. genome. Phylogenetic analysis revealed a distant origin of the nrdJm gene with the most closely related sequences found in mesophiles or moderate thermophiles from the Firmicutes phylum. GC-content, codon usage and the ratio of coding to non-coding substitutions (dN/dS) suggest extensive adaptation of the gene in the virus in terms of nucleotide composition and amino acid sequence. The NrdJm enzyme is a monomeric B-12-dependent RNR with nucleoside triphosphate specificity. It exhibits a temperature optimum at 60-70 degrees C, which is in the range of the growth optimum of Thermus spp. Experiments in combination with the Thermus thermophilus thioredoxin system show that the enzyme is able to retrieve electrons from the host NADPH pool via host thioredoxin and thioredoxin reductases. This is different from other characterized viral RNRs such as T4 phage RNR, where a viral thioredoxin is present. We hence show that the monomeric class II RNR, present in Thermus viruses, was likely transferred from an organism phylogenetically distant from the one they were isolated from, and adapted to the new host in genetic signature and amino acids sequence.

  • 271.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Helmholtz Zentrum Dresden Rossendorf, Germany.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University, Sweden.
    Simone, Domenico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Swedish University of Agricultural Sciences, Sweden.
    Bertilsson, Stefan
    Uppsala University, Sweden;Swedish University of Agricultural Sciences, Sweden.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters2019In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 4, p. 1-6, article id e01470-19Article in journal (Refereed)
    Abstract [en]

    Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two "modern marine" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic "thoroughly mixed" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H-2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or "geogases." IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omits studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.

  • 272.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Helmholtz Zentrum Dresden Rossendorf, Germany.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Turner, Stephanie
    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. Univ Copenhagen, Denmark.
    Bertilsson, Stefan
    Uppsala University.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling2018In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 94, no 8, article id fiy121Article in journal (Refereed)
    Abstract [en]

    The deep biosphere is the largest 'bioreactor' on earth, and microbes inhabiting this biome profoundly influence global nutrient and energy cycles. An important question for deep biosphere microbiology is whether or not specific populations are viable. To address this, we used quantitative PCR and high throughput 16S rRNA gene sequencing of total and viable cells (i.e. with an intact cellular membrane) from three groundwaters with different ages and chemical constituents. There were no statistically significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities. This suggests that populations were adapted to prevailing oligo trophic conditions and that non-viable cells are rapidly degraded and recycled into new biomass. With higher concentrations of organic carbon, the modem marine and undefined mixed waters hosted a community with a larger range of predicted growth strategies than the ultra-oligo trophic old saline water. These strategies included fermentative and potentially symbiotic lifestyles by candidate phyla that typically have streamlined genomes. In contrast, the old saline waters had more 16S rRNA gene sequences in previously cultured lineages able to oxidize hydrogen and fix carbon dioxide. This matches the paradigm of a hydrogen and carbon dioxide-fed chemolithoauto trophic deep biosphere.

  • 273.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Granada, Spain.
    Romero-Gonzalez, Maria
    Univ Sheffield, UK.
    Guenther, Alix
    Helmholtz Zentrum Dresden Rossendorf, Germany.
    Solari, Pier L.
    Synchrotron SOLEIL, France.
    Merroun, Mohamed L.
    Univ Granada, Spain.
    Effect of U(VI) aqueous speciation on the binding of uranium by the cell surface of Rhodotorula mucilaginosa, a natural yeast isolate from bentonites2018In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 199, p. 351-360Article in journal (Refereed)
    Abstract [en]

    This study presents the effect of aqueous uranium speciation (U-hydroxides and U-hydroxo-carbonates) on the interaction of this radionuclide with the cells of the yeast Rhodotorula mucigilanosa BII-R8. This strain was isolated from Spanish bentonites considered as reference materials for the engineered barrier components of the future deep geological repository of radioactive waste. X-ray absorption and infrared spectroscopy showed that the aqueous uranium speciation has no effect on the uranium binding process by this yeast strain. The cells bind mobile uranium species (U-hydroxides and U-hydroxo-carbonates) from solution via a time-dependent process initiated by the adsorption of uranium species to carboxyl groups. This leads to the subsequent involvement of organic phosphate groups forming uranium complexes with a local coordination similar to that of the uranyl mineral phase meta-autunite. Scanning transmission electron microscopy with high angle annular dark field analysis showed uranium accumulations at the cell surface associated with phosphorus containing ligands. Moreover, the effect of uranium mobile species on the cell viability and metabolic activity was examined by means of flow cytometry techniques, revealing that the cell metabolism is more affected by higher concentrations of uranium than the cell viability. The results obtained in this work provide new insights on the interaction of uranium with bentonite natural yeast from genus Rhodotorula under deep geological repository relevant conditions. (C) 2018 The Authors. Published by Elsevier Ltd.

  • 274.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Helmholtz Zentrum, Germany.
    Simone, Domenico
    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.
    Soler, Lucile
    Uppsala University.
    Nilsson, Emelie
    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.
    Lantz, Henrik
    Uppsala University.
    Bertilsson, Stefan
    Uppsala University.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere2018In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 9, no 6, article id e01792-18Article in journal (Refereed)
    Abstract [en]

    The continental subsurface is suggested to contain a significant part of the earth's total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the Aspo Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20 years, defined as "modern marine," and an "old saline" groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available. IMPORTANCE A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the Aspo Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbonfed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 165 rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes.

  • 275.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Granada, Spain.
    Vilchez-Vargas, Ramiro
    Univ Ghent, Belgium;Otto von Guericke Univ, Germany.
    Jroundi, Fadwa
    Univ Granada, Spain.
    Boon, Nico
    Univ Ghent, Belgium.
    Pieper, Dietmar
    Helmholtz Ctr Infect Res, Germany.
    Merroun, Mohamed L.
    Univ Granada, Spain.
    Microbial community changes induced by uranyl nitrate in bentonite clay microcosms2018In: Applied Clay Science, ISSN 0169-1317, E-ISSN 1872-9053, Vol. 160, p. 206-216Article in journal (Refereed)
    Abstract [en]

    Deep geological repository (DGR) is one of the internationally accepted options to dispose radioactive wastes. Bentonite formations from Almeria, Spain, were selected as reference material for artificial barriers for the future Spanish repository. However, the safety of this long-term disposal could be compromised not only by physicochemical factors but also by microbial processes. The highly radioactive waste must be safely stored at least for 100,000 years for the radioactivity to decrease to similar levels to those of natural uranium. To simulate a scenario where the mobilization of radionuclides from the repository to the host formations may occur, long-term microcosms were studied. After being exposed to uranyl nitrate for 5 months, the response of the bentonite microbial community to the addition of this radionuclide was evaluated. High throughput 16S rRNA gene sequencing revealed that the structure of the microbial community after the uranyl nitrate treatment differs to that of the control microcosms. The microbial diversity was dominated by Firmicutes and Proteobacteria. Moreover, after the uranyl nitrate treatment OTUs annotated as Paracoccus and Bacillus were highly enriched. The mineralogy of bentonites was not affected by the uranyl nitrate treatment as was demonstrated by X-ray diffraction analysis. In addition, the study of uranium-bacteria interaction revealed the ability of isolates to biomineralize uranium as uranium phosphate mineral phases. Thus, the changes induced by the release of uranium in the microbial population may also affect the mobility of this radionuclide, making it less mobile and therefore less harmful for this environment.

  • 276.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Åström, Mats E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bertilsson, Stefan
    Uppsala University.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 2880Article in journal (Refereed)
    Abstract [en]

    The continental deep biosphere is suggested to contain a substantial fraction of the earth's total biomass and microorganisms inhabiting this environment likely have a substantial impact on biogeochemical cycles. However, the deep microbial community is still largely unknown and can be influenced by parameters such as temperature, pressure, water residence times, and chemistry of the waters. In this study, 21 boreholes representing a range of deep continental groundwaters from the Aspo Hard Rock Laboratory were subjected to high-throughput 16S rRNA gene sequencing to characterize how the different water types influence the microbial communities. Geochemical parameters showed the stability of the waters and allowed their classification into three groups. These were (i) waters influenced by infiltration from the Baltic Sea with a "modern marine (MM)" signature, (ii) a "thoroughly mixed (TM)" water containing groundwaters of several origins, and (iii) deep "old saline (OS)" waters. Decreasing microbial cell numbers positively correlated with depth. In addition, there was a stronger positive correlation between increased cell numbers and dissolved organic carbon for the MM compared to the OS waters. This supported that the MM waters depend on organic carbon infiltration from the Baltic Sea while the ancient saline waters were fed by "geogases" such as carbon dioxide and hydrogen. The 16S rRNA gene relative abundance of the studied groundwaters revealed different microbial community compositions. Interestingly, the TM water showed the highest dissimilarity compared to the other two water types, potentially due to the several contrasting water types contributing to this groundwater. The main identified microbial phyla in the groundwaters were Gammaproteobacteria, unclassified sequences, Campylobacterota (formerly Epsilonproteobacteria), Patescibacteria, Deltaproteobacteria, and Alphaproteobacteria. Many of these taxa are suggested to mediate ferric iron and nitrate reduction, especially in the MM waters. This indicated that nitrate reduction may be a neglected but important process in the deep continental biosphere. In addition to the high number of unclassified sequences, almost 50% of the identified phyla were archaeal or bacterial candidate phyla. The percentage of unknown and candidate phyla increased with depth, pointing to the importance and necessity of further studies to characterize deep biosphere microbial populations.

  • 277.
    Lysholm, Fredrik
    et al.
    Linköping University ; Karolinska Institutet.
    Wetterbom, Anna
    Karolinska Institutet.
    Lindau, Cecilia
    Karolinska Institutet ; Karolinska University Hospital.
    Darban, Hamid
    Karolinska Institutet.
    Bjerkner, Annelie
    Karolinska Institutet ; Karolinska University Hospital.
    Fahlander, Kristina
    Karolinska Institutet ; Karolinska University Hospital.
    Lindberg, A. Michael
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Persson, Bengt
    Linköping University ; Karolinska Institutet.
    Allander, Tobias
    Karolinska Institutet ; Karolinska University Hospital.
    Andersson, Björn
    Karolinska Institutet.
    Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 2, article id e30875Article in journal (Refereed)
    Abstract [en]

    The human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the human virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.

  • 278.
    Maal-Bared, Rasha
    et al.
    University of Ottawa, Canada.
    Dixon, Brent
    Bureau of Microbial Hazards, Food Directorate, Health Canada, Canada.
    Axelsson Olsson, Diana
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fate of internalized Campylobacter jejuni and Mycobacterium avium from encysted and excysted Acanthamoeba polyphaga2019In: Experimental parasitology, ISSN 0014-4894, E-ISSN 1090-2449, Vol. 199, p. 104-110Article in journal (Refereed)
    Abstract [en]

    Association of the water- and foodborne pathogen Campylobacter jejuni with free-living Acanthamoeba spp. trophozoites enhances C. jejuni survival and resistance to biocides and starvation. When facing less than optimal environmental conditions, however, the Acanthamoeba spp. host can temporarily transform from trophozoite to cyst and back to trophozoite, calling the survival of the internalized symbiont and resulting public health risk into question. Studies investigating internalized C. jejuni survival after A. castellanii trophozoite transformation have neither been able to detect its presence inside the Acanthamoeba cyst after encystation nor to confirm its presence upon excystation of trophozoites through culture-based techniques. The purpose of this study was to detect C. jejuni and Mycobacterium avium recovered from A. polyphaga trophozoites after co-culture and induction of trophozoite encystation using three different encystation methods (Neff's medium, McMillen's medium and refrigeration), as well as after cyst excystation. Internalized M. avium was used as a positive control, since studies have consistently detected the organism after co-culture and after host excystation. Concentrations of C. jejuni in A. polyphaga trophozoites were 4.5 × 105 CFU/ml, but it was not detected by PCR or culture post-encystation. This supports the hypothesis that C. jejuni may be digested during encystation of the amoebae. M. avium was recovered at a mean concentration of 1.9 × 104 from co-cultured trophozoites and 4.4 × 101 CFU/ml after excystation. The results also suggest that M. avium recovery post-excystation was statistically significantly different based on which encystation method was used, ranging from 1.3 × 101 for Neff's medium to 5.4 × 101 CFU/ml for refrigeration. No M. avium was recovered from A. polyphaga cysts when trophozoites were encysted by McMillen's medium. Since C. jejuni internalized in cysts would be more likely to survive harsh environmental conditions and disinfection, a better understanding of potential symbioses between free-living amoebae and campylobacters in drinking water distribution systems and food processing environments is needed to protect public health. Future co-culture experiments examining survival of internalized C. jejuni should carefully consider the encystation media used, and include molecular detection tools to falsify the hypothesis that C. jejuni may be present in a viable but not culturable state.

  • 279. Mangold, Stefanie
    et al.
    Potrykus, Joanna
    Bjorn, Erik
    Lovgren, Lars
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Extreme zinc tolerance in acidophilic microorganisms from the bacterial and archaeal domains2013In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 17, no 1, p. 75-85Article in journal (Refereed)
    Abstract [en]

    Zinc can occur in extremely high concentrations in acidic, heavy metal polluted environments habited by acidophilic prokaryotes. Although these organisms are able to thrive in such severely ntaminated ecosystems their resistance mechanisms have not been well studied. Bioinformatic alysis of a range of acidophilic bacterial and archaeal genomes identified homologues of several own zinc homeostasis systems. These included primary and secondary transporters, such as the imary heavy metal exporter ZntA and Nramp super-family secondary importer MntH. Three idophilic model microorganisms, the archaeon 'Ferroplasma acidarmanus', the Gram negative cterium Acidithiobacillus caldus, and the Gram positive bacterium Acidimicrobium ferrooxidans, were lected for detailed analyses. Zinc speciation modeling of the growth media demonstrated that a large action of the free metal ion is complexed, potentially affecting its toxicity. Indeed, many of the tative zinc homeos! asis genes were constitutively expressed and with the exception of 'F. acidarmanus' ZntA, they were t up-regulated in the presence of excess zinc. Proteomic analysis revealed that zinc played a role in idative stress in At. caldus and Am. ferrooxidans. Furthermore, 'F. acidarmanus' kept a constant level intracellular zinc over all conditions tested whereas the intracellular levels increased with increasing nc exposure in the remaining organisms.

  • 280. Mangold, Stefanie
    et al.
    Rao Jonna, Venkateswara
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Response of Acidithiobacillus caldus toward suboptimal pH conditions.2013In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 17, no 4, p. 689-696Article in journal (Refereed)
    Abstract [en]

    Maintenance of a circumneutral intracellular pH is important for any organism. Acidophilic microorganisms thrive at low pH while maintaining their intracellular pH around 6.5. However, the mechanisms contributing to acidophile pH homeostasis are not well characterized. The authors investigated the proteomic response and cytoplasmic membrane fatty acid profiles of Acidithiobacillus caldus toward three pH values: 1.1, 2.5, and 4.0. Major rearrangements were observed but lower pH elicited larger changes. Differentially expressed transcription factors suggested tight transcriptional control of pH induced genes. Enzymes involved in sulfur metabolism were up-regulated at pH 1.1 suggesting either that: (1) cells required more energy for maintenance or (2) increased metabolic activity was a specific acid stress response to export intracellular protons via 1° electron transport proton pumps. Furthermore, glutamate decarboxylase, an important enzyme in Escherichia coli acid resistance, was uniquely expressed at pH 1.1. Other proteins previously shown to be involved in neutrophilic acid response, such as spermidine synthase, PspA, and toluene tolerance protein, were differentially expressed in At. caldus but require further investigation to show a direct link to pH homeostasis. Their roles in acidophilic organisms are discussed. Active modulation of fatty acid profiles was detected and suggested a more rigid membrane at low pH.

  • 281.
    Mangold, Stefanie
    et al.
    Umeå University.
    Valdés, Jorge
    Andres Bello Univ, Dept Ciencias Biol, Santiago, Chile.
    Holmes, David S
    Andres Bello Univ, Dept Ciencias Biol, Santiago, Chile.
    Dopson, Mark
    Umeå University.
    Sulfur metabolism in the extreme acidophile acidithiobacillus caldus.2011In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 2, p. Article ID: 17-Article in journal (Refereed)
    Abstract [en]

    Given the challenges to life at low pH, an analysis of inorganic sulfur compound (ISC) oxidation was initiated in the chemolithoautotrophic extremophile Acidithiobacillus caldus. A. caldus is able to metabolize elemental sulfur and a broad range of ISCs. It has been implicated in the production of environmentally damaging acidic solutions as well as participating in industrial bioleaching operations where it forms part of microbial consortia used for the recovery of metal ions. Based upon the recently published A. caldus type strain genome sequence, a bioinformatic reconstruction of elemental sulfur and ISC metabolism predicted genes included: sulfide-quinone reductase (sqr), tetrathionate hydrolase (tth), two sox gene clusters potentially involved in thiosulfate oxidation (soxABXYZ), sulfur oxygenase reductase (sor), and various electron transport components. RNA transcript profiles by semi quantitative reverse transcription PCR suggested up-regulation of sox genes in the presence of tetrathionate. Extensive gel based proteomic comparisons of total soluble and membrane enriched protein fractions during growth on elemental sulfur and tetrathionate identified differential protein levels from the two Sox clusters as well as several chaperone and stress proteins up-regulated in the presence of elemental sulfur. Proteomics results also suggested the involvement of heterodisulfide reductase (HdrABC) in A. caldus ISC metabolism. A putative new function of Hdr in acidophiles is discussed. Additional proteomic analysis evaluated protein expression differences between cells grown attached to solid, elemental sulfur versus planktonic cells. This study has provided insights into sulfur metabolism of this acidophilic chemolithotroph and gene expression during attachment to solid elemental sulfur.

  • 282.
    Marin-Beltran, Isabel
    et al.
    CSIC, Spain;Univ Algarve, Portugal.
    Logue, Jürg Brendan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University, Sweden.
    Andersson, Anders F.
    KTH Royal Instute of Technology, Sweden.
    Peters, Francesc
    CSIC, Inst Ciencies Mar, Barcelona, Spain..
    Atmospheric Deposition Impact on Bacterial Community Composition in the NW Mediterranean2019In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, article id 858Article in journal (Refereed)
    Abstract [en]

    Atmospheric deposition is a source of inorganic nutrients and organic matter to the ocean, and can favor the growth of some planktonic species over others according to their nutrient requirements. Atmospheric inputs from natural and anthropogenic sources are nowadays increasing due to desertification and industrialization, respectively. While the impact of mineral dust (mainly from the Saharan desert) on phytoplankton and bacterial community composition has been previously assessed, the effect of anthropogenic aerosols on marine bacterial assemblages remains poorly studied. Since marine bacteria play a range of roles in the biogeochemical cycles of inorganic nutrients and organic carbon, it is important to determine which taxa of marine bacteria may benefit from aerosol fertilization and which not. Here, we experimentally assessed the effect of Saharan dust and anthropogenic aerosols on marine bacterioplankton community composition across a spatial and temporal range of trophic conditions in the northwestern Mediterranean Sea. Results from 16S rDNA sequencing showed that bacterial diversity varied significantly with seasonality and geographical location. While atmospheric deposition did not yield significant changes in community composition when all the experiments where considered together, it did produce changes at certain places and during certain times of the year. These effects accounted for shifts in the bacterial community's relative abundance of up to 28%. The effect of aerosols was overall greatest in summer, both types of atmospheric particles stimulating the groups Alphaproteobacteria, Betaproteobacteria, and Cyanobacteria in the location with the highest anthropogenic footprint. Other bacterial groups benefited from one or the other aerosol depending on the season and location. Anthropogenic aerosols increased the relative abundance of groups belonging to the phylum Bacteriodetes (Cytophagia, Flavobacteriia, and Sphingobacteriia), while Saharan dust stimulated most the phytoplanktonic group of Cyanobacteria and, more specifically, Synechococcus.

  • 283.
    Martínez-García, Sandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Hawaii, USA.
    Microbial respiration in the mesopelagic zone at Station ALOHA2017In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 62, no 1, p. 320-333Article in journal (Refereed)
    Abstract [en]

    Measurements of the temporal and depth variability of microbial community respiration (MCR) in the mesopelagic zone (200-1,000 m) at Station ALOHA were made approximately monthly from November 2011 to October 2012 using the in vivo INT method. MCR in the summed and in each of the 0.2-0.8 mu m and >0.8 mu m size-fractions in the upper mesopelagic zone (200-350 m) (mean [+/- SE], 107.1 [+/- 16.3], 57.5 [+/- 8.4], and 49.6 [+/- 9.0] mu mol O-2 m(-3)day(-1), respectively) were higher than in the lower mesopelagic zone (350-1000 m) (56.1 [+/- 4.5], 30.8 [+/- 2.9], and 25.3 [+/- 3.1] mu mol O-2 m(-3)day(-1), respectively). The average > 0.8 mu m/0.2-0.8 m MCR in the mesopelagic zone was 0.97 [+/- 0.16]) and was indistinguishable in the upper and lower portions of the mesopelagic zone. A recurrent local peak in MCR was found at 600-650 m for both non-winter and winter measurements. Total depth-integrated MCR (200-1,000 m) was higher during the non-winter than during winter months (55.7 [+/- 3.4] and 44.8 [+/- 2.4] mmol O-2 m(-2) day(-1)). Variability of total MCR rates was controlled by changes in the >0.8 mu m size fraction, and was possibly related to higher primary production and export from the euphotic zone during the non-winter period. These findings suggest seasonal variability in respiration rates in the mesopelagic zone at Station ALOHA and support the current steady-state model where export flux controls respiration in the mesopelagic zone

  • 284. Massana, R.
    et al.
    Unrein, F.
    Rodriguez-Martinez, R.
    Forn, I.
    Lefort, T.
    Pinhassi, Jarone
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Not, F.
    Grazing rates and functional diversity of uncultured heterotrophic flagellates2009In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 3, no 5, p. 588-596Article in journal (Refereed)
    Abstract [en]

    Aquatic assemblages of heterotrophic protists are very diverse and formed primarily by organisms that remain uncultured. Thus, a critical issue is assigning a functional role to this unknown biota. Here we measured grazing rates of uncultured protists in natural assemblages (detected by fluorescent in situ hybridization (FISH)), and investigated their prey preference over several bacterial tracers in short-term ingestion experiments. These included fluorescently labeled bacteria (FLB) and two strains of the Roseobacter lineage and the family Flavobacteriaceae, of various cell sizes, which were offered alive and detected by catalyzed reporter deposition-FISH after the ingestion. We obtained grazing rates of the globally distributed and uncultured marine stramenopiles groups 4 and 1 (MAST-4 and MAST-1C) flagellates. Using FLB, the grazing rate of MAST-4 was somewhat lower than whole community rates, consistent with its small size. MAST-4 preferred live bacteria, and clearance rates with these tracers were up to 2 nl per predator per h. On the other hand, grazing rates of MAST-1C differed strongly depending on the tracer prey used, and these differences could not be explained by cell viability. Highest rates were obtained using FLB whereas the flavobacteria strain was hardly ingested. Possible explanations would be that the small flavobacteria cells were outside the effective size range of edible prey, or that MAST-1C selects against this particular strain. Our original dual FISH protocol applied to grazing experiments reveals important functional differences between distinct uncultured protists and offers the possibility to disentangle the complexity of microbial food webs.

  • 285.
    Mazur-Marzec, Hanna
    et al.
    University of Gdansk, Poland.
    Bertos-Fortis, Mireia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Torunska-Sitarz, Anna
    University of Gdansk, Poland.
    Fidor, Anna
    University of Gdansk, Poland.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Chemical and Genetic Diversity of Nodularia spumigena from the Baltic Sea2016In: Marine Drugs, ISSN 1660-3397, E-ISSN 1660-3397, Vol. 14, no 11, article id 209Article in journal (Refereed)
    Abstract [en]

    Nodularia spumigena is a toxic, filamentous cyanobacterium occurring in brackish waters worldwide, yet forms extensive recurrent blooms in the Baltic Sea. N. spumigena produces several classes of non-ribosomal peptides (NRPs) that are active against several key metabolic enzymes. Previously, strains from geographically distant regions showed distinct NRP metabolic profiles. In this work, conspecific diversity in N. spumigena was studied using chemical and genetic approaches. NRP profiles were determined in 25 N. spumigena strains isolated in different years and from different locations in the Baltic Sea using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genetic diversity was assessed by targeting the phycocyanin intergenic spacer and flanking regions (cpcBA-IGS). Overall, 14 spumigins, 5 aeruginosins, 2 pseudaeruginosins, 2 nodularins, 36 anabaenopeptins, and one new cyanopeptolin-like peptide were identified among the strains. Seven anabaenopeptins were new structures; one cyanopeptolin-like peptide was discovered in N. spumigena for the first time. Based on NRP profiles and cpcBA-IGS sequences, the strains were grouped into two main clusters without apparent influence of year and location, indicating persistent presence of these two subpopulations in the Baltic Sea. This study is a major step in using chemical profiling to explore conspecific diversity with a higher resolution than with a sole genetic approach.

  • 286. Middelboe, Mathias
    et al.
    Holmfeldt, Karin
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Riemann, Lasse
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nybroe, Ole
    Haaber, Jakob
    Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties2009In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 11, no 8, p. 1971-1982Article in journal (Refereed)
    Abstract [en]

    Genetic, structural and physiological differences between strains of the marine bacterium Cellulophaga baltica MM#3 (Flavobacteriaceae) developing in response to the activity of two virulent bacteriophages, Theta S(M) and Theta S(T), was investigated during 3 weeks incubation in chemostat cultures. A distinct strain succession towards increased phage resistance and a diversification of the metabolic properties was observed. During the incubation the bacterial population diversified from a single strain, which was sensitive to 24 tested Cellulophaga phages, into a multistrain and multiresistant population, where the dominant strains had lost susceptibility to up to 22 of the tested phages. By the end of the experiment the cultures reached a quasi steady state dominated by Theta S(T)-resistant and Theta S(M) + Theta S(T)-resistant strains coexisting with small populations of phage-sensitive strains sustaining both phages at densities of > 10(6) plaque forming units (pfu) ml(-1). Loss of susceptibility to phage infection was associated with a reduction in the strains' ability to metabolize various carbon sources as demonstrated by BIOLOG assays. This suggested a cost of resistance in terms of reduced physiological capacity. However, there was no direct correlation between the degree of resistance and the loss of metabolic properties, suggesting either the occurrence of compensatory mutations in successful strains or that the cost of resistance in some strains was associated with properties not resolved by the BIOLOG assay. The study represents the first direct demonstration of phage-driven generation of functional diversity within a marine bacterial host population with significant implications for both phage susceptibility and physiological properties. We propose, therefore, that phage-mediated selection for resistant strains contributes significantly to the extensive microdiversity observed within specific bacterial species in marine environments.

  • 287.
    Moniuszko-Malinowska, Anna
    et al.
    Med Univ Bialystok, Poland.
    Dunaj, Justyna
    Med Univ Bialystok, Poland.
    Andersson, Martin O.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Swiecicka, Izabela
    Univ Bialystok, Poland.
    Drewnowska, Justyna M.
    Univ Bialystok, Poland.
    Czupryna, Piotr
    Med Univ Bialystok, Poland.
    Grygorczuk, Sambor
    Med Univ Bialystok, Poland.
    Krol, Monika
    Med Univ Bialystok, Poland.
    Zajkowska, Joanna
    Med Univ Bialystok, Poland.
    Pancewicz, Slawomir
    Med Univ Bialystok, Poland.
    Absence of molecular evidence for Candidatus Neoehrlichia mikurensis presence in symptomatic patients in Poland2019In: Travel Medicine and Infectious Disease, ISSN 1477-8939, E-ISSN 1873-0442, Vol. 32, p. 1-2, article id 101514Article in journal (Refereed)
  • 288.
    Morales, Teresita A
    et al.
    Stockholm University.
    Dopson, Mark
    Umeå University.
    Athar, Rana
    Umeå University.
    Herbert, Roger B
    Uppsala University.
    Analysis of bacterial diversity in acidic pond water and compost after treatment of artificial acid mine drainage for metal removal.2005In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 90, no 5, p. 543-551Article in journal (Refereed)
    Abstract [en]

    The microbial population of a sludge amended leaf compost material utilized for treatment of artificial acid mine drainage was studied by culture-independent molecular methods. Iron-rich and sulfurous wastewater (artificial acid mine drainage) was circulated through a column bioreactor for 16 months. After 12 months the column was inoculated with a mixed culture from an acidic pond receiving acid mine drainage from a tailings impoundment at a decommissioned site in Kristineberg, North Sweden. Hydrogen sulfide odor and the formation of black precipitates indicated that sulfate-reduction occurred in the column. 16S rDNA gene analysis by denaturing gradient gel electrophoresis, cloning, and sequencing as well as fluorescent in situ hybridization confirmed the presence of microorganisms closely related to sulfate-reducing bacteria and microorganisms from the genera Pseudoxanthmonas, Dechlorosoma, Desulfovibrio, Agrobacterium, Methylocapsa, Rhodococcus, Sulfobacillus, and some unidentified bacteria. Sulfate-reducing bacteria were found in the column bioreactor 2 weeks after inoculation, but not thereafter. This suggests they were in low abundance, even though sulfate remediation rates were significant. Instead, the population contained species similar to those previously found to utilize humic substances released from the compost material.

  • 289.
    Mullapudi, Edukondalu
    et al.
    Masaryk Univ, Czech Republic.
    Novacek, Jiri
    Masaryk Univ, Czech Republic.
    Palkova, Lenka
    Masaryk Univ, Czech Republic.
    Kulich, Pavel
    Vet Res Inst, Brno, Czech Republic.
    Lindberg, A. Michael
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    van Kuppeveld, Frank J. M.
    Radboud Univ Nijmegen, Netherlands.
    Plevka, Pavel
    Masaryk Univ, Czech Republic.
    Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 32016In: Journal of Virology, ISSN 0022-538X, E-ISSN 1098-5514, Vol. 90, no 17, p. 7628-7639Article in journal (Refereed)
    Abstract [en]

    In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the uncoating of the nonenveloped human cardiovirus Saffold virus 3 (SAFV-3) of the family Picornaviridae. SAFVs cause diseases ranging from gastrointestinal disorders to meningitis. We present a structure of a native SAFV-3 virion determined to 2.5 angstrom by X-ray crystallography and an 11-angstrom-resolution cryo-electron microscopy reconstruction of an "altered" particle that is primed for genome release. The altered particles are expanded relative to the native virus and contain pores in the capsid that might serve as channels for the release of VP4 subunits, N termini of VP1, and the RNA genome. Unlike in the related enteroviruses, pores in SAFV-3 are located roughly between the icosahedral 3- and 5-fold axes at an interface formed by two VP1 and one VP3 subunit. Furthermore, in native conditions many cardioviruses contain a disulfide bond formed by cysteines that are separated by just one residue. The disulfide bond is located in a surface loop of VP3. We determined the structure of the SAFV-3 virion in which the disulfide bonds are reduced. Disruption of the bond had minimal effect on the structure of the loop, but it increased the stability and decreased the infectivity of the virus. Therefore, compounds specifically disrupting or binding to the disulfide bond might limit SAFV infection. IMPORTANCE A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from the capsid in order to initiate infection. This process is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the genome release of Human Saffold virus 3. Saffold viruses cause diseases ranging from gastrointestinal disorders to meningitis. We show that before the genome is released, the Saffold virus 3 particle expands, and holes form in the previously compact capsid. These holes serve as channels for the release of the genome and small capsid proteins VP4 that in related enteroviruses facilitate subsequent transport of the virus genome into the cell cytoplasm.

  • 290.
    Muradrasoli, Shaman
    et al.
    Uppsala University ; Swedish University of Agricultural Sciences.
    Bálint, Adám
    Swedish University of Agricultural Sciences ; National Veterinary Institute.
    Wahlgren, John
    Karolinska Institutet ; Swedish Institute for Infectious Disease Control.
    Waldenström, Jonas
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Swedish Institute for Infectious Disease Control.
    Belák, Sándor
    Swedish University of Agricultural Sciences ; National Veterinary Institute.
    Blomberg, Jonas
    Uppsala University.
    Olsen, Björn
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Uppsala University.
    Prevalence and phylogeny of coronaviruses in wild birds from the Bering Strait area (Beringia)2010In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 5, no 10, article id e13640Article in journal (Refereed)
    Abstract [en]

    Coronaviruses (CoVs) can cause mild to severe disease in humans and animals, their host range and environmental spread seem to have been largely underestimated, and they are currently being investigated for their potential medical relevance. Infectious bronchitis virus (IBV) belongs to gamma-coronaviruses and causes a costly respiratory viral disease in chickens. The role of wild birds in the epidemiology of IBV is poorly understood. In the present study, we examined 1,002 cloacal and faecal samples collected from 26 wild bird species in the Beringia area for the presence of CoVs, and then we performed statistical and phylogenetic analyses. We detected diverse CoVs by RT-PCR in wild birds in the Beringia area. Sequence analysis showed that the detected viruses are gamma-coronaviruses related to IBV. These findings suggest that wild birds are able to carry gamma-coronaviruses asymptomatically. We concluded that CoVs are widespread among wild birds in Beringia, and their geographic spread and frequency is higher than previously realised. Thus, Avian CoV can be efficiently disseminated over large distances and could be a genetic reservoir for future emerging pathogenic CoVs. Considering the great animal health and economic impact of IBV as well as the recent emergence of novel coronaviruses such as SARS-coronavirus, it is important to investigate the role of wildlife reservoirs in CoV infection biology and epidemiology.

  • 291.
    Muthusamy, Sarala Devi
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Functional Profiling Of Metabolic Regulation In Marine Bacteria2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Oceans are powered by active, metabolically diverse microorganisms, which are important in regulating biogeochemical cycles on Earth. Most of the ocean surface is often limited by nutrients, influencing bacterial growth and activities. Bacterial adaptation to fluctuating environmental conditions involves extensive reprogramming, and redirection of bacterial metabolism and physiology. In this thesis, I investigated the molecular mechanisms of bacterial adaptation strategies to sustain their growth and survival, focusing on the regulation of gene and protein expression in heterotrophic marine bacteria.

    Comparative proteomics analyses of the growth and non-growth conditions, uncovered central adaptations that marine bacteria employ to allow them to change their metabolism to support exponential growth in response to nutrients and to readjust to stationary phase under nutrient limitation. Our results highlight that during nutrient rich conditions three distinct bacteria lineages have great similarities in their proteome. On the other hand, we observed pronounced differences in behavior between taxa during stationary phase.

    Analyses of the proteorhodopsin containing bacterium Vibrio sp. AND4 during starvation showed that significantly improved survival in the light compared to darkness. Notably, proteins involved in promoting cell vitality and survival had higher relative abundance under light. In contrast, cells in the dark need to degrade their endogenous resources to support their basic cellular demands under starvation. Thus, light strongly influences how PR-containing bacteria organize their molecular composition in response to starvation.

    Study of alternative energy generation metabolisms in the Alphaproteobacteria Phaeobacter sp. MED193 showed that the addition of thiosulfate enhanced the bacterial growth yields. Concomitantly, inorganic sulfur oxidation gene expression increased with thiosulfate compared to controls. Moreover, thiosulfate stimulated protein synthesis and anaplerotic CO2 fixation. These findings imply that this bacterium could use their lithotrophic potential to gain additional energy from sulfur oxidation for both improving their growth and survival.

    This thesis concludes that analyses in model organisms under defined growth conditions gives invaluable knowledge about the regulatory networks and physiological strategies that ensure the growth and survival of heterotrophic bacteria. This is critically important for interpreting bacterial responses to dynamic environmental changes.

    Moreover, these analyses are crucial for understanding genetic and proteomic responses in microbial communities or uncultivated organisms in terms of defining ecological niches of planktonic bacteria

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  • 292.
    Muthusamy, Sarala Devi
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    González, José M.
    Univ La Laguna, Dept Microbiol, Tenerife, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dynamics of metabolic activities and gene expression in the Roseobacter clade bacterium Phaeobacter sp. MED193 during growth with thiosulfate2014In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 80, no 22, p. 6933-6942Article in journal (Refereed)
    Abstract [en]

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

  • 293.
    Muthusamy, Sarala Devi
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Branca, Rui Miguel Mamede
    Sci Life Lab, Stockholm ; Karolinska Institutet.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Otago, New Zealand.
    Gonzalez, Jose M.
    Univ La Laguna, Spain.
    Lehtio, Janne
    Sci Life Lab, Stockholm ; Karolinska Institutet.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2301-2319Article, review/survey (Refereed)
    Abstract [en]

    Much of the phenotype of a microorganism consists of its repertoire of metabolisms and how and when its proteins are deployed under different growth conditions. Hence, analyses of protein expression could provide important understanding of how bacteria adapt to different environmental settings. To characterize the flexibility of proteomes of marine bacteria, we investigated protein profiles of three important marine bacterial lineages - Oceanospirillaceae (Neptuniibacter caesariensis strain MED92), Roseobacter (Phaeobacter sp. MED193) and Flavobacteria (Dokdonia sp. MED134) - during transition from exponential to stationary phase. As much as 59-80% of each species' total proteome was expressed. Moreover, all three bacteria profoundly altered their expressed proteomes during growth phase transition, from a dominance of proteins involved in translation to more diverse proteomes, with a striking appearance of enzymes involved in different nutrient-scavenging metabolisms. Whereas the three bacteria shared several overarching metabolic strategies, they differed in important details, including distinct expression patterns of membrane transporters and proteins in carbon and phosphorous metabolism and storage compounds. These differences can be seen as signature metabolisms - metabolisms specific for lineages. These findings suggest that quantitative proteomics can inform about the divergent ecological strategies of marine bacteria in adapting to changes in environmental conditions.

  • 294.
    Naguib, Mahmoud M.
    et al.
    Uppsala University, Sweden;Anim Hlth Res Inst, Egypt.
    Verhagen, Josanne H.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Mostafa, Ahmed
    Justus Liebig Univ Giessen, Germany;NRC, Egypt.
    Wille, Michelle
    WHO Collaborating Ctr Reference & Res Influenza, Australia.
    Li, Ruiyun
    Imperial Coll London, UK.
    Graaf, Annika
    Friedrich Loeffler Inst, Germany.
    Jarhult, Josef D.
    Uppsala University, Sweden.
    Ellström, Patrik
    Uppsala University, Sweden.
    Zohari, Siamak
    National Veterinary Institute, Sweden.
    Lundkvist, Åke
    Uppsala University, Sweden.
    Olsen, Björn
    Uppsala University, Sweden.
    Global patterns of avian influenza A (H7): virus evolution and zoonotic threats2019In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 43, no 6, p. 608-621Article, review/survey (Refereed)
    Abstract [en]

    Avian influenza viruses (AIVs) continue to impose a negative impact on animal and human health worldwide. In particular, the emergence of highly pathogenic AIV H5 and, more recently, the emergence of low pathogenic AIV H7N9 have led to enormous socioeconomical losses in the poultry industry and resulted in fatal human infections. While H5N1 remains infamous, the number of zoonotic infections with H7N9 has far surpassed those attributed to H5. Despite the clear public health concerns posed by AIV H7, it is unclear why specifically this virus subtype became endemic in poultry and emerged in humans. In this review, we bring together data on global patterns of H7 circulation, evolution and emergence in humans. Specifically, we discuss data from the wild bird reservoir, expansion and epidemiology in poultry, significant increase in their zoonotic potential since 2013 and genesis of highly pathogenic H7. In addition, we analysed available sequence data from an evolutionary perspective, demonstrating patterns of introductions into distinct geographic regions and reassortment dynamics. The integration of all aspects is crucial in the optimisation of surveillance efforts in wild birds, poultry and humans, and we emphasise the need for a One Health approach in controlling emerging viruses such as AIV H7.

  • 295.
    Naguib, Mahmoud M.
    et al.
    Uppsala University, Sweden;Animal Health Research Institute, Egypt.
    Verhagen, Josanne H.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Samy, Ahmed
    Animal Health Research Institute, Egypt;The Pirbright Institute, UK.
    Eriksson, Per
    Uppsala University, Sweden.
    Fife, Mark
    The Pirbright Institute, UK.
    Lundkvist, Åke
    Uppsala University, Sweden.
    Ellström, Patrik
    Uppsala University, Sweden.
    Järhult, Josef D.
    Uppsala University, Sweden.
    Avian influenza viruses at the wild–domestic bird interface in Egypt2019In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 9, no 1, p. 1-9, article id 1575687Article, review/survey (Refereed)
    Abstract [en]

    Wild birds of the orders Anseriformes (mainly ducks, geese and swans) and Charadriiformes (mainly gulls, terns and waders) constitute the natural reservoir for low pathogenic avian influenza (LPAI) viruses. In Egypt, highly pathogenic avian influenza (HPAI) H5N1 and LPAI H9N2 viruses are endemic in domestic poultry, forming a threat to animal and human health and raising questions about the routes of introduction and mechanisms of persistence. Recently, HPAI H5N8 virus was also introduced into Egyptian domestic birds. Here we review the literature on the role of wild birds in the introduction and endemicity of avian influenza viruses in Egypt. Dabbling ducks in Egypt harbor an extensive LPAI virus diversity and may constitute the route of introduction for HPAI H5N1 and HPAI H5N8 viruses into Egypt through migration, however their role in the endemicity of HPAI H5N1, LPAI H9N2 and potentially other avian influenza virus (AIV) strains–by means of reassortment of viral genes–is less clear. Strengthened surveillance programs, in both domestic and wild birds, that include all LPAI virus subtypes and full genome sequencing are needed to better assess the wild–domestic bird interface and form a basis for evidence-based measures to limit and prevent AIV transmission between wild and domestic birds. © 2019, © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

  • 296.
    Nasrin, Shamima
    et al.
    Auburn Univ, USA.
    Ganji, Suresh
    Univ Mississippi, USA.
    Kakirde, Kavita S.
    Auburn Univ, USA.
    Jacob, Melissa R.
    Univ Mississippi, USA.
    Wang, Mei
    Univ Mississippi, USA.
    Ravu, Ranga Rao
    Univ Mississippi, USA.
    Cobine, Paul A.
    Auburn Univ, USA.
    Khan, Ikhlas A.
    Univ Mississippi, USA.
    Wu, Cheng-Cang
    Lucigen Corp, USA.
    Mead, David A.
    Varigen Biosci Corp, USA.
    Li, Xing-Cong
    Univ Mississippi, USA.
    Liles, Mark R.
    Auburn Univ, USA;Varigen Biosci Corp, USA.
    Chloramphenicol Derivatives with Antibacterial Activity Identified by Functional Metagenomics2018In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 81, no 6, p. 1321-1332Article in journal (Refereed)
    Abstract [en]

    A functional metagenomic approach identified novel and diverse soil-derived DNAs encoding inhibitors to methicillin-resistant Staphylococcus aureus (MRSA). A metagenomic DNA soil library containing 19 200 recombinant Escherichia coli BAC clones with 100 Kb average insert size was screened for antibiotic activity. Twenty-seven clones inhibited MRSA, seven of which were found by LC-MS to possess modified chloramphenicol (Cm) derivatives, including three new compounds whose structures were established as 1-acetyl-3-propanoylchloramphenicol, 1-acety1-3-butanoyl-chloramphenicol, and 3-butanoyl-1-propanoylchloramphenicol. Cm was used as the selectable antibiotic for cloning, suggesting that heterologously expressed enzymes resulted in derivatization of Cm into new chemical entities with biological activity. An esterase was found to be responsible for the enzymatic regeneration of Cm, and the gene trfA responsible for plasmid copy induction was found to be responsible for inducing antibacterial activity in some clones. Six additional acylchloramphenicols were synthesized for structure and antibacterial activity relationship studies, with 1-p-nitrobenzoylchloramphenicol the most active against Mycobacterium intracellulare and Mycobacterium tuberculosis, with MICs of 12.5 and 50.0 mu g/mL, respectively.

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  • 297. Nedwell, D.
    et al.
    Hall, S.E.
    Andersson, A.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Seasonal changes in the distribution and exchange of inorganic nitrogen between sediment and water in the Northern Baltic (Gulf of Bothnia)1983In: Estuarine, Coastal and Shelf Science, ISSN 0272-7714, E-ISSN 1096-0015, Vol. 17, no 2, p. 169-179Article in journal (Refereed)
  • 298.
    Ni, Gaofeng
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Canizales, Sebastian
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Wetsus, European Ctr Excellence Sustainable Water Technol, Netherlands.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Simone, Domenico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Palwai, Viraja R.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundin, Daniel
    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. Helmholtz Zentrum Dresden Rossendorf, Germany.
    Sleutels, Tom
    Wetsus, European Ctr Excellence Sustainable Water Technol, Netherlands.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 2308Article in journal (Refereed)
    Abstract [en]

    Thiocyanate is a toxic compound produced by the mining and metallurgy industries that needs to be remediated prior to its release into the environment. If the industry is situated at high altitudes or near the poles, economic factors require a low temperature treatment process. Microbial fuel cells are a developing technology that have the benefits of both removing such toxic compounds while recovering electrical energy. In this study, simultaneous thiocyanate degradation and electrical current generation was demonstrated and it was suggested that extracellular electron transfer to the anode occurred. Investigation of the microbial community by 16S rRNA metatranscriptome reads supported that the anode attached and planktonic anolyte consortia were dominated by a Thiobacillus-like population. Metatranscriptomic sequencing also suggested thiocyanate degradation primarily occurred via the 'cyanate' degradation pathway. The generated sulfide was metabolized via sulfite and ultimately to sulfate mediated by reverse dissimilatory sulfite reductase, APS reductase, and sulfate adenylyltransferase and the released electrons were potentially transferred to the anode via soluble electron shuttles. Finally, the ammonium from thiocyanate degradation was assimilated to glutamate as nitrogen source and carbon dioxide was fixed as carbon source. This study is one of the first to demonstrate a low temperature inorganic sulfur utilizing microbial fuel cell and the first to provide evidence for pathways of thiocyanate degradation coupled to electron transfer.

  • 299.
    Ni, Gaofeng
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. European Ctr Excellence Sustainable Water Technol, Netherlands.
    Harnawan, Pebrianto
    European Ctr Excellence Sustainable Water Technol, Netherlands.
    Seidel, Laura
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Heijne, Annemiek Ter
    Wageningen Univ, Netherlands.
    Sleutels, Tom
    European Ctr Excellence Sustainable Water Technol, Netherlands.
    Buisman, Cees J. N.
    European Ctr Excellence Sustainable Water Technol, Netherlands;Wageningen Univ, Netherlands.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Haloalkaliphilic microorganisms assist sulfide removal in a microbial electrolysis cell2019In: Journal of Hazardous Materials, ISSN 0304-3894, E-ISSN 1873-3336, Vol. 363, p. 197-204Article in journal (Refereed)
    Abstract [en]

    Several industrial processes produce toxic sulfide containing streams that are often scrubbed using caustic solutions. An alternative, cost effective sulfidetreatment method is bioelectrochemical sulfide removal. For the first time, a haloalkaliphilic sulfide-oxidizing microbial consortium was introduced to the anodic chamber of a microbial electrolysis cell operated at alkaline pH and with 1.0 M sodium ions. Under anode potential control, the highest sulfideremoval rate was 2.16 mM/day and chemical analysis supported that the electrical current generation was from the sulfide oxidation. Biotic operation produced a maximum current density of 3625 mA/m(2) compared to 210 mA/m2 while under abiotic operation. Furthermore, biotic electrical production was maintained for a longer period than for abiotic operation, potentially due to the passivation of the electrode by elemental sulfur during abiotic operation. The use of microorganisms reduced the energy input in this study compared to published electrochemical sulfide removal technologies. Sulfide-oxidizing populations dominated both the planktonic and electrode-attached communities with 16S rRNA gene sequences aligning within the genera Thioctikalivibrio, Thioalkaihnicrobium, and Desulfurivibrio. The dominance of the Desulfurivibrio-like population on the anode surface offered evidence for the first haloalkaliphilic bacterium able to couple electrons from sulfide oxidation to extracellular electron transfer to the anode.

  • 300.
    Ni, Gaofeng
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Simone, Domenico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Swedish University of Agricultural Sciences.
    Palma, Daniela
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University.
    Wu, Xiaofen
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Turner, Stephanie
    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.
    A novel inorganic sulfur compound metabolizing Ferroplasma-like population is suggested to mediate extracellular electron transfer2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, article id 2945Article in journal (Refereed)
    Abstract [en]

    Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed 'acid mine drainage (AMD)'] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of 'microbial fuel cells' that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbemineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-likepopulation had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylylsulfate released electrons and the extracellular electrontransfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganicsulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.

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