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  • 1.
    Abbott, Benjamin W.
    et al.
    Univ Rennes 1, OSUR, CNRS, UMR ECOBIO 6553, F-35014 Rennes, France.;Univ Alaska Fairbanks, Inst Arctic Biol, Fairbanks, AK USA.;Univ Alaska Fairbanks, Dept Biology& Wildlife, Fairbanks, AK USA..
    Jones, Jeremy B.
    Univ Alaska Fairbanks, Inst Arctic Biol, Fairbanks, AK USA.;Univ Alaska Fairbanks, Dept Biology& Wildlife, Fairbanks, AK USA..
    Schuur, Edward A. G.
    No Arizona Univ, Ctr Ecosyst Sci & Soc, Flagstaff, AZ 86011 USA..
    Chapin, F. Stuart, III
    Univ Alaska Fairbanks, Inst Arctic Biol, Fairbanks, AK USA.;Univ Alaska Fairbanks, Dept Biology& Wildlife, Fairbanks, AK USA..
    Bowden, William B.
    Univ Vermont, Rubenstein Sch Environm & Nat Resources, Burlington, VT 05405 USA..
    Bret-Harte, M. Syndonia
    Univ Alaska Fairbanks, Inst Arctic Biol, Fairbanks, AK USA.;Univ Alaska Fairbanks, Dept Biology& Wildlife, Fairbanks, AK USA..
    Epstein, Howard E.
    Univ Virginia, Dept Environm Sci, Charlottesville, VA 22903 USA..
    Flannigan, Michael D.
    Univ Alberta, Dept Renewable Resources, Edmonton, AB T6G 2M7, Canada..
    Harms, Tamara K.
    Univ Alaska Fairbanks, Inst Arctic Biol, Fairbanks, AK USA.;Univ Alaska Fairbanks, Dept Biology& Wildlife, Fairbanks, AK USA..
    Hollingsworth, Teresa N.
    Univ Alaska Fairbanks, PNW Res Stn, USDA Forest Serv, Fairbanks, AK USA..
    Mack, Michelle C.
    No Arizona Univ, Ctr Ecosyst Sci & Soc, Flagstaff, AZ 86011 USA..
    McGuire, A. David
    Univ Alaska Fairbanks, Alaska Cooperat Fish & Wildlife Res Unit, US Geol Survey, Anchorage, AK USA..
    Natali, Susan M.
    Woods Hole Res Ctr, Woods Hole, MA USA..
    Rocha, Adrian V.
    Univ Notre Dame, Dept Biol Sci, Notre Dame, IN 46556 USA.;Univ Notre Dame, Environm Change Initiat, Notre Dame, IN 46556 USA..
    Tank, Suzanne E.
    Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2M7, Canada..
    Turetsky, Merritt R.
    Univ Guelph, Dept Integrat Biol, Guelph, ON N1G 2W1, Canada..
    Vonk, Jorien E.
    Vrije Univ Amsterdam, Dept Earth Sci, Amsterdam, Netherlands..
    Wickland, Kimberly P.
    US Geol Survey, Natl Res Program, Boulder, CO USA..
    Aiken, George R.
    US Geol Survey, Natl Res Program, Boulder, CO USA..
    Alexander, Heather D.
    Mississippi State Univ, Forest & Wildlife Res Ctr, Mississippi State, MS 39762 USA..
    Amon, Rainer M. W.
    Texas A&M Univ, Galveston, TX USA..
    Benscoter, Brian W.
    Florida Atlantic Univ, Boca Raton, FL 33431 USA..
    Bergeron, Yves
    Univ Quebec Abitibi Temiscamingue, Forest Res Inst, Rouyn Noranda, PQ, Canada..
    Bishop, Kevin
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. wedish Univ Agr Sci, Dept Aquat Sci & Assessment, S-90183 Umea, Sweden..
    Blarquez, Olivier
    Univ Montreal, Dept Geog, Montreal, PQ H3C 3J7, Canada..
    Bond-Lamberty, Ben
    Pacific NW Natl Lab, Richland, WA 99352 USA..
    Breen, Amy L.
    Univ Alaska Fairbanks, Int Arctic Res Ctr, Scenarios Network Alaska & Arctic Planning, Fairbanks, AK USA..
    Buffam, Ishi
    Univ Cincinnati, Cincinnati, OH 45221 USA..
    Cai, Yihua
    Xiamen Univ, State Key Lab Marine Environm Sci, Xiamen, Peoples R China..
    Carcaillet, Christopher
    Ecole Prat Hautes Etud, UMR5023, CNRS Lyon 1, Lyon, France..
    Carey, Sean K.
    McMaster Univ, Hamilton, ON L8S 4L8, Canada..
    Chen, Jing M.
    Univ Toronto, Toronto, ON M5S 1A1, Canada..
    Chen, Han Y. H.
    Lakehead Univ, Fac Nat Resources Management, Thunder Bay, ON P7B 5E1, Canada..
    Christensen, Torben R.
    Lund Univ, Arctic Res Ctr, S-22100 Lund, Sweden.;Aarhus Univ, DK-8000 Aarhus C, Denmark..
    Cooper, Lee W.
    Univ Maryland, Ctr Environm Sci, Bethesda, MD USA..
    Cornelissen, J. Hans C.
    Vrije Univ Amsterdam, Syst Ecol, Amsterdam, Netherlands..
    de Groot, William J.
    Nat Resources Canada, Canadian Forest Serv, Toronto, ON, Canada..
    DeLuca, Thomas H.
    Univ Washington, Sch Environm & Forest Sci, Seattle, WA 98195 USA..
    Dorrepaal, Ellen
    Umea Univ, Dept Ecol & Environm Sci, Climate Impacts Res Ctr, S-90187 Umea, Sweden..
    Fetcher, Ned
    Wilkes Univ, Inst Environm Sci & Sustainabil, Wilkes Barre, PA 18766 USA..
    Finlay, Jacques C.
    Univ Minnesota, Dept Ecol Evolut & Behav, Minneapolis, MN 55455 USA..
    Forbes, Bruce C.
    Univ Lapland, Arctic Ctr, Rovaniemi, Finland..
    French, Nancy H. F.
    Michigan Technol Univ, Michigan Tech Res Inst, Houghton, MI 49931 USA..
    Gauthier, Sylvie
    Nat Resources Canada, Canadian Forest Serv, Laurentian Forestry Ctr, Toronto, ON, Canada..
    Girardin, Martin P.
    Nat Resources Canada, Canadian Forest Serv, Laurentian Forestry Ctr, Toronto, ON, Canada..
    Goetz, Scott J.
    Woods Hole Res Ctr, Woods Hole, MA USA..
    Goldammer, Johann G.
    Max Planck Inst Chem, Global Fire Monitoring Ctr, Berlin, Germany..
    Gough, Laura
    Towson Univ, Dept Biol Sci, Towson, MD USA..
    Grogan, Paul
    Queens Univ, Dept Biol, Kingston, ON K7L 3N6, Canada..
    Guo, Laodong
    Univ Wisconsin Milwaukee, Sch Freshwater Sci, Milwaukee, WI USA..
    Higuera, Philip E.
    Univ Montana, Dept Ecosyst & Conservat Sci, Missoula, MT 59812 USA..
    Hinzman, Larry
    Univ Alaska Fairbanks, Fairbanks, AK USA..
    Hu, Feng Sheng
    Univ Illinois, Dept Plant Biol, Chicago, IL 60680 USA.;Univ Illinois, Dept Geol, Chicago, IL 60680 USA..
    Hugelius, Gustaf
    Stockholm Univ, Dept Phys Geog, Stockholm, Sweden..
    Jafarov, Elchin E.
    Univ Colorado Boulder, Inst Arctic & Alpine Res, Boulder, CO USA..
    Jandt, Randi
    Univ Alaska Fairbanks, Alaska Fire Sci Consortium, Fairbanks, AK USA..
    Johnstone, Jill F.
    Univ Saskatchewan, Dept Biol, Saskatoon, SK S7N 0W0, Canada..
    Karlsson, Jan
    Umea Univ, Dept Ecol & Environm Sci, Climate Impacts Res Ctr, S-90187 Umea, Sweden..
    Kasischke, Eric S.
    Univ Maryland, Dept Geog Sci, Bethesda, MD USA..
    Kattner, Gerhard
    Helmholtz Ctr Polar & Marine Res, Alfred Wegener Inst, Berlin, Germany..
    Kelly, Ryan
    Neptune & Co Inc, North Wales, PA USA..
    Keuper, Frida
    Umea Univ, Dept Ecol & Environm Sci, Climate Impacts Res Ctr, S-90187 Umea, Sweden.;INRA, AgroImpact UPR1158, New York, NY USA..
    Kling, George W.
    Univ Michigan, Ann Arbor, MI 48109 USA..
    Kortelainen, Pirkko
    Finnish Environm Inst, Helsinki, Finland..
    Kouki, Jari
    Univ Eastern Finland, Sch Forest Sci, Joensuu, Finland..
    Kuhry, Peter
    Stockholm Univ, Dept Phys Geog, Stockholm, Sweden..
    Laudon, Hjalmar
    Swedish Univ Agr Sci, Dept Forest Ecol & Management, S-90183 Umea, Sweden..
    Laurion, Isabelle
    Inst Natl Rech Sci, Ctr Eau Terre Environm, Toronto, ON, Canada..
    Macdonald, Robie W.
    Inst Ocean Sci, Dept Fisheries & Oceans, Toronto, ON, Canada..
    Mann, Paul J.
    Northumbria Univ, Dept Geog, Newcastle Upon Tyne NE1 8ST, Tyne & Wear, England..
    Martikainen, Pertti J.
    Univ Eastern Finland, Dept Environm & Biol Sci, Joensuu, Finland..
    McClelland, James W.
    Univ Texas Austin, Inst Marine Sci, Austin, TX 78712 USA..
    Molau, Ulf
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden..
    Oberbauer, Steven F.
    Florida Int Univ, Dept Biol Sci, Miami, FL 33199 USA..
    Olefeldt, David
    Univ Alberta, Dept Revewable Resources, Edmonton, AB T6G 2M7, Canada..
    Pare, David
    Nat Resources Canada, Canadian Forest Serv, Laurentian Forestry Ctr, Toronto, ON, Canada..
    Parisien, Marc-Andre
    Nat Resources Canada, Canadian Forest Serv, No Forestry Ctr, Toronto, ON, Canada..
    Payette, Serge
    Univ Laval, Ctr Etud Nord, Quebec City, PQ G1K 7P4, Canada..
    Peng, Changhui
    Univ Quebec, Ctr CEF, ESCER, Montreal, PQ H3C 3P8, Canada.;Northwest A&F Univ, Coll Forestry, State Key Lab Soil Eros & Dryland Farming Loess P, Xian, Peoples R China..
    Pokrovsky, Oleg S.
    CNRS, Georesources & Environm, Toulouse, France.;Tomsk State Univ, BIO GEO CLIM Lab, Tomsk, Russia..
    Rastetter, Edward B.
    Marine Biol Lab, Ctr Ecosyst, Woods Hole, MA 02543 USA..
    Raymond, Peter A.
    Yale Univ, Sch Forestry & Environm Studies, New Haven, CT 06520 USA..
    Raynolds, Martha K.
    Univ Alaska Fairbanks, Inst Arctic Biol, Fairbanks, AK USA..
    Rein, Guillermo
    Univ London Imperial Coll Sci Technol & Med, Dept Mech Engn, London SW7 2AZ, England..
    Reynolds, James F.
    Lanzhou Univ, Sch Life Sci, Lanzhou 730000, Peoples R China.;Duke Univ, Nicholas Sch Environm, Durham, NC 27706 USA..
    Robards, Martin
    Arctic Beringia Program, Wildlife Conservat Soc, New York, NY USA..
    Rogers, Brendan M.
    Woods Hole Res Ctr, Woods Hole, MA USA..
    Schaedel, Christina
    No Arizona Univ, Ctr Ecosyst Sci & Soc, Flagstaff, AZ 86011 USA..
    Schaefer, Kevin
    Univ Colorado Boulder, Cooperat Inst Res Environm Sci, Natl Snow & Ice Data Ctr, Boulder, CO USA..
    Schmidt, Inger K.
    Univ Copenhagen, Dept Geosci & Nat Resource Management, DK-1168 Copenhagen, Denmark..
    Shvidenko, Anatoly
    Int Inst Appl Syst Anal, A-2361 Laxenburg, Austria.;Sukachev Inst Forest, Moscow, Russia..
    Sky, Jasper
    Cambridge Ctr Climate Change Res, Cambridge, England..
    Spencer, Robert G. M.
    Florida State Univ, Dept Earth Ocean & Atmospher Sci, Tallahassee, FL 32306 USA..
    Starr, Gregory
    Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA..
    Striegl, Robert G.
    US Geol Survey, Natl Res Program, Boulder, CO USA..
    Teisserenc, Roman
    Univ Toulouse, CNRS, INPT, ECOLAB,UPS, Toulouse, France..
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Virtanen, Tarmo
    Univ Helsinki, Dept Environm Sci, FIN-00014 Helsinki, Finland..
    Welker, Jeffrey M.
    Univ Alaska Anchorage, Anchorage, AK USA..
    Zimov, Sergei
    Russian Acad Sci, Northeast Sci Stn, Moscow 117901, Russia..
    Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire: an expert assessment2016In: Environmental Research Letters, ISSN 1748-9326, E-ISSN 1748-9326, Vol. 11, no 3, article id 034014Article in journal (Refereed)
    Abstract [en]

    As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export. Models predict that some portion of this release will be offset by increased production of Arctic and boreal biomass; however, the lack of robust estimates of net carbon balance increases the risk of further overshooting international emissions targets. Precise empirical or model-based assessments of the critical factors driving carbon balance are unlikely in the near future, so to address this gap, we present estimates from 98 permafrost-region experts of the response of biomass, wildfire, and hydrologic carbon flux to climate change. Results suggest that contrary to model projections, total permafrost-region biomass could decrease due to water stress and disturbance, factors that are not adequately incorporated in current models. Assessments indicate that end-of-the-century organic carbon release from Arctic rivers and collapsing coastlines could increase by 75% while carbon loss via burning could increase four-fold. Experts identified water balance, shifts in vegetation community, and permafrost degradation as the key sources of uncertainty in predicting future system response. In combination with previous findings, results suggest the permafrost region will become a carbon source to the atmosphere by 2100 regardless of warming scenario but that 65%-85% of permafrost carbon release can still be avoided if human emissions are actively reduced.

  • 2.
    Ahlgren, Joakim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    De Brabandere, Heidi
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Reitzel, Kasper
    Rydin, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Waldebäck, Monica
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Sediment Phosphorus Extractants for Phosphorus-31 Nuclear Magnetic Resonance Analysis: A Quantitative Evaluation2007In: Journal of Environmental Quality, ISSN 0047-2425, E-ISSN 1537-2537, Vol. 36, no 3, p. 892-898Article in journal (Refereed)
    Abstract [en]

    The influence of pre-extractant, extractant, and post-extractant on total extracted amounts of P and organic P compound groups measured with 31P nuclear magnetic resonance (31P-NMR) in lacustrine sediment was examined. The main extractants investigated were sodium hydroxide (NaOH) and sodium hydroxide ethylenediaminetetraacetic acid (NaOH-EDTA) with bicarbonate buffered dithionite (BD) or EDTA as pre-extractants. Post extractions were conducted using either NaOH or NaOH-EDTA, depending on the main extractant. Results showed that the most efficient combination of extractants for total P yield was NaOH with EDTA as pre-extractant, yielding almost 50% more than the second best procedure. The P compound groups varying the most between the different extraction procedures were polyphosphates and pyrophosphates. NaOH with BD as pre-extractant was the most efficient combination for these compound groups.

  • 3.
    Ahlgren, Joakim
    et al.
    Institute of Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
    Reitzel, Kasper
    Institute of Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
    De Brabandere, Heidi
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Analytical Chemistry.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry I.
    Rydin, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Release of Organic P Forms from Lake Sediments2011In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 45, no 2, p. 565-572Article in journal (Refereed)
    Abstract [en]

    The effects of different physical and chemical conditions on the decomposition and release of organic and inorganic P compound groups from the sediment of Lake Erken were investigated in a series of laboratory experiments. Conditions investigated were temperature, oxygen level, and the effects of additions of carbon substrate (glucose) and poison (formalin). The effects on the P compound groups were determined by measurements with 31P NMR before and after the experiments, as well as analysis of P in effluent water throughout the experiment. Phosphate analysis of the effluent water showed that oxygen level was the most influential in terms of release rates, with the sediments under anoxic conditions generally releasing more phosphate than the other treatments. 31P NMR showed that the various treatments did influence the P compound group composition of the sediment. In particular, the addition of glucose led to a decrease in orthophosphate and polyphosphate while the addition of formalin led to a decrease in phosphorus lipids, DNAphosphate and polyphosphate. Oxic conditions resulted in an increase in polyphosphates, and anoxic conditions in a decrease in these. Temperature did not seem to affect the composition significantly.

  • 4.
    Ahmed Osman, Omneya
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Beier, Sara
    Leibniz Inst Balt Sea Res, Warnemunde, Germany..
    Grabherr, Manfred
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Interactions of Freshwater Cyanobacteria with Bacterial Antagonists2017In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 83, no 7, article id UNSP e02634Article in journal (Refereed)
    Abstract [en]

    Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera Pseudomonas, Stenotrophomonas, Acinetobacter, and Delftia from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1: 1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. L, D-Transpeptidase was the only significantly upregulated lytic gene in Stenotrophomonas rhizophila EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes. IMPORTANCE Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms.

  • 5. Almeida, Rafael M.
    et al.
    Barros, Nathan
    Cole, Jonathan J.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Roland, Fabio
    Correspondence: Emissions from Amazonian dams2013In: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 3, no 12, p. 1005-1005Article in journal (Other academic)
  • 6. Almeida, Rafael M.
    et al.
    Barros, Nathan
    Cole, Jonathan J.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Roland, Fábio
    Emissions from Amazonian dams2013In: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 3, no 12, p. 1005-1005Article in journal (Refereed)
  • 7.
    Almeida, Rafael M.
    et al.
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Nobrega, Gabriel N.
    Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Ciencia Solo, Piracicaba, Brazil..
    Junger, Pedro C.
    Univ Fed Rio de Janeiro, Lab Limnol, Rio De Janeiro, Brazil..
    Figueiredo, Aline V.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Andrade, Anizio S.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    de Moura, Caroline G. B.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Tonetta, Denise
    Univ Fed Santa Catarina, Lab Freshwater Ecol, Florianopolis, SC, Brazil..
    Oliveira, Ernandes S., Jr.
    Radboud Univ Nijmegen, Dept Aquat Ecol & Environm Biol, Inst Water & Wetland Res, NL-6525 ED Nijmegen, Netherlands..
    Araujo, Fabiana
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Rust, Felipe
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Pineiro-Guerra, Juan M.
    Univ Republica, Dept Ecol Teor & Aplicada, Ctr Univ Reg Este, Montevideo, Uruguay.;Univ Republica, Fac Ciencias, Montevideo, Uruguay..
    Mendonca, Jurandir R., Jr.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Medeiros, Leonardo R.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Pinheiro, Lorena
    Univ Fed Estado Rio de Janeiro, Dept Ciencias Nat, Rio De Janeiro, Brazil..
    Miranda, Marcela
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Costa, Mariana R. A.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Melo, Michaela L.
    Univ Fed Sao Carlos, Lab Microbial Proc & Biodivers, BR-13560 Sao Carlos, SP, Brazil..
    Nobre, Regina L. G.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Benevides, Thiago
    Univ Fed Rio de Janeiro, Lab Limnol, Rio De Janeiro, Brazil..
    Roland, Fabio
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    de Klein, Jeroen
    Wageningen Univ, Aquat Ecol & Environm Sci, NL-6700 AP Wageningen, Netherlands..
    Barros, Nathan O.
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Mendonca, Raquel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil.
    Becker, Vanessa
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Huszar, Veral. M.
    Univ Fed Rio de Janeiro, Museu Nacl, Lab Ficol, Rio De Janeiro, Brazil..
    Kosten, Sarian
    Radboud Univ Nijmegen, Dept Aquat Ecol & Environm Biol, Inst Water & Wetland Res, NL-6525 ED Nijmegen, Netherlands..
    High Primary Production Contrasts with Intense Carbon Emission in a Eutrophic Tropical Reservoir2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 717Article in journal (Refereed)
    Abstract [en]

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

  • 8. Almeida, Rafael M.
    et al.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Huszar, Vera L. M.
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Mendonca, Raquel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Barros, Nathan
    Boemer, Gina
    Arantes, Joao Durval, Jr.
    Roland, Fabio
    Phosphorus transport by the largest Amazon tributary (Madeira River, Brazil) and its sensitivity to precipitation and damming2015In: INLAND WATERS, ISSN 2044-2041, E-ISSN 2044-205X, Vol. 5, no 3, p. 275-282Article in journal (Refereed)
    Abstract [en]

    Originating in the Bolivian and Peruvian Andes, the Madeira River is the largest tributary of the Amazon River in terms of discharge. Andean rivers transport large quantities of nutrient-rich suspended sediments and are the main source of phosphorus (P) to the Amazon basin. Here, we show the seasonal variability in concentrations and loads of different P forms (total, particulate, dissolved, and soluble reactive P) in the Madeira River through 8 field campaigns between 2009 and 2011. At our sampling reach in Porto Velho, Brazil, the Madeira River transports similar to 177-247 Gg yr(-1) of P, mostly linked to particles (similar to 85%). Concentrations and loads of all P forms have a maximum at rising waters and a minimum at low waters. Total P concentrations were substantially higher at a given discharge at rising water than at a similar discharge at falling water. The peak of P concentrations matched the peak of rainfall in the upper basin, suggesting an influence of precipitation-driven erosion. Projected precipitation increase in the eastern slopes of the Andes could enhance sediment yield and hence the P transport in the Madeira River. Because most of the P is particulate, however, we hypothesize that the planned proliferation of hydropower dams in the Madeira basin has the potential to reduce P loads substantially, possibly counteracting any precipitation-related increases. In the long term, this could be detrimental to highly productive downstream floodplain forests that are seasonally fertilized with P-rich deposits.

  • 9.
    Alonso-Saez, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Unanue, Marian
    Latatu, Ainhoa
    Azua, Inigo
    Ayo, Begona
    Artolozaga, Itxaso
    Iriberri, Juan
    Changes in marine prokaryotic community induced by varying types of dissolved organic matter and subsequent grazing pressure2009In: Journal of Plankton Research, ISSN 0142-7873, E-ISSN 1464-3774, Vol. 31, no 11, p. 1373-1383Article in journal (Refereed)
    Abstract [en]

    We analysed changes in the abundance, biomass, activity and composition of coastal marine prokaryotic communities after the addition of organic substrates, such as glucose, leucine and yeast extract, and the effect of grazing pressure exerted by nanoflagellates. The addition of a carbon source (i.e. glucose) promoted the growth of Gammaproteobacteria, while a combined source of C and N (i.e. leucine) favoured the development of Alphaproteobacteria. The addition of yeast extract, a complex substrate rich in N and growth factors, promoted the proliferation of Alphaproteobacteria and Gammaproteobacteria. Grazing pressure exerted by nanoflagellates produced marked differences on the size structure of the prokaryotic biomass. A pronounced tendency to filamentation and aggregation was observed in the glucose treatment, while in the case of yeast extract, small and mainly freely dispersed prokaryotes were maintained throughout the incubations. Thus, the final community in the yeast extract treatment showed a high percentage of edible biomass, while an important fraction of potentially grazing-resistant prokaryotes (more than 50% of total prokaryotic biomass) was detected in the microcosms enriched with glucose. These results suggest a marked effect of DOM sources on the development of grazing-resistant prokaryotes.

  • 10.
    Alonso-Saez, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Vazquez-Dominguez, Evaristo
    Cardelus, Clara
    Pinhassi, Jarone
    Sala, M. Montserrat
    Lekunberri, Itziar
    Balague, Vanessa
    Vila-Costa, Maria
    Unrein, Fernando
    Massana, Ramon
    Simo, Rafel
    Gasol, Josep M.
    Factors controlling the year-round variability in carbon flux through bacteria in a coastal marine system2008In: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 11, no 3, p. 397-409Article in journal (Refereed)
    Abstract [en]

    Data from several years of monthly samplings are combined with a 1-year detailed study of carbon flux through bacteria at a NW Mediterranean coastal site to delineate the bacterial role in carbon use and to assess whether environmental factors or bacterial assemblage composition affected the in situ rates of bacterial carbon processing. Leucine (Leu) uptake rates [as an estimate of bacterial heterotrophic production (BHP)] showed high interannual variability but, on average, lower values were found in winter (around 50 pM Leu(-1) h(-1)) as compared to summer (around 150 pM Leu(-1) h(-1)). Leu-to-carbon conversion factors ranged from 0.9 to 3.6 kgC mol Leu(-1), with generally higher values in winter. Leu uptake was only weakly correlated to temperature, and over a full-year cycle (in 2003), Leu uptake peaked concomitantly with winter chlorophyll a (Chl a) maxima, and in periods of high ectoenzyme activities in spring and summer. This suggests that both low molecular weight dissolved organic matter (DOM) released by phytoplankton, and high molecular weight DOM in periods of low Chl a, can enhance BHP. Bacterial respiration (BR, range 7-48 mu g C l(-1) d(-1)) was not correlated to BHP or temperature, but was significantly correlated to DOC concentration. Total bacterial carbon demand (BHP plus BR) was only met by dissolved organic carbon produced by phytoplankton during the winter period. We measured bacterial growth efficiencies by the short-term and the long-term methods and they ranged from 3 to 42%, increasing during the phytoplankton blooms in winter (during the Chl a peaks), and in spring. Changes in bacterioplankton assemblage structure (as depicted by denaturing gradient gel electrophoresis fingerprinting) were not coupled to changes in ecosystem functioning, at least in bacterial carbon use.

  • 11.
    Alonso-Saez, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zeder, Michael
    Harding, Tommy
    Pernthaler, Jakob
    Lovejoy, Connie
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pedros-Alio, Carlos
    Winter bloom of a rare betaproteobacteriurn in the Arctic Ocean2014In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 5, p. 425-Article in journal (Refereed)
    Abstract [en]

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

  • 12.
    Alonso-Sáez, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Andersson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Heinrich, Friederike
    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.
    High archaeal diversity in Antarctic circumpolar deep waters2011In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 3, no 6, p. 689-697Article in journal (Refereed)
    Abstract [en]

    Archaea are abundant in polar oceans but important ecological aspects of this group remain enigmatic, such as patterns of diversity and biogeography. Here, we provide the first high-throughput sequencing population study of Antarctic archaea based on 198 bp fragments of the 16S rRNA gene, targeting different water masses across the Amundsen and Ross Seas. Our results suggest that archaeal community composition is strongly shaped by hydrography and significantly influenced by environmental parameters. Archaeal communities from cold continental shelf waters (SW) of the Ross Sea were similar over depth with a single thaumarchaeal phylotype dominating Antarctic surface waters (AASW) and deeper SW (contributing up to 80% of reads). However, this phylotype contributed less than 8% of reads in circumpolar deep waters (CDW). A related thaumarchaeon (98% identity) was almost absent in AASW, but contributed up to 30% of reads in CDW, suggesting ecological differentiation of closely related phylotypes. Significantly higher archaeal richness and evenness were observed in CDW, with Shannon indices (c. 2.5) twice as high as for AASW, and high contributions of Group II Euryarchaeota. Based on these results, we suggest that CDW is a hotspot of archaeal diversity and may play an important role in the dispersal of archaeal phylotypes to other oceanic water masses.

  • 13.
    Alonso-Sáez, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Waller, A. S.
    Mende, D. R.
    Bakker, K.
    Farnelid, H.
    Yager, P. L.
    Lovejoy, C.
    Tremblay, J. -E
    Potvin, M.
    Heinrich, Friederike
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Estrada, M.
    Riemann, L.
    Bork, P.
    Pedrós-Alió, C.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Role for urea in nitrification by polar marine Archaea2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 44, p. 17989-17994Article in journal (Refereed)
    Abstract [en]

    Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.

  • 14.
    Andersson, Anders F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Pelve, Erik A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lindeberg, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lundgren, Magnus
    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 Cell and Molecular Biology, Microbiology.
    Nilsson, Peter
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Replication-biased genome organisation in the crenarchaeon Sulfolobus2010In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, p. 454-Article in journal (Refereed)
    Abstract [en]

    Background: Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. Results: We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what would be anticipated by gene dosage effects alone. In addition, early replicating regions are denser in archaeal core genes (enriched in essential functions), display lower intergenic distances, and are devoid of mobile genetic elements. Conclusion: The strong replication-biased structuring of the Sulfolobus chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication. The higher-level chromosomal organisation could be of importance for minimizing the impact of DNA damage, and may also be linked to transcriptional regulation.

  • 15. Andersson, Eva
    et al.
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Comparison of a mass balance and an ecosystem model approach when evaluating the carbon cycling in a lake ecosystem2006In: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 35, no 8, p. 476-483Article in journal (Refereed)
  • 16.
    Andersson, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Abundance data adaptation experiment2017Data set
  • 17.
    Andersson, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bacterial abundance data from sterilization experiment2017Data set
  • 18.
    Andersson, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Extent and limitations of functional redundancy among bacterial communities towards dissolved organic matter2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    One of the key processes in the carbon cycle on our planet is the degradation of dissolved organic matter (DOM) in aquatic environments. The use of organic matter by bacteria links energy from DOM to higher trophic levels of the ecosystem when bacteria are consumed by other organisms. This is referred to as the microbial loop. In this thesis I examined if the communities were functionally redundant in their ability to utilize organic matter, or if variation in bacterial composition and richness is of importance. To test this overarching question several experiments were conducted that include methods such as illumina sequencing of the 16S rRNA gene for taxonomic identification of bacterial communities, flow cytometry to follow the growth of communities and spectroscopic measurement to describe the composition of the organic matter pool. Initially we demonstrated how to optimally sterilize organic matter for experimental studies in order to preserve its natural complexity. In further experiments we found that bacterial communities are redundant in their utilization of organic matter and can maintain optimal performance towards a range of organic matter pools. Related to this we found that pre-adaptation to organic matter played a small role as communities performed equally well regardless of their environmental history. We saw a small effect of richness and composition of bacterial communities on the efficiency of organic matter use, but conclude that this is of minor importance relative to abiotic factors. Still, we also show that organic matter can put strong selection pressure on bacterial communities with regards to richness and composition. Additionally we found that the supply rate of a carbon compound greatly influenced the energy utilization of the compound, i.e. a higher growth rate can be maintained if substrate is delivered in pulses relative to a continuous flow. Finally we conclude that the variation in bacterial communities is unlikely to have a major influence on carbon cycling in boreal lakes, but to enable a finer understanding, the genetics underlying the carbon utilization needs to be further explored. 

    List of papers
    1. Effects of sterilization on composition and bacterial utilization of dissolved organic carbon
    Open this publication in new window or tab >>Effects of sterilization on composition and bacterial utilization of dissolved organic carbon
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Sterilization of dissolved organic carbon (DOC) is an essential step in research on interactions between DOC and organisms, for example where the effect of different microbial communities on DOC is studied or vice versa. Few studies have, however, gone beyond acknowledging that sterilization of DOC influences its characteristics. Here we aimed to provide further knowledge that enables scientists to better tailor their sterilization methods to their research question. To meet this aim, we conducted a sterilization experiment with DOC from 4 boreal lakes treated with 4 sterilization methods, 2 filtrations (0.2 µm, 0.1 µm) and 2 autoclaving approaches (single autoclaving and double with intermediate pH adjustment). Quantity and spectroscopic properties of DOC were compared before and after sterilization and DOC was further tested as a substrate for bacterial growth. We found that the filtration methods better preserved the qualities of DOC, particularly the 0.2 µm filtration. On the contrary, autoclaving caused major inconsistent shifts in both qualitative and quantitative measurements of DOC as well as an increase of the maximum abundance of bacteria in growth experiments. Nonetheless, there remains a trade-off between retaining the quality of DOC and achieving sterile conditions. Therefore, the sterilization method of choice should be guided by the scientific question at hand.    

    Keyword
    sterilization, autoclave, filtration, dissolved organic carbon, excitation emission matrices, parallel factor analysis
    National Category
    Biological Sciences
    Research subject
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-331676 (URN)
    Available from: 2017-10-16 Created: 2017-10-16 Last updated: 2017-10-23
    2. Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors
    Open this publication in new window or tab >>Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors
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    2017 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 12, p. 5078-5087Article in journal (Refereed) Published
    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. 

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-275178 (URN)10.1111/1462-2920.13979 (DOI)000418352800021 ()29124844 (PubMedID)
    Funder
    Swedish Research Council, 2012-3892
    Available from: 2016-02-01 Created: 2016-02-01 Last updated: 2018-01-30Bibliographically approved
    3. Response and effect interactions between bacterial communities and organic matter
    Open this publication in new window or tab >>Response and effect interactions between bacterial communities and organic matter
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The interaction between bacteria and dissolved organic matter (DOM) is crucial for the global carbon cycling. Despite decades of research there are, however, few consistent patterns regarding the relationship between bacterial diversity and community composition and DOM. Here we hypothesized that one reason for such inconsistences among studies is that bacterial communities can adapt to a DOM source over time, whereby a change in the functioning of a community can be, at least partly, decoupled from its composition and diversity. To test this idea we performed a reciprocal transplant experiment with medium (i.e. DOM source) and bacterial communities from two boreal lakes. In this experiment the two communities were allowed to adapt to their indigenous and their foreign source of DOM over 42 days. Bacterial community composition (BCC) was measured throughout the experiment. In addition we measured the capacity of the communities to use DOM, in repeated short (5 days) separated bioassays. The results show a response of bacterial community composition to the DOM sources which was influenced by the origin of the community. In contrast, we could not show an effect of BCC on DOM-processing and functional performance. Indeed, communities of different origin processed the two DOM sources equally well even at the beginning of the experiment. This work demonstrates that the DOM pool can be a strong selective force for BCC but not vice versa. 

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-331696 (URN)
    Available from: 2017-10-17 Created: 2017-10-17 Last updated: 2017-10-23
    4. The relative importance of richness and BCC for DOC degradation
    Open this publication in new window or tab >>The relative importance of richness and BCC for DOC degradation
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The importance of biodiversity has been of primary interest for ecologist the last 20 years, giving rise to biodiversity ecosystem function (BEF) studies. Within the traditional field of ecology reoccurring patterns have emerged but within microbial ecology the importance of species richness for functioning is still poorly understood with few consistent patterns. In this study we examined the effect of species richness for dissolved organic matter degradation in lakes. This was examined within a smaller span of species richness compared to what is typically in microbial BEF experiments. Bacterial communities of reduced species richness were exposed to a range of DOC environments to test if reduced richness changed the functioning of communities and if the effect was similar among DOC environments. This was conducted in a full factorial design of 3 levels, with 6 dilutions, 5 media and 3 inocula resulting in 90 treatments. Overall, richness and community composition appeared to have effects on DOC degradation, but these effects were minor compared to the variation caused by the different DOC sources. Further, the importance of species richness varied among media and, thus, the chemical complexity of the environment influenced the biodiversity-ecosystem functioning relationship. 

    National Category
    Biological Sciences
    Research subject
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-331693 (URN)
    Available from: 2017-10-17 Created: 2017-10-17 Last updated: 2017-10-23
  • 19.
    Andersson, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Spectroscopic data / carbon quality measurements1987Data set
  • 20.
    Andersson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Berga, Mercè
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    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.
    The spatial structure of bacterial communities is influenced by historical environmental conditions2014In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 95, no 5, p. 1134-1140Article in journal (Refereed)
    Abstract [en]

    The spatial structure of ecological communities, including that of bacteria, is often influenced by species sorting by contemporary environmental conditions. Moreover, historical processes, i.e., ecological and evolutionary events that have occurred at some point in the past, such as dispersal limitation, drift, priority effects, or selection by past environmental conditions, can be important, but are generally investigated much less. Here, we conducted a field study using 16 rock pools, where we specifically compared the importance of past vs. contemporary environmental conditions for bacterial community structure by correlating present differences in bacterial community composition among pools to environmental conditions measured on the same day, as well as to those measured 2, 4, 6, and 8 d earlier. The results prove that selection by past environmental conditions exists, since we were able to show that bacterial communities are, to a greater extent, an imprint of past compared to contemporary environmental conditions. We suggest that this is the result of a combination of different mechanisms, including priority effects that cause rapid adaptation to new environmental conditions of taxa that have been initially selected by past environmental conditions, and slower rates of turnover in community composition compared to environmental conditions.

  • 21.
    Andersson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Catalán, Núria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. ICRA, Catalan Institute of Water Research.
    Rahman, Zeeshanur
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Effects of sterilization on composition and bacterial utilization of dissolved organic carbonManuscript (preprint) (Other academic)
    Abstract [en]

    Sterilization of dissolved organic carbon (DOC) is an essential step in research on interactions between DOC and organisms, for example where the effect of different microbial communities on DOC is studied or vice versa. Few studies have, however, gone beyond acknowledging that sterilization of DOC influences its characteristics. Here we aimed to provide further knowledge that enables scientists to better tailor their sterilization methods to their research question. To meet this aim, we conducted a sterilization experiment with DOC from 4 boreal lakes treated with 4 sterilization methods, 2 filtrations (0.2 µm, 0.1 µm) and 2 autoclaving approaches (single autoclaving and double with intermediate pH adjustment). Quantity and spectroscopic properties of DOC were compared before and after sterilization and DOC was further tested as a substrate for bacterial growth. We found that the filtration methods better preserved the qualities of DOC, particularly the 0.2 µm filtration. On the contrary, autoclaving caused major inconsistent shifts in both qualitative and quantitative measurements of DOC as well as an increase of the maximum abundance of bacteria in growth experiments. Nonetheless, there remains a trade-off between retaining the quality of DOC and achieving sterile conditions. Therefore, the sterilization method of choice should be guided by the scientific question at hand.    

  • 22.
    Andersson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Rahman, Zeeshanur
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi.
    Catalán, Núria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Catalan Institute for Water Research (ICRA).
    Lindström, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    The relative importance of richness and BCC for DOC degradationManuscript (preprint) (Other academic)
    Abstract [en]

    The importance of biodiversity has been of primary interest for ecologist the last 20 years, giving rise to biodiversity ecosystem function (BEF) studies. Within the traditional field of ecology reoccurring patterns have emerged but within microbial ecology the importance of species richness for functioning is still poorly understood with few consistent patterns. In this study we examined the effect of species richness for dissolved organic matter degradation in lakes. This was examined within a smaller span of species richness compared to what is typically in microbial BEF experiments. Bacterial communities of reduced species richness were exposed to a range of DOC environments to test if reduced richness changed the functioning of communities and if the effect was similar among DOC environments. This was conducted in a full factorial design of 3 levels, with 6 dilutions, 5 media and 3 inocula resulting in 90 treatments. Overall, richness and community composition appeared to have effects on DOC degradation, but these effects were minor compared to the variation caused by the different DOC sources. Further, the importance of species richness varied among media and, thus, the chemical complexity of the environment influenced the biodiversity-ecosystem functioning relationship. 

  • 23.
    Andersson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Rahman, Zeeshanur
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi.
    Catalán, Núria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Catalan Institute for Water Research (ICRA).
    Tranvik, Lars
    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.
    Lindström, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Response and effect interactions between bacterial communities and organic matterManuscript (preprint) (Other academic)
    Abstract [en]

    The interaction between bacteria and dissolved organic matter (DOM) is crucial for the global carbon cycling. Despite decades of research there are, however, few consistent patterns regarding the relationship between bacterial diversity and community composition and DOM. Here we hypothesized that one reason for such inconsistences among studies is that bacterial communities can adapt to a DOM source over time, whereby a change in the functioning of a community can be, at least partly, decoupled from its composition and diversity. To test this idea we performed a reciprocal transplant experiment with medium (i.e. DOM source) and bacterial communities from two boreal lakes. In this experiment the two communities were allowed to adapt to their indigenous and their foreign source of DOM over 42 days. Bacterial community composition (BCC) was measured throughout the experiment. In addition we measured the capacity of the communities to use DOM, in repeated short (5 days) separated bioassays. The results show a response of bacterial community composition to the DOM sources which was influenced by the origin of the community. In contrast, we could not show an effect of BCC on DOM-processing and functional performance. Indeed, communities of different origin processed the two DOM sources equally well even at the beginning of the experiment. This work demonstrates that the DOM pool can be a strong selective force for BCC but not vice versa. 

  • 24. Arnold, M. C.
    et al.
    Bier, R. L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindberg, T. T.
    Bernhardt, E. S.
    Di Giulio, R. T.
    Biofilm mediated uptake of selenium in streams with mountaintop coal mine drainage2017In: Limnologica, ISSN 0075-9511, E-ISSN 1873-5851, Vol. 65, p. 10-13Article in journal (Refereed)
    Abstract [en]

    Selenium (Se) may cause reproductive toxicity, yet the characteristics of Se bioaccumulation in aquatic food webs are understudied. Stream biofilms were grown in two reaches of Mud River, West Virginia (WV), including one downstream of a coal mine complex and an adjacent, unmined watershed. Mined stream biofilms contained significantly higher Se concentrations compared to unmined biofilms. An inverse relationship between water Se concentrations and biofilm accumulation factors was observed; mined-stream biofilms had an average bioconcentration factor (BCF) of 688 ± 350 fold while unmined-stream biofilms had an average BCF of 14505 ± 2700 fold.

  • 25. Arvola, Lauri
    et al.
    George, Glen
    Livingstone, David M.
    Järvinen, Marko
    Blenckner, Thorsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution.
    Dokulil, Martin T.
    Jennings, Eleanor
    Aonghusa, Caitriona Nic
    Nõges, Peeter
    Nõges, Tiina
    Weyhenmeyer, Gesa. A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    The impact of changing climate on the thermal characteristics of lakes2010In: The impact of climate change on European lakes / [ed] D.G. George, Springer , 2010, p. 85-101Chapter in book (Other academic)
  • 26.
    Attermeyer, Katrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Leibniz Inst Freshwater Ecol & Inland Fisheries C, Muggelseedamm 310, D-12587 Berlin, Germany..
    Flury, S.
    Leibniz Inst Freshwater Ecol & Inland Fisheries C, Muggelseedamm 310, D-12587 Berlin, Germany.;Univ Geneva, Fac Sci, Blvd Carl Vogt 66, CH-1211 Geneva, Switzerland..
    Jayakumar, R.
    IITM, IGCS, Madras 600036, Tamil Nadu, India.;IITM, Environm & Water Resources Engn Div, Dept Civil Engn, Madras 600036, Tamil Nadu, India..
    Fiener, P.
    Univ Augsburg, Dept Geog, Alter Postweg 118, D-86159 Augsburg, Germany..
    Steger, K.
    IITM, IGCS, Madras 600036, Tamil Nadu, India..
    Arya, V.
    IITM, Environm & Water Resources Engn Div, Dept Civil Engn, Madras 600036, Tamil Nadu, India..
    Wilken, F.
    Univ Augsburg, Dept Geog, Alter Postweg 118, D-86159 Augsburg, Germany.;BTU, Chair Soil Protect & Recultivat, Konrad Wachsmann Allee 6, D-03013 Cottbus, Germany..
    van Geldern, R.
    Univ Erlangen Nurnberg, GeoZentrum Nordbayern, Schlossgarten 5, D-91054 Erlangen, Germany..
    Premke, K.
    Leibniz Inst Freshwater Ecol & Inland Fisheries C, Muggelseedamm 310, D-12587 Berlin, Germany.;Leibniz Ctr Agr Landscape Res ZALF, Inst Landscape Biogeochem, Eberswalder Str 84, D-15374 Muncheberg, Germany..
    Invasive floating macrophytes reduce greenhouse gas emissions from a small tropical lake2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 20424Article in journal (Refereed)
    Abstract [en]

    Floating macrophytes, including water hyacinth (Eichhornia crassipes), are dominant invasive organisms in tropical aquatic systems, and they may play an important role in modifying the gas exchange between water and the atmosphere. However, these systems are underrepresented in global datasets of greenhouse gas (GHG) emissions. This study investigated the carbon (C) turnover and GHG emissions from a small (0.6 km(2)) water-harvesting lake in South India and analysed the effect of floating macrophytes on these emissions. We measured carbon dioxide (CO2) and methane (CH4) emissions with gas chambers in the field as well as water C mineralization rates and physicochemical variables in both the open water and in water within stands of water hyacinths. The CO2 and CH4 emissions from areas covered by water hyacinths were reduced by 57% compared with that of open water. However, the C mineralization rates were not significantly different in the water between the two areas. We conclude that the increased invasion of water hyacinths and other floating macrophytes has the potential to change GHG emissions, a process that might be relevant in regional C budgets.

  • 27.
    Attermeyer, Katrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Chemical Analytics and Biogeochemistry, Germany.
    Grossart, Hans-Peter
    Leibniz-Institute of Freshwater Ecology and InlandFisheries, Experimental Limnology, Germany; Institute for Biochemistry and Biology, Potsdam University, Germany.
    Flury, Sabine
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Chemical Analytics and Biogeochemistry, Germany; Faculty of Science, University of Geneva, Switzerland.
    Premke, Katrin
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Chemical Analytics and Biogeochemistry, Germany; Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Germany.
    Bacterial processes and biogeochemical changes in the water body of kettle holes: mainly driven by autochthonous organic matter?2017In: Aquatic Sciences, ISSN 1015-1621, E-ISSN 1420-9055, Vol. 79, no 3, p. 675-687Article in journal (Refereed)
    Abstract [en]

    Kettle holes are small inland waters formed from glacially-created depressions often situated in agricultural landscapes. Due to their high perimeter-to-area ratio facilitating a high aquatic-terrestrial coupling, kettle holes can accumulate high concentrations of organic carbon and nutrients, fueling microbial activities and turnover rates. Thus, they represent hotspots of carbon turnover in the landscape, but their bacterial activities and controlling factors have not been well investigated. Therefore, we aimed to assess the relative importance of various environmental factors on bacterial and biogeochemical processes in the water column of kettle holes and to disentangle their variations. In the water body of ten kettle holes in north-eastern Germany, we measured several physico-chemical and biological parameters such as carbon quantity and quality, as well as bacterial protein production (BP) and community respiration (CR) in spring, early summer and autumn 2014. Particulate organic matter served as an indicator of autochthonous production and represented an important parameter to explain variations in BP and CR. This notion is supported by qualitative absorbance indices of dissolved molecules in water samples and C:N ratios of the sediments, which demonstrate high fractions of autochthonous organic matter (OM) in the studied kettle holes. In contrast, dissolved chemical parameters were less important for bacterial activities although they revealed strong differences throughout the growing season. Pelagic bacterial activities and dynamics might thus be regulated by autochthonous OM in kettle holes implying a control of important biogeochemical processes by internal primary production rather than facilitated exchange with the terrestrial surrounding due to a high perimeter-to-area ratio.

  • 28. Bagatini, Inessa Lacativa
    et al.
    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.
    Klaveness, Dag
    Tessarolli, Leticia Piton
    Henriques Vieira, Armando Augusto
    Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 1, p. e85950-Article in journal (Refereed)
    Abstract [en]

    Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways.

  • 29.
    Baho, Didier
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Resistance and resilience of microbial communities - temporal and spatial insurance against perturbations2010Independent thesis Advanced level (degree of Master (One Year)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Bacterial communities are fundamental components of many processes occurring in aquatic ecosystems, since through microbial activities substantial amount of matter and energy is transferred from a pool of DOC to higher trophic levels. Previous studies highlighted the beneficial effects of diversity on ecosystem functioning, however studies on the resistance and resilience in microbial communities are scarce. Similarly, studies focusing on factors that might improve resistance or resilience of communities such as the influence of refuges are equally missing, although an understanding of the underlying mechanisms could be very useful in the field of conservation management. In this study, chemostat cultures were used to investigate the influence of a spatial and a temporal refuge on bacterioplankton communities’ resistance and resilience measured in terms of functioning and community composition after applying a salinity pulse disturbance. Respiration rate and substrate utilization were used to estimate bacterial functioning while community composition was determined by using T-RFLP. The perturbation was found to affect bacterial functioning and community composition. Moreover our findings indicate that the resistance and resilience measured in terms of bacterial functioning and community composition were significantly influenced by the provision of refuges.  

  • 30.
    Baho, Didier
    et al.
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Peter, Hannes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Resistance and resilience of microbial communities: temporal and spatial insurance against perturbations2012In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 14, no 9, p. 2283-2292Article in journal (Refereed)
    Abstract [en]

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

  • 31. Barros, Nathan
    et al.
    Cole, Jonathan J.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Prairie, Yves T.
    Bastviken, David
    Huszar, Vera L. M.
    del Giorgio, Paul
    Roland, Fabio
    Carbon emission from hydroelectric reservoirs linked to reservoir age and latitude2011In: Nature Geoscience, ISSN 1752-0894, E-ISSN 1752-0908, Vol. 4, no 9, p. 593-596Article in journal (Refereed)
    Abstract [en]

    Hydroelectric reservoirs cover an area of 3.4 x 10(5) km(2) and comprise about 20% of all reservoirs. In addition, they contain large stores of formerly terrestrial organic carbon. Significant amounts of greenhouse gases are emitted(2), especially in the early years following reservoir creation, but the global extent of these emissions is poorly known. Previous estimates of emissions from all types of reservoir indicate that these human-made systems emit 321 Tg of carbon per year (ref. 4). Here we assess the emissions of carbon dioxide and methane from hydroelectric reservoirs, on the basis of data from 85 globally distributed hydroelectric reservoirs that account for 20% of the global area of these systems. We relate the emissions to reservoir age, location biome, morphometric features and chemical status. We estimate that hydroelectric reservoirs emit about 48 Tg C as CO(2) and 3 Tg C as CH(4), corresponding to 4% of global carbon emissions from inland waters. Our estimates are smaller than previous estimates on the basis of more limited data. Carbon emissions are correlated to reservoir age and latitude, with the highest emission rates from the tropical Amazon region. We conclude that future emissions will be highly dependent on the geographic location of new hydroelectric reservoirs.

  • 32.
    Bartels, Pia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ecology across Boundaries: Food web coupling among and within ecosystems2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cross-boundary movements of energy and material are ubiquitous. Freshwater ecosystems receive nutrients, dissolved, and particulate organic matter from adjacent terrestrial ecosystems, whereas terrestrial ecosystems mainly receive prey organisms and detritus deposited by physical processes such as floods from freshwater ecosystems. Within lakes, fish are considered as integrators between habitats due to their high mobility, although they often occupy either near-shore littoral or open-water pelagic habitats and develop habitat-specific morphologies. Such intra-population divergence in morphological traits might limit the use of multiple habitats.

    In this thesis, I first focused on quantity and quality of reciprocal fluxes of particulate organic matter between freshwater and terrestrial ecosystems and responses of recipient consumers. Freshwater ecosystems generally received higher amounts of externally-produced resources than terrestrial ecosystems. Despite this discrepancy, aquatic and terrestrial consumer responses were similar, likely due to the differences in resource quality. Second, I investigated the potential of particulate organic carbon (POC) supporting benthic food webs in lakes; a pathway that has largely been neglected in previous studies. I found that POC can substantially subsidize the benthic food web and that the effects on the benthic food web were transferred to the pelagic habitat, thus emphasizing the importance of benthic pathways for pelagic production. Third, I examined how water transparency can affect intra-population divergence in perch (Perca fluviatilis). I observed that increased water transparency can considerably increase morphological divergence between littoral and pelagic populations likely due to its effects on foraging. Finally, I investigated the effects of such intra-population divergence on littoral-pelagic food web coupling. I found that low morphological divergence corresponded with high overlap in resource use, whereas strong morphological divergence resulted in low overlap in resource use. Here littoral populations mainly utilized littoral resources and pelagic populations primarily utilized pelagic resources, indicating that habitat coupling might be strongly limited when intra-population divergence is high.

    In conclusion, although different ecosystems seem separated by distinct physical boundaries, these boundaries are often crossed. However, the development of habitat-specific adaptive traits might limit movement between apparently contiguous habitats.

    List of papers
    1. Reciprocal subsidies between freshwater and terrestrial ecosystems structure consumer-resource dynamics
    Open this publication in new window or tab >>Reciprocal subsidies between freshwater and terrestrial ecosystems structure consumer-resource dynamics
    Show others...
    2012 (English)In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 93, no 5, p. 1173-1182Article in journal (Refereed) Published
    Abstract [en]

    Cross-ecosystem movements of material and energy, particularly reciprocal resource fluxes across the freshwater-land interface, have received major attention. Freshwater ecosystems may receive higher amounts of subsidies (i.e., resources produced outside the focal ecosystem) than terrestrial ecosystems, potentially leading to increased secondary production in freshwaters. Here we used a meta-analytic approach to quantify the magnitude and direction of subsidy inputs across the freshwater-land interface and to determine subsequent responses in recipient animals. Terrestrial and freshwater ecosystems differed in the magnitude of subsidies they received, with aquatic ecosystems generally receiving higher subsidies than terrestrial ecosystems. Surprisingly, and despite the large discrepancy in magnitude, the contribution of these subsidies to animal carbon inferred from stable isotope composition did not differ between freshwater and terrestrial ecosystems, likely due to the differences in subsidy quality. The contribution of allochthonous subsidies was highest to primary consumers and predators, suggesting that bottom-up and top-down effects may be affected considerably by the input of allochthonous resources. Future work on subsidies will profit from a food web dynamic approach including indirect trophic interactions and propagating effects.

    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-160772 (URN)10.1890/11-1210.1 (DOI)000304368100022 ()
    Available from: 2011-10-31 Created: 2011-10-31 Last updated: 2017-12-08Bibliographically approved
    2. Terrestrial subsidies to lake food webs: An experimental approach
    Open this publication in new window or tab >>Terrestrial subsidies to lake food webs: An experimental approach
    Show others...
    2012 (English)In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 168, no 3, p. 807-818Article in journal (Refereed) Published
    Abstract [en]

    Cross-ecosystem movements of material and energy are ubiquitous. Aquatic ecosystems typically receive material that also includes organic matter from the surrounding catchment. Terrestrial-derived (allochthonous) organic matter can enter aquatic ecosystems in dissolved or particulate form. Several studies have highlighted the importance of dissolved organic carbon to aquatic consumers, but less is known about allochthonous particulate organic carbon (POC). Similarly, most studies showing the effects of allochthonous organic carbon (OC) on aquatic consumers have investigated pelagic habitats; the effects of allochthonous OC on benthic communities are less well studied. Allochthonous inputs might further decrease primary production through light reduction, thereby potentially affecting autotrophic resource availability to consumers. Here, an enclosure experiment was carried out to test the importance of POC input and light availability on the resource use in a benthic food web of a clear-water lake. Corn starch (a C-4 plant) was used as a POC source due to its insoluble nature and its distinct carbon stable isotope value (delta C-13). The starch carbon was closely dispersed over the bottom of the enclosures to study the fate of a POC source exclusively available to sediment biota. The addition of starch carbon resulted in a clear shift in the isotopic signature of surface-dwelling herbivorous and predatory invertebrates. Although the starch carbon was added solely to the sediment surface, the carbon originating from the starch reached zooplankton. We suggest that allochthonous POC can subsidize benthic food webs directly and can be further transferred to pelagic systems, thereby highlighting the importance of benthic pathways for pelagic habitats.

    Keyword
    Allochthonous, Cross-ecosystem, Autochthonous, Aquatic-terrestrial linkage, Benthic
    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-160774 (URN)10.1007/s00442-011-2141-7 (DOI)000301706800020 ()
    Available from: 2011-10-31 Created: 2011-10-31 Last updated: 2017-12-08Bibliographically approved
    3. Water transparency drives intra-population divergence in Eurasian perch (Perca fluviatilis)
    Open this publication in new window or tab >>Water transparency drives intra-population divergence in Eurasian perch (Perca fluviatilis)
    2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 8, p. e43641-Article in journal (Refereed) Published
    Abstract [en]

    Trait combinations that lead to a higher efficiency in resource utilization are important drivers of divergent natural selection and adaptive radiation. However, variation in environmental features might constrain foraging in complex ways and therefore impede the exploitation of critical resources. We tested the effect of water transparency on intra-population divergence in morphology of Eurasian perch (Perca fluviatilis) across seven lakes in central Sweden. Morphological divergence between near-shore littoral and open-water pelagic perch substantially increased with increasing water transparency. Reliance on littoral resources increased strongly with increasing water transparency in littoral populations, whereas littoral reliance was not affected by water transparency in pelagic populations. Despite the similar reliance on pelagic resources in pelagic populations along the water transparency gradient, the utilization of particular pelagic prey items differed with variation in water transparency in pelagic populations. Pelagic perch utilized cladocerans in lakes with high water transparency and copepods in lakes with low water transparency. We suggest that under impaired visual conditions low utilization of littoral resources by littoral perch and utilization of evasive copepods by pelagic perch may lead to changes in morphology. Our findings indicate that visual conditions can affect population divergence in predator populations through their effects on resource utilization.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-158689 (URN)10.1371/journal.pone.0043641 (DOI)000308063700123 ()
    Available from: 2011-09-13 Created: 2011-09-13 Last updated: 2017-12-08Bibliographically approved
    4. Intra-population niche separation mediated by water transparency limits habitat coupling
    Open this publication in new window or tab >>Intra-population niche separation mediated by water transparency limits habitat coupling
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-160776 (URN)
    Available from: 2011-10-31 Created: 2011-10-31 Last updated: 2013-02-11
  • 33.
    Bartels, Pia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Cucherousset, Julien
    Gudasz, Cristian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Jansson, Mats
    Karlsson, Jan
    Persson, Lennart
    Premke, Katrin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Rubach, Anja
    Steger, Kristin
    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.
    Eklöv, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Terrestrial subsidies to lake food webs: An experimental approach2012In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 168, no 3, p. 807-818Article in journal (Refereed)
    Abstract [en]

    Cross-ecosystem movements of material and energy are ubiquitous. Aquatic ecosystems typically receive material that also includes organic matter from the surrounding catchment. Terrestrial-derived (allochthonous) organic matter can enter aquatic ecosystems in dissolved or particulate form. Several studies have highlighted the importance of dissolved organic carbon to aquatic consumers, but less is known about allochthonous particulate organic carbon (POC). Similarly, most studies showing the effects of allochthonous organic carbon (OC) on aquatic consumers have investigated pelagic habitats; the effects of allochthonous OC on benthic communities are less well studied. Allochthonous inputs might further decrease primary production through light reduction, thereby potentially affecting autotrophic resource availability to consumers. Here, an enclosure experiment was carried out to test the importance of POC input and light availability on the resource use in a benthic food web of a clear-water lake. Corn starch (a C-4 plant) was used as a POC source due to its insoluble nature and its distinct carbon stable isotope value (delta C-13). The starch carbon was closely dispersed over the bottom of the enclosures to study the fate of a POC source exclusively available to sediment biota. The addition of starch carbon resulted in a clear shift in the isotopic signature of surface-dwelling herbivorous and predatory invertebrates. Although the starch carbon was added solely to the sediment surface, the carbon originating from the starch reached zooplankton. We suggest that allochthonous POC can subsidize benthic food webs directly and can be further transferred to pelagic systems, thereby highlighting the importance of benthic pathways for pelagic habitats.

  • 34.
    Bartels, Pia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Cucherousset, Julien
    Steger, Kristin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eklöv, Peter
    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.
    Hillebrand, Helmut
    Reciprocal subsidies between freshwater and terrestrial ecosystems structure consumer-resource dynamics2012In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 93, no 5, p. 1173-1182Article in journal (Refereed)
    Abstract [en]

    Cross-ecosystem movements of material and energy, particularly reciprocal resource fluxes across the freshwater-land interface, have received major attention. Freshwater ecosystems may receive higher amounts of subsidies (i.e., resources produced outside the focal ecosystem) than terrestrial ecosystems, potentially leading to increased secondary production in freshwaters. Here we used a meta-analytic approach to quantify the magnitude and direction of subsidy inputs across the freshwater-land interface and to determine subsequent responses in recipient animals. Terrestrial and freshwater ecosystems differed in the magnitude of subsidies they received, with aquatic ecosystems generally receiving higher subsidies than terrestrial ecosystems. Surprisingly, and despite the large discrepancy in magnitude, the contribution of these subsidies to animal carbon inferred from stable isotope composition did not differ between freshwater and terrestrial ecosystems, likely due to the differences in subsidy quality. The contribution of allochthonous subsidies was highest to primary consumers and predators, suggesting that bottom-up and top-down effects may be affected considerably by the input of allochthonous resources. Future work on subsidies will profit from a food web dynamic approach including indirect trophic interactions and propagating effects.

  • 35.
    Bartels, Pia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Hirsch, Philipp E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Svanbäck, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eklöv, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Intra-population niche separation mediated by water transparency limits habitat couplingManuscript (preprint) (Other academic)
  • 36.
    Bartels, Pia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Hirsch, Philipp E
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Svanbäck, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eklöv, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Water transparency drives intra-population divergence in Eurasian perch (Perca fluviatilis)2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 8, p. e43641-Article in journal (Refereed)
    Abstract [en]

    Trait combinations that lead to a higher efficiency in resource utilization are important drivers of divergent natural selection and adaptive radiation. However, variation in environmental features might constrain foraging in complex ways and therefore impede the exploitation of critical resources. We tested the effect of water transparency on intra-population divergence in morphology of Eurasian perch (Perca fluviatilis) across seven lakes in central Sweden. Morphological divergence between near-shore littoral and open-water pelagic perch substantially increased with increasing water transparency. Reliance on littoral resources increased strongly with increasing water transparency in littoral populations, whereas littoral reliance was not affected by water transparency in pelagic populations. Despite the similar reliance on pelagic resources in pelagic populations along the water transparency gradient, the utilization of particular pelagic prey items differed with variation in water transparency in pelagic populations. Pelagic perch utilized cladocerans in lakes with high water transparency and copepods in lakes with low water transparency. We suggest that under impaired visual conditions low utilization of littoral resources by littoral perch and utilization of evasive copepods by pelagic perch may lead to changes in morphology. Our findings indicate that visual conditions can affect population divergence in predator populations through their effects on resource utilization.

  • 37.
    Bartels, Pia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Hirsch, Philipp Emanuel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Svanbäck, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Eklöv, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Dissolved Organic Carbon Reduces Habitat Coupling by Top Predators in Lake Ecosystems2016In: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 19, p. 955-967Article in journal (Refereed)
    Abstract [en]

    Increasing input of terrestrial dissolved organic carbon (DOC) has been identified as a widespread environmental phenomenon in many aquatic ecosystems. Terrestrial DOC influences basal trophic levels: it can subsidize pelagic bacterial production and impede benthic primary production via light attenuation. However, little is known about the impacts of elevated DOC concentrations on higher trophic levels, especially on top consumers. Here, we used Eurasian perch (Perca fluviatilis) to investigate the effects of increasing DOC concentrations on top predator populations. We applied stable isotope analysis and geometric morphometrics to estimate long-term resource and habitat utilization of perch. Habitat coupling, the ability to exploit littoral and pelagic resources, strongly decreased with increasing DOC concentrations due to a shift toward feeding predominantly on pelagic resources. Simultaneously, resource use and body morphology became increasingly alike for littoral and pelagic perch populations with increasing DOC, suggesting more intense competition in lakes with high DOC. Eye size of perch increased with increasing DOC concentrations, likely as a result of deteriorating visual conditions, suggesting a sensory response to environmental change. Increasing input of DOC to aquatic ecosystems is a common result of environmental change and might affect top predator populations in multiple and complex ways.

  • 38. Bastviken, David
    et al.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Downing, John A.
    Crill, Patrick M.
    Enrich-Prast, Alex
    Freshwater Methane Emissions Offset the Continental Carbon Sink2011In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 331, no 6013Article in journal (Refereed)
    Abstract [en]

    Inland waters (lakes, reservoirs, streams, and rivers) are often substantial methane (CH(4)) sources in the terrestrial landscape. They are, however, not yet well integrated in global greenhouse gas (GHG) budgets. Data from 474 freshwater ecosystems and the most recent global water area estimates indicate that freshwaters emit at least 103 teragrams of CH(4) year(-1), corresponding to 0.65 petagrams of C as carbon dioxide (CO(2)) equivalents year(-1), offsetting 25% of the estimated land carbon sink. Thus, the continental GHG sink may be considerably overestimated, and freshwaters need to be recognized as important in the global carbon cycle.

  • 39.
    Beier, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bacterial Degradation and Use of Chitin in Aquatic Habitats2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Chitin belongs to the most abundant biopolymers on earth where it has an important role as a structural element in crustaceans, insects, fungi and some phytoplankton. Missing evidence for long-term accumulation of chitin in nature implies fast turnover and as chitin is composed of aminosugar subunits it holds central roles in both carbon and nitrogen cycles. The aim of this thesis was to contribute to a better understanding of organic matter cycling by learning more about the diversity, function and ecology of bacteria that degrade chitin. A metagenome-enabled study of the spatial distribution of chitinolytic bacteria in aquatic ecosystems identified salinity as the major environmental factor for shaping their community composition. To address the role of alternative environmental variables controlling chitinolytic communities, a temporally resolved study was completed in a dimictic freshwater lake. Pronounced seasonal change in the indigenous chitinolytic community was observed and parallel measured environmental parameters pointed to the availability and crystalline form of chitin as significant controlling factors.  The different ecological niches occupied by microbes that utilize chitin for growth were studied in an experimental study. Single-cell quantification of chitinolytic cells and cells incorporating chitin hydrolysis products suggested that commensal use of chitin hydrolysis products without simultaneous chitinase activity could be an important ecological strategy in freshwater bacterioplankton communities. Members of the ubiquitous and often quantitatively dominant group of freshwater Actinobacteria Ac1 were identified as particularly active in this “cheater” lifestyle. Further experiments based on artificially created gradients in bacterial diversity demonstrated the importance of specific bacterial populations and community composition rather than overall community richness in controlling more specific functions such as chitin and cellulose degradation. To conclude, results of this thesis provide insight into the biogeography, niche-separation and species interactions of the functional community of chitin degraders and the influence of general bacterial diversity to the respective system functioning.

     

     

     

     

    List of papers
    1. Mechanisms and ecology of bacterial chitin degradation
    Open this publication in new window or tab >>Mechanisms and ecology of bacterial chitin degradation
    (English)Manuscript (preprint) (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-131084 (URN)
    Available from: 2010-09-22 Created: 2010-09-22 Last updated: 2011-03-21
    2.
    The record could not be found. The reason may be that the record is no longer available or you may have typed in a wrong id in the address field.
    3. Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing
    Open this publication in new window or tab >>Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing
    Show others...
    2012 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 14, no 9, p. 2467-2479Article in journal (Refereed) Published
    Abstract [en]

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

    Keyword
    chitinase genes, lake, temporal dynamics, seasonality, pyrosequencing
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-131091 (URN)10.1111/j.1462-2920.2012.02764.x (DOI)000308300600018 ()
    Available from: 2010-09-22 Created: 2010-09-22 Last updated: 2017-12-12Bibliographically approved
    4. Uncoupling of chitinase activity and uptake of hydrolyses products in freshwater bacterioplankton
    Open this publication in new window or tab >>Uncoupling of chitinase activity and uptake of hydrolyses products in freshwater bacterioplankton
    2011 (English)In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 56, no 4, p. 1179-1188Article in journal (Refereed) Published
    Abstract [en]

    We investigated to what extent chitinolytic bacteria subsidize bacterial populations that do not produce chitinolytic enzymes but still use the products of chitin hydrolysis. Applying single-cell techniques to untreated and chitin-enriched lake water, we show that the number of planktonic cells taking up chitin hydrolysis products by far exceeds the number of cells expressing chitinases. Flavobacteria, Actinobacteria, and specifically members of the abundant and ubiquitous freshwater Ac1 cluster of the Actinobacteria, increased in abundance and were enriched in response to the chitin amendment. Flavobacteria were frequently observed in dense clusters on chitin particles, suggesting that they are actively involved in the hydrolysis and solubilization of chitin. In contrast, Actinobacteria were exclusively planktonic. We propose that planktonic Actinobacteria contain commensals specialized in the uptake of small hydrolysis products without expressing or possibly even possessing the machinery for chitin hydrolysis. More research is needed to assess the importance of such "cheater'' substrate acquisition strategies in the turnover and degradation of polymeric organic matter in aquatic ecosystems.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-131094 (URN)10.4319/lo.2011.56.4.1179 (DOI)000294603400001 ()
    Available from: 2010-09-22 Created: 2010-09-22 Last updated: 2017-12-12Bibliographically approved
    5. Function-specific response to depletion of microbial diversity
    Open this publication in new window or tab >>Function-specific response to depletion of microbial diversity
    Show others...
    2011 (English)In: The ISME Journal, ISSN 1751-7362, Vol. 5, no 2, p. 351-361Article in journal (Refereed) Published
    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.

    Keyword
    cellulose, chitin, functional diversity, species traits, T-RFLP
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-131083 (URN)10.1038/ismej.2010.119 (DOI)000290020000018 ()20686511 (PubMedID)
    Available from: 2010-09-22 Created: 2010-09-22 Last updated: 2017-11-30Bibliographically approved
  • 40.
    Beier, Sara
    et al.
    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.
    Bacterial chitin degradation: mechanisms and ecophysiological strategies2013In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 4, p. 149-Article, review/survey (Refereed)
    Abstract [en]

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

  • 41.
    Beier, Sara
    et al.
    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.
    Mechanisms and ecology of bacterial chitin degradationManuscript (preprint) (Other academic)
  • 42.
    Beier, Sara
    et al.
    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.
    Uncoupling of chitinase activity and uptake of hydrolyses products in freshwater bacterioplankton2011In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 56, no 4, p. 1179-1188Article in journal (Refereed)
    Abstract [en]

    We investigated to what extent chitinolytic bacteria subsidize bacterial populations that do not produce chitinolytic enzymes but still use the products of chitin hydrolysis. Applying single-cell techniques to untreated and chitin-enriched lake water, we show that the number of planktonic cells taking up chitin hydrolysis products by far exceeds the number of cells expressing chitinases. Flavobacteria, Actinobacteria, and specifically members of the abundant and ubiquitous freshwater Ac1 cluster of the Actinobacteria, increased in abundance and were enriched in response to the chitin amendment. Flavobacteria were frequently observed in dense clusters on chitin particles, suggesting that they are actively involved in the hydrolysis and solubilization of chitin. In contrast, Actinobacteria were exclusively planktonic. We propose that planktonic Actinobacteria contain commensals specialized in the uptake of small hydrolysis products without expressing or possibly even possessing the machinery for chitin hydrolysis. More research is needed to assess the importance of such "cheater'' substrate acquisition strategies in the turnover and degradation of polymeric organic matter in aquatic ecosystems.

  • 43.
    Beier, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Jones, Christopher M.
    Mohit, Vani
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Hallin, Sara
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Global Phylogeography of Chitinase Genes in Aquatic Metagenomes2011In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 77, no 3, p. 1101-1106Article in journal (Refereed)
    Abstract [en]

    Phylogeny-based analysis of chitinase and 16S rRNA genes from metagenomic data suggests that salinity is a major driver for the distribution of both chitinolytic and total bacterial communities in aquatic systems. Additionally, more acidic chitinase proteins were observed with increasing salinity. Congruent habitat separation was further observed for both genes according to latitude and proximity to the coastline. However, comparison of chitinase and 16S rRNA genes extracted from different geographic locations showed little congruence in distribution. There was no indication that dispersal limited the global distribution of either gene.

  • 44.
    Beier, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Kim, Ok-Sun
    Junier, Pilar
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Witzel, Karl-Paul
    Betaproteobacterial ammonia oxidizers in root zones of aquatic macrophytes2010In: Fundamental and Applied Limnology, ISSN 1863-9135, Vol. 177, no 4, p. 241-255Article in journal (Refereed)
    Abstract [en]

    Enhanced nitrification and coupled denitrification in macrophyte root zones may contribute to the depletion of nitrogen from the rhizosphere and are both critical processes for agriculture and rhizoremediation. We examined one factor likely to affect these processes: the ammonia oxidizing betaproteobacterial community composition, and whether or not it is influenced by plant species (Eleocharis acicularis, Eleocharis palustris, Typha angustifolia) or sediment characteristics. Genes coding for ammonia monooxygenase (amoA) and 16S rRNA of betaproteobacterial ammonia oxidizers were targeted. The betaproteobacterial ammonia oxidizing community in root surface biofilms was distinct from the surrounding rhizosphere sediment. In contrast, communities in rhizosphere and bulk sediment samples were very similar. Our results showed the occurrence of Nitrosomonas europaea-like bacteria nearly exclusively in the rhizoplane biofilms, while sequences affiliated with the Nitrosomonas oligotropha, Nitrosomonas communis and Nitrosospira-lineages were more frequently detected in the surrounding sediment. Our results further suggest that the presence of N. europaea on macrophyte roots depends on the sampling site rather than on the studied macrophyte species. We propose that the rhizoplane of aquatic macrophytes is a natural habitat for N. europaea.

  • 45.
    Beier, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Mohit, Vani
    Département de Biologie, Québec-Océan and Institut de biologie integrative et des systèmes, Université Laval.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Östman, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing2012In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 14, no 9, p. 2467-2479Article in journal (Refereed)
    Abstract [en]

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

  • 46. Beisner, Beatrix E.
    et al.
    Peres-Neto, Pedro R.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Barnett, Alain
    Longhi, Maria Lorena
    The role of environmental and spatial processes in structuring lake communities from bacteria to fish2006In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 87, no 12, p. 2985-2991Article in journal (Refereed)
    Abstract [en]

    We assessed the relative roles of local environmental conditions and dispersal on community structure in a landscape of lakes for the major trophic groups. We use taxonomic presence–absence and abundance data for bacteria, phytoplankton, zooplankton, and fish from 18 lakes in southern Quebec, Canada. The question of interest was whether communities composed of organisms with more limited dispersal abilities, because of size and life history (zooplankton and fish) would show a different effect of lake distribution than communities composed of good dispersers (bacteria and phytoplankton). We examine the variation in structure attributable to local environmental (i.e., lake chemical and physical variables) vs. dispersal predictors (i.e., overland and watercourse distances between lakes) using variation partitioning techniques. Overall, we show that less motile species (crustacean zooplankton and fish) are better predicted by spatial factors than by local environmental ones. Furthermore, we show that for zooplankton abundances, both overland and watercourse dispersal pathways are equally strong, though they may select for different components of the community, while for fish, only watercourses are relevant dispersal pathways. These results suggest that crustacean zooplankton and fish are more constrained by dispersal and therefore more likely to operate as a metacommunity than are bacteria and phytoplankton within this studied landscape.

  • 47. Bendall, Matthew L
    et al.
    Stevens, Sarah LR
    Chan, Leong-Keat
    Malfatti, Stephanie
    Schwientek, Patrick
    Tremblay, Julien
    Schackwitz, Wendy
    Martin, Joel
    Pati, Amrita
    Bushnell, Brian
    Froula, Jeff
    Kang, Dongwan
    Tringe, Susannah G
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Moran, Mary A
    Shade, Ashley
    Newton, Ryan J
    McMahon, Katherine D
    Malmstrom, Rex R
    Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 7, p. 1589-1601Article in journal (Refereed)
    Abstract [en]

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005-2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the /`ecotype model/' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.

  • 48.
    Bennke, Christin M.
    et al.
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Reintjes, Greta
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Schattenhofer, Martha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Ellrott, Andreas
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Wulf, Jörg
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Zeder, Michael
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.;Technobiol GmbH, Buchrain, Switzerland..
    Fuchs, Bernhard M.
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Modification of a High-Throughput Automatic Microbial Cell Enumeration System for Shipboard Analyses2016In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 82, no 11, p. 3289-3296Article in journal (Refereed)
    Abstract [en]

    In the age of ever-increasing "-omics" studies, the accurate and statistically robust determination of microbial cell numbers within often-complex samples remains a key task in microbial ecology. Microscopic quantification is still the only method to enumerate specific subgroups of microbial clades within complex communities by, for example, fluorescence in situ hybridization (FISH). In this study, we improved an existing automatic image acquisition and cell enumeration system and adapted it for usage at high seas on board an oceanographic research ship. The system was evaluated by testing settings such as minimal pixel area and image exposure times ashore under stable laboratory conditions before being brought on board and tested under various wind and wave conditions. The system was robust enough to produce high-quality images even with ship heaves of up to 3m and pitch and roll angles of up to 6.3 degrees. On board the research ship, on average, 25% of the images acquired from plankton samples on filter membranes could be used for cell enumeration. Automated enumeration was highly correlated with manual counts (r(2)>0.9). Even the smallest of microbial cells in the open ocean, members of the alphaproteobacterial SAR11 clade, could be confidently detected and enumerated. The automated image acquisition and cell enumeration system developed here enables an accurate and reproducible determination of microbial cell counts in planktonic samples and allows insight into the abundance and distribution of specific microorganisms already on board within a few hours.

    IMPORTANCE In this research article, we report on a new system and software pipeline, which allows for an easy and quick image acquisition and the subsequent enumeration of cells in the acquired images. We put this pipeline through vigorous testing and compared it to manual microscopy counts of microbial cells on membrane filters. Furthermore, we tested this system at sea on board a marine research vessel and counted bacteria on board within a few hours after the retrieval of water samples. The imaging and counting system described here has been successfully applied to a number of laboratory-based studies and allowed the quantification of thousands of samples and FISH preparations (see, e.g., H. Teeling, B. M. Fuchs, D. Becher, C. Klockow, A. Gardebrecht, C. M. Bennke, M. Kassabgy, S. Huang, A. J. Mann, J. Waldmann, M. Weber, A. Klindworth, A. Otto, J. Lange, J. Bernhardt, C. Reinsch, M. Hecker, J. Peplies, F. D. Bockelmann, U. Callies, G. Gerdts, A. Wichels, K. H. Wiltshire, F. O. Glockner, T. Schweder, and R. Amann, Science 336:608-611, 2012, http://dx.doi.org/10.1126/science.1218344). We adjusted the standard image acquisition software to withstand ship movements. This system will allow for more targeted sampling of the microbial community, leading to a better understanding of the role of microorganisms in the global oceans.

  • 49. Benson, Barbara J.
    et al.
    Magnuson, John J.
    Jensen, Olaf P.
    Card, Virginia M.
    Hodgkins, Glenn
    Korhonen, Johanna
    Livingstone, David M.
    Stewart, Kenton M.
    Weyhenmeyer, Gesa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Granin, Nick G.
    Extreme events, trends, and variability in Northern Hemisphere lake-ice phenology (1855-2005)2012In: Climatic Change, ISSN 0165-0009, E-ISSN 1573-1480, Vol. 112, no 2, p. 299-323Article in journal (Refereed)
    Abstract [en]

    Often extreme events, more than changes in mean conditions, have the greatest impact on the environment and human well-being. Here we examine changes in the occurrence of extremes in the timing of the annual formation and disappearance of lake ice in the Northern Hemisphere. Both changes in the mean condition and in variability around the mean condition can alter the probability of extreme events. Using long-term ice phenology data covering two periods 1855-6 to 2004-5 and 1905-6 to 2004-5 for a total of 75 lakes, we examined patterns in long-term trends and variability in the context of understanding the occurrence of extreme events. We also examined patterns in trends for a 30-year subset (1975-6 to 2004-5) of the 100-year data set. Trends for ice variables in the recent 30-year period were steeper than those in the 100- and 150-year periods, and trends in the 150-year period were steeper than in the 100-year period. Ranges of rates of change (days per decade) among time periods based on linear regression were 0.3-1.6 later for freeze, 0.5-1.9 earlier for breakup, and 0.7-4.3 shorter for duration. Mostly, standard deviation did not change, or it decreased in the 150-year and 100-year periods. During the recent 50-year period, standard deviation calculated in 10-year windows increased for all ice measures. For the 150-year and 100-year periods changes in the mean ice dates rather than changes in variability most strongly influenced the significant increases in the frequency of extreme lake ice events associated with warmer conditions and decreases in the frequency of extreme events associated with cooler conditions.

  • 50.
    Berga, Mercè
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Yinghua, Zha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Székely, Anna
    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.
    Testing responses of bacterial communities to environmental change using whole ecosystem manipulation experimentsManuscript (preprint) (Other academic)
1234567 1 - 50 of 547
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