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  • 1.
    Agervald, Åsa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Baebprasert, Wipawee
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Zhang, Xiaohui
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Incharoensakdi, Aran
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Stensjö, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    The CyAbrB transcription factor CalA regulates the iron superoxide dismutase in Nostoc sp. strain PCC 71202010In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 12, no 10, p. 2826-2837Article in journal (Refereed)
    Abstract [en]

    P>In the present investigation the results of induced over-production of the CyAbrB transcription factor CalA (Cyanobacterial AbrB-like, annotated as Alr0946) in the cyanobacterium Nostoc sp. PCC 7120 were analysed. The CalA overexpression strain showed a bleaching phenotype with lower growth rate and truncated filaments 2 days after induction of overexpression. The phenotype was even more pronounced when illumination was increased from 35 to 125 mu mol m-2 s-1. Using gel-based quantitative proteomics, the induced overexpression of CalA was shown to downregulate the abundance of FeSOD, one of two types of superoxide dismutases in Nostoc sp. PCC 7120. The change in protein abundance was also accompanied by lower transcript as well as activity levels. Purified recombinant CalA from Nostoc sp. PCC 7120 was shown to interact with the promoter region of alr2938, encoding FeSOD, indicating a transcriptional regulation of FeSOD by CalA. The bleaching phenotype is in line with a decreased tolerance against oxidative stress and indicates that CalA is involved in regulation of cellular responses in which FeSOD has an important and specific function in the filamentous cyanobacterium Nostoc sp. PCC 7120.

  • 2.
    Ast, Jennifer C
    et al.
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Dunlap, Paul V
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group.2005In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 7, no 10, p. 1641-54Article in journal (Refereed)
    Abstract [en]

    Substantial ambiguity exists regarding the phylogenetic status of facultatively psychrophilic luminous bacteria identified as Photobacterium phosphoreum, a species thought to be widely distributed in the world's oceans and believed to be the specific bioluminescent light-organ symbiont of several deep-sea fishes. Members of the P. phosphoreum species group include luminous and non-luminous strains identified phenotypically from a variety of different habitats as well as phylogenetically defined lineages that appear to be evolutionarily distinct. To resolve this ambiguity and to begin developing a meaningful knowledge of the geographic distributions, habitats and symbiotic relationships of bacteria in the P. phosphoreum species group, we carried out a multilocus, fine-scale phylogenetic analysis based on sequences of the 16S rRNA, gyrB and luxABFE genes of many newly isolated luminous strains from symbiotic and saprophytic habitats, together with previously isolated luminous and non-luminous strains identified as P. phosphoreum from these and other habitats. Parsimony analysis unambiguously resolved three evolutionarily distinct clades, phosphoreum, iliopiscarium and kishitanii. The tight phylogenetic clustering within these clades and the distinct separation between them indicates they are different species, P. phosphoreum, Photobacterium iliopiscarium and the newly recognized 'Photobacterium kishitanii'. Previously reported non-luminous strains, which had been identified phenotypically as P. phosphoreum, resolved unambiguously as P. iliopiscarium, and all examined deep-sea fishes (specimens of families Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae and Acropomatidae) were found to harbour 'P. kishitanii', not P. phosphoreum, in their light organs. This resolution revealed also that 'P. kishitanii' is cosmopolitan in its geographic distribution. Furthermore, the lack of phylogenetic variation within 'P. kishitanii' indicates that this facultatively symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine-scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.

  • 3.
    Baho, Didier
    et al.
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Peter, Hannes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Resistance and resilience of microbial communities: temporal and spatial insurance against perturbations2012In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 14, no 9, p. 2283-2292Article in journal (Refereed)
    Abstract [en]

    Bacteria play fundamental roles for many ecosystem processes; however, little empirical evidence is available on how environmental perturbations affect their composition and function. We investigated how spatial and temporal refuges affect the resistance and resilience of a freshwater bacterioplankton community upon a salinity pulse perturbation in continuous cultures. Attachment to a surface avoided the flushing out of cells and enabled re-colonization of the liquid phase after the perturbation, hence serving as a temporal refuge. A spatial refuge was established by introduction of bacteria from an undisturbed reservoir upstream of the continuous culture vessel, acting analogous to a regional species pool in a metacommunity. The salinity pulse affected bacterial community composition and the rates of respiration and the pattern of potential substrate utilization as well as the correlation between composition and function. Compared with the no-refuge treatment, the temporal refuge shortened return to pre-perturbation conditions, indicating enhanced community resilience. Composition and function were less disturbed in the treatment providing a spatial refuge, suggesting higher resistance. Our results highlight that spatial and temporal dynamics in general and refuges in particular need to be considered for conceptual progress in how microbial metacommunities are shaped by perturbations.

  • 4.
    Balmonte, John Paul
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Buckley, Andrew
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Hoarfrost, Adrienne
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Ghobrial, Sherif
    Univ New Hampshire, Inst Study Earth Oceans & Space, Durham, NH 03824 USA.
    Ziervogel, Kai
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Teske, Andreas
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Arnosti, Carol
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Community structural differences shape microbial responses to high molecular weight organic matter2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 2, p. 557-571Article in journal (Refereed)
    Abstract [en]

    The extent to which differences in microbial community structure result in variations in organic matter (OM) degradation is not well understood. Here, we tested the hypothesis that distinct marine microbial communities from North Atlantic surface and bottom waters would exhibit varying compositional succession and functional shifts in response to the same pool of complex high molecular weight (HMW-OM). We also hypothesized that microbial communities would produce a broader spectrum of enzymes upon exposure to HMW-OM, indicating a greater potential to degrade these compounds than reflected by initial enzymatic activities. Our results show that community succession in amended mesocosms was congruent with cell growth, increased bacterial production and most notably, with substantial shifts in enzymatic activities. In all amended mesocosms, closely related taxa that were initially rare became dominant at time frames during which a broader spectrum of active enzymes were detected compared to initial timepoints, indicating a similar response among different communities. However, succession on the whole-community level, and the rates, spectra and progression of enzymatic activities, reveal robust differences among distinct communities from discrete water masses. These results underscore the crucial role of rare bacterial taxa in ocean carbon cycling and the importance of bacterial community structure for HMW-OM degradation.

  • 5.
    Beier, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Mohit, Vani
    Département de Biologie, Québec-Océan and Institut de biologie integrative et des systèmes, Université Laval.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Östman, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing2012In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 14, no 9, p. 2467-2479Article in journal (Refereed)
    Abstract [en]

    Seasonal variation in activity of enzymes involved in polymer degradation, including chitinases, has been observed previously in freshwater environments. However, it is not known whether the seasonal dynamics are due to shifts in the activity of bacteria already present, or shifts in community structure towards emergence or disappearance of chitinolytic organisms. We traced seasonal shifts in the chitinase gene assemblage in a temperate lake and linked these communities to variation in chitinase activity. Chitinase genes from 20 samples collected over a full yearly cycle were characterized by pyrosequencing. Pronounced temporal shifts in composition of the chitinase gene pool (beta diversity) occurred along with distinct shifts in richness (alpha diversity) as well as chitin processing. Changes in the chitinase gene pool correlated mainly with temperature, abundance of crustacean zooplankton and phytoplankton blooms. Also changes in the physical structure of the lake, e.g. stratification and mixing were associated with changes in the chitinolytic community, while differences were minor between surface and suboxic hypolimnetic water. The lake characteristics influencing the chitinolytic community are all linked to changes in organic particles and we suggest that seasonal changes in particle quality and availability foster microbial communities adapted to efficiently degrade them.

  • 6.
    Berga, Mercè
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Östman, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Combined effects of zooplankton grazing and dispersal on the diversity and assembly mechanisms of bacterial metacommunities2015In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, no 7, p. 2275-2287Article in journal (Refereed)
    Abstract [en]

    Effects of dispersal and the presence of predators on diversity, assembly and functioning of bacterial communities are well studied in isolation. In reality, however, dispersal and trophic interactions act simultaneously and can therefore have combined effects, which are poorly investigated. We performed an experiment with aquatic metacommunities consisting of three environmentally different patches and manipulated dispersal rates among them as well as the presence or absence of the keystone species Daphnia magnaDaphnia magnareduced both local and regional diversity, whereas dispersal increased local diversity but decreased beta-diversity having no net effect on regional diversity. Dispersal modified the assembly mechanisms of bacterial communities by increasing the degree of determinism. Additionally, the combination of the D. magna and dispersal increased the importance of deterministic processes, presumably because predator-tolerant taxa were spread in the metacommunity via dispersal. Moreover, the presence of D. magna affected community composition, increased community respiration rates but did not affect bacterial production or abundance, whereas dispersal slightly increased bacterial production. In conclusion, our study suggests that predation by a keystone species such as D. magna and dispersal additively influence bacterial diversity, assembly processes and ecosystem functioning.

  • 7.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    How to see more: double hybridization to reveal ecological differentiation among close bacterial relatives2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2110-2111Article in journal (Other academic)
  • 8.
    Comte, Jérôme
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Berga, Mercè
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Biological Oceanography, Leibniz-Institute for Baltic Sea Research, Germany.
    Severin, Ina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2391-2404Article in journal (Refereed)
    Abstract [en]

    The diversity and composition of lake bacterial communities are driven by the interplay between local contemporary environmental conditions and dispersal of cells from the surroundings, i.e. the metacommunity. Still, a conceptual understanding ofthe relative importance of the two types of factors is lacking. For instance, it is unknown which sources ofdispersal are most important and under which circumstances. Here, we investigated the seasonal variation in the importance of dispersal from different sources (mixing, precipitation, surface runoff and sediment resuspension) for lake bacterioplankton community and population dynamics. For that purpose, two small forest lakes and their dispersal sources were sampled over a period of 10 months.The influence of dispersal on communities and populations was determined by 454 sequencing of the 16S rRNA gene and Source Tracker analysis. On the community level direct effects of dispersal were questionable from all sources. Instead we found that the community of the preceding sampling occasion, representing growth of resident bacteria, was of great importance. On the population level, however, dispersal of individual taxa from the inlet could be occasionally important even under low water flow. The effect of sediment resuspension and precipitation appeared small.

  • 9.
    Comte, Jérôme
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Environm & Climate Change Canada, Canada Ctr Inland Waters, Watershed Hydrol & Ecol Res Div, Water Sci & Technol, Burlington, ON L7S 1A1, Canada..
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Berga, Mercè
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Leibniz Inst Balt Sea Res, Biol Oceanog, Seestr 15, D-18119 Rostock, Germany..
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 1, p. 251-260Article in journal (Refereed)
    Abstract [en]

    Dispersal can modify how bacterial community composition (BCC) changes in response to environmental perturbations, yet knowledge about the functional consequences of dispersal is limited. Here we hypothesize that changes in bacterial community production in response to a salinity disturbance depend on the possibility to recruit cells from different dispersal sources. To investigate this, we conducted an in situ mesocosm experiment where bacterial communities of an oligotrophic lake were exposed to different salinities (0, 18, 36 psu) for two weeks and subjected to dispersal of cells originating from sediments, air (mesocosms open to air deposition), both or none. BCC was determined using 454 pyrosequencing of the 16S rRNA gene and bacterial production was measured by 3H leucine uptake. Bacterial production differed significantly among salinity treatments and dispersal treatments, being highest at high salinity. These changes were associated with changes in BCC and it was found that the identity of the main functional contributors differed at different salinities. Our results further showed that after a salinity perturbation, the response of bacterial communities depended on the recruitment of taxa, including marine representatives (e.g. Alphaproteobacteria Loktanella, Erythrobacter and the Gammaproteobacterium Rheiheimera) from dispersal sources, in which atmospheric deposition appeared to play a major role.

  • 10.
    Dinasquet, Julie
    et al.
    Linnaeus Univ, Dept Nat Sci, Kalmar, Sweden.;Univ Copenhagen, Marine Biol Sect, Helsingor, Denmark.;Scripps Inst Oceanog, Div Marine Biol Res, La Jolla, CA 92093 USA..
    Richert, Inga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. UFZ Helmholtz Ctr Environm Res, Microbial Ecosyst Serv Grp, Dept Environm Microbiol, Leipzig, Germany..
    Logares, Ramiro
    CSIC, Inst Marine Sci, Barcelona, Spain..
    Yager, Patricia
    Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA..
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Riemann, Lasse
    Univ Copenhagen, Marine Biol Sect, Helsingor, Denmark..
    Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2453-2467Article in journal (Refereed)
    Abstract [en]

    The number of icebergs produced from ice-shelf disintegration has increased over the past decade in Antarctica. These drifting icebergs mix the water column, influence stratification and nutrient condition, and can affect local productivity and food web composition. Data on whether icebergs affect bacterioplankton function and composition are scarce, however. We assessed the influence of iceberg drift on bacterial community composition and on their ability to exploit carbon substrates during summer in the coastal Southern Ocean. An elevated bacterial production and a different community composition were observed in iceberg-influenced waters relative to the undisturbed water column nearby. These major differences were confirmed in short-term incubations with bromodeoxyuridine followed by CARD-FISH. Furthermore, one-week bottle incubations amended with inorganic nutrients and carbon substrates (a mix of substrates, glutamine, Nacetylglucosamine, or pyruvate) revealed contrasting capacity of bacterioplankton to utilize specific carbon substrates in the iceberg-influenced waters compared with the undisturbed site. Our study demonstrates that the hydrographical perturbations introduced by a drifting iceberg can affect activity, composition, and substrate utilization capability of marine bacterioplankton. Consequently, in a context of global warming, increased frequency of drifting icebergs in polar regions holds the potential to affect carbon and nutrient biogeochemistry at local and possibly regional scales.

  • 11.
    Dunlap, Paul V
    et al.
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Jiemjit, Anchalee
    Ast, Jennifer C
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Pearce, Meghan M
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Marques, Ryan R
    Lavilla-Pitogo, Celia R
    Genomic polymorphism in symbiotic populations of Photobacterium leiognathi.2004In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 6, no 2, p. 145-58Article in journal (Refereed)
    Abstract [en]

    Photobacterium leiognathi forms a bioluminescent symbiosis with leiognathid fishes, colonizing the internal light organ of the fish and providing its host with light used in bioluminescence displays. Strains symbiotic with different species of the fish exhibit substantial phenotypic differences in symbiosis and in culture, including differences in 2-D PAGE protein patterns and profiles of indigenous plasmids. To determine if such differences might reflect a genetically based symbiont-strain/host-species specificity, we profiled the genomes of P. leiognathi strains from leiognathid fishes using PFGE. Individual strains from 10 species of leiognathid fishes exhibited substantial genomic polymorphism, with no obvious similarity among strains; these strains were nonetheless identified as P. leiognathi by 16S rDNA sequence analysis. Profiling of multiple strains from individual host specimens revealed an oligoclonal structure to the symbiont populations; typically one or two genomotypes dominated each population. However, analysis of multiple strains from multiple specimens of the same host species, to determine if the same strain types consistently colonize a host species, demonstrated substantial heterogeneity, with the same genomotype only rarely observed among the symbiont populations of different specimens of the same host species. Colonization of the leiognathid light organ to initiate the symbiosis therefore is likely to be oliogoclonal, and specificity of the P. leiognathi/leiognathid fish symbiosis apparently is maintained at the bacterial species level rather than at the level of individual, genomotypically defined strain types.

  • 12.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Zaremba-Niedzwiedzka, Katarzyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Martinez Garcia, Manuel
    McMahon, Katherine
    Stepanauskas, Ramunas
    Andersson, Siv G.E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics2014In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 16, no 9, p. 2682-2698Article in journal (Refereed)
    Abstract [en]

    Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared to freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.

  • 13.
    Ekman, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Sandh, Gustaf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Nenninger, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Oliveira, Paulo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Stensjö, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Cellular and functional specificity among ferritin-like proteins in the multicellular cyanobacterium Nostoc punctiforme.2014In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 16, no 3, p. 829-844Article in journal (Refereed)
    Abstract [en]

    Ferritin-like proteins constitute a remarkably heterogeneous protein family, including ferritins, bacterioferritins and Dps proteins. The genome of the filamentous heterocyst-forming cyanobacterium Nostoc punctiforme encodes five ferritin-like proteins. In the present paper, we report a multidimensional characterization of these proteins. Our phylogenetic and bioinformatics analyses suggest both structural and physiological differences among the ferritin-like proteins. The expression of these five genes responded differently to hydrogen peroxide treatment, with a significantly higher rise in transcript level for Npun_F3730 as compared with the other four genes. A specific role for Npun_F3730 in the cells tolerance against hydrogen peroxide was also supported by the inactivation of Npun_F3730, Npun_R5701 and Npun_R6212; among these, only the ΔNpun_F3730 strain showed an increased sensitivity to hydrogen peroxide compared with wild type. Analysis of promoter-GFP reporter fusions of the ferritin-like genes indicated that Npun_F3730 and Npun_R5701 were expressed in all cell types of a diazotrophic culture, while Npun_F6212 was expressed specifically in heterocysts. Our study provides the first comprehensive analysis combining functional differentiation and cellular specificity within this important group of proteins in a multicellular cyanobacterium.

  • 14. Grogan, Dennis W
    et al.
    Ozarzak, Melissa A
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Molecular Evolution.
    Variation in gene content among geographically diverse Sulfolobus isolates2008In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 10, no 1, p. 137-146Article in journal (Refereed)
    Abstract [en]

    The ability of competitive (i.e., comparative) genomic hybridization (CGH) to assess similarity across entire microbial genomes suggests that it should reveal diversification within and between natural populations of free-living prokaryotes. We used CGH to measure relatedness of genomes drawn from Sulfolobus populations that had been shown in a previous study to be diversified along geographical lines. Eight isolates representing a wide range of spatial separation were compared with respect to gene-specific tags based on a closely related reference strain (Sulfolobus solfataricus P2). For the purpose of assessing genetic divergence, 232 loci identified as polymorphic were assigned one of two alleles based on the corresponding fluorescence intensities from the arrays. Clustering of these binary genotypes was stable with respect to changes in the threshold and similarity criteria, and most of the groupings were consistent with an isolation-by-distance model of diversification. These results indicate that increasing spatial separation of geothermal sites correlates not only with minor sequence polymorphisms in conserved genes of Sulfolobus (demonstrated in the previous study), but also with the regions of difference (RDs) that occur between genomes of conspecifics. In view of the abundance of RDs in prokaryotic genomes and the relevance that some RDs may have for ecological adaptation, the results further suggest that CGH on microarrays may have advantages for investigating patterns of diversification in other free-living archaea and bacteria.

  • 15. Henche, Anna-Lena
    et al.
    Ghosh, Abhrajyoti
    Yu, Xiong
    Jeske, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Egelman, Edward
    Albers, Sonja-Verena
    Structure and function of the adhesive type IV pilus of Sulfolobus acidocaldarius2012In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 14, no 12, p. 3188-3202Article in journal (Refereed)
    Abstract [en]

    Archaea display a variety of type IV pili on their surface and employ them in different physiological functions. In the crenarchaeon Sulfolobus acidocaldarius the most abundant surface structure is the aap pilus (archaeal adhesive pilus). The construction of in frame deletions of the aap genes revealed that all the five genes (aapA, aapX, aapE, aapF, aapB) are indispensible for assembly of the pilus and an impact on surface motility and biofilm formation was observed. Our analyses revealed that there exists a regulatory cross-talk between the expression of aap genes and archaella (formerly archaeal flagella) genes during different growth phases. The structure of the aap pilus is entirely different from the known bacterial type IV pili as well as other archaeal type IV pili. An aap pilus displayed 3 stranded helices where there is a rotation per subunit of ∼ 138° and a rise per subunit of ∼ 5.7 Å. The filaments have a diameter of ∼ 110 Å and the resolution was judged to be ∼ 9 Å. We concluded that small changes in sequence might be amplified by large changes in higher-order packing. Our finding of an extraordinary stability of aap pili possibly represents an adaptation to harsh environments that S. acidocaldarius encounters.

  • 16. Jezberova, Jitka
    et al.
    Jezbera, Jan
    Brandt, Ulrike
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Hahn, Martin W.
    Ubiquity of Polynucleobacter necessarius ssp asymbioticus in lentic freshwater habitats of a heterogenous 2000 km2 area2010In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 12, no 3, p. 658-669Article in journal (Refereed)
    Abstract [en]

    We present a survey on the distribution and habitat range of Polynucleobacter necessarius ssp. asymbioticus (PnecC), a numerically and functionally important taxon in the plankton of freshwater systems. We systematically sampled stagnant freshwater habitats in a heterogeneous 2000 km2 area, together with ecologically different habitats outside this area. In total, 137 lakes, ponds and puddles were investigated, which represent an enormous diversity of habitats differing, e.g. in depth (< 10 cm - 171 m) and pH (3.9-8.5). PnecC bacteria were detected by cultivation-independent methods in all investigated habitats, and their presence was confirmed by cultivation of strains from selected habitats representing the whole studied ecological range. The determined relative abundance of the subspecies ranged from values close to the detection limit of FISH (0.2%) to 67% (average 14.5%), and the highest observed absolute abundance was 5.3 x 106 cells ml-1. Statistical analyses revealed that the abundance of PnecC bacteria was partially controlled by factors linked to concentrations of humic substances, which support the hypothesis that these bacteria utilize photodegradation products of humic substances. Based on the revealed statistical relationships, an average relative abundance of this subspecies of 20% in global freshwater habitats was extrapolated. Our study provides important implications for the current debate on ubiquity and biogeography in microorganisms.

  • 17.
    Langenheder, Silke
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Prosser, James I.
    Resource availability influences the diversity of a functional group of heterotrophic soil bacteria.2008In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 10, no 9, p. 2245-2256Article in journal (Refereed)
    Abstract [en]

    Resource availability is a key factor regulating biodiversity and ecosystem functioning, but the relationship between resource availability and diversity has only been rarely investigated in microbial communities. The aim of this study was to determine how diversity and community structure of a functional group of soil bacteria are influenced by resource concentration. To achieve this, we used soil microcosms to investigate degradation of benzoate, which served as a model compound, by soil bacterial communities. Microcosms were supplied with 13C-labelled benzoate at four concentrations and RNA-stable isotope probing followed by molecular fingerprinting analysis of 16S rRNA genes was employed to identify bacteria able to assimilate benzoate at different concentrations. The composition of the benzoate degrader community differed at different concentrations and there was a significant decrease in taxa evenness at the highest substrate concentration. Active organisms could be grouped into generalists, occurring at all substrate concentrations, specialists, active at one particular benzoate concentration only, and taxa that were active at either the two lowest or two highest concentrations. The study comprises the first explicit demonstration that resource availability has an effect on the diversity of a functional group of heterotrophic soil bacteria.

  • 18.
    Lebret, Karen
    et al.
    Lund University.
    Kritzberg, Emma S.
    Figueroa, Rosa
    Rengefors, Karin
    Genetic diversity within and genetic differentiation between blooms of a microalgal species2012In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 14, no 9, p. 2395-2404Article in journal (Refereed)
    Abstract [en]

    The field of genetic diversity in protists, particularly phytoplankton, is under expansion. However, little is known regarding variation in genetic diversity within populations over time. The aim of our study was to investigate intrapopulation genetic diversity and genetic differentiation in the freshwater bloom-forming microalga Gonyostomum semen (Raphidophyceae). The study covered a 2-year period including all phases of the bloom. Amplified fragment length polymorphism (AFLP) was used to determine the genetic structure and diversity of the population. Our results showed a significant differentiation between samples collected during the two blooms from consecutive years. Also, an increase of gene diversity and a loss of differentiation among sampling dates were observed over time within a single bloom. The latter observations may reflect the continuous germination of cysts from the sediment. The life cycle characteristics of G. semen, particularly reproduction and recruitment, most likely explain a high proportion of the observed variation. This study highlights the importance of the life cycle for the intraspecific genetic diversity of microbial species, which alternates between sexual and asexual reproduction.

  • 19. Leong, Su-lin L.
    et al.
    Lantz, Henrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pettersson, Olga Vinnere
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Frisvad, Jens C.
    Thrane, Ulf
    Heipieper, Hermann J.
    Dijksterhuis, Jan
    Grabherr, Manfred
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pettersson, Mats
    Tellgren-Roth, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Schnurer, Johan
    Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date2015In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, no 2, p. 496-513Article in journal (Refereed)
    Abstract [en]

    Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its dry' but nutrient-rich environment, X.bisporus appears to have relinquished abilities for combative interactions. Elements to sense/signal osmotic stress, e.g. HogA pathway, were present in X.bisporus. However, transcriptomes at optimal (approximate to 0.89) versus low a(w) (0.68) revealed differential expression of only a few stress-related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X.bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus was previously proposed to be a chaophile', preferring solutes that disorder biomolecular structures. Both X.bisporus and the closely related xerophile, Xerochrysium xerophilum, with low membrane unsaturation indices, could represent a phylogenetic cluster of chaophiles'.

  • 20.
    Logares, Ramiro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Daugbjerg, Niels
    Boltovskoy, Andrés
    Kremp, Anke
    Laybourn-Parry, Johanna
    Rengefors, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Recent evolutionary diversification of a protist lineage.2008In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 10, no 5, p. 1231-1243Article in journal (Refereed)
    Abstract [en]

    Here, we have identified a protist (dinoflagellate) lineage that has diversified recently in evolutionary terms. The species members of this lineage inhabit cold-water marine and lacustrine habitats, which are distributed along a broad range of salinities (0–32) and geographic distances (0–18 000 km). Moreover, the species present different degrees of morphological and sometimes physiological variability. Altogether, we analysed 30 strains, generating 55 new DNA sequences. The nuclear ribosomal DNA (nrDNA) sequences (including rapidly evolving introns) were very similar or identical among all the analysed isolates. This very low nrDNA differentiation was contrasted by a relatively high cytochrome b (COB) mitochondrial DNA (mtDNA) polymorphism, even though the COB evolves very slowly in dinoflagellates. The 16 Maximum Likelihood and Bayesian phylogenies constructed using nr/mtDNA indicated that the studied cold-water dinoflagellates constitute a monophyletic group (supported also by the morphological analyses), which appears to be evolutionary related to marine-brackish and sometimes toxic Pfiesteria species. We conclude that the studied dinoflagellates belong to a lineage which has diversified recently and spread, sometimes over long distances, across low-temperature environments which differ markedly in ecology (marine versus lacustrine communities) and salinity. Probably, this evolutionary diversification was promoted by the variety of natural selection regimes encountered in the different environments.

  • 21.
    Martijn, Joran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lind, Anders E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Schön, Max E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Spiertz, Ian
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Juzokaite, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bunikis, Ignas
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pettersson, Olga V.
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Wageningen Univ, Dept Agrotechnol & Food Sci, Lab Microbiol, NL-6708 WE Wageningen, Netherlands.
    Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 7, p. 2485-2498Article in journal (Refereed)
    Abstract [en]

    Amplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions and to discover novel lineages. However, traditional short amplicons often do not contain enough information to confidently resolve their phylogeny. Here we present a cost-effective protocol that amplifies a large part of the rRNA operon and sequences the amplicons with PacBio technology. We tested our method on a mock community and developed a read-curation pipeline that reduces the overall read error rate to 0.18%. Applying our method on four environmental samples, we captured near full-length rRNA operon amplicons from a large diversity of prokaryotes. The method operated at moderately high-throughput (22286-37,850 raw ccs reads) and generated a large amount of putative novel archaeal 23S rRNA gene sequences compared to the archaeal SILVA database. These long amplicons allowed for higher resolution during taxonomic classification by means of long (similar to 1000 bp) 16S rRNA gene fragments and for substantially more confident phylogenies by means of combined near full-length 16S and 23S rRNA gene sequences, compared to shorter traditional amplicons (250 bp of the 16S rRNA gene). We recommend our method to those who wish to cost-effectively and confidently estimate the phylogenetic diversity of prokaryotes in environmental samples at high throughput.

  • 22.
    Mondav, Rhiannon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
    McCalley, Carmody K
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH 03824, USA.
    Hodgkins, Suzanne B
    Department of Earth Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306-4320, USA.
    Frolking, Steve
    Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH 03824, USA.
    Saleska, Scott R
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
    Rich, Virginia I
    Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721, USA.
    Chanton, Jeff P
    Department of Earth Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306-4320, USA.
    Crill, Patrick M
    Department of Geology and Geochemistry, Stockholm University, Stockholm 10691, Sweden.
    Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 8, p. 3201-3218Article in journal (Refereed)
    Abstract [en]

    Biogenic production and release of methane (CH4 ) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa site (intact permafrost and low radiative forcing signature) had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog (thawing permafrost and low radiative forcing signature) had lower alpha diversity and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering. Hydrogenotrophic methanogens and Acidobacteria dominated the bog shifting from palsa-like to fen-like at the waterline. The fen (no underlying permafrost, high radiative forcing signature) had the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota and was significantly enriched in methanogens. The Mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing.

  • 23.
    Münzner, Karla
    et al.
    Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden.
    Berggren, Martin
    Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden.
    In situ plankton community respiration measurements show low respiratory quotients in a eutrophic lake2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 4, p. 1425-1435Article in journal (Refereed)
    Abstract [en]

    Planktonic community respiration is an important carbon cycling process, typically quantified by converting measured values of dissolved O2 consumption rates into CO2 production rates assuming a respiratory quotient of 1 (RQ = CO2 per O2 by moles). However, the true variability in planktonic RQs between different aquatic ecosystems is poorly understood. We conducted in situ RQ measurements in a eutrophic lake dominated by algal‐derived substances and found that RQs were significantly below 1. In fact, many RQ values were extremely low (0.2–0.6), below theoretical RQs for oxidation of algal organic matter substrates (0.7–0.8), suggesting that other factors than substrate control need to be considered to understand the RQ. This view was further supported by lack of correlations between RQ and microbial variables known to be strongly substrate dependent, including bacterial growth efficiency and the functional capacity of the bacterioplankton community to degrade different compounds. Based on the measured dynamics in methane and nutrient pools, we discuss that methane oxidation and nitrification likely occurred in the lake, contributing to the unusually low RQs. Our findings demonstrate that planktonic RQs in productive lakes can systematically be below 1, suggesting that CO2 emissions from these lakes may currently be overestimated.

    The full text will be freely available from 2020-02-29 13:45
  • 24.
    Pent, Mari
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Hiltunen, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Poldmaa, Kadri
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Furneaux, Brendan R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hildebrand, Falk
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies2018In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 20, no 5, p. 1641-1650Article in journal (Refereed)
    Abstract [en]

    Despite increasing knowledge on host-associated microbiomes, little is known about mechanisms underlying fungus-microbiome interactions. This study aimed to examine the relative importance of host genetic, geographic and environmental variations in structuring fungus-associated microbiomes. We analyzed the taxonomic composition and function of microbiomes inhabiting fungal fruiting-bodies in relation to host genetic variation, soil pH and geographic distance between samples. For this, we sequenced the metagenomes of 40 fruiting-bodies collected from six fairy rings (i.e., genets) of a sapro-trophic fungus Marasmius oreades. Our analyses revealed that fine genetic variations between host fungi could strongly affect their associated microbiome, explaining, respectively, 25% and 37% of the variation in microbiome structure and function, whereas geographic distance and soil pH remained of secondary importance. These results, together with the smaller genome size of fungi compared to other eukaryotes, suggest that fruiting-bodies are suitable for further genome-centric studies on hostmicrobiome interactions.

  • 25. Ribbeck-Busch, Kathrin
    et al.
    Roder, Anja
    Hasse, Dirk
    de Boer, Wietse
    Martínez, José Luis
    Hagemann, Martin
    Berg, Gabriele
    A molecular biological protocol to distinguish potentially human pathogenic Stenotrophomonas maltophilia from plant-associated Stenotrophomonas rhizophila.2005In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 7, no 11Article in journal (Refereed)
    Abstract [en]

    In recent years, the importance of the Gram-negative bacterium Stenotrophomonas as an opportunistic pathogen as well as in biotechnology has increased. The aim of the present study was to develop new methods for distinguishing between strains closely related to the potentially human pathogenic Stenotrophomonas maltophilia and those closely related to the plant-associated Stenotrophomonas rhizophila. To accomplish this, 58 strains were characterized by 16S rDNA sequencing and amplified ribosomal DNA restriction analysis (ARDRA), and the occurrence of specific functional genes. Based on 16S rDNA sequences, an ARDRA protocol was developed which allowed differentiation between strains of the S. maltophilia and the S. rhizophila group. As it was known that only salt-treated cells of S. rhizophila were able to synthesize the compatible solute glucosylglycerol (GG), the ggpS gene responsible for GG synthesis was used for differentiation between both species and it was confirmed that it only occurred in S. rhizophila strains. As a further genetic marker the smeD gene, which is part of the genes coding for the multidrug efflux pump SmeDEF from S. maltophilia, was used. Based on the results we propose a combination of fingerprinting techniques using the 16S rDNA and the functional genes ggpS and smeD to distinguish both Stenotrophomonas species.

  • 26.
    Ricão Canelhas, Monica
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. eDNA Solut Ltd, Bjorkasgatan 16, S-43131 Molndal, Sweden.
    Andersson, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. eDNA Solut Ltd, Bjorkasgatan 16, S-43131 Molndal, Sweden.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 12, p. 5078-5087Article in journal (Refereed)
    Abstract [en]

    Aquatic environments are typically not homogenous, but characterized by changing substrate concentration gradients and nutrient patches. This heterogeneity in substrate availability creates a multitude of niches allowing bacteria with different substrate utilization strategies to hypothetically coexist even when competing for the same substrate. To study the impact of heterogeneous distribution of organic substrates on bacterioplankton, bioreactors with freshwater bacterial communities were fed artificial freshwater medium with acetate supplied either continuously or in pulses. After a month-long incubation, bacterial biomass and community-level substrate uptake rates were twice as high in the pulsed treatment compared to the continuously fed reactors even if the same total amount of acetate was supplied to both treatments. The composition of the bacterial communities emerging in the two treatments differed significantly with specific taxa overrepresented in the respective treatments. The higher estimated growth yield in cultures that received pulsed substrate inputs, imply that such conditions enable bacteria to use resources more efficiently for biomass production. This finding agrees with established concepts of basal maintenance energy requirements and high energetic costs to assimilate substrates at low concentration. Our results further imply that degradation of organic matter is influenced by temporal and spatial heterogeneity in substrate availability. 

  • 27. Salka, Ivette
    et al.
    Wurzbacher, Christian
    Garcia, Sarahi L
    ena School for Microbial Communication (JSMC) and Microbial Ecology Group, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany..
    Labrenz, Matthias
    Jürgens, Klaus
    Grossart, Hans-Peter
    Distribution of acI-Actinorhodopsin genes in Baltic Sea salinity gradients indicates adaptation of facultative freshwater photoheterotrophs to brackish waters2014In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 16, no 2, p. 586-597Article in journal (Refereed)
    Abstract [en]

    Knowledge onActinobacteriarhodopsin gene (actR)diversity and spatial distribution is scarce. The BalticSea is characterized by strong salinity gradientsleading to the coexistence of marine and freshwaterbacteria and hence is an ideal study area to elucidatethe dispersion and phylogenetic affiliation ofactRindependence on salinity. ActRDGGE fingerprints insummer 2008 revealed between 3 and 19 distinctbands within a salinity range of 2.4–27 PSU. Environ-mentalactRclone sequences were obtained from sta-tions distributed along the whole salinity gradient.Overall, 20 differentactRsequence groups (opera-tional taxonomic units) were found, with up to 11different ones per station. Phylogenetically, theactRsequences were predominantly (80%) affiliated with freshwater acI-Actinobacteriawhose 16S rRNA geneaccounted for 2–33% of total 16S rRNA genes in both the Bothnian Sea and central Baltic Sea. However, atsalinities above 14 PSU, acI-16S rRNA gene accounted for less than 1%. In contrast, the diversity of actRremained high. Changes in actRgene diversity were significantly correlated with salinity, oxygen, silica orabundance of Synechococcussp. Our results demonstrate a wide distribution of freshwater actRalong theBaltic Sea salinity gradient indicating that some fresh-water Actinobacteriamight have adapted to higher salinities.

  • 28.
    Savio, Domenico
    et al.
    Vienna Univ Technol, CWRS, A-1040 Vienna, Austria.;Vienna Univ Technol, Inst Chem Engn, Res Grp Environm Microbiol & Mol Ecol, A-1040 Vienna, Austria..
    Sinclair, Lucas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ijaz, Umer Z.
    Univ Glasgow, Sch Engn, Glasgow, Lanark, Scotland..
    Parajka, Juraj
    Vienna Univ Technol, CWRS, A-1040 Vienna, Austria.;Vienna Univ Technol, Inst Hydraul Engn & Water Resource Management, A-1040 Vienna, Austria..
    Reischer, Georg H.
    Vienna Univ Technol, Inst Chem Engn, Res Grp Environm Microbiol & Mol Ecol, A-1040 Vienna, Austria.;Interuniv Cooperat Ctr Water & Hlth, London, England..
    Stadler, Philipp
    Vienna Univ Technol, CWRS, A-1040 Vienna, Austria.;Vienna Univ Technol, Inst Water Qual Resource & Waste Management, A-1040 Vienna, Austria..
    Blaschke, Alfred P.
    Vienna Univ Technol, CWRS, A-1040 Vienna, Austria.;Vienna Univ Technol, Inst Hydraul Engn & Water Resource Management, A-1040 Vienna, Austria..
    Bloeschl, Guenter
    Vienna Univ Technol, CWRS, A-1040 Vienna, Austria.;Vienna Univ Technol, Inst Hydraul Engn & Water Resource Management, A-1040 Vienna, Austria..
    Mach, Robert L.
    Vienna Univ Technol, Inst Chem Engn, Res Grp Environm Microbiol & Mol Ecol, A-1040 Vienna, Austria..
    Kirschner, Alexander K. T.
    Interuniv Cooperat Ctr Water & Hlth, London, England.;Med Univ Vienna, Inst Hyg & Appl Immunol Water Hyg, Vienna, Austria..
    Farnleitner, Andreas H.
    Vienna Univ Technol, CWRS, A-1040 Vienna, Austria.;Vienna Univ Technol, Inst Chem Engn, Res Grp Environm Microbiol & Mol Ecol, A-1040 Vienna, Austria.;Interuniv Cooperat Ctr Water & Hlth, London, England..
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bacterial diversity along a 2600 km river continuum2015In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, no 12, p. 4994-5007Article in journal (Refereed)
    Abstract [en]

    The bacterioplankton diversity in large rivers has thus far been under-sampled despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA-gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free-living and particle-associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the Polynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and groundwater-affiliated bacteria. Based on views of the meta-community and River Continuum Concept, we interpret the observed taxonomic patterns and accompanying changes in alpha and beta diversity with the intention of laying the foundation for a unified concept for river bacterioplankton diversity.

  • 29.
    Schulz, Frederik
    et al.
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Althanstr 14, Vienna, Austria..
    Martijn, Joran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wascher, Florian
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Althanstr 14, Vienna, Austria..
    Lagkouvardos, Ilias
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Althanstr 14, Vienna, Austria..
    Kostanjsek, Rok
    Univ Ljubljana, Dept Biol, Vecna Pot 111, Ljubljana, Slovenia..
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Horn, Matthias
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Althanstr 14, Vienna, Austria..
    A Rickettsiales symbiont of amoebae with ancient features2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 8, p. 2326-2342Article in journal (Refereed)
    Abstract [en]

    The Rickettsiae comprise intracellular bacterial symbionts and pathogens infecting diverse eukaryotes. Here, we provide a detailed characterization of CandidatusJidaibacter acanthamoeba', a rickettsial symbiont of Acanthamoeba. The bacterium establishes the infection in its amoeba host within 2h where it replicates within vacuoles. Higher bacterial loads and accelerated spread of infection at elevated temperatures were observed. The infection had a negative impact on host growth rate, although no increased levels of host cell lysis were seen. Phylogenomic analysis identified this bacterium as member of the Midichloriaceae. Its 2.4Mb genome represents the largest among Rickettsiales and is characterized by a moderate degree of pseudogenization and a high coding density. We found an unusually large number of genes encoding proteins with eukaryotic-like domains such as ankyrins, leucine-rich repeats and tetratricopeptide repeats, which likely function in host interaction. There are a total of three divergent, independently acquired type IV secretion systems, and 35 flagellar genes representing the most complete set found in an obligate intracellular Alphaproteobacterium. The deeply branching phylogenetic position of CandidatusJidaibacter acanthamoeba' together with its ancient features place it closely to the rickettsial ancestor and helps to better understand the transition from a free-living to an intracellular lifestyle.

  • 30.
    Vredenburg, Jana
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Varela, Ana Rita
    Hasan, Badrul
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Narciso-da-Rocha, Carlos
    Bonnedahl, Jonas
    Stedt, Johan
    Martins da Costa, Paulo
    Manaia, Célia M.
    Quinolone resistant E. coli isolated from birds of prey in Portugal are genetically distinct from those isolated from water environments in gulls in Portugal, Spain and Sweden2014In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 16, no 4, p. 995-1004Article in journal (Refereed)
    Abstract [en]

    The influence of geographic distribution and type of habitat on the molecular epidemiology of ciprofloxacin resistant Escherichia coli was investigated. Ciprofloxacin resistant E. coli from wastewater, urban water with faecal contamination and faeces of gulls, pigeons and birds of prey, from Portugal, Spain and Sweden were compared based on multi-locus sequence typing (MLST) and quinolone resistance genetic determinants. Multi-locus sequence typing allowed the differentiation of E. coli lineages associated with birds of prey from those inhabiting gulls and waters. E. coli lineages of clinical relevance, such as the complex ST131, were detected in wastewater, streams and gulls in Portugal, Spain and Sweden. Quinolone resistance was due to gyrA and parC mutations, although distinct mutations were detected in birds of prey and in wastewater, streams and gulls isolates. These differences were correlated with specific MLST lineages, suggesting resistance inheritance. Among the plasmid-mediated quinolone resistance genes, only aac(6 ')-ib-cr and qnrS were detected in wastewater, streams and gulls isolates, but not in birds of prey. The horizontal transfer of the gene aac(6 ')-ib-cr could be inferred from its occurrence in different MLST lineages.

  • 31.
    Wedén, Christina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Danell, Eric
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Species recognition in the truffle genus Tuber: the synonyms Tuber aestivum and Tuber uncinatum2005In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 7, no 10, p. 1535-1546Article in journal (Refereed)
    Abstract [en]

    The two morphologically similar truffles Tuber aestivum and T. uncinatum have caused confusion because T. uncinatum is regarded by different authors, as either a distinct species, variety, subspecies, or synonym of T. aestivum. A clarification of the relationship between the two truffles would help both conservation biology and cultivation. We aimed both to test the reliability of the only quantitative morphological character used to distinguish the two taxa, i.e. the height of the spore reticulum, and to compare sequences of the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region. Our study included 117 fruit bodies of T. aestivum and T. uncinatum, originating from eight European countries. The results showed that the spore reticulum height is not diagnostic. The phylogenetic analysis of ITS sequences from 81 fruit bodies and an additional 32 sequences from GenBank showed that T. aestivum and T. uncinatum were intermingled in one highly supported (100% bootstrap) monophyletic clade, separate from its sister species Tuber mesentericum. We conclude that T. aestivum and T. uncinatum are synonyms and the species should be named T. aestivum, as the oldest name has priority. For traders, T. aestivum syn. T. uncinatum should be used until conformity has been reached.

1 - 31 of 31
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