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  • 101.
    Nilsson, Louise K. J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology. Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Sharma, Anil
    International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
    Bhatnagar, Raj K.
    International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Terenius, Olle
    Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Presence of Aedes and Anopheles mosquito larvae is correlated to bacteria found in domestic water-storage containers2018In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 94, no 6, article id fiy058Article in journal (Refereed)
    Abstract [en]

    Water-storage containers are common in households where access to water is scarce and often act as breeding sites for vector mosquitoes. Bacteria in these containers may be important for attracting or repelling ovipositing mosquitoes. We hypothesized that bacterial community composition in water-storage containers would represent either inhibitory or suitable environmental conditions for mosquito larvae. To investigate this, we characterized the bacterial community composition in water-storage containers and correlated these communities to Aedes and Anopheles larval densities. Water samples were collected over two years from 13 containers in an Indian village and analyzed by high throughput 16S rRNA gene amplicon sequencing. Comparisons of bacterial community composition between water with and without mosquito larvae showed that Xanthomonadaceae, Comamonadaceae and Burkholderiaceae were more common (P < 0.05) in absence of larvae, while Lachnospiraceae, Synechococcaceae, Alcaligenaceae and Cryomorphaceae were more common (P < 0.05) in presence of larvae. Indicator analysis identified operational taxonomic units designated as CL500–29 marine group (Acidimicrobiaceae) and FukuN101 (Microbacteriaceae) for absence and presence of larvae, respectively. These results contribute to the understanding of which bacteria, directly or indirectly, can be linked to absence or presence of mosquitoes around households and set the basis for potential measures to be taken against these vector mosquitoes.

  • 102. Obertegger, Ulrike
    et al.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pindo, Massimo
    Larger, Simone
    Flaim, Giovanna
    Temporal variability of bacterioplankton is habitat driven2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 21, p. 4322-4335Article in journal (Refereed)
    Abstract [en]

    Temporal dynamics of bacterioplankton are rarely investigated for multiple habitats and years within individual lakes, limiting our understanding of the variability of bacterioplankton community (BC) composition with respect to environmental factors. We assessed the BC composition of a littoral and two pelagic habitats (euphotic zone and hypolimnion) of Lake Tovel monthly from April 2014 to May 2017 by high-throughput sequencing of the V3?V4 hypervariable region of the 16S rRNA gene. The three habitats differed in temperature, light, oxygen and hydrology. In particular, the littoral was the most hydrologically unstable because it receives most of the lake inflow, the hypolimnion was the most stable because of its hydrologically sheltered position, and the pelagic euphotic habitat was intermediate. Consequently, we hypothesized different temporal patterns of BC composition for all three habitats according to their environmental differences. We applied PERMANOVA, nonmetric multidimensional scaling and source?sink analysis to characterize BC composition. Overall, BCs were different among habitats with the littoral showing the highest variability and the hypolimnion the highest stability. The BC of rainy 2014 was distinct from the BCs of other years irrespective of the habitats considered. Seasonal differences in BCs were limited to spring, probably linked to meltwater inflow and mixing. Thus, temporal effects related to year and season were linked to the hydrological gradient of habitats. We suggest that despite potential within-lake dispersal of bacterioplankton by water flow and mixing, local environmental conditions played a major role in Lake Tovel, fostering distinct BCs in the three habitats.

  • 103.
    Osman, Omneya Ahmed
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Isolation And Characterization Of Surface Active Compounds Produced By Halophilic Bacteria2012In: Book of Proceedings: 5th International Symposium on Biosorption and Bioremediation / [ed] Petra Lovecká, Martina Nováková, Petra Prouzová, Ondrej Uhlik, Prague: ICT Press , 2012, p. 164-168Conference paper (Other academic)
    Abstract [en]

    Biosurfactants or bioemulsifiers produced by microorganisms is considered an essential step in hydrocarbon biodegradation in the marine environment. Four bacterial strains isolated from Maruit lake, Egypt displayed hemolytic activity when grown on blood agar. 16S rRNA sequencing revealed that these strains were affiliated to Halomonas, Chromohalobacter and Halobacillus. Bacterial adhesion to benzene, xylene and lubricant motor oil ranged between 60-80 % indicating the presence of surface active compounds. The 4 strains had the capacity to produce surface active compounds when grown with 1% of motor oil, rapeseed oil and olive oil as sole carbon source and in the presence of different NaCl concentrations (0.0, 0.5 and 1.0 M). Most of the strains showed enhanced growth in the presence of 0.5 and 1.0 M NaCl, emphasizing the importance of NaCl in controlling the growth of halophilic bacteria. Drop collapse test was positive in all strains. Surface tension measurements ranged between 72-58 mN/m for motor oil, olive oil and rapeseed oil. All the isolates exhibit emusification stability of 69-100% with the tested oils. Resultant emulsion found stable without any phase separation. We concluded that these strains have a potential application as a bioemulsifiers which can grow in different types of oils.

  • 104.
    Osman, Omneya
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Gudasz, Cristian
    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.
    Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change2014In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 88, no 3, p. 468-481Article in journal (Refereed)
    Abstract [en]

    The abundance and composition of genes involved in the catabolism of aromatic compounds provide important information on the biodegradation potential of organic pollutants and naturally occurring compounds in the environment. We studied catechol 2, 3 dioxygenase (C23O) and benzylsuccinate synthase (bssA) genes coding for key enzymes of aerobic and anaerobic degradation of aromatic compounds in experimental incubations with sediments from two contrasting lakes; humic lake Svarttjärn and eutrophic Vallentunasjön, respectively. Sediment cores from both lakes were incubated continuously for 5 months at constant temperatures ranging from 1.0 to 21.0 °C. The difference in C23O gene composition of the sediment analyzed at the end of the experiment was larger between lakes, than among temperature treatments within each lake. The abundance of C23O gene copies and measured respiration was positively correlated with temperature in Vallentunasjön, whereas putative C23O genes were present in lower concentrations in Svarttjärn sediments. Putative bssA genes were only detected in Svarttjärn. For both lakes, the two catabolic genes were most abundant in the surface sediment. The results emphasize the important role of temperature and nutrient availability in controlling the functional potential of sediment microorganisms and reveal differences between systems with contrasting trophic status. A better understanding of catabolic pathways and enzymes will enable more accurate forecasting of the functional properties of ecosystems under various scenarios of environmental change.

  • 105.
    Peter, Hannes
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Beier, Sara
    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.
    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.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Function-specific response to depletion of microbial diversity2011In: The ISME Journal, ISSN 1751-7362, Vol. 5, no 2, p. 351-361Article in journal (Refereed)
    Abstract [en]

    Recent meta-analyses suggest that ecosystem functioning increases with biodiversity, but contradictory results have been presented for some microbial functions. Moreover, observations of only one function underestimate the functional role of diversity because of species-specific trade-offs in the ability to carry out different functions. We examined multiple functions in batch cultures of natural freshwater bacterial communities with different richness, achieved by a dilution-to-extinction approach. Community composition was assessed by molecular fingerprinting of 16S rRNA and chitinase genes, representing the total community and a trait characteristic for a functional group, respectively. Richness was positively related to abundance and biomass, negatively correlated to cell volumes and unrelated to maximum intrinsic growth rate. The response of chitin and cellulose degradation rates depended on the presence of a single phylotype. We suggest that species identity and community composition rather than richness matters for specific microbial processes.

  • 106.
    Peura, Sari
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Jones, Roger I.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Resistant Microbial Cooccurrence Patterns Inferred by Network Topology2015In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 81, no 6, p. 2090-2097Article in journal (Refereed)
    Abstract [en]

    Although complex cooccurrence patterns have been described for microbes in natural communities, these patterns have scarcely been interpreted in the context of ecosystem functioning and stability. Here we constructed networks from species cooccurrences between pairs of microorganisms which were extracted from five individual aquatic time series, including a dystrophic and a eutrophic lake as well as an open ocean site. The resulting networks exhibited higher clustering coefficients, shorter path lengths, and higher average node degrees and levels of betweenness than those of random networks. Moreover, simulations demonstrated that taxa with a large number of cooccurrences and placement at convergence positions in the network, so-called "hubs" and "bottlenecks," confer resistance against random removal of "taxa." Accordingly, we refer to cooccurrences at convergence positions as system-relevant interdependencies, as they, like hubs and bottlenecks, determine network topology. These topology features of the cooccurrence networks point toward microbial community dynamics being resistant over time and thus could provide indicators for the state of ecosystem stability.

  • 107.
    Peura, Sari
    et al.
    Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
    Eiler, Alexander
    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.
    Nykanen, Hannu
    Univ Jyvaskyla, Dept Biol & Environm Sci, Jyvaskyla 40014, Finland.
    Tiirola, Marja
    Univ Jyvaskyla, Dept Biol & Environm Sci, Jyvaskyla 40014, Finland.
    Jones, Roger I.
    Univ Jyvaskyla, Dept Biol & Environm Sci, Jyvaskyla 40014, Finland.
    Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD12012In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 6, no 9, p. 1640-1652Article in journal (Refereed)
    Abstract [en]

    Lakes have a central role in the carbon cycle of the boreal landscape. These systems typically stratify in summer and their hypolimnetic microbial communities influence burial of biogenic organic matter in sediments. The composition of bacterial communities in these suboxic habitats was studied by pyrosequencing of 16S rRNA amplicons from five lakes with variable dissolved organic carbon (DOC) concentrations. Bacterioplankton communities in the hypolimnetic waters were clearly different from the surface layer with candidate division OD1, Chlorobi and Bacteroidetes as dominant community members. Several operational taxonomic units (OTUs) affiliated with candidate division OD1 were abundant and consistently present in the suboxic hypolimnion in these boreal lakes. The overall representation of this group was positively correlated with DOC and methane concentrations. Network analysis of time-series data revealed contrasting temporal patterns but suggested similar ecological roles among the abundant OTUs affiliated with candidate division OD1. Together, stable isotope data and taxonomic classification point to methane oxidation and autotrophic denitrification as important processes in the suboxic zone of boreal lakes. Our data revealed that while hypolimnetic bacterial communities are less dynamic, they appear to be more diverse than communities from the oxic surface layer. An appreciable proportion of the hypolimnetic bacteria belong to poorly described phyla.

  • 108.
    Peura, Sari
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sinclair, Lucas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 12102Article in journal (Refereed)
    Abstract [en]

    Thousands of net-heterotrophic and strongly stratifying lakes dominate the boreal landscape. Besides their central role as emitters of greenhouse gases, we have only recently begun to understand the microbial systems driving the metabolic processes and elemental cycles in these lakes. Using shotgun metagenomics, we show that the functional potential differs among lake types, with humic lakes being particularly enriched in carbon degradation genes. Most of the metabolic pathways exhibit oxygen- and temperature-dependent stratification over depth, coinciding with shifts in bacterial community composition, implying that stratification is a major factor controlling lake metabolism. In the bottom waters, rare and poorly characterized taxa, such as epsilon-Proteobacteria, but also autotrophs, such as photolithotrophic Chlorobia were abundant. These oxygen-depleted layers exhibited high genetic potential for mineralization, but also for fixation of carbon and nitrogen, and genetic markers for both methane production and oxidation were present. Our study provides a first glimpse of the genetic versatility of freshwater anoxic zones, and demonstrates the potential for complete turnover of carbon compounds within the water column.

  • 109. Polymanakou, Paraskevi
    et al.
    Stephanou, Euripides
    Tselepides, Anastasios
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Organic Matter Preservation and Microbial Community Accumulations in Deep-Hypersaline Anoxic Basins2007In: Geomicrobiology Journal, ISSN 0149-0451, E-ISSN 1521-0529, Vol. 24, no 1, p. 19-29Article in journal (Refereed)
    Abstract [en]

    The Eastern Mediterranean Sea hosts several deep hypersaline anoxic basins (DHABs) such as the Bannock, L'Atalante, Discovery, and Urania which, due to strong salinity gradients, have a limited exchange with the overlying seawater. In the present study, a series of environmental variables associated with the origin and quality of organic matter were thoroughly investigated in an attempt to understand the function of these unique ecosystems. The redox potential of sediments collected from the brines as well as from reference sites varied from -136 to 543 mV and salinity varied from 38 to 380 psu. Principal component analysis of chemical characteristics, including salinity, redox potential, organic carbon and nitrogen content, and C/N ratio grouped the sediments into two major clusters according to their redox state. Aliphatic hydrocarbon analysis revealed that the organic matter in the DHABs was predominantly of terrestrial origin but there was also evidence for petroleum inputs and for organic matter of phototrophic origin. Phospholipid linked fatty acids (PLFA) which were employed to assess the composition of microbial communities were found in greater abundance in stations situated inside the anoxic basins providing also strong evidence for the presence of methanotrophs and sulfate reducers. These results may represent an enhanced preservation of organic matter and an accumulation of microorganisms in these extreme environments. Heterogeneity in microbial community fatty acid profiles was documented between the anoxic sediments and the oxic and suboxic stations. However there were no significant correlations between PLFA and organic matter parameters. Redox conditions appear to influence microbial community composition, highlighting the role of the redox state as a regulator of organic matter preservation and microbial community accumulations in these ancient hypersaline anoxic lakes.

  • 110. Polymenakou, Paraskevi N
    et al.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Tselepides, Anastasios
    Stephanou, Euripides G
    Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries.2005In: Microbial Ecology, ISSN 0095-3628, Vol. 50, no 3, p. 447-462Article in journal (Refereed)
  • 111. Polymenakou, Paraskevi
    et al.
    Tselepides, Anastasios
    Stephanou, Euripides
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Carbon speciation and composition of natural microbial communities in polluted and pristine sediments of the Eastern Mediterranean Sea2006In: Marine Pollution Bulletin, ISSN 0025-326X, E-ISSN 1879-3363, Vol. 52, no 11, p. 1396-1405Article in journal (Refereed)
    Abstract [en]

    Sediment samples collected from polluted (Augusta Bay) and pristine regions of the Eastern Mediterranean Sea (South Ionian Sea, Thracian Sea) were analyzed for black carbon, aliphatic hydrocarbons and phospholipid ester-linked fatty acids (PLFA). The aim of the study was to investigate the anthropogenic and biogenic inputs into the Eastern Mediterranean Sea and to evaluate the effects of refractory organic matter (e.g. black carbon) and the level of hydrocarbon contamination on benthic microbial community composition. Black carbon, generally considered to be chemically and biologically inert, comprised a significant but highly variable fraction of the sedimentary carbon pool in the analyzed sediments with a ratio to total organic carbon ranging from 0.02 to 0.66. Principal component analysis of the chemical characteristics of the sediments (organic carbon content, black carbon, bioavailable organic carbon, chlorophyll a, phaeopigments, aliphatic hydrocarbons) revealed clustering of samples along a gradient from the most productive and contaminated region of Augusta Bay to the carbon-poor and pristine sediments of the Thracian Sea. PLFA analysis revealed that gram-negative bacteria and microeukaryotes were most abundant in Augusta Bay and in the most impacted station of the Thracian Sea. The high levels of branched and odd-chain fatty acids recorded for these stations is probably linked to the elevated amounts of hydrocarbons at these stations; e.g. microbial communities may have developed the ability to degrade either naturally occurring aliphatic hydrocarbons or hydrocarbons derived from oil contamination.

  • 112. Polymenakou,, P.N.
    et al.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Tselepides,, A.
    Stephanou, E.G.
    Links between Geographic Location, Environmental Factors, and Microbial Community Composition in Sediments of the Eastern Mediterranean Sea.2005In: Microbial Ecology, Vol. 49:, p. 367-378.Article in journal (Refereed)
    Abstract [en]

    (2005)

  • 113. Polz, M.
    et al.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bärlocher, F.
    Nikolcheva, L.
    Newell, S.Y.
    Kuehn, K.A.
    Community structure and interactions of aquatic microorganisms associated with decomposing litter2007In: Plant litter decomposition. Methods in Ecology, Blackwell Publishers , 2007Chapter in book (Other academic)
  • 114. Polz, Martin
    et al.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Acinas, Silvia
    Hunt, Dana
    A(r)Ray of Hope in Analysis of Function and Diversity of Microbial Communties2003In: Biological Bulletin, Vol. 204, p. 196-199Article in journal (Refereed)
  • 115.
    Pullin, M J
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Goldstone, J V
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Voelker, B M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Effects of sunlight and hydroxyl radical on dissolved organic matter: Bacterial growth efficiency and production of carboxylic acids and other substrates2004In: Limnol. Oceanogr., Vol. 49, no 6, p. 2011-2022Article in journal (Refereed)
    Abstract [en]

    This study examines the importance of several possible mechanisms causing sunlight-mediated changes in the amounts of bacterial utilization and biomass growth on dissolved organic matter (DOM) from allochthonous sources. Our results demonstrate that, while hydroxyl radical reactions with DOM can be an important process increasing its bioavailability, other photoreactions will cause most of the sunlight-induced increases unless hydroxyl production rates are high (>~ 7 mmol L-1 d-1). Low molecular weight carboxylic acids could not account for most of the observed sunlight and hydroxyl-induced increases in DOM bioavailability. Both sunlight and hydroxyl-mediated reactions significantly decreased the bacterial growth efficiency of DOM, indicating that photochemical reactions affect not only the fraction of the total DOM pool available to bacteria on ecologically relevant timescales but also the substrate quality and ultimately the environmental fate of this material. Extrapolation of these results to field conditions suggests that photochemical and biochemical mineralization could be an important sink of DOC and source of bioavailable carbon in the Plum Island estuary during the summer months.

  • 116.
    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.

  • 117.
    Richert, Inga
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Julie, Dinasquet
    Logares, Ramiro
    Riemann, Lasse
    Scofield, Douglas
    Wendeberg, Annelie
    Bertilsson, Stefan
    Spatial patterns of marine bacterioplankton along gradients of primary production in the Amundsen Sea Polynya, Southern OceanManuscript (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.

  • 118.
    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)
  • 119.
    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. 

  • 120.
    Ricão Canelhas, Monica
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Denfeld, Blaize A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Weyhenmeyer, Gesa A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bastviken, David
    Linköping University, Department of Thematic Studies, Environmental Change.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Methane oxidation at the water-ice interface of an ice-covered lake2016In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 61, no S1, p. S78-S90Article in journal (Refereed)
    Abstract [en]

    Lakes are important components of the global methane (CH4) cycle. In seasonally ice-covered lakes, CH4 transported by ebullition (bubbling) from anoxic sediments gets trapped at the water-ice interface. If not oxidized by methane-oxidizing bacteria (MOB), this can potentially lead to high episodic CH4 emissions at ice-melt. To understand the fate of CH4 trapped below ice, we measured depth-distributions of CH4 concentrations in the water column near bubbles trapped below ice in Lake Erken. We also performed a 21 d incubation experiment at low temperature (2.3 ± 0.2°C) to investigate the potential for CH4 oxidation. During most sampling occasions, we found steep CH4 concentration gradients just below the ice with a 13-fold decrease from the surface to a depth of 20 cm. In vitro incubations revealed that CH4oxidation can occur at low temperatures typical for the water-ice interface. CH4 oxidation was observed as a significant decrease in CH4 concentration, a significant increase in stable isotope 13C signature, and an increase in MOB during the incubation. Thus, CH4 accumulating in the top 20 cm of the water column, fed by diffusion from CH4 in trapped bubbles, may fuel significant CH4 oxidation. Since northern latitude lakes can be ice-covered for many months of the year and significant amounts of CH4 accumulate below the ice, the extent of CH4oxidation under these low temperature-conditions is important for understanding the potential CH4 emissions to the atmosphere during ice-melt.

  • 121.
    Ricão Canelhas, Monica
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eiler, Alexander
    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.
    Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?2016In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 92, no 2, article id UNSP fiw005Article in journal (Refereed)
    Abstract [en]

    A wide range of carbon compounds sustain bacterial activity and growth in freshwater ecosystems and the amount and quality of these substrates influence bacterial diversity and metabolic function. Biologically labile low-molecular-weight compounds, such as dissolved free amino acids, are particularly important substrates and can fuel as much as 20% of the total heterotrophic production. In this study, we show that extensive laboratory incubations with variable amino acids as substrates caused only minimal differences in bacterial growth rate, growth yield, quantitative amino acid usage, community composition and diversity. This was in marked contrast to incubations under dark or light regimes, where significant responses were observed in bacterial community composition and with higher diversity in the dark incubations. While a few individual taxa still responded to amendment with specific amino acids, our results suggest that compositional shifts in the specific supply of amino acids and possibly also other labile organic substrates have a minor impact on heterotrophic bacterioplankton communities, at least in nutrient rich lakes and compared to other prevailing environmental factors.

  • 122.
    Roger, Fabian
    et al.
    Univ Gothenburg, Dept Marine Sci, Box 461, SE-40530 Gothenburg, Sweden.
    Bertilsson, Stefan
    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.
    Osman, Omneya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Gamfeldt, Lars
    Univ Gothenburg, Dept Marine Sci, Box 461, SE-40530 Gothenburg, Sweden.
    Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality2016In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 97, no 10, p. 2716-2728Article in journal (Refereed)
    Abstract [en]

    Bacteria are essential for many ecosystem services but our understanding of factors controlling their functioning is incomplete. While biodiversity has been identified as an important driver of ecosystem processes in macrobiotic communities, we know much less about bacterial communities. Due to the high diversity of bacterial communities, high functional redundancy is commonly proposed as explanation for a lack of clear effects of diversity. The generality of this claim has, however, been questioned. We present the results of an outdoor dilution-to-extinction experiment with four lake bacterial communities. The consequences of changes in bacterial diversity in terms of effective number of species, phylogenetic diversity, and functional diversity were studied for (1) bacterial abundance, (2) temporal stability of abundance, (3) nitrogen concentration, and (4) multifunctionality. We observed a richness gradient ranging from 15 to 280 operational taxonomic units (OTUs). Individual relationships between diversity and functioning ranged from negative to positive depending on lake, diversity dimension, and aspect of functioning. Only between phylogenetic diversity and abundance did we find a statistically consistent positive relationship across lakes. A literature review of 24 peer-reviewed studies that used dilution-to-extinction to manipulate bacterial diversity corroborated our findings: about 25% found positive relationships. Combined, these results suggest that bacteria-driven community functioning is relatively resistant to reductions in diversity.

  • 123.
    Samad, Md Sainur
    et al.
    Univ Otago, Dept Microbiol & Immunol, Dunedin, New Zealand..
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Seasonal Variations in Abundance and Diversity of Bacterial Mathanotrophs in Five Temperate Lakes2017In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, article id 142Article in journal (Refereed)
    Abstract [en]

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

  • 124.
    Segura, Javier
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umea, Sweden.
    Nilsson, Mats B.
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umea, Sweden.
    Schleucher, Jürgen
    Umea Univ, Dept Med Biochem & Biophys, SE-90187 Umea, Sweden.
    Haei, Mahsa
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umea, Sweden.
    Sparrman, Tobias
    Umea Univ, Dept Chem, SE-90187 Umea, Sweden.
    Szekely, Anna 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.
    Öquist, Mats G.
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umea, Sweden.
    Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures2019In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 135, p. 438-448Article in journal (Refereed)
    Abstract [en]

    Boreal peatlands are key high-latitude ecosystem types and act as a carbon (C) sink storing an estimated 25% of the world's soil C. These environments are currently seeing the most substantial changing climate, especially during the winter. CO2 emissions during the winter can correspond to 80% of the growing season's net CO2 assimilation. Yet, our conceptual understanding of the controls on microbial metabolic activity in peat soils at temperatures <= 0 degrees C is poor. We used stable isotope probing of peat samples and tracked the fate of C-13-glucose using C-13-NMR. We show that microorganisms in frozen boreal peat soils utilize monomeric C-substrates to sustain both catabolic and anabolic metabolism at temperatures down to -5 degrees C. The C-13-substrate was transformed into C-13-CO2, different metabolites, and incorporated into membrane phospholipid fatty acids. The 16S rRNA-based community analyses revealed the activity at -3 degrees C changes the composition of the bacterial cornmunity over relevant timescales. Below 0 degrees C, small temperature changes have strong effects on process rates and small differences in winter soil temperature may affect C dynamics of northern peatlands. Understanding biological processes at low and below zero temperatures are central for the overall functioning of these systems representing one of the world's major soil C pools.

  • 125. Shade, Ashley
    et al.
    Carey, Cayelan C.
    Kara, Emily
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    McMahon, Katherine D.
    Smith, Matthew C.
    Can the black box be cracked?: The augmentation of microbial ecology by high-resolution, automated sensing technologies2009In: The ISME Journal, ISSN 1751-7362, Vol. 3, no 8, p. 881-888Article, review/survey (Refereed)
    Abstract [en]

    Automated sensing technologies, 'ASTs,' are tools that can monitor environmental or microbial-related variables at increasingly high temporal resolution. Microbial ecologists are poised to use AST data to couple microbial structure, function and associated environmental observations on temporal scales pertinent to microbial processes. In the context of aquatic microbiology, we discuss three applications of ASTs: windows on the microbial world, adaptive sampling and adaptive management. We challenge microbial ecologists to push AST potential in helping to reveal relationships between microbial structure and function.

  • 126.
    Sinclair, Lucas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ahmed Osman, Omneya
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eiler, Alexander
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 2, article id e0116955Article in journal (Refereed)
    Abstract [en]

    As new sequencing technologies become cheaper and older ones disappear, laboratories switch vendors and platforms. Validating the new setups is a crucial part of conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates as well as 70 samples from alkaline soda lakes, we evaluated the performance of the method with regards to estimates of alpha and beta diversity. Using different purification and DNA quantification procedures we always found up to 5-fold differences in the yield of sequences between individually barcodes samples. Using either a one-step or a two-step PCR preparation resulted in significantly different estimates in both alpha and beta diversity. Comparing with a previous method based on 454 pyrosequencing, we found that our Illumina protocol performed in a similar manner – with the exception for evenness estimates where correspondence between the methods was low. We further quantified the data loss at every processing step eventually accumulating to 50% of the raw reads. When evaluating different OTU clustering methods, we observed a stark contrast between the results of QIIME with default settings and the more recent UPARSE algorithm when it comes to the number of OTUs generated. Still, overall trends in alpha and beta diversity corresponded highly using both clustering methods. Our procedure performed well considering the precisions of alpha and beta diversity estimates, with insignificant effects of individual barcodes. Comparative analyses suggest that 454 and Illumina sequence data can be combined if the same PCR protocol and bioinformatic workflows are used for describing patterns in richness, beta-diversity and taxonomic composition.

  • 127.
    Swalethorp, Rasmus
    et al.
    University of California, Scripps Institution of Oceanography, San Diego, USA; Technical University of Denmark, National Institute of Aquatic Resources (DTU Aqua), Lyngby, Denmark; University of Gothenburg, Department of Marine Sciences, Gothenburg, Sweden.
    Dinasquet, Julie
    University of California, Scripps Institution of Oceanography, San Diego, USA; University of Copenhagen, Department of Biology, Marine Biological Section, Copenhagen, Denmark; Linnaeus University, Department of Natural Sciences, Växjö, Sweden.
    Logares, Ramiro
    CSIC, Institute of Marine Sciences (ICM), Barcelona, Spain.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kjellerup, Sanne
    Technical University of Denmark, National Institute of Aquatic Resources (DTU Aqua), Lyngby, Denmark; University of Gothenburg, Department of Marine Sciences, Gothenburg, Sweden.
    Krabberød, Anders K.
    University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Oslo, Norway.
    Moksnes, Per Olav
    University of Gothenburg, Department of Marine Sciences, Gothenburg, Sweden.
    Nielsen, Torkel G.
    Technical University of Denmark, National Institute of Aquatic Resources (DTU Aqua), Lyngby, Denmark.
    Riemann, Lasse
    University of Copenhagen, Department of Biology, Marine Biological Section, Copenhagen, Denmark.
    Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom2018In: Progress in Oceanography, ISSN 0079-6611, E-ISSN 1873-4472, Vol. 170, p. 1-10Article in journal (Refereed)
    Abstract [en]

    In Antarctica, summer is a time of extreme environmental shifts resulting in large coastal phytoplankton blooms fueling the food web. Despite the importance of the microbial loop in remineralizing biomass from primary production, studies of how microzooplankton communities respond to such blooms in the Southern Ocean are rather scarce. Microzooplankton (ciliate and dinoflagellate) communities were investigated combining microscopy and 18S rRNA sequencing analyses in the Amundsen Sea Polynya during an extensive summer bloom of Phaeocystis antarctica. The succession of microzooplankton was further assessed during a 15-day induced bloom microcosm experiment. Dinoflagellates accounted for up to 59 % of the microzooplankton biomass in situ with Gymnodinium spp., Protoperidium spp. and Gyrodinium spp. constituting 89 % of the dinoflagellate biomass. Strobilidium spp., Strombidium spp. and tintinids represented 90 % of the ciliate biomass. Gymnodinium, Gyrodinium and tintinnids are known grazers of Phaeocystis, suggesting that this prymnesiophyte selected for the key microzooplankton taxa. Availability of other potential prey, such as diatoms, heterotrophic nanoflagellates and bacteria, also correlated to changes in microzooplankton community structure. Overall, both heterotrophy and mixotrophy appeared to be key trophic strategies of the dominant microzooplankton observed, suggesting that they influence carbon flow in the microbial food web through top-down control on the phytoplankton community.

  • 128.
    Szabó, Katalin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Itor, Paul
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Importance of rare and abundant populations for the structure and functional potential of freshwater bacterial communities2007In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 47, no 1, p. 1-10Article in journal (Refereed)
    Abstract [en]

    Lakewater microcosms were inoculated with freshwater bacterioplankton, to determine how the elimination of less abundant populations affects the structure and basic functional features (growth) of microbial communities. The number of bacteria added to individual microcosms varied from <1 to 2.6 × 10 7 cells. Cultures amended with 11 mg C l_1 of either isolated humic substances or phenol, as well as unamended controls, were studied in parallel. All cultures inoculated with 260 cells or more showed vigorous growth, whereas an inoculum size of 2.6 to 26 cells resulted in growth in the control and humic enrichment cultures only. All cultures were harvested at steady state within 14 d of inoculation. The biomass yield was only slightly affected by the dilution factor. The catechol 2,3-dioxygenase gene (encoding the enzyme responsible for starting the meta pathway of aromatic compound degradation) was detected in all phenol and in the least diluted humic enrichment cultures. Dominant members of the emerging bacterial communities were detected by terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA genes. The number of detected community members was much higher in the humic treatment than in the phenol and control treatments. Based on the T-RFLP data, dilution of the inoculum significantly affected the resulting community composition (p < 0.0001). Rare, opportunistic populations were apparently able to exploit the humic enrichment cultures. Phenol appeared to be detrimental to the most abundant members of the original inoculum, but promoted the growth of relatively rare species carrying the catechol 2,3-dioxygenase gene. Thus, community functioning following an environmental perturbation can depend on the presence of rare as well as abundant species.

  • 129.
    Szabó, Katalin É.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Makk, Judit
    Kiss, Keve Tihamér
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Ács, Éva
    Tóth, Bence
    Kiss, Áron Keve
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Sequential colonization of river periphyton analysed by microscopy and molecular fingerprinting2008In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 53, no 7, p. 1359-1371Article in journal (Refereed)
    Abstract [en]

    1. An artificial glass substratum was incubated in the River Danube for a period of 28 days in order to detect the sequential colonization of microorganisms.

    2. Light and fluorescent microscopy showed that microalgae and the picoalgal fraction on the slides increased rapidly over the first 2 weeks of colonization. Diatoms were numerically the most abundant component of the periphyton and their species richness and diversity increased rapidly in the early phase of colonization whereas diversity subsequently increased moderately.

    3. Evenness of the diatom community was initially high, lower in the intermediate phase and again higher later on. Succession involving early, intermediate and late colonizer species was observed. Community composition during the first 5 days of colonization was very different from later stages whereas there were only minor changes subsequently.

    4. Molecular community analysis by means of terminal restriction fragment length polymorphism analysis of PCR amplified 16S rRNA and 18S rRNA genes pointed to even larger differences between the composition of samples obtained early and late in the period.

    5. The number of 18S rRNA and 16S rRNA terminal restriction fragments (T-RF-s) was variable over the colonization period and the fragment patterns of both the bacterial and eukaryotic portion of the microbial community were variable, with most T-RF-s unique to a single sample, suggesting a wide diversity and dynamic properties of periphytic organisms.

  • 130.
    Szabó-Taylor, Katalin É.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Kiss, Keve T.
    Logares, Ramiro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Acs, Eva
    Toth, Bence
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Composition and dynamics of microeukaryote communities in the River Danube2010In: Fottea, ISSN 1802-5439, Vol. 10, no 1, p. 99-113Article in journal (Refereed)
    Abstract [en]

    The diversity of microeukaryote communities inhabiting rivers is still poorly known. Here, we have analyzed the periphytic and planktonic microeukaryote communities present in one section of the River Danube by two different methods: 18S rRNA-based terminal restriction fragment length polymorphism with fragment sequencing and microscopical analysis of the phytoplankton and periphyton. Both data sets were then related to environmental variables. Molecular fingerprinting revealed diverse communities with fluctuating composition, with the majority of sequences affiliated to the groups Bacillariophyta, Synurophyceae and Chlorophyceae. This was in accordance with microscopical data. The total number of detected T-RFs during the study period was 145, with more than half of the T-RFs being restricted to either plankton or periphyton. This suggests that the likely different natural selection regimes experienced by microeukaryotes in these two environments may promote the presence of different lineages in each of them. Significant correlations were found between phytoplankton chlorophyll a content, phosphorus content, temperature, and the T RFLP pattern of the planktonic microeukaryotic community, suggesting that the former environmental factors are especially important in structuring the planktonic microeukaryote communities in the River Danube. These data, together with earlier studies suggest that molecular methods are an invaluable addition in pursuit of the better understanding of the diversity and fluctuation of freshwater microeukaryotic communities.

  • 131.
    Söderqvist, Karin
    et al.
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Ahmed Osman, Omneya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wolff, Cecilia
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vågsholm, Ivar
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Boqvist, Sofia
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Emerging microbiota during cold storage and temperature abuse of ready-to-eat salad​2017In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 7, no 1, article id 1328963Article in journal (Refereed)
    Abstract [en]

    Introduction: Ready-to-eat (RTE) leafy vegetables have a natural leaf microbiota that changes during different processing and handling steps from farm to fork. The objectives of this study were (i) to compare the microbiota of RTE baby spinach and mixed-ingredient salad before and after seven days of storage at 8°C or 15°C; (ii) to explore associations between bacterial communities and the foodborne pathogens Listeria monocytogenes, pathogenic Yersinia enterocolitica, and pathogen model organism Escherichia coli O157:H7 gfp+ when experimentally inoculated into the salads before storage; and (iii) to investigate if bacterial pathogens may be detected in the 16S rRNA amplicon dataset. Material and methods: The microbiota was studied by means of Illumina 16S rRNA amplicon sequencing. Subsets of samples were inoculated with low numbers (50-100 CFU g(-1)) of E. coli O157:H7 gfp+, pathogenic Y. enterocolitica or L. monocytogenes before storage. Results and discussion: The composition of bacterial communities changed during storage of RTE baby spinach and mixed-ingredient salad, with Pseudomonadales as the most abundant order across all samples. Although pathogens were present at high viable counts in some samples, they were only detected in the community-wide dataset in samples where they represented approximately 10% of total viable counts. Positive correlations were identified between viable counts of inoculated strains and the abundance of Lactobacillales, Enterobacteriales, and Bacillales, pointing to positive interactions or similar environmental driver variables that may make it feasible to use such bacterial lineages as indicators of microbial health hazards in leafy vegetables. The data from this study contribute to a better understanding of the bacteria present in RTE salads and may help when developing new types of biocontrol agents.​.

  • 132. Tenssay, Zeleke W.
    et al.
    Ashenafi, Mogessie
    Eiler, Alexander
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    ISOLATION AND CHARACTERIZATION OF BACILLUS THURINGIENSIS FROM SOILS IN CONTRASTING AGROECOLOGICAL ZONES OF ETHIOPIA2009In: SINET: An Ethiopian Journal of Science, ISSN 0379-2897, Vol. 32, no 2, p. 117-128Article in journal (Refereed)
  • 133.
    Tranvik, Lars
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Contrasting effects of solar UV radiation on dissolved organic sources for bacterial growth2001In: Ecology Letters, ISSN 0906-7590, Vol. 4, no 5, p. 458-463Article in journal (Refereed)
    Abstract [en]

    In most groups of organisms, the species richness decreases from the tropics to the poles. The mechanisms causing this latitudinal diversity gradient are still controversial. We present data from a comprehensive weighted meta-analysis on the strength of t

  • 134.
    Tranvik, Lars
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Olofsson, Hans
    Bertilsson, Stefan
    Photochemical effects on bacterial degradation of dissolved organic matter in lake water2000In: Microbial Biosystems: New Frontiers, 2000, p. 193-200Chapter in book (Refereed)
  • 135.
    Troell, Karin
    et al.
    Natl Vet Inst, Dept Microbiol, S-75007 Uppsala, Sweden..
    Hallstrom, Bjorn
    Publ Hlth Agcy Sweden, Dept Microbiol, Solna, Sweden..
    Divne, Anna-Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Alsmark, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy. Natl Vet Inst, Dept Microbiol, S-75007 Uppsala, Sweden..
    Arrighi, Romanico
    Publ Hlth Agcy Sweden, Dept Microbiol, Solna, Sweden..
    Huss, Mikael
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Beser, Jessica
    Publ Hlth Agcy Sweden, Dept Microbiol, Solna, Sweden..
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes2016In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 17, article id 471Article in journal (Refereed)
    Abstract [en]

    Background: Infectious disease involving multiple genetically distinct populations of pathogens is frequently concurrent, but difficult to detect or describe with current routine methodology. Cryptosporidium sp. is a widespread gastrointestinal protozoan of global significance in both animals and humans. It cannot be easily maintained in culture and infections of multiple strains have been reported. To explore the potential use of single cell genomics methodology for revealing genome-level variation in clinical samples from Cryptosporidium-infected hosts, we sorted individual oocysts for subsequent genome amplification and full-genome sequencing. Results: Cells were identified with fluorescent antibodies with an 80 % success rate for the entire single cell genomics workflow, demonstrating that the methodology can be applied directly to purified fecal samples. Ten amplified genomes from sorted single cells were selected for genome sequencing and compared both to the original population and a reference genome in order to evaluate the accuracy and performance of the method. Single cell genome coverage was on average 81 % even with a moderate sequencing effort and by combining the 10 single cell genomes, the full genome was accounted for. By a comparison to the original sample, biological variation could be distinguished and separated from noise introduced in the amplification. Conclusions: As a proof of principle, we have demonstrated the power of applying single cell genomics to dissect infectious disease caused by closely related parasite species or subtypes. The workflow can easily be expanded and adapted to target other protozoans, and potential applications include mapping genome-encoded traits, virulence, pathogenicity, host specificity and resistance at the level of cells as truly meaningful biological units.

  • 136. Turner, David R
    et al.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Fransson, Agneta
    Pakhomov, Evgeny
    The SWEDARP 1997/98 marine expedition: overview2004In: Deep Sea Research II,, Vol. 51, p. 2745-2756.Article in journal (Refereed)
    Abstract [en]

    The SWEDARP 1997/98 expedition aboard the S.A. Agulhas focused on three study areas along the 6°E meridian: 60°S, the location of the spring ice edge; 56°S, the location of the winter ice edge; and 50.5°S, the Antarctic Polar Front. This intensive study was preceded by a north–south transect through the area measuring surface water properties while under way. An extensive measurement programme included hydrography, tracers, nutrients, organic carbon, trace metals, bacteria, and primary and secondary producers (including production and grazing rates). Analysis of the results from the three study areas does not identify a single factor limiting primary production: water column stability and the optical regime, and probably iron supply contributed to the control of primary production. The study area acted as a sink for atmospheric CO2 at the time of measurement, while analysis of water column carbon inventories indicated a net CO2 source integrated over the spring season.

  • 137.
    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.

  • 138. Widenfalk, Anneli
    et al.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Sundh, Ingvar
    Goedkoop, Willem
    Effects of pesticides on community composition and activity of sediment microbes: responses at various levels of microbial community organization2008In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 152, no 3, p. 576-584Article in journal (Refereed)
    Abstract [en]

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology.

  • 139. Wu, Xiaofen
    et al.
    Holmfeldt, Karin
    Hubalek, Valerie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lundin, Daniel
    Åström, Mats
    Bertilsson, Stefan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Dopson, Mark
    Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 5, p. 1192-1203Article in journal (Refereed)
    Abstract [en]

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 mu m filter. Such cells of <0.22 mu m would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 mu m populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

  • 140.
    Wu, Xiaofen
    et al.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMIS, S-39182 Kalmar, Sweden..
    Pedersen, Karsten
    Microbial Analyt Sweden AB, Molnlycke, Sweden..
    Edlund, Johanna
    Microbial Analyt Sweden AB, Molnlycke, Sweden..
    Eriksson, Lena
    Microbial Analyt Sweden AB, Molnlycke, Sweden..
    Astrom, Mats
    Linnaeus Univ, Dept Biol & Environm Sci, Kalmar, Sweden..
    Andersson, Anders F.
    KTH Royal Inst Technol, Sch Biotechnol, Sci Life Lab, Stockholm, Sweden..
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMIS, S-39182 Kalmar, Sweden..
    Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters2017In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, article id 37Article in journal (Refereed)
    Abstract [en]

    Background: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. Results: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide-and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria. Conclusions: Populations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.

  • 141.
    Xu, Jingying
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Lulea Univ Technol, Dept Civil Environm & Nat gesources Engn, S-97187 Lulea, Sweden.
    Bravo, Andrea Garcia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lagerkvist, Anders
    Lulea Univ Technol, Dept Civil Environm & Nat gesources Engn, S-97187 Lulea, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Sjöblom, Rolf
    Lulea Univ Technol, Dept Civil Environm & Nat gesources Engn, S-97187 Lulea, Sweden.
    Kumpiene, Jurate
    Lulea Univ Technol, Dept Civil Environm & Nat gesources Engn, S-97187 Lulea, Sweden.
    Sources and remediation techniques for mercury contaminated soil2015In: Environment International, ISSN 0160-4120, E-ISSN 1873-6750, Vol. 74, p. 42-53Article, review/survey (Refereed)
    Abstract [en]

    Mercury (Hg) in soils has increased by a factor of 3 to 10 in recent times mainly due to combustion of fossil fuels combined with long-range atmospheric transport processes. Other sources as chlor-alkali plants, gold mining and cement production can also be significant, at least locally. This paper summarizes the natural and anthropogenic sources that have contributed to the increase of Hg concentration in soil and reviews major remediation techniques and their applications to control soil Hg contamination. The focus is on soil washing, stabilisation/solidification, thermal treatment and biological techniques; but also the factors that influence Hg mobilisation in soil and therefore are crucial for evaluating and optimizing remediation techniques are discussed. Further research on bioremediation is encouraged and future study should focus on the implementation of different remediation techniques under field conditions.

  • 142. Yager, Patricia L.
    et al.
    Sherrell, R. M.
    Stammerjohn, S. E.
    Ducklow, H. W.
    Schofield, O. M E.
    Ingall, E. D.
    Wilson, S. E.
    Lowry, K. E.
    Williams, C. M.
    Riemann, Lasse
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Alderkamp, A-C
    Dinasquet, J.
    Logares, R.
    Richert, Inga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Sipler, R.E.
    Melara, A.J.
    Mu, L.
    Newstead, R.G.
    Post, A.F.
    Swalethorp, R.
    van Dijken, G.L.
    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.

  • 143. Yager, Patricia L.
    et al.
    Sherrell, Robert M.
    Stammerjohn, Sharon E.
    Alderkamp, Anne-Carlijn
    Schofield, Oscar
    Abrahamsen, E. Povl
    Arrigo, Kevin R.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Garay, D. Lollie
    Guerrero, Raul
    Lowry, Kate E.
    Moksnes, Per-Olav
    Ndungu, Kuria
    Post, Anton F.
    Randall-Goodwin, Evan
    Riemann, Lasse
    Severmann, Silke
    Thatje, Sven
    van Dijken, Gert L.
    Wilson, Stephanie
    ASPIRE The Amundsen Sea Polynya International Research Expedition2012In: Oceanography, ISSN 1042-8275, Vol. 25, no 3, p. 40-53Article in journal (Refereed)
    Abstract [en]

    In search of an explanation for some of the greenest waters ever seen in coastal Antarctica and their possible link to some of the fastest melting glaciers and declining summer sea ice, the Amundsen Sea Polynya International Research Expedition (ASPIRE) challenged the capabilities of the US Antarctic Program and RVIB Nathaniel B. Palmer during Austral summer 2010-2011. We were well rewarded by both an extraordinary research platform and a truly remarkable oceanic setting. Here we provide further insights into the key questions that motivated our sampling approach during ASPIRE and present some preliminary findings, while highlighting the value of the Palmer for accomplishing complex, multifaceted oceanographic research in such a challenging environment.

  • 144.
    Zaremba-Niedzwiedzka, Katarzyna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Viklund, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Zhao, Weizhou
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ast, Jennifer
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Scandinavian Languages.
    Sczyrba, Alexander
    Woyke, Tanja
    McMahon, Katherina
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Stepanauskas, Ramunas
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade2013In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 14, no 11, article id R130Article in journal (Refereed)
    Abstract [en]

    Background: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt-and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. Results: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. Conclusions: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.

  • 145.
    Zink, Eren
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Cultural Anthropology and Ethnology.
    Elvander, Marianne
    Lindberg, Ann
    Järhult, Josef D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Målqvist, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, International Maternal and Child Health (IMCH), International Child Health and Nutrition.
    Boqvist, Sofia
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Magnusson, Ulf
    Chandler, Rebecca
    Hur ska vi klara de nya epidemierna?2017Other (Other (popular science, discussion, etc.))
  • 146. Öztürk, Murat
    et al.
    Croot, Peter L.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Abrahamsson, Katarina
    Karlsone,, Bengt
    David, Roland
    Fransson, Agneta
    Sakshaug, Egil
    Iron enrichment and photoreduction of iron under UV and PAR in the presence of hydroxycarboxylic acid: implications for phytoplankton growth in the Southern Ocean2004In: Deep Sea Research Part II:: Topical Studies in Oceanography, Vol. 51, p. 2841-2856Article in journal (Refereed)
    Abstract [en]

    Iron(III) photoreduction and the responses of phytoplankton under ultraviolet (UV) and photosynthetically available radiation (PAR) were investigated with the presence of hydroxycarboxylic acid (glucaric acid (GA), a model compound for organic acids excreted by phytoplankton). The incubation experiments were carried out on board using seawater samples collected in the location of the winter ice edge (WIE) and the spring ice edge (SIE) of the Southern Ocean. In this paper, we focus on the results of experiment in WIE. Throughout the experiments, dissolved Fe(II), major nutrients and in vivo fluorescence were monitored regularly. In addition, Chl-a, POC/PON, cell densities of phytoplankton and bacteria, bacterial production, organic peroxide, hydrogen peroxide and total CO2 were measured.

    The results from the WIE show that iron enrichment had a substantial effect on phytoplankton growth rate. Fe(III) addition in the presence of GA (FeGA) gave higher Fe(II) concentration and higher growth rate of phytoplankton than those in controls. Our results suggest that hydroxycarboxylic acid had a significant chemical and biological impact. The presence of GA influenced iron photochemistry and iron availability to phytoplankton. Phytoplankton growth responses to iron enrichments in incubations under UV and PAR were completely dissimilar. It seems that FeGA addition prominently changes the harmful effect of UV on the phytoplankton population. This study provides preliminary information on how the photoreduction of iron(III) and the phytoplankton growth are affected by iron enrichment in the presence of hydroxycarboxylic acid.

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