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  • 1. Bengtson, Per
    et al.
    Bastviken, David
    Stockholm University, Faculty of Science, Department of Geology and Geochemistry.
    de Boer, Wietse
    Oberg, Gunilla
    Possible role of reactive chlorine in microbial antagonism and organic matter chlorination in terrestrial environments2009In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 11, no 6, p. 1330-1339Article, review/survey (Refereed)
    Abstract [en]

    Several studies have demonstrated that extensive formation of organically bound chlorine occurs both in soil and in decaying plant material. Previous studies suggest that enzymatic formation of reactive chlorine outside cells is a major source. However, the ecological role of microbial-induced extracellular chlorination processes remains unclear. In the present paper, we assess whether or not the literature supports the hypothesis that extracellular chlorination is involved in direct antagonism against competitors for the same resources. Our review shows that it is by no means rare that biotic processes create conditions that render biocidal concentrations of reactive chlorine compounds, which suggest that extracellular production of reactive chlorine may have an important role in antagonistic microbial interactions. To test the validity, we searched the UniprotPK database for microorganisms that are known to produce haloperoxidases. It appeared that many of the identified haloperoxidases from terrestrial environments are originating from organisms that are associated with living plants or decomposing plant material. The results of the in silico screening were supported by various field and laboratory studies on natural chlorination. Hence, the ability to produce reactive chlorine seems to be especially common in environments that are known for antibiotic-mediated competition for resources (interference competition). Yet, the ability to produce haloperoxidases is also recorded, for example, for plant endosymbionts and parasites, and there is little or no empirical evidence that suggests that these organisms are antagonistic.

  • 2.
    Brindefalk, Björn
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Ekman, Martin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Ininbergs, Karolina
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Dupont, Christopher L.
    Yooseph, Shibu
    Pinhassi, Jarone
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4442-4455Article in journal (Refereed)
    Abstract [en]

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

  • 3. Cardini, Ulisse
    et al.
    van Hoytema, Nanne
    Bednarz, Vanessa N.
    Rix, Laura
    Foster, Rachel A.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Al-Rshaidat, Mamoon M. D.
    Wild, Christian
    Microbial dinitrogen fixation in coral holobionts exposed to thermal stress and bleaching2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 8, p. 2620-2633Article in journal (Refereed)
    Abstract [en]

    Coral holobionts (i.e., coral-algal-prokaryote symbioses) exhibit dissimilar thermal sensitivities that may determine which coral species will adapt to global warming. Nonetheless, studies simultaneously investigating the effects of warming on all holobiont members are lacking. Here we show that exposure to increased temperature affects key physiological traits of all members (herein: animal host, zooxanthellae and diazotrophs) of both Stylophora pistillata and Acropora hemprichii during and after thermal stress. S. pistillata experienced severe loss of zooxanthellae (i.e., bleaching) with no net photosynthesis at the end of the experiment. Conversely, A. hemprichii was more resilient to thermal stress. Exposure to increased temperature (+ 6 degrees C) resulted in a drastic increase in daylight dinitrogen (N-2) fixation, particularly in A. hemprichii (threefold compared with controls). After the temperature was reduced again to in situ levels, diazotrophs exhibited a reversed diel pattern of activity, with increased N-2 fixation rates recorded only in the dark, particularly in bleached S. pistillata (twofold compared to controls). Concurrently, both animal hosts, but particularly bleached S. pistillata, reduced both organic matter release and heterotrophic feeding on picoplankton. Our findings indicate that physiological plasticity by coral-associated diazotrophs may play an important role in determining the response of coral holobionts to ocean warming.

  • 4.
    Celepli, Narin
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Sundh, John
    Ekman, Martin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Dupont, Chris L.
    Yooseph, Shibu
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Ininbergs, Karolina
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 2, p. 673-686Article in journal (Refereed)
    Abstract [en]

    Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradients in salinity and nutrient concentrations. Here, we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa. Cyanobacteria in the Baltic Sea differed genetically from those in adjacent limnic and marine waters as well as from cultivated and sequenced picocyanobacterial strains. Diversity peaked at brackish salinities 3.5-16psu, with low N:P ratios. A shift in community composition from brackish to marine strains was accompanied by a change in the repertoire and expression of genes involved in salt acclimation. Overall, the pre-bloom cyanobacterial population was more genetically diverse, widespread and abundant than previously documented, with unicellular picocyanobacteria being the most abundant clade along the entire Baltic Sea salinity gradient.

  • 5.
    Klawonn, Isabell
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Nahar, N.
    Walve, Jakob
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Andersson, B.
    Olofsson, M.
    Barthel Svedén, Jennie
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Littmann, S.
    Whitehouse, M. J.
    Kuypers, M. M. M.
    Ploug, Helle
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Cell-specific nitrogen- and carbon-fixation of cyanobacteria in a temperate marine system (Baltic Sea)2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4596-4609Article in journal (Refereed)
    Abstract [en]

    We analysed N-2- and carbon (C) fixation in individual cells of Baltic Sea cyanobacteria by combining stable isotope incubations with secondary ion mass spectrometry (SIMS). Specific growth rates based on N-2- and C-fixation were higher for cells of Dolichospermum spp. than for Aphanizomenon sp. and Nodularia spumigena. The cyanobacterial biomass, however, was dominated by Aphanizomenon sp., which contributed most to total N-2-fixation in surface waters of the Northern Baltic Proper. N-2-fixation by Pseudanabaena sp. and colonial picocyanobacteria was not detectable. N-2-fixation by Aphanizomenon sp., Dolichospermum spp. and N. spumigena populations summed up to total N-2-fixation, thus these genera appeared as sole diazotrophs within the Baltic Sea's euphotic zone, while their mean contribution to total C-fixation was 21%. Intriguingly, cell-specific N-2-fixation was eightfold higher at a coastal station compared to an offshore station, revealing coastal zones as habitats with substantial N-2-fixation. At the coastal station, the cell-specific C-to N-2-fixation ratio was below the cellular C: N ratio, i.e. N-2 was assimilated in excess to C-fixation, whereas the C-to N-2-fixation ratio exceeded the C: N ratio in offshore sampled diazotrophs. Our findings highlight SIMS as a powerful tool not only for qualitative but also for quantitative N-2-fixation assays in aquatic environments.

  • 6. Marzocchi, Ugo
    et al.
    Bonaglia, Stefano
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    van de Velde, Sebastiaan
    Hall, Per O. J.
    Schramm, Andreas
    Risgaard-Petersen, Nils
    Meysman, Filip J. R.
    Transient bottom water oxygenation creates a niche for cable bacteria in long‐term anoxic sediments of the Eastern Gotland Basin2018In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 20, no 8, p. 3031-3041Article in journal (Refereed)
    Abstract [en]

    Cable bacteria have been reported in sediments from marine and freshwater locations, but the environmental factors that regulate their growth in natural settings are not well understood. Most prominently, the physiological limit of cable bacteria in terms of oxygen availability remains poorly constrained. In this study, we investigated the presence, activity and diversity of cable bacteria in relation to a natural gradient in bottom water oxygenation in a depth transect of the Eastern Gotland Basin (Baltic Sea). Cable bacteria were identified by FISH at the oxic and transiently oxic sites, but not at the permanently anoxic site. Three species of the candidate genus Electrothrix, i.e. marina, aarhusiensis and communis were found coexisting within one site. The highest filament density (33 m cm−2) was associated with a 6.3 mm wide zone depleted in both oxygen and free sulphide, and the presence of an electric field resulting from the electrogenic sulphur oxidizing metabolism of cable bacteria. However, the measured filament densities and metabolic activities remained low overall, suggesting a limited impact of cable bacteria at the basin level. The observed bottom water oxygen levels (< 5 μM) are the lowest so far reported for cable bacteria, thus expanding their known environmental distribution.

  • 7. Matos, Marina N.
    et al.
    Lozada, Mariana
    Anselmino, Luciano E.
    Musumeci, Matías A.
    Henrissat, Bernard
    Jansson, Janet K.
    Mac Cormack, Walter P.
    Carroll, JoLynn
    Sjöling, Sara
    Lundgren, Leif
    Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Dionisi, Hebe M.
    Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4471-4484Article in journal (Refereed)
    Abstract [en]

    Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.

  • 8. Mondav, Rhiannon
    et al.
    McCalley, Carmody K.
    Hodgkins, Suzanne B.
    Frolking, Steve
    Saleska, Scott R.
    Rich, Virginia I.
    Chanton, Jeff P.
    Crill, Patrick M.
    Stockholm University, Faculty of Science, Department of Geology and Geochemistry.
    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, review/survey (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.

  • 9.
    Ogonowski, Martin
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. Aquabiota Water Research AB, Sweden.
    Motiei, Asa
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Ininbergs, Karolina
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Hell, Eva
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Gerdes, Zandra
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Udekwu, Klas I.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Bacsik, Zoltan
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Gorokhova, Elena
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Evidence for selective bacterial community structuring on microplastics2018In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 20, no 8, p. 2796-2808Article in journal (Refereed)
    Abstract [en]

    In aquatic ecosystems, microplastics are a relatively new anthropogenic substrate that can readily be colonized by biofilm-forming organisms. To examine the effects of substrate type on microbial community assembly, we exposed ambient Baltic bacterioplankton to plastic substrates commonly found in marine environments (polyethylene, polypropylene and polystyrene) as well as native (cellulose) and inert (glass beads) particles for 2 weeks under controlled conditions. The source microbial communities and those of the biofilms were analyzed by Illumina sequencing of the 16S rRNA gene libraries. All biofilm communities displayed lower diversity and evenness compared with the source community, suggesting substrate-driven selection. Moreover, the plastics-associated communities were distinctly different from those on the non-plastic substrates. Whereas plastics hosted greater than twofold higher abundance of Burkholderiales, the non-plastic substrates had a significantly higher proportion of Actinobacteria and Cytophagia. Variation in the community structure, but not the cell abundance, across the treatments was strongly linked to the substrate hydrophobicity. Thus, microplastics host distinct bacterial communities, at least during early successional stages.

  • 10.
    Robador, Alberto
    et al.
    Max-Planck Institute for marine Microbiology.
    Brüchert, Volker
    Stockholm University, Faculty of Science, Department of Geology and Geochemistry.
    Jørgensen, Bo Barker
    Max-Planck Institute for marine Microbiology.
    The impact of temperature change on the activity and community composition of sulfate-reducing abcteria in arctic versus temperate marine sediments2009In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 11, no 7, p. 1692-1703Article in journal (Refereed)
    Abstract [en]

    Arctic regions may be particularly sensitive to climate warming and, consequently, rates of carbon mineralization in warming marine sediment may also be affected. Using long-term (24 months) incubation experiments at 0°C, 10°C and 20°C, the temperature response of metabolic activity and community composition of sulfate-reducing bacteria were studied in the permanently cold sediment of north-western Svalbard (Arctic Ocean) and compared with a temperate habitat with seasonally varying temperature (German Bight, North Sea). Short-term <sup>35</sup>S-sulfate tracer incubations in a temperature-gradient block (between −3.5°C and +40°C) were used to assess variations in sulfate reduction rates during the course of the experiment. Warming of arctic sediment resulted in a gradual increase of the temperature optima ( T<sub>opt</sub>) for sulfate reduction suggesting a positive selection of psychrotolerant/mesophilic sulfate-reducing bacteria (SRB). However, high rates at in situ temperatures compared with maximum rates showed the predominance of psychrophilic SRB even at high incubation temperatures. Changing apparent activation energies ( E<sub>a</sub>) showed that increasing temperatures had an initial negative impact on sulfate reduction that was weaker after prolonged incubations, which could imply an acclimatization response rather than a selection process of the SRB community. The microbial community composition was analysed by targeting the 16S ribosomal RNA using catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH). The results showed the decline of specific groups of SRB and confirmed a strong impact of increasing temperatures on the microbial community composition of arctic sediment. Conversely, in seasonally changing sediment sulfate reduction rates and sulfate-reducing bacterial abundance changed little in response to changing temperature.

  • 11. Tischer, Karolin
    et al.
    Kleinsteuber, Sabine
    Schleinitz, Kathleen M.
    Fetzer, Ingo
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Helmholtz Centre for Environmental Research, Germany.
    Spott, Oliver
    Stange, Florian
    Lohse, Ute
    Franz, Janett
    Neumann, Franziska
    Gerling, Sarah
    Schmidt, Christian
    Hasselwander, Eyk
    Harms, Hauke
    Wendeberg, Annelie
    Microbial communities along biogeochemical gradients in a hydrocarbon-contaminated aquifer2013In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 15, no 9, p. 2603-2615Article in journal (Refereed)
    Abstract [en]

    Micro-organisms are known to degrade a wide range of toxic substances. How the environment shapes microbial communities in polluted ecosystems and thus influences degradation capabilities is not yet fully understood. In this study, we investigated microbial communities in a highly complex environment: the capillary fringe and subjacent sediments in a hydrocarbon-contaminated aquifer. Sixty sediment sections were analysed using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting, cloning and sequencing of bacterial and archaeal 16S rRNA genes, complemented by chemical analyses of petroleum hydrocarbons, methane, oxygen and alternative terminal electron acceptors. Multivariate statistics revealed concentrations of contaminants and the position of the water table as significant factors shaping the microbial community composition. Micro-organisms with highest T-RFLP abundances were related to sulphate reducers belonging to the genus Desulfosporosinus, fermenting bacteria of the genera Sedimentibacter and Smithella, and aerobic hydrocarbon degraders of the genus Acidovorax. Furthermore, the acetoclastic methanogens Methanosaeta, and hydrogenotrophic methanogens Methanocella and Methanoregula were detected. Whereas sulphate and sulphate reducers prevail at the contamination source, the detection of methane, fermenting bacteria and methanogenic archaea further downstream points towards syntrophic hydrocarbon degradation.

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