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  • 1.
    Almeida, Rafael M.
    et al.
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Nobrega, Gabriel N.
    Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Ciencia Solo, Piracicaba, Brazil..
    Junger, Pedro C.
    Univ Fed Rio de Janeiro, Lab Limnol, Rio De Janeiro, Brazil..
    Figueiredo, Aline V.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Andrade, Anizio S.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    de Moura, Caroline G. B.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Tonetta, Denise
    Univ Fed Santa Catarina, Lab Freshwater Ecol, Florianopolis, SC, Brazil..
    Oliveira, Ernandes S., Jr.
    Radboud Univ Nijmegen, Dept Aquat Ecol & Environm Biol, Inst Water & Wetland Res, NL-6525 ED Nijmegen, Netherlands..
    Araujo, Fabiana
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Rust, Felipe
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Pineiro-Guerra, Juan M.
    Univ Republica, Dept Ecol Teor & Aplicada, Ctr Univ Reg Este, Montevideo, Uruguay.;Univ Republica, Fac Ciencias, Montevideo, Uruguay..
    Mendonca, Jurandir R., Jr.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Medeiros, Leonardo R.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Pinheiro, Lorena
    Univ Fed Estado Rio de Janeiro, Dept Ciencias Nat, Rio De Janeiro, Brazil..
    Miranda, Marcela
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Costa, Mariana R. A.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Melo, Michaela L.
    Univ Fed Sao Carlos, Lab Microbial Proc & Biodivers, BR-13560 Sao Carlos, SP, Brazil..
    Nobre, Regina L. G.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Benevides, Thiago
    Univ Fed Rio de Janeiro, Lab Limnol, Rio De Janeiro, Brazil..
    Roland, Fabio
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    de Klein, Jeroen
    Wageningen Univ, Aquat Ecol & Environm Sci, NL-6700 AP Wageningen, Netherlands..
    Barros, Nathan O.
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Mendonca, Raquel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil.
    Becker, Vanessa
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Huszar, Veral. M.
    Univ Fed Rio de Janeiro, Museu Nacl, Lab Ficol, Rio De Janeiro, Brazil..
    Kosten, Sarian
    Radboud Univ Nijmegen, Dept Aquat Ecol & Environm Biol, Inst Water & Wetland Res, NL-6525 ED Nijmegen, Netherlands..
    High Primary Production Contrasts with Intense Carbon Emission in a Eutrophic Tropical Reservoir2016Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, artikkel-id 717Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent studies from temperate lakes indicate that eutrophic systems tend to emit less carbon dioxide (Co-2) and bury more organic carbon (OC) than oligotrophic ones, rendering them CO2 sinks in some cases. However, the scarcity of data from tropical systems is critical for a complete understanding of the interplay between eutrophication and aquatic carbon (C) fluxes in warm waters. We test the hypothesis that a warm eutrophic system is a source of both CO2 and CH4 to the atmosphere, and that atmospheric emissions are larger than the burial of OC in sediments. This hypothesis was based on the following assumptions: (i) OC mineralization rates are high in warm water systems, so that water column CO2 production overrides the high C uptake by primary producers, and (ii) increasing trophic status creates favorable conditions for CH4 production. We measured water-air and sediment-water CO2 fluxes, CH4 diffusion, ebullition and oxidation, net ecosystem production (NEP) and sediment OC burial during the dry season in a eutrophic reservoir in the semiarid northeastern Brazil. The reservoir was stratified during daytime and mixed during nighttime. In spite of the high rates of primary production (4858 +/- 934 mg C m(-2) d(-1)), net heterotrophy was prevalent due to high ecosystem respiration (5209 +/- 992 mg C m(-2) d(-1)). Consequently, the reservoir was a source of atmospheric CO2 (518 +/- 182 mg C m(-2) d(-1)). In addition, the reservoir was a source of ebullitive (17 +/- 10 mg C m(-2) d(-1)) and diffusive CH4 (11 +/- 6 mg C m(-2) d(-1)). OC sedimentation was high (1162 mg C m(-2) d(-1)), but our results suggest that the majority of it is mineralized to CO2 (722 +/- 182 mg C m(-2) d(-1)) rather than buried as OC (440 mg C m(-2) d(-1)). Although temporally resolved data would render our findings more conclusive, our results suggest that despite being a primary production and OC burial hotspot, the tropical eutrophic system studied here was a stronger CO2 and CH4 source than a C sink, mainly because of high rates of OC mineralization in the water column and sediments.

  • 2.
    Alonso-Saez, Laura
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Zeder, Michael
    Harding, Tommy
    Pernthaler, Jakob
    Lovejoy, Connie
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Pedros-Alio, Carlos
    Winter bloom of a rare betaproteobacteriurn in the Arctic Ocean2014Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 5, s. 425-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Extremely low abundance microorganisms (members of the "rare biosphere") are believed to include dormant taxa, which can sporadically become abundant following environmental triggers. Yet, microbial transitions from rare to abundant have seldom been captured in situ, and it is uncertain how widespread these transitions are. A bloom of a single ribotype (>= 99% similarity in the 16S ribosomal RNA gene) of a widespread betaproteobacterium (Janthinobacterium sp.) occurred over 2 weeks in Arctic marine waters. The Janthinobactenum population was not detected microscopically in situ in January and early February, but suddenly appeared in the water column thereafter, eventually accounting for up to 20% of bacterial cells in mid February. During the bloom, this bacterium was detected at open water sites up to 50 km apart, being abundant down to more than 300 m. This event is one of the largest monospecific bacterial blooms reported in polar oceans. It is also remarkable because Betaproteobacteria are typically found only in low abundance in marine environments. In particular, Janthinobacterium were known from non-marine habitats and had previously been detected only in the rare biosphere of seawater samples, including the polar oceans. The Arctic Janthinobacterium formed mucilagenous monolayer aggregates after short (ca. 8 h) incubations, suggesting that biofilm formation may play a role in maintaining rare bacteria in pelagic marine environments. The spontaneous mass occurrence of this opportunistic rare taxon in polar waters during the energy-limited season extends current knowledge of how and when microbial transitions between rare and abundant occur in the ocean.

  • 3.
    Ansell, Brendan R. E.
    et al.
    Univ Melbourne, Fac Vet & Agr Sci, Melbourne, Vic, Australia..
    Baker, Louise
    Walter & Eliza Hall Inst Med Res, Populat Hlth & Immun Div, Melbourne, Vic, Australia..
    Emery, Samantha J.
    Walter & Eliza Hall Inst Med Res, Populat Hlth & Immun Div, Melbourne, Vic, Australia..
    McConville, Malcolm J.
    Univ Melbourne, Mol Sci & Biotechnol Inst Bio21, Melbourne, Vic, Australia..
    Svärd, Staffan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Gasser, Robin B.
    Univ Melbourne, Fac Vet & Agr Sci, Melbourne, Vic, Australia..
    Jex, Aaron R.
    Univ Melbourne, Fac Vet & Agr Sci, Melbourne, Vic, Australia.;Walter & Eliza Hall Inst Med Res, Populat Hlth & Immun Div, Melbourne, Vic, Australia..
    Transcriptomics Indicates Active and Passive Metronidazole Resistance Mechanisms in Three Seminal Giardia Lines2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 398Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Giardia duodenalis is an intestinal parasite that causes 200-300 million episodes of diarrhoea annually. Metronidazole (Mtz) is a front-line anti-giardial, but treatment failure is common and clinical resistance has been demonstrated. Mtz is thought to be activated within the parasite by oxidoreductase enzymes, and to kill by causing oxidative damage. In G. duodenalis, Mtz resistance involves active and passive mechanisms. Relatively low activity of iron-sulfur binding proteins, namely pyruvate: ferredoxin oxidoreductase (PFOR), ferredoxins, and nitroreductase-1, enable resistant cells to passively avoid Mtz activation. Additionally, low expression of oxygen-detoxification enzymes can allow passive (non-enzymatic) Mtz detoxification via futile redox cycling. In contrast, active resistance mechanisms include complete enzymatic detoxification of the pro-drug by nitroreductase-2 and enhanced repair of oxidized biomolecules via thioredoxin-dependent antioxidant enzymes. Molecular resistance mechanisms may be largely founded on reversible transcriptional changes, as some resistant lines revert to drug sensitivity during drug-free culture in vitro, or passage through the life cycle. To comprehensively characterize these changes, we undertook strand-specific RNA sequencing of three laboratory-derived Mtz-resistant lines, 106-2ID(10), 713-M3, and WB-M3, and compared transcription relative to their susceptible parents. Common up-regulated genes encoded variant-specific surface proteins (VSPs), a high cysteine membrane protein, calcium and zinc channels, a Mad-2 cell cycle regulator and a putative fatty acid a alpha-oxidase. Down-regulated genes included nitroreductase-1, putative chromate and quinone reductases, and numerous genes that act proximal to PFOR. Transcriptional changes in 106-2ID(10) diverged from those in 713-r and WB-r (r <= 0.2), which were more similar to each other (r = 0.47). In 106-2ID(10), a nonsense mutation in nitroreductase-1 transcripts could enhance passive resistance whereas increased transcription of nitroreductase-2, and a MATE transmembrane pump system, suggest active drug detoxification and efflux, respectively. By contrast, transcriptional changes in 713-M3 and WB-M3 indicated a higher oxidative stress load, attributed to Mtz- and oxygen-derived radicals, respectively. Quantitative comparisons of orthologous gene transcription between Mtz-resistant G. duodenalis and Trichomonas vaginalis, a closely related parasite, revealed changes in transcripts encoding peroxidases, heat shock proteins, and FMN-binding oxidoreductases, as prominent correlates of resistance. This work provides deep insight into Mtz-resistant G. duodenalis, and illuminates resistance-associated features across parasitic species.

  • 4.
    Atterby, Clara
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    Mourkas, Evangelos
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Univ Bath, Dept Biol & Biochem, Milner Ctr Evolut, Bath, Avon, England.
    Meric, Guillaume
    Univ Bath, Dept Biol & Biochem, Milner Ctr Evolut, Bath, Avon, England.
    Pascoe, Ben
    Univ Bath, Dept Biol & Biochem, Milner Ctr Evolut, Bath, Avon, England;MRC CLIMB Consortium, Bath, Avon, England.
    Wang, Helen
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Waldenström, Jonas
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
    Sheppard, Samuel K.
    Univ Bath, Dept Biol & Biochem, Milner Ctr Evolut, Bath, Avon, England;MRC CLIMB Consortium, Bath, Avon, England.
    Olsen, Björn
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    Järhult, Josef D.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    Ellström, Patrik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    The Potential of Isolation Source to Predict Colonization in Avian Hosts: A Case Study in Campylobacter jejuni Strains From Three Bird Species2018Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikkel-id 591Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 5.
    Beier, Sara
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bacterial chitin degradation: mechanisms and ecophysiological strategies2013Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 4, s. 149-Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Chitin is one the most abundant polymers in nature and interacts with both carbon and nitrogen cycles. Processes controlling chitin degradation are summarized in reviews published some 20 years ago, but the recent use of culture-independent molecular methods has led to a revised understanding of the ecology and biochemistry of this process and the organisms involved. This review summarizes different mechanisms and the principal steps involved in chitin degradation at a molecular level while also discussing the coupling of community composition to measured chitin hydrolysis activities and substrate uptake. Ecological consequences are then highlighted and discussed with a focus on the cross feeding associated with the different habitats that arise because of the need for extracellular hydrolysis of the chitin polymer prior to metabolic use. Principal environmental drivers of chitin degradation are identified which are likely to influence both community composition of chitin degrading bacteria and measured chitin hydrolysis activities.

  • 6.
    Berga, Mercè
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Germany.
    Zha, Yinghua
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Székely, Anna J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Langenheder, Silke
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 948Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Disturbances and environmental change are important factors determining the diversity,composition, and functioning of communities. However, knowledge about how naturalbacterial communities are affected by such perturbations is still sparse. We performeda whole ecosystem manipulation experiment with freshwater rock pools where weapplied salinity disturbances of different intensities. The aim was to test how thecompositional and functional resistance and resilience of bacterial communities,alpha- and beta-diversity and the relative importance of stochastic and deterministiccommunity assembly processes changed along a disturbance intensity gradient.We found that bacterial communities were functionally resistant to all salinity levels (3, 6, and 12 psu) and compositionally resistant to a salinity increase to 3 psu andresilient to increases of 6 and 12 psu. Increasing salinities had no effect on local richnessand evenness, beta-diversity and the proportion of deterministically vs. stochasticallyassembled communities. Our results show a high functional and compositional stabilityof bacterial communities to salinity changes of different intensities both at localand regional scales, which possibly reflects long-term adaptation to environmentalconditions in the study system.

  • 7.
    Cardoso, Simone J.
    et al.
    Laboratory of Aquatic Ecology, Federal University of Juiz de Fora, Juiz de Fora, Brazil.
    Vidal, Luciana O.
    Laboratory of Aquatic Ecology, Federal University of Juiz de Fora, Juiz de Fora, Brazil.
    Mendonça, Raquel F.
    Laboratory of Aquatic Ecology, Federal University of Juiz de Fora, Juiz de Fora, Brazil.
    Tranvik, Lars J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Sobek, Sebastian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Fábio, Roland
    Laboratory of Aquatic Ecology, Federal University of Juiz de Fora, Juiz de Fora, Brazil.
    Spatial variation of sediment mineralization supports differential CO2 emissions from a tropical hydroelectric reservoir2013Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 4, s. 101-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Substantial amounts of organic matter (OM) from terrestrial ecosystems are buried as sediments in inland waters. It is still unclear to what extent this OM constitutes a sink of carbon, and how much of it is returned to the atmosphere upon mineralization to carbon dioxide (CO2). The construction of reservoirs affects the carbon cycle by increasing OM sedimentation at the regional scale. In this study we determine the OM mineralization in the sediment of three zones (river, transition, and dam) of a tropical hydroelectric reservoir in Brazil as well as identify the composition of the carbon pool available for mineralization. We measured sediment organic carbon mineralization rates and related them to the composition of the OM, bacterial abundance and pCO2 of the surface water of the reservoir. Terrestrial OM was an important substrate for the mineralization. In the river and transition zones most of the OM was allochthonous (56 and 48%, respectively) while the dam zone had the lowest allochthonous contribution (7%). The highest mineralization rates were found in the transition zone (154.80 ± 33.50 mg C m-2 d-1) and the lowest in the dam (51.60 ± 26.80 mg C m-2 d-1). Moreover, mineralization rates were significantly related to bacterial abundance (r2= 0.50, p < 0.001) and pCO2 in the surface water of the reservoir (r2 = 0.73, p < 0.001). The results indicate that allochthonous OM has different contributions to sediment mineralization in the three zones of the reservoir. Further, the sediment mineralization, mediated by heterotrophic bacteria metabolism, significantly contributes to CO2supersaturation in the water column, resulting in higher pCO2 in the river and transition zones in comparison with the dam zone, affecting greenhouse gas emission estimations from hydroelectric reservoirs.

  • 8.
    Douchi, Damien
    et al.
    Natl Renewable Energy Lab, Biosci Ctr, Golden, CO 80401 USA.
    Liang, Feiyan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Cano, Melissa
    Natl Renewable Energy Lab, Biosci Ctr, Golden, CO 80401 USA.
    Xiong, Wei
    Natl Renewable Energy Lab, Biosci Ctr, Golden, CO 80401 USA.
    Wang, Bo
    Natl Renewable Energy Lab, Biosci Ctr, Golden, CO 80401 USA.
    Maness, Pin-Ching
    Natl Renewable Energy Lab, Biosci Ctr, Golden, CO 80401 USA.
    Lindblad, Peter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Yu, Jianping
    Natl Renewable Energy Lab, Biosci Ctr, Golden, CO 80401 USA.
    Membrane-Inlet Mass Spectrometry Enables a Quantitative Understanding of Inorganic Carbon Uptake Flux and Carbon Concentrating Mechanisms in Metabolically Engineered Cyanobacteria2019Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, artikkel-id 1356Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Photosynthesis uses solar energy to drive inorganic carbon (Ci) uptake, fixation, and biomass formation. In cyanobacteria, Ci uptake is assisted by carbon concentrating mechanisms (CCM), and CO2 fixation is catalyzed by RubisCO in the Calvin-Benson-Bassham (CBB) cycle. Understanding the regulation that governs CCM and CBB cycle activities in natural and engineered strains requires methods and parameters that quantify these activities. Here, we used membrane-inlet mass spectrometry (MIMS) to simultaneously quantify Ci concentrating and fixation processes in the cyanobacterium Synechocystis 6803. By comparing cultures acclimated to ambient air conditions to cultures transitioning to high Ci conditions, we show that acclimation to high Ci involves a concurrent decline of Ci uptake and fixation parameters. By varying light input, we show that both CCM and CBB reactions become energy limited under low light conditions. A strain over-expressing the gene for the CBB cycle enzyme fructose-bisphosphate aldolase showed higher CCM and carbon fixation capabilities, suggesting a regulatory link between CBB metabolites and CCM capacity. While the engineering of an ethanol production pathway had no effect on CCM or carbon fixation parameters, additional fructose-bisphosphate aldolase gene over-expression enhanced both activities while simultaneously increasing ethanol productivity. These observations show that MIMS can be a useful tool to study the extracellular Ci flux and how CBB metabolites regulate Ci uptake and fixation.

  • 9.
    Eiler, Alexander
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Hayakawa, Darin H
    Rappé, Michael S
    Non-random assembly of bacterioplankton communities in the subtropical North Pacific Ocean2011Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 2Artikkel i tidsskrift (Fagfellevurdert)
  • 10.
    Eriksson, Per
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Lindskog, Cecilia
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Klinisk och experimentell patologi.
    Lorente-Leal, Victor
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Waldenström, Jonas
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
    González-Acuna, Daniel
    Univ Concepcion, Fac Ciencias Vet, Chillan, Chile.
    Järhult, Josef D.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    Lundkvist, Åke
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Olsen, Björn
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    Jourdain, Elsa
    INRA, UMR0346 EPIA, VetAgro Sup, St Genes Champanelle, France.
    Ellström, Patrik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    Attachment Patterns of Human and Avian Influenza Viruses to Trachea and Colon of 26 Bird Species: Support for the Community Concept2019Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, artikkel-id 815Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Avian influenza A viruses (AIVs) have a broad host range, but are most intimately associated with waterfowl (Anseriformes) and, in the case of the H13 and H16 subtypes, gulls (Charadriiformes). Host associations are multifactorial, but a key factor is the ability of the virus to bind host cell receptors and thereby initiate infection. The current study aims at investigating the tissue attachment pattern of a panel of AIVs, comprising H3N2, H6N1, H12N5, and H16N3, to avian trachea and colon tissue samples obtained from host species of different orders. Virus attachment was not restricted to the bird species or order from which the virus was isolated. Instead, extensive virus attachment was observed to several distantly related avian species. In general, more virus attachment and receptor expression were observed in trachea than in colon samples. Additionally, a human seasonal H3N2 virus was studied. Unlike the studied AIVs, this virus mainly attached to tracheae from Charadriiformes and a very limited set of avian cola. In conclusion, the reported results highlight the importance of AIV attachment to trachea in many avian species. Finally, the importance of chickens and mallards in AIVs dynamics was illustrated by the abundant AIV attachment observed.

  • 11.
    Flaviani, Flavia
    et al.
    Univ Cape Town, Biopharming Res Unit, Dept Mol & Cell Biol, Cape Town, South Africa;Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Schroeder, Declan C.
    Univ Reading, Sch Biol Sci, Reading, Berks, England;Univ Minnesota Twin Cities, Coll Vet Med, Minneapolis, MN 55455 USA;Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Lebret, Karen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Balestreri, Cecilia
    Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Highfield, Andrea C.
    Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Schroeder, Joanna L.
    Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Thorpe, Sally E.
    NERC, British Antarctic Survey, Cambridge, England.
    Moore, Karen
    Univ Exeter, Exeter Sequencing Serv, Biosci, Exeter, Devon, England.
    Pasckiewicz, Konrad
    Univ Exeter, Exeter Sequencing Serv, Biosci, Exeter, Devon, England.
    Pfaff, Maya C.
    Oceans & Coasts, Dept Environm Affairs, Cape Town, South Africa.
    Rybicki, Edward P.
    Univ Cape Town, Biopharming Res Unit, Dept Mol & Cell Biol, Cape Town, South Africa.
    Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current2018Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikkel-id 1474Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while gamma-Proteobacteria dominated the South-East Indian Ocean. A combination of gamma- and alpha-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order Caudovirales across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity.

  • 12.
    Galand, Pierre E.
    et al.
    Centre d’Estudis Avançats de Blanes-Consejo Superior de Investigaciones Científicas.
    Alonso-Sáez, Laura
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Lovejoy, Connie
    Université Laval.
    Casamayor, Emilio O.
    Centre d’Estudis Avançats de Blanes-Consejo Superior de Investigaciones Científicas.
    Contrasting activity patterns determined by BrdU incorporation in bacterial ribotypes from the Arctic Ocean in winter2013Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 4, s. 118-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The winter Arctic Ocean is one of the most unexplored marine environments from a microbiological perspective. Heterotrophic bacteria maintain their activity at a baseline level during the extremely low-energy conditions of the winter, but little is known about the specific phylotypes that have the potential to survive and grow in such harsh environment. In this study, we aimed at identifying actively growing ribotypes in winter Arctic Ocean seawater cultures by experimental incubations with the thymidine analog bromodeoxyuridine (BrdU), followed by immunocapturing, terminal restriction fragment length polymorphism fingerprinting, cloning, and sequencing the 16S rRNA gene. We incubated water collected at different months over the Arctic winter and showed that the actively growing bacterial fraction, taking up BrdU, represented only a subset of the total community. Among the BrdU-labeled bacterial taxa we identified the Flavobacteria Polaribacter, theAlphaproteobacteria SAR11, the Gammaproteobacteria Arctic 96B-16 cluster and, predominately, members of Colwellia spp. Interestingly,Colwellia sequences formed three clusters (93 and 97% pairwise 16S rRNA identity) that contributed in contrasting ways to the active communities in the incubations. Polaribacter, Arctic 96B-16 and one cluster of Colwellia were more abundant in the active community represented by the BrdU-labeled DNA. In contrast, SAR11 and two otherColwellia clusters were underrepresented in the BrdU-labeled community compared to total communities. Despite the limitation of the long incubations needed to label slow growing arctic communities, the BrdU approach revealed the potential for active growth in low-energy conditions in some relevant groups of polar bacteria, includingPolaribacter and Arctic 96B-16. Moreover, under similar incubation conditions, the growth of different Colwellia ribotypes varied, suggesting that related clusters of Colwellia may have distinct metabolic features.

  • 13.
    Graham, Emily B.
    et al.
    Univ Colorado, Inst Arctic & Alpine Res, Boulder, CO 80309 USA.;Pacific NW Natl Lab, Div Biol Sci, Richland, WA 99352 USA..
    Knelman, Joseph E.
    Univ Colorado, Inst Arctic & Alpine Res, Boulder, CO 80309 USA.;Joint Genome Inst, US Dept Energy, Walnut Creek, CA USA..
    Schindlbacher, Andreas
    Bundesforsch & Ausblldungszentrum VVald, Fed Res & Tr 3Thing Ctr Forests, Dept Forest Ecol, Vienna, Austria..
    Siciliano, Steven
    Univ Saskatchewan, Dept Soil Sci, Saskatoon, SK, Canada..
    Breulmann, Marc
    Helmholtz Ctr Environm Res, Ctr Environm Biotechnol, Leipzig, Germany..
    Yannarell, Anthony
    Univ Illinois, Dept Nat Resources & Environm Sci, Urbana, IL USA..
    Bemans, J. M.
    Univ Calif Merced, Life & Environm Sci & Sierra Nevada Res Inst, Merced, CA USA..
    Abell, Guy
    Flinders Univ S Australia, Sch Med, Adelaide, SA 5001, Australia..
    Philippot, Laurent
    Inst Natl Rech Agron Agroecol, Dijon, France..
    Prosser, James
    Univ Aberdeen, Inst Biol & Environm Sci, Aberdeen, Scotland..
    Foulquier, Arnaud
    UR MALY, Irstea, Ctr Lyon Villeurbanne, Villeurbanne, France..
    Yuste, Jorge C.
    CSIC, Museo Nacl Ciencias Nat, Dept Biogeog & Global Change, Madrid, Spain..
    Glanville, Helen C.
    Bangor Univ, Environm Ctr Wales, Gwynedd, England..
    Jones, Davey L.
    Bangor Univ, Environm Ctr Wales, Gwynedd, England..
    Angel, Foey
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Vienna, Austria..
    Salminen, Janne
    Hame Univ Appl Sci, Hameenlinna, Finland..
    Newton, Ryan J.
    Univ Wisconsin, Sch Freshwater Sci, Milwaukee, WI 53201 USA..
    Buergmann, Helmut
    Eawag Swiss Fed Inst Aquat Sci & Technol, Dept Surface Waters, Kastanienbaum, Switzerland..
    Ingram, Lachlan J.
    Univ Sydney, Ctr Carbon Water & Food, Sydney, NSW 2006, Australia..
    Hamer, Ute
    Univ Munster, Inst Landscape Ecol, D-48149 Munster, Germany..
    Siljanen, Henri M. P.
    Univ Eastern Finland, Dept Environm & Biol Sci, Kuopio, Finland..
    Peltoniemi, Krista
    Nat Resources Inst, Vantaa, Finland..
    Potthast, Karin
    Tech Univ Dresden, Inst Soil Sci & Site Ecol, D-01062 Dresden, Germany..
    Baneras, Lluis
    Univ Girona, Fac Ciencies, Inst Aquat Ecol, Girona, Spain..
    Hartmann, Martin
    Inst Sustainabil Sci Agroscope, Zurich, Switzerland..
    Banerjee, Samiran
    CSIRO Agr Flagship, Crace, ACT, Australia..
    Yu, Ri-Qing
    Univ Texas Tyler, Dept Biol, Tyler, TX 75799 USA..
    Nogaro, Geraldine
    EDF R&D, Alat Hydraul & Environm Lab, Chatou, France..
    Richter, Andreas
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Vienna, Austria..
    Koranda, Marianne
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Div Terr Ecosyst Res, Vienna, Austria..
    Castle, Sarah C.
    Univ Montana, Dept Ecosyst & Conservat Sci, Missoula, MT 59812 USA..
    Goberna, Marta
    CSIC, Ctr Invest & Docencia Econ, Valencia, Spain..
    Song, Bongkeun
    Virginia Inst Marine Sci, Dept Biol Sci, Gloucester Point, VA USA..
    Chatterjee, Amitava
    N Dakota State Univ, AES Sch Nat Resources Sci, Fargo, ND 58105 USA..
    Nunes, Olga C.
    Lopes, Ana R.
    Univ Porto, Fac Engn, Lab Proc Engn Environm Biotechnol & Energy, LEPABE, Rua Campo Alegre 823, P-4100 Oporto, Portugal..
    Cao, Yiping
    Southern Calif Coastal Water Res Project Author, Costa Mesa, CA USA..
    Kaisermann, Aurore
    INRA Bordeaux, Interact Sol Plante Atmosphere, UMR, Villenave Dornon, France..
    Hallin, Sara
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden..
    Strickland, Michael S.
    State Univ, Virginia Polytech Inst, Dept Biol Sci, Blacksburg, VA USA..
    Garcia-Pausas, Jordi
    Ctr Tecnol Forestal Catalunya, Solsona, Spain..
    Barba, Josep
    Ctr Recerca Ecol & Aplicac Forestals, Barcelona, Spain..
    Kang, Hojeong
    Yonsei Univ, Sch Civil & Environm Engn, Seoul 120749, South Korea..
    Isobe, Kazuo
    Univ Tokyo, Dept Appl Biol Chem, Tokyo, Japan..
    Papaspyrou, Sokratis
    Univ Cadiz, Dept Biomed Biotechnol & Publ Hlth, Puerto Real, Spain..
    Pastorelli, Roberta
    Res Ctr Agrobiol & Pedol, Florence, Italy..
    Lagomarsino, Alessandra
    Res Ctr Agrobiol & Pedol, Florence, Italy..
    Lindström, Eva S.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Basiliko, Nathan
    Laurentian Univ, Vale Living Lakes Ctr, Sudbury, ON P3E 2C6, Canada.;Laurentian Univ, Dept Biol, Sudbury, ON P3E 2C6, Canada..
    Nemergut, Diana R.
    Univ Colorado, Inst Arctic & Alpine Res, Boulder, CO 80309 USA.;Duke Univ, Dept Biol, Durham, NC USA..
    Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?2016Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, artikkel-id 214Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

  • 14.
    Gumpert, Heidi
    et al.
    Tech Univ Denmark, Dept Syst Biol, Lyngby, Denmark.;Univ Copenhagen, Hvidovre Hosp, Dept Clin Microbiol, Hvidovre, Denmark..
    Kubicek-Sutherland, Jessica Z.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Porse, Andreas
    Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Lyngby, Denmark..
    Karami, Nahid
    Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Dept Infect Dis, Gothenburg, Sweden..
    Munck, Christian
    Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Lyngby, Denmark..
    Linkevicius, Marius
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Adlerberth, Ingegerd
    Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Dept Infect Dis, Gothenburg, Sweden..
    Wold, Agnes E.
    Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Dept Infect Dis, Gothenburg, Sweden..
    Andersson, Dan I.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Sommer, Morten O. A.
    Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Lyngby, Denmark..
    Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiotain the Absence of Antibiotic Treatment2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 1852Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The microbial ecosystem residing in the human gut is believed to play an important role in horizontal exchange of virulence and antibiotic resistance genes that threatens human health. While the diversity of gut-microorganisms and their genetic content has been studied extensively, high-resolution insight into the plasticity, and selective forces shaping individual genomes is scarce. In a longitudinal study, we followed the dynamics of co-existing Escherichia coli lineages in an infant not receiving antibiotics. Using whole genome sequencing, we observed large genomic deletions, bacteriophage infections, as well as the loss and acquisition of plasmids in these lineages during their colonization of the human gut. In particular, we captured the exchange of multidrug resistance genes, and identified a clinically relevant conjugative plasmid mediating the transfer. This resistant transconjugant lineage was maintained for months, demonstrating that antibiotic resistance genes can disseminate and persist in the gut microbiome; even in absence of antibiotic selection. Furthermore, through in vivo competition assays, we suggest that the resistant transconjugant can persist through a fitness advantage in the mouse gut in spite of a fitness cost in vitro. Our findings highlight the dynamic nature of the human gut microbiota and provide the first genomic description of antibiotic resistance gene transfer between bacteria in the unperturbed human gut. These results exemplify that conjugative plasmids, harboring resistance determinants, can transfer and persists in the gut in the absence of antibiotic treatment.

  • 15. Keller, Andreas Hardy
    et al.
    Schleinitz, Kathleen M.
    Starke, Robert
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Vogt, Carsten
    Kleinsteuber, Sabine
    Metagenome-based metabolic reconstruction reveals the ecophysiological function of Epsilonproteobacteria in a hydrocarbon-contaminated sulfidic aquifer2015Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, artikkel-id 1396Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The population genome of an uncultured bacterium assigned to the Campylobacterales (Epsilonproteobacteria) was reconstructed from a metagenome dataset obtained by whole-genome shotgun pyrosequencing. Genomic DNA was extracted from a sulfate-reducing, m-xylene-mineralizing enrichment culture isolated from groundwater of a benzene-contaminated sulfidic aquifer. The identical epsilonproteobacterial phylotype has previously been detected in toluene- or benzene-mineralizing, sulfate-reducing consortia enriched from the same site. Previous stable isotope probing (SIP) experiments with 13C6-labeled benzene suggested that this phylotype assimilates benzene-derived carbon in a syntrophic benzene-mineralizing consortium that uses sulfate as terminal electron acceptor. However, the type of energy metabolism and the ecophysiological function of this epsilonproteobacterium within aromatic hydrocarbon-degrading consortia and in the sulfidic aquifer are poorly understood. Annotation of the epsilonproteobacterial population genome suggests that the bacterium plays a key role in sulfur cycling as indicated by the presence of an sqr gene encoding a sulfide quinone oxidoreductase and psr genes encoding a polysulfide reductase. It may gain energy by using sulfide or hydrogen/formate as electron donors. Polysulfide, fumarate, as well as oxygen are potential electron acceptors. Auto- or mixotrophic carbon metabolism seems plausible since a complete reductive citric acid cycle was detected. Thus the bacterium can thrive in pristine groundwater as well as in hydrocarbon-contaminated aquifers. In hydrocarbon-contaminated sulfidic habitats, the epsilonproteobacterium may generate energy by coupling the oxidation of hydrogen or formate and highly abundant sulfide with the reduction of fumarate and/or polysulfide, accompanied by efficient assimilation of acetate produced during fermentation or incomplete oxidation of hydrocarbons. The highly efficient assimilation of acetate was recently demonstrated by a pulsed 13C2-acetate protein SIP experiment. The capability of nitrogen fixation as indicated by the presence of nif genes may provide a selective advantage in nitrogen-depleted habitats. Based on this metabolic reconstruction, we propose acetate capture and sulfur cycling as key functions of Epsilonproteobacteria within the intermediary ecosystem metabolism of hydrocarbon-rich sulfidic sediments.

  • 16.
    Knöppel, Anna
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Knopp, Michael
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Albrecht, Lisa M
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Lundin, Erik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Lustig, Ulrika
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Näsvall, Joakim
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Andersson, Dan I
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Genetic adaptation to growth under laboratory conditions in Escherichia coli and Salmonella enterica2018Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikkel-id 756Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Experimental evolution under controlled laboratory conditions is becoming increasingly important to address various evolutionary questions, including, for example, the dynamics and mechanisms of genetic adaptation to different growth and stress conditions. In such experiments, mutations typically appear that increase the fitness under the conditions tested (medium adaptation), but that are not necessarily of interest for the specific research question. Here, we have identified mutations that appeared during serial passage of E. coli and S. enterica in four different and commonly used laboratory media and measured the relative competitive fitness and maximum growth rate of 111 genetically re-constituted strains, carrying different single and multiple mutations. Little overlap was found between the mutations that were selected in the two species and the different media, implying that adaptation occurs via different genetic pathways. Furthermore, we show that commonly occurring adaptive mutations can generate undesired genetic variation in a population and reduce the accuracy of competition experiments. However, by introducing media adaptation mutations with large effects into the parental strain that was used for the evolution experiment, the variation (standard deviation) was decreased 10-fold, and it was possible to measure fitness differences between two competitors as small as |s| < 0.001.

  • 17. Krause, Sascha
    et al.
    Le Roux, Xavier
    Niklaus, Pascal A.
    Van Bodegom, Peter M.
    Lennon, Jay T.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Grossart, Hans-Peter
    Philippot, Laurent
    Bodelier, Paul L. E.
    Trait-based approaches for understanding microbial biodiversity and ecosystem functioning2014Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 5, s. 251-Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    In ecology, biodiversity-ecosystem functioning (BEE) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEE of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEE using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEE studies are often inadequate to unravel BEE relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEE relationships and thus generating systematic principles in microbial ecology and more generally ecology.

  • 18.
    Leavitt, Steven D.
    et al.
    Brigham Young Univ, Dept Biol, Provo, UT 84602 USA.;Brigham Young Univ, Monte L Bean Life Sci Museum, Provo, UT 84602 USA..
    Westberg, Martin
    Uppsala universitet, Enheten för musik och museer, Evolutionsmuseet.
    Nelsen, Matthew P.
    Field Museum, Sci & Educ, Chicago, IL USA..
    Elix, John A.
    Australian Natl Univ, Res Sch Chem, Canberra, ACT, Australia..
    Timdal, Einar
    Univ Oslo, Nat Hist Museum, Oslo, Norway..
    Sohrabi, Mohammad
    Iranian Res Org Sci & Technol, Dept Biotechnol, Tehran, Iran..
    Clair, Larry L. St.
    Brigham Young Univ, Dept Biol, Provo, UT 84602 USA.;Brigham Young Univ, Monte L Bean Life Sci Museum, Provo, UT 84602 USA..
    Williams, Laura
    Univ Kaiserslautern, Biol Inst, Plant Ecol & Systemat, Kaiserslautern, Germany..
    Wedin, Mats
    Swedish Museum Nat Hist, Dept Bot, Stockholm, Sweden..
    Lumbsch, H. T.
    Field Museum, Sci & Educ, Chicago, IL USA..
    Multiple, Distinct Intercontinental Lineages but Isolation of Australian Populations in a Cosmopolitan Lichen-Forming Fungal Taxon, Psora decipiens (Psoraceae, Ascomycota)2018Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikkel-id 283Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Multiple drivers shape the spatial distribution of species, including dispersal capacity, niche incumbency, climate variability, orographic barriers, and plate tectonics. However, biogeographic patterns of fungi commonly do not fit conventional expectations based on studies of animals and plants. Fungi, in general, are known to occur across exceedingly broad, intercontinental distributions, including some important components of biological soil crust communities (BSCs). However, molecular data often reveal unexpected biogeographic patterns in lichenized fungal species that are assumed to have cosmopolitan distributions. The lichen-forming fungal species Psora decipiens is found on all continents, except Antarctica and occurs in BSCs across diverse habitats, ranging from hot, arid deserts to alpine habitats. In order to better understand factors that shape population structure in cosmopolitan lichen-forming fungal species, we investigated biogeographic patterns in the cosmopolitan taxon P. decipiens, along with the closely related taxa P. crenata and P. saviczii. We generated a multi-locus sequence dataset based on a worldwide sampling of these taxa in order to reconstruct evolutionary relationships and explore phylogeographic patterns. Both P. crenata and P. decipiens were not recovered as monophyletic; and P. saviczii specimens were recovered as a monophyletic clade closely related to a number of lineages comprised of specimens representing P. decipiens. Striking phylogeographic patterns were observed for P. crenata, with populations from distinct geographic regions belonging to well-separated, monophyletic lineages. South African populations of P. crenata were further divided into well-supported sub-clades. While well-supported phylogenetic substructure was also observed for the nominal taxon P. decipiens, nearly all lineages were comprised of specimens collected from intercontinental populations. However, all Australian specimens representing P. decipiens were recovered within a single well-supported monophyletic clade consisting solely of Australian samples. Our study supports up to 10 candidate species-level lineages in P. decipiens, based on genealogical concordance and coalescent-based species delimitation analyses. Our results support the general pattern of the biogeographic isolation of lichen-forming fungal populations in Australia, even in cases where closely related congeners have documented intercontinental distributions. Our study has important implications for understanding factors influencing diversification and distributions of lichens associated with BSC.

  • 19.
    Lemmens, Liesbeth
    et al.
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Brussels, Belgium.
    Tilleman, Laurentijn
    Univ Ghent, Fac Pharmaceut Sci, Lab Pharmaceut Biotechnol, Ghent, Belgium.
    De Koning, Ezra
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Brussels, Belgium.
    Valegård, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Lindås, Ann-Christin
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, Stockholm, Sweden.
    Van Nieuwerburgh, Filip
    Univ Ghent, Fac Pharmaceut Sci, Lab Pharmaceut Biotechnol, Ghent, Belgium.
    Maes, Dominique
    Vrije Univ Brussel, Dept Bioengn Sci, Struct Biol Brussels, Brussels, Belgium.
    Peeters, Eveline
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Brussels, Belgium.
    YtrASa, a GntR-Family Transcription Factor, Represses Two Genetic Loci Encoding Membrane Proteins in Sulfolobus acidocaldarius2019Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, artikkel-id 2084Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In bacteria, the GntR family is a widespread family of transcription factors responsible for the regulation of a myriad of biological processes. In contrast, despite their occurrence in archaea only a little information is available on the function of GntR-like transcription factors in this domain of life. The thermoacidophilic crenarchaeon Sulfolobus acidocaldarius harbors a GntR-like regulator belonging to the YtrA subfamily, encoded as the first gene in an operon with a second gene encoding a putative membrane protein. Here, we present a detailed characterization of this regulator, named YtrA(Sa), with a focus on regulon determination and mechanistic analysis with regards to DNA binding. Genome-wide chromatin immunoprecipitation and transcriptome experiments, the latter employing a ytrA(Sa) overexpression strain, demonstrate that the regulator acts as a repressor on a very restricted regulon, consisting of only two targets including the operon encoding its own gene and a distinct genetic locus encoding another putative membrane protein. For both targets, a conserved 14-bp semi-palindromic binding motif was delineated that covers the transcriptional start site and that is surrounded by additional half-site motifs. The crystallographic structure of YtrA(Sa) was determined, revealing a compact dimeric structure in which the DNA-binding motifs are oriented ideally to enable a specific high-affinity interaction with the core binding motif. This study provides new insights into the functioning of a YtrA-like regulator in the archaeal domain of life.

  • 20.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
    Åström, Mats
    Linnaeus Univ, Dept Biol & Environm Sci, Kalmar, Sweden.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
    Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers2018Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikkel-id 2880Artikkel i tidsskrift (Fagfellevurdert)
    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 Äspö 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.

  • 21.
    Owen, Sian V.
    et al.
    Univ Liverpool, Inst Integrat Biol, Liverpool, Merseyside, England..
    Wenner, Nicolas
    Univ Liverpool, Inst Integrat Biol, Liverpool, Merseyside, England..
    Canals, Rocio
    Univ Liverpool, Inst Integrat Biol, Liverpool, Merseyside, England..
    Makumi, Angela
    Katholieke Univ Leuven, Fac Biosci Engn, Food Microbiol Lab, Dept Microbial & Mol Syst, Leuven, Belgium..
    Hammarlöf, Disa L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Gordon, Melita A.
    Univ Liverpool, Inst Infect & Global Hlth, Liverpool, Merseyside, England.;Malawi Liverpool Wellcome Trust Clin Res Programm, Blantyre, Malawi..
    Aertsen, Abram
    Katholieke Univ Leuven, Fac Biosci Engn, Food Microbiol Lab, Dept Microbial & Mol Syst, Leuven, Belgium..
    Feasey, Nicholas A.
    Univ Liverpool Liverpool Sch Trop Med, Liverpool, Merseyside, England..
    Hinton, Jay C. D.
    Univ Liverpool, Inst Integrat Biol, Liverpool, Merseyside, England..
    Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP12017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 235Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the past 30 years, Salmonella bloodstream infections have become a significant health problem in sub-Saharan Africa and are responsible for the deaths of an estimated 390,000 people each year. The disease is predominantly caused by a recently described sequence type of Salmonella Typhimurium: ST313, which has a distinctive set of prophage sequences. We have thoroughly characterized the ST313-associated prophages both genetically and experimentally. ST313 representative strain D23580 contains five full-length prophages: BTP1, Gifsy-2D23580, ST64BD23580, Gifsy-1D23580, and BTP5. We show that common S. Typhimurium prophages Gifsy-2, Gifsy-1, and ST64B are inactivated in ST313 by mutations. Prophage BTP1 was found to be a functional novel phage, and the first isolate of the proposed new species "Salmonella virus BTP1", belonging to the P22virus genus. Surprisingly, similar to 10(9) BTP1 virus particles per ml were detected in the supernatant of non-induced, stationary-phase cultures of strain D23580, representing the highest spontaneously induced phage titer so far reported for a bacterial prophage. High spontaneous induction is shown to be an intrinsic property of prophage BTP1, and indicates the phage-mediated lysis of around 0.2% of the lysogenic population. The fact that BTP1 is highly conserved in ST313 poses interesting questions about the potential fitness costs and benefits of novel prophages in epidemic S. Typhimurium ST313.

  • 22.
    Pasqua, Martina
    et al.
    Sapienza Univ Roma, Dept Biol & Biotechnol C Darwin, Ist Pasteur Italia, Rome, Italy.
    Michelacci, Valeria
    European Union, Dept Vet Publ Hlth & Food Safety, Reference Lab Escherichia Coli, Ist Super Sanita, Rome, Italy.
    Di Martino, Maria Letizia
    Sapienza Univ Roma, Dept Biol & Biotechnol C Darwin, Ist Pasteur Italia, Rome, Italy;Uppsala Univ, Sci Life Lab, Dept Med Biochem & Microbiol, Uppsala, Sweden.
    Tozzoli, Rosangela
    European Union, Dept Vet Publ Hlth & Food Safety, Reference Lab Escherichia Coli, Ist Super Sanita, Rome, Italy.
    Grossi, Milena
    Sapienza Univ Roma, Dept Biol & Biotechnol C Darwin, Ist Pasteur Italia, Rome, Italy.
    Colonna, Bianca
    Sapienza Univ Roma, Dept Biol & Biotechnol C Darwin, Ist Pasteur Italia, Rome, Italy.
    Morabito, Stefano
    European Union, Dept Vet Publ Hlth & Food Safety, Reference Lab Escherichia Coli, Ist Super Sanita, Rome, Italy.
    Prosseda, Gianni
    Sapienza Univ Roma, Dept Biol & Biotechnol C Darwin, Ist Pasteur Italia, Rome, Italy.
    The Intriguing Evolutionary Journey of Enteroinvasive E-coli (EIEC) toward Pathogenicity2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 2390Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Among the intestinal pathogenic Escherichia coli, enteroinvasive E. coli (EIEC) are a group of intracellular pathogens able to enter epithelial cells of colon, multiplicate within them, and move between adjacent cells with a mechanism similar to Shigella, the ethiological agent of bacillary dysentery. Despite EIEC belong to the same pathotype of Shigella, they neither have the full set of traits that define Shigella nor have undergone the extensive gene decay observed in Shigella. Molecular analysis confirms that EIEC are widely distributed among E. coli phylogenetic groups and correspond to bioserotypes found in many E. coli serogroups. Like Shigella, also in EIEC the critical event toward a pathogenic life-style consisted in the acquisition by horizontal gene transfer of a large F-type plasmid (pINV) containing the genes required for invasion, intracellular survival, and spreading through the intestinal mucosa. In Shigella, the ample gain in virulence determinants has been counteracted by a substantial loss of functions that, although important for the survival in the environment, are redundant or deleterious for the life inside the host. The pathoadaptation process that has led Shigella to modify its metabolic profile and increase its pathogenic potential is still in infancy in EIEC, although maintenance of some features typical of E. coli might favor their emerging relevance as intestinal pathogens worldwide, as documented by recent outbreaks in industrialized countries. In this review, we will discuss the evolution of EIEC toward Shigella-like invasive forms going through the epidemiology, including the emergence of new virulent strains, their genome organization, and the complex interactions they establish with the host.

  • 23.
    Pelve, Erik A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Fontanez, Kristina M.
    Fluid Screen Inc, Cambridge, MA USA;MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
    DeLong, Edward F.
    Univ Hawaii Manoa, Dept Oceanog, Daniel K Inoue Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
    Bacterial Succession on Sinking Particles in the Ocean's Interior2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 2269Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sinking particles formed in the photic zone and moving vertically through the water column are a main mechanism for nutrient transport to the deep ocean, and a key component of the biological carbon pump. The particles appear to be processed by a microbial community substantially different from the surrounding waters. Single cell genomics and metagenomics were employed to describe the succession of dominant bacterial groups during particle processing. Sinking particles were extracted from sediment traps at Station Aloha in the North Pacific Subtropical Gyre (NPSG) during two different trap deployments conducted in July and August 2012. The microbial communities in poisoned vs. live sediment traps differed significantly from one another, consistent with prior observations by Fontanez et al. (2015). Partial genomes from these communities were sequenced from cells belonging to the genus Arcobacter (commensalists potentially associated with protists such as Radiolaria), and Vibrio carnpbellii (a group previously reported to be associated with crustacea). These bacteria were found in the particle-associated communities at specific depths in both trap deployments, presumably due to their specific host-associations. Partial genomes were also sequenced from cells belonging to Idiomarina and Kangiella that were enriched in live traps over a broad depth range, that represented a motile copiotroph and a putatively non-motile algicidal saprophyte, respectively. Planktonic bacterial cells most likely caught in the wake of the particles belonging to Actinomarina and the SAR11 Glade were also sequenced. Our results suggest that similar groups of eukaryote-associated bacteria are consistently found on sinking particles at different times, and that particle remineralization involves specific, reproducible bacterial succession events in oligotrophic ocean waters.

  • 24.
    Pent, Mari
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia..
    Poldmaa, Kadri
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia..
    Bahram, Mohammad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia.
    Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 836Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales-the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements.

  • 25.
    Ponce-de-Leon, Miguel
    et al.
    Univ Complutense Madrid, Fac Ciencias Quim, Dept Bioquim & Biol Mol 1, Madrid, Spain..
    Tamarit, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Calle-Espinosa, Jorge
    Univ Complutense Madrid, Fac Ciencias Quim, Dept Bioquim & Biol Mol 1, Madrid, Spain..
    Mori, Matteo
    Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA..
    Latorre, Amparo
    Univ Valencia, Dept Genet, Valencia, Spain.;Univ Valencia, CSIC, Inst Integrat Syst Biol, Valencia, Spain..
    Montero, Francisco
    Univ Complutense Madrid, Fac Ciencias Quim, Dept Bioquim & Biol Mol 1, Madrid, Spain..
    Pereto, Juli
    Univ Valencia, CSIC, Inst Integrat Syst Biol, Valencia, Spain.;Univ Valencia, Dept Bioquim & Biol Mol, Valencia, Spain..
    Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 2290Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism-which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphid Cinara cedri that harbors two co-primary endosymbionts, Buchnera aphidicola BCc and Ca. Serratia symbiotica SCc, and in which some metabolic pathways are partitioned between different partners. Here we present a genome-scale metabolic network (GEM) for the bacterial consortium from the cedar aphid iBSCc. The analysis of this GEM allows us the confirmation of cases of metabolic complementation previously described by genome analysis (i.e., tryptophan and biotin biosynthesis) and the redefinition of an event of metabolic pathway sharing between the two endosymbionts, namely the biosynthesis of tetrahydrofolate. In silico knock-out experiments with iBSCc showed that the consortium metabolism is a highly integrated yet fragile network. We also have explored the evolutionary pathways leading to the emergence of metabolic complementation between reduced metabolisms starting from individual, complete networks. Our results suggest that, during the establishment of metabolic complementation in endosymbionts, adaptive evolution is significant in the case of tryptophan biosynthesis, whereas vitamin production pathways seem to adopt suboptimal solutions.

  • 26.
    Samad, Md Sainur
    et al.
    Univ Otago, Dept Microbiol & Immunol, Dunedin, New Zealand..
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Seasonal Variations in Abundance and Diversity of Bacterial Mathanotrophs in Five Temperate Lakes2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 142Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Lakes are significant sources of methane (CH4) to the atmosphere. Within these systems, methanotrophs consume CH4 and act as a potential biofilter mitigating the emission of this potent greenhouse gas. However, it is still not well understood how spatial and temporal variation in environmental parameters influence the abundance, diversity, and community structure of methanotrophs in lakes. To address this gap in knowledge, we collected water samples from three depths (surface, middle, and bottom) representing oxic to suboxic or anoxic zones of five different Swedish lakes in winter (ice-covered) and summer. Methanotroph abundance was determined by quantitative real time polymerase chain reaction and a comparison to environmental variables showed that temperature, season as well as depth, phosphate concentration, dissolved oxygen, and CH4 explained the observed variation in methanotroph abundance. Due to minimal differences in methane concentrations (0.19 and 0.29 mu M for summer and winter, respectively), only a weak and even negative correlation was observed between CH4 and methanotrophs, which was possibly due to usage of CH4. Methanotrophs were present at concentrations ranging from 105 to 106 copies/l throughout the oxic (surface) and suboxic/anoxic (bottom) water mass of the lakes, but always contributed less than 1.3% to the total microbial community. Relative methanotroph abundance was significantly higher in winter than in summer and consistently increased with depth in the lakes. Phylogenetic analysis of pmoA genes in two clone libraries from two of the ice-covered lakes (Ekoln and Ramsen) separated the methanotrophs into five distinct clusters of Methylobacter sp. (Type I). Terminal restriction fragment length polymorphism analysis of the pmoA gene further revealed significant differences in methanotrophic communities between lakes as well as between winter and summer while there were no significant differences between water layers. The study provides new insights into diversity, abundance, community composition and spatial as well as temporal distribution of freshwater methanotrophs in low-methane dimictic lakes.

  • 27.
    Shen, Dandan
    et al.
    Leibniz Inst Balt Sea Res, Sect Biol Oceanog, Warnemunde, Germany.
    Langenheder, Silke
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Juergens, Klaus
    Leibniz Inst Balt Sea Res, Sect Biol Oceanog, Warnemunde, Germany.
    Dispersal Modifies the Diversity and Composition of Active Bacterial Communities in Response to a Salinity Disturbance2018Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikkel-id 2188Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dispersal can influence the response of bacterial communities to environmental changes and disturbances. However, the extent to which dispersal contributes to the community response in dependence of the character and strength of the disturbance remains unclear. Here, we conducted a transplant experiment using dialysis bags in which bacterioplankton originating from brackish and marine regions of the Saint Lawrence Estuary were reciprocally incubated in the two environments for 5 days. Dispersal treatments were set-up by subjecting half of the microcosms in each environment to an exchange of cells between the marine and brackish assemblages at a daily exchange rate of 6% (v/v), and the other half of microcosms were kept as the nondispersal treatments. Bacterial 16S rRNA sequencing was then used to examine the diversity and composition of the active communities. Alpha diversity of the marine communities that were exposed to the brackish environment was elevated greatly by dispersal, but declined in the absence of dispersal. This indicates that dispersal compensated the loss of diversity in the marine communities after a disturbance by introducing bacterial taxa that were able to thrive and coexist with the remaining community members under brackish conditions. On the contrary, alpha diversity of the brackish communities was not affected by dispersal in either environment. Furthermore, dispersal led to an increase in similarity between marine and brackish communities in both of the environments, with a greater similarity when the communities were incubated in the brackish environment. These results suggest that the higher initial diversity in the brackish than in the marine starting community made the resident community less susceptible to dispersing bacteria. Altogether, this study shows that dispersal modifies the diversity and composition of the active communities in response to a salinity disturbance, and enables the local adjustment of specific bacteria under brackish environmental conditions.

  • 28. Timmusk, Salme
    et al.
    Kim, Seong-Bin
    Nevo, Eviatar
    Abd El Daim, Islam
    Ek, Bo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Analytisk kemi.
    Bergquist, Jonas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Analytisk kemi.
    Behers, Lawrence
    Sfp-type PPTase inactivation promotes bacterial biofilm formation and ability to enhance wheat drought tolerance2015Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, artikkel-id 387Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Paenibacillus polymyxa is a common soil bacterium with broad range of practical applications. An important group of secondary metabolites in P polymyxa are non-ribosomal peptide and polyketide derived metabolites (NRPs/PKs). Modular non-ribosomal peptide synthetases catalyze main steps in the biosynthesis of the complex secondary metabolites. Here we report on the inactivation of an A26 Sfp-type 4'-phosphopantetheinyl transferase (Sfp-type PPTase). The inactivation of the gene resulted in loss of NRPs/PKs production. In contrast to the former Bacillus spp. model the mutant strain compared to wild type showed greatly enhanced biofilm formation ability. A26 Delta sfp biofilm promotion is directly mediated by NRPs/PKs, as exogenous addition of the wild type metabolite extracts restores its biofilm formation level. Wheat inoculation with bacteria that had lost their Sfp-type PPTase gene resulted in two times higher plant survival and about three times increased biomass under severe drought stress compared to wild type. Challenges with P. polymyxa genetic manipulation are discussed.

  • 29. Vestö, Kim
    et al.
    Huseby, Douglas L
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Snygg, Lina
    Wang, Helen
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Karolinska Inst, Dept Microbiol Tumor & Cell Biol.
    Hughes, Diarmaid
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Rhen, Mikael
    Muramyl Endopeptidase Spr Contributes to Intrinsic Vancomycin Resistance in Salmonella enterica Serovar Typhimurium2018Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikkel-id 2941Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The impermeability barrier provided by the outer membrane of enteric bacteria, a feature lacking in Gram-positive bacteria, plays a major role in maintaining resistance to numerous antimicrobial compounds and antibiotics. Here we demonstrate that mutational inactivation of spr, coding for a muramyl endopeptidase, significantly sensitizes Salmonella enterica serovar Typhimurium to vancomycin without any accompanying apparent growth defect or outer membrane destabilization. A similar phenotype was not achieved by deleting the genes coding for muramyl endopeptidases MepA, PbpG, NlpC, YedA, or YhdO. The spr mutant showed increased autolytic behavior in response to not only vancomycin, but also to penicillin G, an antibiotic for which the mutant displayed a wild-type MIC. A screen for suppressor mutations of the spr mutant phenotype revealed that deletion of tsp (prc), encoding a periplasmic carboxypeptidase involved in processing Spr and PBP3, restored intrinsic resistance to vancomycin and reversed the autolytic phenotype of the spr mutant. Our data suggest that Spr contributes to intrinsic antibiotic resistance in S. Typhimurium without directly affecting the outer membrane permeability barrier. Furthermore, our data suggests that compounds targeting specific cell wall endopeptidases might have the potential to expand the activity spectrum of traditional Gram-positive antibiotics.

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