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  • 1.
    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.

  • 2.
    Richert, Inga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Microbial Ecosystem Services Group, Leipzig, Germany.
    Environmental filtering of bacteria in low productivity habitats2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Microbes fulfill important ecosystem functions by contributing as drivers of global nutrient cycles. Their distribution patterns are mainly controlled by environmental heterogeneities. So far, little is known about the mode of action of particular environmental drivers on the microbiota, particularly in low productivity habitats.

    The aim of this thesis was to investigate the relationships between local environmental drivers and the microbial responses at the level of communities, individuals and realized function, using three structurally different model habitats sharing the feature of overall low productivity. Using a hypothesis-based approach and extensive 16S rRNA amplicon mapping of bacterioplankton colonizing the polar Southern Ocean, I identified how the seasonal formation of open-water polynyas and coupled phytoplankton production affected the diversity of surface bacterial communities and resulted in a cascading effect influencing the underlying dark polar water masses. Additional laboratory experiments, with cultures exposed to light, resulted in reduction in alpha diversity and promoted opportunistic populations with most bacterial populations thriving in the cultures typically reflected the dominants in situ.

    Furthermore it was experimentally tested how induced cyclic water table fluctuations shaping environmental heterogeneity in a constructed wetland on temporal scale, by directly affecting redox conditions. Twelve months of water table fluctuations resulted in enhanced microbial biomass, however a shift in community composition did not lead to a significant increase in pollutant removal efficiency when compared to a static control wetland. I detected phyla that have previously been proposed as key players in anaerobic benzene break-down using a protocol that was developed for single cell activity screening using isotope-substrate uptake and microautoradiography combined with taxonomic identification based on fluorescent in situ hybridization targeting the 16S rRNA. Eventually, I provide an example of how anthropogenic pollution with polyaromatic hydrocarbons induced a strong environmental filtering on intrinsic microbial communities in lake sediments.

    In conclusion, my studies reveal that microorganisms residing in low productivity habitats are greatly influenced by environmental heterogeneity across both spatial and temporal scales. However, such variation in community composition or overall abundance does not always translate to altered community function.

     

    List of papers
    1. Spatial patterns of marine bacterioplankton along gradients of primary production in the Amundsen Sea Polynya, Southern Ocean
    Open this publication in new window or tab >>Spatial patterns of marine bacterioplankton along gradients of primary production in the Amundsen Sea Polynya, Southern Ocean
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    During austral summers, the Southern Ocean's biota experience a sharp increase in primary production and a steepening of biotic and abiotic gradients, resulting from increased solar radiation and retreating ice.  In one of the largest ice-free patches - the Amundsen Sea Polynya - we aimed to identify connections between spatial diversity patterns of heterotrophic bacterioplankton and gradients of phytoplankton biomass. We gathered samples from throughout the depth profile at 15 sites during the austral summer of 2010/2011, collecting bacterioplankton and measuring several biotic and abiotic factors in the surrounding seawater.  We assessed bacterial community structure by targeting the 16S rRNA gene for pyrosequencing. Our overall goal was to identify patterns of spatial diversity in heterotrophic bacterioplankton and to generate and test mechanistic hypotheses for bacterioplankton community structure related to phytoplankton biomass, biotic and abiotic nutrients, and hydrological relationships due to depth and water mass.

    We found that processes acting within the photic surface related to the level of phytoplankton biomass induce a strong filtering effect by decreasing bacterioplankton community richness while increasing bacterioplankton abundance as phytoplankton biomass increases. We also found that the bacterioplankton community in the photic surface represents a subset of that found in the underlying dark water masses, likely reformed annually as the polynya appears; bacterial communities in surface waters reflect the communities found beneath, though as phytoplankton biomass increases, the similarity of these communities between different sites within the polynya increases, likely due to the filtering effect. The high phytoplankton biomass in the photic surface represents an important pool of organic matter and inorganic nutrients, fueling the underlying dark water with nutrients in a cascading effect; we found that in contrast to the community response in shallower water, the bacterioplankton community at the bottom of the phytoplankton biomass increased in diversity as phytoplankton biomass in overlying waters increased, while deeper waters remained largely unaffected. We propose that this lack of, response in deeper water masses gives rise to the observed high group dispersal in bacterial community composition in all water masses and the relatively homogenous community in the bottom water mass.

    Keywords
    marine bacterioplankton, community dynamics, Southern Ocean
    National Category
    Biological Sciences
    Research subject
    Biology with specialization in Microbiology
    Identifiers
    urn:nbn:se:uu:diva-229137 (URN)
    Funder
    Swedish Research Council
    Available from: 2014-08-01 Created: 2014-08-01 Last updated: 2015-05-07
    2. The impact of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya
    Open this publication in new window or tab >>The impact of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Although the Antarctic Ocean is perpetually cold, mostly ice-covered and dark, it is a highly productive and diverse marine ecosystem. During austral summer, ice-free patches (polynyas) form, exposing marine organisms to sunlight, while mobilizing large amounts of nutrients from the melting ice. As a result, intense phytoplankton blooms form that sustain life across the entire Antarctic food web. This seasonality is likely to shape microbial communities, but the main environmental drivers controlling these communities and the biogeochemical processes they mediate are largely unknown.

    In this study, the remote Amundsen Sea Polynya (ASP) was used as a model system to identify the influence of some of the most important environmental drivers of the Southern Ocean. We studied the dynamics in occurrence and activity of abundant members of the bacterioplankton community, directly in environmental samples as well as in microcosm experiments, by using next-generation sequencing of bar-coded 16S rRNA genes in combination with immunochemical detection of DNA-synthesis using bromodeoxyuridine as a tracer.

    We found that the photic zone harbored a bacterioplankton community with a low species richness. Here, the dominant populations were related to taxa known to benefit from high organic carbon and nutrient loads (copiotrophs). In contrast, the dark water masses below the photic zone hosted bacterial communities of higher richness, and were dominated by oligotrophs. Results from enrichment studies suggested that indirect impacts of light via photosynthetic production and competition for dissolved nutrients provided in the water masses are the two main factors shaping bacterial communities of the ASP.

    Keywords
    marine bacterioplankton, population dynamics, Southern Ocean
    National Category
    Biological Sciences
    Research subject
    Biology with specialization in Microbiology
    Identifiers
    urn:nbn:se:uu:diva-229138 (URN)
    Available from: 2014-08-01 Created: 2014-08-01 Last updated: 2014-09-08
    3. The effect of water table fluctuation on microbial benzene utilization in a constructed wetland
    Open this publication in new window or tab >>The effect of water table fluctuation on microbial benzene utilization in a constructed wetland
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Microbial degradation of benzene in anoxic habitats is so low that it’s hardly detectable. In this study benzene-utilizing taxa residing in a mostly anoxic wetland were identified and visualized by applying single-cell techniques and phylogenetic identification based on 16S rRNA amplicon sequencing. We also tested whether cyclic water table fluctuations had a positive effect on benzene removal rates.

    We found that cyclic water table changes in a constructed wetland with horizontal water flow created fluctuations in redox conditions and resulted in an increase of microbial biomass. However, it did not enhance the removal of recalcitrant hydrocarbon contaminants, at least not within one year of operation. Benzene remained persistent, despite the increased microbial biomass. A slight decrease in ammonia and nitrate concentrations may hint towards an increase in microbial denitrification as a result of the artificially induced hydrodynamic changes.

    Despite the low benzene uptake rates, we successfully visualized and identified anaerobic benzene-degrading microbes, by using 14C-benzene-Microautoradiography (MAR) and Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH) with a probe set targeting proposed anaerobic benzene-utilizers. We found Deltaproteobacteria, Firmicutes, Archaea and Azoarcus (Betaproteobacteria) to actively take up benzene anaerobically

    Our MAR-CARD-FISH protocol can be applied to visualize benzene- or other aromatic hydrocarbon-utilizing microbes in contaminated sediments and soils and can help to reveal physical associations of different taxa involved in the recalcitrant hydrocarbon break-down.

    Keywords
    constructed wetland, benzene, anoxic, bacteria, fluctuation
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-229139 (URN)
    Available from: 2014-08-01 Created: 2014-08-01 Last updated: 2014-09-08
    4. Bacterial communities in a tar-contaminated lake sediment
    Open this publication in new window or tab >>Bacterial communities in a tar-contaminated lake sediment
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Organic anthropogenic pollutants, such as polycyclic aromatic hydrocarbons (PAHs) are widespread in nature and even low concentrations can be harmful for many organisms. To assess if also microbiota residing in freshwater sediments respond to such contaminants a lake sediment adjacent to the former discharge of a factory that conducted tar distillation in the early 20th century in central Sweden were studied. We compared the bacterial community composition (BCC) at sites affected by high tar loads to BCC in a linked, but pristine sediment, and a downstream site that is likely influenced by regular diffusive loads of PAHs. PAH and VOC (Volatile Organic Carbon) concentrations were analyzed whereas sediment aliquots were used for molecular identification of the local BCC. Here we took the opportunity to compare the bacteria abundance-data retrieved from two distinct approaches; two OTU tables were generated based on either paired-end MiSeq Illumina 16S rRNA gene amplicon sequencing or direct HiSeq Illumina-based metagenome sequencing of sediment DNA extracts. Both methods revealed that the high PAH loads adjacent to the tar factory significantly alters the BCC compared to the less affected sites, even though they both partly result in contrasting outcome. The highly contaminated sediments hosted a bacterial community that was low in richness, featuring taxa known to colonize habitats with high PAH loads. For instance the relative abundance of Sphingomonadales and Burkhoderiales, both orders, within the phylum Proteobacteria, increased relative to the pristine site as well as Acidimicrobiales, one subclass of Actinobacteria. Interestingly the sediment downstream of the former factory outlet was colonized by bacteria which were very similar in community composition to the pristine site upstream of the factory outlet, implying a capacity of the natural sediment microbiota to cope with low levels of PAH contamination. 

    National Category
    Microbiology
    Research subject
    Biology with specialization in Microbiology
    Identifiers
    urn:nbn:se:uu:diva-229140 (URN)
    Available from: 2014-08-01 Created: 2014-08-01 Last updated: 2014-09-08
  • 3.
    Richert, Inga
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Microbial Ecosystem Services Group, Leipzig, Germany.
    Dinasquet, Julie
    Logares, Ramiro
    Riemann, Lasse
    Yager, Patricia L
    Wendeberg, Annelie
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    The influence of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya2015In: Elementa: Science of the Anthropocene, ISSN 2325-1026, Vol. 3, no 1, article id 44Article in journal (Refereed)
    Abstract [en]

    Despite being perpetually cold, seasonally ice-covered and dark, the coastal Southern Ocean is highly productive and harbors a diverse microbiota. During the austral summer, ice-free coastal patches (or polynyas) form, exposing pelagic organisms to sunlight, triggering intense phytoplankton blooms. This strong seasonality is likely to influence bacterioplankton community composition (BCC). For the most part, we do not fully understand the environmental drivers controlling high-latitude BCC and the biogeochemical cycles they mediate. In this study, the Amundsen Sea Polynya was used as a model system to investigate important environmental factors that shape the coastal Southern Ocean microbiota. Population dynamics in terms of occurrence and activity of abundant taxa was studied in both environmental samples and microcosm experiments by using 454 pyrosequencing of 16S rRNA genes. We found that the BCC in the photic epipelagic zone had low richness, with dominant bacterial populations being related to taxa known to benefit from high organic carbon and nutrient loads (copiotrophs). In contrast, the BCC in deeper mesopelagic water masses had higher richness, featuring taxa known to benefit from low organic carbon and nutrient loads (oligotrophs). Incubation experiments indicated that direct impacts of light and competition for organic nutrients are two important factors shaping BCC in the Amundsen Sea Polynya.

  • 4.
    Richert, Inga
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Yager, Patricia L.
    Dinasquet, Julie
    Logares, Ramiro
    Riemann, Lasse
    Wendeberg, Annelie
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Summer comes to the Southern Ocean: How phytoplankton shape bacterioplankton communities far into the deep dark sea2019In: Ecosphere, ISSN 2150-8925, E-ISSN 2150-8925, Vol. 10, no 3, article id e02641Article in journal (Refereed)
  • 5.
    Yager, Patricia L.
    et al.
    Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
    Sherrell, R. M.
    Rutgers State Univ, Dept Marine & Coastal Sci, New Brunswick, NJ USA.
    Stammerjohn, S. E.
    Univ Colorado, Inst Arctic & Alpine Res, Boulder, CO 80309 USA.
    Ducklow, H. W.
    Columbia Univ, Lamont Doherty Earth Observ, Palisades, NY USA.
    Schofield, O. M E.
    Rutgers State Univ, Dept Marine & Coastal Sci, New Brunswick, NJ USA.
    Ingall, E. D.
    Georgia Inst Technol, Sch Earth & Atmospher Sci, Atlanta, GA 30332 USA.
    Wilson, S. E.
    Bangor Univ, Sch Ocean Sci, Bangor, Gwynedd, Wales.
    Lowry, K. E.
    Stanford Univ, Dept Earth Syst Sci, Stanford, CA 94305 USA.
    Williams, C. M.
    Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
    Riemann, Lasse
    Univ Copenhagen, Marine Biol Sect, Helsingor, Denmark.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Alderkamp, A-C
    Stanford Univ, Dept Earth Syst Sci, Stanford, CA 94305 USA.
    Dinasquet, J.
    Univ Copenhagen, Marine Biol Sect, Helsingor, Denmark; Linnaeus Univ, Dept Nat Sci, Kalmar, Sweden.
    Logares, R.
    CSIC, Inst Marine Sci, Barcelona, Spain.
    Richert, Inga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sipler, R.E.
    Coll William & Mary, Virginia Inst Marine Sci, Gloucester Pt, VA USA.
    Melara, A.J.
    Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
    Mu, L.
    Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
    Newstead, R.G.
    Bangor Univ, Sch Ocean Sci, Bangor, Gwynedd, Wales.
    Post, A.F.
    Florida Atlantic Univ, Oceanog Inst, Harbor Branch, Boca Raton, FL 33431 USA.
    Swalethorp, R.
    Tech Univ Denmark, Sect Oceanog & Climate, Natl Inst Aquat Resources DTU Aqua, Charlottenlund, Denmark; Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    van Dijken, G.L.
    Stanford Univ, Dept Earth Syst Sci, Stanford, CA 94305 USA.
    A carbon budget for the Amundsen Sea Polynya, Antarctica: estimating net community production and export in a highly productive polar ecosystem2016In: Elementa: Science of the Anthropocene, ISSN 2325-1026, Vol. 4, article id 000140Article in journal (Refereed)
    Abstract [en]

    Polynyas, or recurring areas of seasonally open water surrounded by sea ice, are foci for energy and material transfer between the atmosphere and the polar ocean. They are also climate sensitive, with both sea ice extent and glacial melt influencing their productivity. The Amundsen Sea Polynya (ASP) is the greenest polynya in the Southern Ocean, with summertime chlorophyll a concentrations exceeding 20 µg L−1. During the Amundsen Sea Polynya International Research Expedition (ASPIRE) in austral summer 2010–11, we aimed to determine the fate of this high algal productivity. We collected water column profiles for total dissolved inorganic carbon (DIC) and nutrients, particulate and dissolved organic matter, chlorophyll a, mesozooplankton, and microbial biomass to make a carbon budget for this ecosystem. We also measured primary and secondary production, community respiration rates, vertical particle flux and fecal pellet production and grazing. With observations arranged along a gradient of increasing integrated dissolved inorganic nitrogen drawdown (ΔDIN; 0.027–0.74 mol N m−2), changes in DIC in the upper water column (ranging from 0.2 to 4.7 mol C m−2) and gas exchange (0–1.7 mol C m−2) were combined to estimate early season net community production (sNCP; 0.2–5.9 mol C m−2) and then compared to organic matter inventories to estimate export. From a phytoplankton bloom dominated by Phaeocystis antarctica, a high fraction (up to ~60%) of sNCP was exported to sub-euphotic depths. Microbial respiration remineralized much of this export in the mid waters. Comparisons to short-term (2–3 days) drifting traps and a year-long moored sediment trap capturing the downward flux confirmed that a relatively high fraction (3–6%) of the export from ~100 m made it through the mid waters to depth. We discuss the climate-sensitive nature of these carbon fluxes, in light of the changing sea ice cover and melting ice sheets in the region.

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