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  • 201.
    Gudasz, Cristian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bastviken, David
    The Department of Thematic Studies - Water and Environmental Studies Linköping university.
    Koehler, Birgit
    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.
    Mineralization of organic carbon in lake sediments: temperature sensitivity and a comparison to soilsManuscript (preprint) (Other academic)
    Abstract [en]

    Temperature alone can explain a great amount of variation in sediment organic carbon (OC) mineralization. Studies on decomposition of soil OC suggest that the temperature sensitivity is different for the decomposition of labile and recalcitrant OC, but lake sediments with different contributions of labile and recalcitrant components have been reported to show similar temperature sensitivities. Sediment mineralization is typically measured in short-term incubations. However, whether the mineralization of OC in sediments dominated by recalcitrant and labile OC have different temperature sensitivities at the longer term is not clear. Here we show that during 5 months of continuous incubation of contrasting boreal lake sediments, sediment mineralization was strongly dependent on temperature and OC quality/origin but temperature sensitivity was similar across lakes and over time. Sediment mineralization showed low overall rates in spite of low apparent activation energy (Ea) compared to published rates of soil and litter mineralization. The fraction of the total OC pool that was lost during 5 months varied between 0.4 and 14%. The non-buried sediment OC pool was lost slowly, with apparent turnover times between 2.5 and 32 years. At a large scale, lake sediments, by showing lower mineralization rates than soils are more effective as carbon sinks.

     

  • 202.
    Gudasz, Cristian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bastviken, David
    Köhler, Birgit
    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.
    Temperature sensitivity of organic carbon mineralization in contrasting lake sediments2015In: Journal of Geophysical Research - Biogeosciences, ISSN 2169-8953, E-ISSN 2169-8961, Vol. 120, no 7, p. 1215-1225Article in journal (Refereed)
    Abstract [en]

    Temperature alone explains a great amount of variation in sediment organic carbon (OC) mineralization. Studies on decomposition of soil OC suggest that (1) temperature sensitivity differs between the fast and slowly decomposition OC and (2) over time, decreasing soil respiration is coupled with increase in temperature sensitivity. In lakes, autochthonous and allochthonous OC sources are generally regarded as fast and slowly decomposing OC, respectively. Lake sediments with different contributions of allochthonous and autochthonous components, however, showed similar temperature sensitivity in short-term incubation experiments. Whether the mineralization of OC in lake sediments dominated by allochthonous or autochthonous OC has different temperature sensitivity in the longer term has not been addressed. We incubated sediments from two boreal lakes that had contrasting OC origin (allochthonous versus autochthonous), and OC characteristics (C/N ratios of 21 and 10) at 1, 3, 5, 8, 13, and 21 degrees C for five months. Compared to soil and litter mineralization, sediment OC mineralization rates were low in spite of low apparent activation energy (E-a). The fraction of the total OC pool that was lost during five months varied between 0.4 and 14.8%. We estimate that the sediment OC pool not becoming long-term preserved was degraded with average apparent turnover times between 3 and 32years. While OC mineralization was strongly dependent on temperature as well as on OC composition and origin, temperature sensitivity was similar across lakes and over time. We suggest that the temperature sensitivity of OC mineralization in lake sediments is similar across systems within the relevant seasonal scales of OC supply and degradation.

  • 203.
    Guillemette, Francois
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    von Wachenfeldt, Eddie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Swedish Univ Agr Sci, Swedish Species Informat Ctr, Uppsala, Sweden..
    Kothawala, Dolly
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bastviken, David
    Linkoping Univ, Dept Themat Studies Environm Change, Linkoping, Sweden..
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Preferential sequestration of terrestrial organic matter in boreal lake sediments2017In: Journal of Geophysical Research - Biogeosciences, ISSN 2169-8953, E-ISSN 2169-8961, Vol. 122, no 4, p. 863-874Article in journal (Refereed)
    Abstract [en]

    The molecular composition and origin has recently been demonstrated to play a critical role in the persistence of organic matter in lake water, but it is unclear to what degree chemical attributes and sources may also control settling and burial of organic matter in lake sediments. Here we compared the annual contribution of allochthonous and autochthonous sources to the organic matter settling in the water column and present in the sediments of 12 boreal lakes. We used the fluorescence properties and elemental composition of the organic matter to trace its origin and found a consistent pattern of increasing contribution of terrestrial compounds in the sediments as compared to the settling matter, with an annual average allochthony of similar to 87% and similar to 57%, respectively. Seasonal data revealed a predominance of in-lake-produced compounds sinking in the water column in summer. Yet only a slight concurrent decrease in the contribution of terrestrial C to lake sediments was observed during the same period, and sediment allochthony increased again to high levels in autumn. Our results reveal a preferential preservation of allochthonous matter in the sediments and highlight the role of lakes as sequesters of organic carbon primarily originating from the surrounding landscape.

  • 204.
    Guillemette, François
    et al.
    Research Center for Watershed - Aquatic Ecosystem Interactions (RIVE), Université du Québec à Trois-Rivières, Québec, Canada.
    Mostovaya, Alina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Seasonal variability in dissolved organic carbon degradation in boreal lakes: links to composition, sources, and baseline metabolismManuscript (preprint) (Other academic)
  • 205.
    Guinea Barrientos, Héctor Estuardo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Swain, Ashok
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Uppsala Centre for Sustainable Development, CSD Uppsala.
    Wallin, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Nyberg, Lars
    Disaster Management Cooperation in Central America: The Case of Rainfall-induced Natural Disasters2015In: Geografiska Annaler. Series A, Physical Geography, ISSN 0435-3676, E-ISSN 1468-0459, Vol. 97, no 1, p. 85-96Article in journal (Refereed)
    Abstract [en]

    Rainfall-induced natural disasters rank first among all natural disasters in Central America. Due to the geographical conditions of the Central American region, it is common that two or more countries are struck by the same rainfall event, for example Hurricane Mitch in 1998 affected the entire Central American region, killing more than 18 000 people. As a consequence, Central American countries have started to promote regional policies and programs that aim for better preparation and response to these events, including disaster management cooperation. However, cooperation poses several challenges that may hinder its goals. In order to analyse these challenges, we present analysis in this paper of the current policy and legal institutions as well as the main challenges that may hinder international disaster management cooperation in Central America.

  • 206. Gurnell, Angela M.
    et al.
    O'Hare, Matthew T.
    O'Hare, Judith M.
    Scarlett, Peter
    Liffen, Thomas M. R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    The geomorphological context and impact of the linear emergent macrophyte, Sparganium erectum L.: a statistical analysis of observations from British rivers2013In: Earth Surface Processes and Landforms, ISSN 0197-9337, E-ISSN 1096-9837, Vol. 38, no 15, p. 1869-1880Article in journal (Refereed)
    Abstract [en]

    This paper explores the geomorphological context and impact of the widely-occurring, linear emergent macrophyte, Sparganium erectum. Forty-seven sites across Britain were selected for field investigation, spanning the range of environmental conditions within which Sparganium erectum had been found to be present in previous analyses of national data sets. A combination of descriptive graphs and statistics, principal components analysis, and Kruskal-Wallis tests were used to explore the large multivariate data set collected at the 47 sites. The analyses showed that Sparganium erectum is present in significant quantities in relatively narrow and shallow (< 18m wide and<0.9m deep to the limit of terrestrial vegetation), low gradient (maximum 0.004) channels of varying bed sediment calibre (cobble to silt). Within these environments, S. erectum stands (features) were associated with fine sediment retention, aggradation and submerged landform construction, leading to bench development and so, potentially, to adjustments in channel form and position. Sediment retention and landform construction within S. erectum features was most strongly apparent within reaches with a relatively high S. erectum cover and the presence of large area S. erectum features. It was also associated more weakly with S. erectum features that were comprised of relatively higher densities of plants with relatively smaller inter-plant spacing and fewer leaves. The sediment retained in S. erectum features and associated bench and bank toe deposits showed larger numbers and species of viable seeds, indicating the potential for colonization and growth of other species on S. erectum features once they aggrade above the low flow water level and are no longer a suitable habitat for S. erectum.

  • 207. Guy-Haim, Tamar
    et al.
    Alexander, Harriet
    Bell, Tom W.
    Bier, Raven L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bortolotti, Lauren E.
    Briseño-Avena, Christian
    Dong, Xiaoli
    Flanagan, Alison M.
    Grosse, Julia
    Grossmann, Lars
    Hasnain, Sarah
    Hovel, Rachel
    Johnston, Cora A.
    Miller, Dan R.
    Muscarella, Mario
    Noto, Akana E.
    Reisinger, Alexander J.
    Smith, Heidi J.
    Stamieszkin, Karen
    What are the type, direction, and strength of species, community, and ecosystem responses to warming in aquatic mesocosm studies and their dependency on experimental characteristics?: A systematic review protocol2017In: Environmental Evidence, ISSN 2047-2382, E-ISSN 2047-2382, Vol. 6, no 1, article id 6Article, review/survey (Refereed)
    Abstract [en]

    Mesocosm experiments have become increasingly popular in climate change research as they bridge the gap between small-scale, less realistic, microcosm experiments, and large-scale, more complex, natural systems. Characteristics of aquatic mesocosm designs (e.g., mesocosm volume, study duration, and replication) vary widely, potentially affecting the magnitude and direction of effect sizes measured in experiments. In this global systematic review we aim to identify the type, direction and strength of climate warming effects on aquatic species, communities and ecosystems in mesocosm experiments. Furthermore, we will investigate the context-dependency of the observed effects on several a priori determined effect moderators (ecological and methodological). Our conclusions will provide recommendations for aquatic scientists designing mesocosm experiments, as well as guidelines for interpretation of experimental results by scientists, policy-makers and the general public. Methods: We will conduct a systematic search using multiple online databases to gather evidence from the scientific literature on the effects of warming experimentally tested in aquatic mesocosms. Data from relevant studies will be extracted and used in a random effects meta-analysis to estimate the overall effect sizes of warming experiments on species performance, biodiversity and ecosystem functions. Experimental characteristics (e.g., mesocosm size and shape, replication-level, experimental duration and design, biogeographic region, community type, crossed manipulation) will be further analysed using subgroup analyses.

  • 208.
    Gómez-Gener, Lluís
    et al.
    Department of Ecology, University of Barcelona.
    Obrador, Biel
    Department of Ecology, University of Barcelona.
    von Schiller, Daniel
    Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country.
    Marcé, Rafael
    Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona.
    Casas-Ruiz, Joan Pere
    Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona.
    Proia, Lorenzo
    Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona.
    Acuña, Vicenç
    Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona.
    Catalán, Núria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Muñoz, Isabel
    Department of Ecology, University of Barcelona.
    Koschorreck, Matthias
    Department Lake Research, Helmholtz Centre for Environmental Research.
    Hot spots for carbon emissions from Mediterranean fluvial networks during summer drought2015In: Biogeochemistry, ISSN 0168-2563, E-ISSN 1573-515X, Vol. 125, no 3, p. 409-426Article in journal (Refereed)
    Abstract [en]

    During summer drought, Mediterranean fluvial networks are transformed into highly heterogeneous landscapes characterized by different environments (i.e., running and impounded waters, isolated river pools and dry beds). This hydrological setting defines novel biogeochemically active areas that could potentially increase the rates of carbon emissions from the fluvial network to the atmosphere. Using chamber methods, we aimed to identify hot spots for carbon dioxide (CO2) and methane (CH4) emissions from two typical Mediterranean fluvial networks during summer drought. The CO2 efflux from dry beds (mean ± SE = 209 ± 10 mmol CO2 m−2 d−1) was comparable to that from running waters (120 ± 33 mmol m−2 d−1) and significantly higher than from impounded waters (36.6 ± 8.5 mmol m−2 d−1) and isolated pools (17.2 ± 0.9 mmol m−2 d−1). In contrast, the CH4 efflux did not significantly differ among environments, although the CH4 efflux was notable in some impounded waters (13.9 ± 10.1 mmol CH4 m−2 d−1) and almost negligible in the remaining environments (mean <0.3 mmol m−2 d−1). Diffusion was the only mechanism driving CO2 efflux in all environments and was most likely responsible for CH4 efflux in running waters, isolated pools and dry beds. In contrast, the CH4 efflux in impounded waters was primarily ebullition-based. Using a simple heuristic approach to simulate potential changes in carbon emissions from Mediterranean fluvial networks under future hydrological scenarios, we show that an extreme drying out (i.e., a four-fold increase of the surface area of dry beds) would double the CO2 efflux from the fluvial network. Correspondingly, an extreme transformation of running waters into impounded waters (i.e., a twofold increase of the surface area of impounded waters) would triple the CH4 efflux. Thus, carbon emissions from dry beds and impounded waters should be explicitly considered in carbon assessments of fluvial networks, particularly under predicted global change scenarios, which are expected to increase the spatial and temporal extent of these environments.

  • 209.
    Habiba, G.
    et al.
    Univ Addis Ababa, Ethiopian Inst Water Resources, Addis Ababa, Ethiopia.
    Abebe, G.
    Univ Addis Ababa, Dept Zool Sci, Addis Ababa, Ethiopia.
    Bravo, Andrea G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ermias, D.
    Hawassa Univ, Addis Ababa, Ethiopia.
    Staffan, Ǻ.
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden.
    Bishop, Kevin
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden.
    Mercury Human Exposure in Populations Living Around Lake Tana (Ethiopia)2017In: Biological Trace Element Research, ISSN 0163-4984, E-ISSN 1559-0720, Vol. 175, no 2, p. 237-243Article in journal (Refereed)
    Abstract [en]

    A survey carried out in Lake Tana in 2015 found that Hg levels in some fish species exceeded internationally accepted safe levels for fish consumption. The current study assesses human exposure to Hg through fish consumption around the Lake Tana. Of particular interest was that a dietary intake of fishes is currently a health risk for Bihar Dar residents and anglers. Hair samples were collected from three different groups: anglers, college students and teachers, and daily laborers. A questionary includes gender, age, weight, activity. Frequency of fish consumption and origin of the eaten fish were completed by each participant. Mercury concentrations in hair were significantly higher (P value <0.05) for anglers (mean ± standard deviation 0.120 ± 0.199 μg/g) than college students (mean ± standard deviation 0.018 ± 0.039 μg/g) or daily workers (mean ± standard deviation 16 ± 9.5 ng/g). Anglers consumed fish more often than daily workers and college group. Moreover, there was also a strong correlation (P value <0.05) between the logarithms of total mercury and age associated with mercury concentration in scalp hair. Mercury concentrations in the hair of men were on average twice the value of the women. Also, users of skin lightening soap on a daily basis had 2.5 times greater mercury in scalp hair than non-users. Despite the different sources of mercury exposure mentioned above, the mercury concentrations of the scalp hair of participants of this study were below levels deemed to pose a threat to health.

  • 210.
    Hamilton, Joshua J.
    et al.
    University of Wisconsin—Madison, Madison, USA.
    Garcia, Sarahi L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Brown, Brittany S.
    University of Wisconsin—Madison, Madison, USA.
    Oyserman, Ben O.
    University of Wisconsin—Madison, Madison, USA.
    Moya-Flores, Francisco
    University of Wisconsin—Madison, Madison, USA.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Malmstrom, Rex R.
    United States Department of Energy Joint Genome Institute, Walnut Creek, USA.
    Forest, Katrina T.
    University of Wisconsin—Madison, Madison, USA.
    McMahon, Katherine D.
    University of Wisconsin—Madison, Madison, USA.
    Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI2017In: mSystems, E-ISSN 2379-5077, Vol. 2, no 4, article id e00091-17Article in journal (Refereed)
    Abstract [en]

    An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the “seed set framework,” which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U S A 105:14482–14487, 2008, https://doi.org/10.1073/pnas.0806162105 ), enables computational analysis of metabolic reconstructions while providing new insights into a microbe’s metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support of the hypothesis that members of the acI are photoheterotrophs.

  • 211. Hampton, Stephanie E.
    et al.
    Galloway, Aaron W. E.
    Powers, Stephen M.
    Ozersky, Ted
    Woo, Kara H.
    Batt, Ryan D.
    Labou, Stephanie G.
    O’Reilly, Catherine M.
    Sharma, Sapna
    Lottig, Noah R.
    Stanley, Emily H.
    North, Rebecca L.
    Stockwell, Jason D.
    Adrian, Rita
    Weyhenmeyer, Gesa A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Arvola, Lauri
    Baulch, Helen M.
    Bertani, Isabella
    Bowman, Larry L.
    Carey, Cayelan C.
    Catalan, Jordi
    Colom-Montero, William
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Domine, Leah M.
    Felip, Marisol
    Granados, Ignacio
    Gries, Corinna
    Grossart, Hans-Peter
    Haberman, Juta
    Haldna, Marina
    Hayden, Brian
    Higgins, Scott N.
    Jolley, Jeff C.
    Kahilainen, Kimmo K.
    Kaup, Enn
    Kehoe, Michael J.
    MacIntyre, Sally
    Mackay, Anson W.
    Mariash, Heather L.
    McKay, Robert M.
    Nixdorf, Brigitte
    Nõges, Peeter
    Nõges, Tiina
    Palmer, Michelle
    Pierson, Don C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Post, David M.
    Pruett, Matthew J.
    Rautio, Milla
    Read, Jordan S.
    Roberts, Sarah L.
    Rücker, Jacqueline
    Sadro, Steven
    Silow, Eugene A.
    Smith, Derek E.
    Sterner, Robert W.
    Swann, George E. A.
    Timofeyev, Maxim A.
    Toro, Manuel
    Twiss, Michael R.
    Vogt, Richard J.
    Watson, Susan B.
    Whiteford, Erika J.
    Xenopoulos, Marguerite A.
    Ecology under lake ice2017In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 20, no 1, p. 98-111Article, review/survey (Refereed)
    Abstract [en]

    Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer ‘growing seasons’. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass.

  • 212. Harrison, John A.
    et al.
    Barros, Nathan
    Bastviken, David
    Deemer, Bridget
    Evans, Christopher
    Grinham, Alistair
    Harby, Atle
    Lovelock, Catherine
    Peacock, Michael
    Prairie, Yves
    Sherman, Bradford
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Dams: weigh pros and cons case by case2019In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 568, no 7751, p. 171-171Article in journal (Other (popular science, discussion, etc.))
  • 213. Hastie, Adam
    et al.
    Lauerwald, Ronny
    Weyhenmeyer, Gesa A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Verpoorter, Charles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Univ Lille, Univ Littoral Cole Opale, CNRS, LOG,UMR 8187, Wimereux, France.
    Regnier, Pierre
    CO2 evasion from boreal lakes: Revised estimate, drivers of spatial variability, and future projections2018In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 24, no 2, p. 711-728Article in journal (Refereed)
    Abstract [en]

    Lakes (including reservoirs) are an important component of the global carbon (C) cycle, as acknowledged by the 5th assessment report of the IPCC. In the context of lakes, the boreal region is disproportionately important contributing to 27% of the worldwide lake area, despite representing just 14% of global land surface area. In this study, we used a statistical approach to derive a prediction equation for the partial pressure of CO2 (pCO2) in lakes as a function of lake area, terrestrial net primary productivity (NPP) and precipitation (r2 = 0.56), and to create the first high resolution, circumboreal map (0.5) of lake pCO2. The map of pCO2 was combined with lake area from the recently published GLOWABO database and three different estimates of the gas transfer velocity k to produce a resulting map of CO2 evasion (FCO2). For the boreal region we estimate an average, lake area weighted,pCO2 of 966 (678- 1325) μatm and a total FCO2 of 189 (74-347) Tg C yr−1, and evaluate the corresponding uncertainties based on Monte Carlo simulation. Our estimate of FCO2 is approximately twofold greater than previous estimates, as a result of methodological and data source differences. We use our results along with published estimates of the other C fluxes through inland waters to derive a C budget for the boreal region, and find that FCO2 from lakes is the most significant flux of the land-ocean aquatic continuum, and of a similar magnitude as emissions from forest fires. Using the model and applying it to spatially resolved projections of terrestrial NPP and precipitation while keeping everything else constant, we predict a 107% increase in boreal lake FCO2 under emission scenario RCP8.5 by 2100. Our projections are largely driven by increases in terrestrial NPP over the same period, showing the very close connection between the terrestrial and aquatic C cycle.

  • 214.
    Hawkes, Jeffrey A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Dittmar, Thorsten
    Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Res Grp Marine Geochem, D-26129 Oldenburg, Germany..
    Patriarca, Claudia
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Evaluation of the Orbitrap Mass Spectrometer for the Molecular Fingerprinting Analysis of Natural Dissolved Organic Matter2016In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 88, no 15, p. 7698-7704Article in journal (Refereed)
    Abstract [en]

    We investigated the application of the LTQ-Orbitrap mass spectrometer (LTQ-Velos Pro, Thermo Fisher) for resolving complex mixtures of natural aquatic dissolved organic matter (DOM) and compared this technique to the more established state-of-the-art technique, Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS, Bruker Daltonics), in terms of the distribution of molecular masses detected and the reproducibility of the results collected. The Orbitrap was capable of excellent reproducibility: Bray-Curtis dissimilarity between duplicate measurements was 2.85 +/- 0.42% (mean +/- standard deviation). The Orbitrap was also capable of the detection of most major ionizable organic molecules in typical aquatic mixtures, with the exception of most sulfur and phosphorus containing masses. This result signifies that the Orbitrap is an appropriate technique for the investigation of very subtle biogeochemical processing of bulk DOM. The lower costs (purchase and maintenance) and wider availability of Orbitrap mass spectrometers in university departments means that the tools necessary for research into DOM processing at the molecular level should be accessible to a much wider group of scientists than before. The main disadvantage of the technique is that substantially fewer molecular formulas can be resolved from a complex mixture (roughly one third as many), meaning some loss of information. In balance, most biogeochemical studies that aim at molecularly fingerprinting the source of natural DOM could be satisfactorily carried out with Orbitrap mass spectrometry. For more targeted metabolomic studies where individual compounds are traced through natural systems, FTICR-MS remains advantageous.

  • 215.
    Hawkes, Jeffrey A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Patriarca, Claudia
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Sjöberg, Per J. R.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Extreme isomeric complexity of dissolved organic matter found across aquatic environments2018In: Limnology and Oceanography Letters, E-ISSN 2378-2242, Vol. 3, no 2, p. 21-30Article in journal (Refereed)
    Abstract [en]

    The natural aquatic environment contains an enormous pool of dissolved reduced carbon, present as ultra‐complex mixtures that are constituted by an unknown number of compounds at vanishingly small concentrations. We attempted to separate individual structural isomers from several samples using online reversed‐phase chromatography with selected ion monitoring/tandem mass spectrometry, but found that isomeric complexity still presented a boundary to investigation even after chromatographic simplification of the samples. However, it was possible to determine that the structural complexity differed among samples. Our results also suggest that extreme structural complexity was a ubiquitous feature of dissolved organic matter (DOM) in all aquatic systems, meaning that this diversity may play similar roles for recalcitrance and degradation of DOM in all tested environments.

  • 216.
    Hawkes, Jeffrey A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Radoman, Nikola
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry. Stockholm Univ, Dept Environm Sci & Analyt Chem, Stockholm, Sweden.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Wallin, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Löfgren, Stefan
    Swedish Univ Agr Sci SLU, Dept Aquat Sci & Assessment, Sect Geochem & Hydrol, Uppsala, Sweden.
    Regional diversity of complex dissolved organic matter across forested hemiboreal headwater streams2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, no 1, article id 16060Article in journal (Refereed)
    Abstract [en]

    Dissolved organic matter (DOM) from soils enters the aquatic environment via headwater streams. Thereafter, it is gradually transformed, removed by sedimentation, and mineralised. Due to the proximity to the terrestrial source and short water residence time, the extent of transformation is minimal in headwaters. DOM has variable composition across inland waters, but the amount of variability in the terrestrial end member is unknown. This gap in knowledge is crucial considering the potential impact large variability would have on modelling DOM degradation. Here, we used a novel liquid chromatography –mass spectrometry method to characterise DOM in 74 randomly selected, forested headwater streams in an 87,000 km2 region of southeast Sweden. We found a large degree of sample similarity across this region, with Bray-Curtis dissimilarity values averaging 8.4 ± 3.0% (mean ± SD). The identified variability could be reduced to two principle coordinates, correlating to varying groundwater flow-paths and regional mean temperature. Our results indicate that despite reproducible effects of groundwater geochemistry and climate, the composition of DOM is remarkably similar across catchments already as it leaves the terrestrial environment, rather than becoming homogeneous as different headwaters and sub-catchments mix.

  • 217.
    Hawkes, Jeffrey A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Sjöberg, Per J. R.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Complexity of dissolved organic matter in the molecular size dimension: insights from coupled size exclusion chromatography electrospray ionisation mass spectrometry2019In: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 218, p. 52-71Article in journal (Refereed)
    Abstract [en]

    This paper investigates the relationship between apparent size distribution and molecular complexity of dissolved organic matter from the natural environment. We used a high pressure size exclusion chromatography (HPSEC) method coupled to UV-Vis diode array detection (UV-DAD) and electrospray ionisation mass spectrometry (ESI-MS) in order to compare the apparent size of natural organic matter, determined by HPSEC-UV and the molecular mass determined online by ESI-MS. We found that there was a clear discrepancy between the two methods, and found evidence for an important pool of organic matter that has a strong UV absorbance and no ESI-MS signal. Contrary to some previous research, we found no evidence that apparently high molecular weight organic matter is constituted by aggregates of low molecular weight (<1000 Da) material. Furthermore, our results suggest that the majority of apparent size variability within the ESI ionisable pool of organic matter is due to secondary interaction and exclusion effects on the HPSEC column, and not true differences in hydrodynamic size or intermolecular aggregation.

  • 218. He, Shaomei
    et al.
    Ivanova, Natalia
    Kirton, Edward
    Allgaier, Martin
    Bergin, Claudia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Scheffrahn, Rudolf H.
    Kyrpides, Nikos C.
    Warnecke, Falk
    Tringe, Susannah G.
    Hugenholtz, Philip
    Comparative Metagenomic and Metatranscriptomic Analysis of Hindgut Paunch Microbiota in Wood- and Dung-Feeding Higher Termites2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 4, p. e61126-Article in journal (Refereed)
    Abstract [en]

    Termites effectively feed on many types of lignocellulose assisted by their gut microbial symbionts. To better understand the microbial decomposition of biomass with varied chemical profiles, it is important to determine whether termites harbor different microbial symbionts with specialized functionalities geared toward different feeding regimens. In this study, we compared the microbiota in the hindgut paunch of Amitermes wheeleri collected from cow dung and Nasutitermes corniger feeding on sound wood by 16S rRNA pyrotag, comparative metagenomic and metatranscriptomic analyses. We found that Firmicutes and Spirochaetes were the most abundant phyla in A. wheeleri, in contrast to N. corniger where Spirochaetes and Fibrobacteres dominated. Despite this community divergence, a convergence was observed for functions essential to termite biology including hydrolytic enzymes, homoacetogenesis and cell motility and chemotaxis. Overrepresented functions in A. wheeleri relative to N. corniger microbiota included hemicellulose breakdown and fixed-nitrogen utilization. By contrast, glycoside hydrolases attacking celluloses and nitrogen fixation genes were overrepresented in N. corniger microbiota. These observations are consistent with dietary differences in carbohydrate composition and nutrient contents, but may also reflect the phylogenetic difference between the hosts.

  • 219.
    He, Shaomei
    et al.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.;Univ Wisconsin, Dept Geosci, Madison, WI USA..
    Stevens, Sarah L. R.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA..
    Chan, Leong-Keat
    DOE Joint Genome Inst, Walnut Creek, CA USA..
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    del Rio, Tijana Glavina
    DOE Joint Genome Inst, Walnut Creek, CA USA..
    Tringe, Susannah G.
    DOE Joint Genome Inst, Walnut Creek, CA USA..
    Malmstrom, Rex R.
    DOE Joint Genome Inst, Walnut Creek, CA USA..
    McMahon, Katherine D.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.;Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA..
    Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes2017In: MSPHERE, ISSN 2379-5042, Vol. 2, no 5, article id e00277-17Article in journal (Refereed)
    Abstract [en]

    Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly) saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called "Planctomycete-specific" cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly) saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called " Planctomycete-specific" cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.

  • 220.
    Heinrich, Friederike
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Abundance and diveristy of Alphaproteobacteria in the Southern Ocean: the dark side of SAR11Manuscript (preprint) (Other academic)
    Abstract [en]

    Alphaproteobacteria represented by lineages such as SAR11 and Roseobacter are ubiquitous and often dominant in marine bacterioplankton communities. The Southern Ocean is no exception even if annual extremes in light regime and autochthonous inputs of organic substrates present an environment that are in many ways very different from other oceanic regions. Using population mapping and community analysis of bacterioplankton during the highly dynamic summer season within the Ross and Amundsen Seas, in combination with experimental incubations under contrasting light regimes, we studied the impact of solar radiation and other environmental factors on individual lineages and populations within class Alphaproteobacteria. Quantitative population tracking by fluorescence in-situ hybridization was combined with pyrosequencing-derived 16S rRNA gene inventories to resolve the community beyond class and abundant lineages. Both experiments and depth-resolved distribution patterns confirm SAR11 as a major component of the bacterial community regardless of water mass and depth. However, the experiments revealed that SAR11 as a lineage was less competitive under solar-exposed conditions whereas the opposite response was observed for Roseobacter. Resolving the SAR11 linage into subclades, clear partitioning of groups between the different water masses and light regimes was observed. Also the diversity within the SAR11 lineage varied with significantly higher richness in the deeper, permanently dark water masses. Using this abundant marine bacterial lineage as a model, we could demonstrate clear separation of closely related bacterial populations between water masses and along environmental gradients of light exposure, oxygen availability, phytoplankton and nutrients. It is evident that such ecologically coherent populations can only be tracked at high phylogenetic resolution and that ecological and evolutionary mechanisms underpinning the observed phylogeographic patterns differ between water masses in the Southern Ocean. 

  • 221.
    Heinrich, Friederike
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Alteration of lake bacterioplankton diversity and community composition during lake stratification and gradual oxygen depletionManuscript (preprint) (Other academic)
    Abstract [en]

    Hypolimnetic waters of many stratifying lakes experience gradual oxygen depletion and seasonal hypoxia as organic matter is degraded with oxygen as terminal electron acceptor. Such changes are known to have dramatic effects on larger organisms, but also resident microbiota are likely to be affected by altered availability of oxygen, nutrients and other chemical constituents. We explored how such seasonal shifts in water mass characteristics influenced the resident bacterioplankton in a mesotrophic temperate lake by tracing the temporal dynamics of bacterial communities and populations at different phylogenetic resolution across the entire period of summer stratification. Compared to the epilimnion, bacterial richness was significantly higher in the hypolimnion where varying hypoxia was also reflected in higher beta diversity. Many abundant groups of freshwater bacteria, such as Actinobacteria acI, Polynucleobacter and freshwater SAR11 (LD12), were abundant in both the epi- and hypolimnion, with distinct temporal and vertical population shifts observed at the 97% population identity level. The mechanisms that lead to closely related populations partitioning into ecotypes are not well understood, but are probably due to fine-tuned physiological adaptions towards oxygen and nutrient concentrations in the lake. The existence of ecotypes partitioned by oxygen availability and the seasonal succession in hypolimnetic bacteria driven by gradual oxygen depletion and associated changes in water chemistry merits further studies on their implications for biogeochemical cycles.

  • 222.
    Heinrich, Friederike
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Drivers of Population Dynamics in Bacterioplankton: Spotlight on Alphaproteobacteria and its dominant SAR11 Lineage2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bacteria are mediators of biogeochemical cycles and are in this way vital for maintaining life on earth. Their distribution, abundance and functioning are driven by environmental heterogeneity and dynamic change in abiotic and biotic factors. Both, freshwater lakes and oceans play central roles in the global carbon cycle and bacteria in these systems perform many services for the ecosystems, such as the transfer of organic carbon from primary producers to higher trophic levels. With estimated relative abundances up to 50% of the total bacterioplankton, the Alphaproteobacteria lineage SAR11 is the most abundant group of aquatic bacteria. It is globally distributed and can be partitioned into multiple sub-clades, one of which is exclusive to freshwaters. Until recently, the distribution, abundance and ecological role of this freshwater SAR11 named LD12 was unknown. The aim of the thesis was to study the drivers and mechanisms that influence the dynamics of aquatic bacterial communities in general and the SAR11 and LD12 groups in particular. The thesis consists of environmental surveys of a mesotrophic Lake Erken and the western Southern Ocean, an experiment and a data-mining exercise to reveal the phylogenetic structure of the SAR11 lineage on various temporal and spatial scales. The analysis of a long-term bacterioplankton community survey in lake Erken provided insights about the dynamics of the entire bacterial community and the LD12 population over an annual cycle. The results demonstrate that LD12 can be an equally abundant member of freshwater communities as marine SAR11 in oceans. LD12 featured strong seasonality and was positively coupled to environmental conditions indicative for an oligotrophic lifestyle. LD12 as well as other dominant lake bacterioplankton also maintained stable populations throughout spatial and temporal varying environments, but at high phylogenetic resolution, habitat preferences were revealed, particularly in response to oxygen concentrations. The later was not the case in LD12 as a single ribotype dominated. This is in stark contrast to the habitat partitioning with light availability, depth and water masses observed for marine SAR11 subclades in the Southern Ocean. The global data-mining corroborated that LD12 as a group was much less diverse than SAR11 furthermore, suggesting that the marine-freshwater barrier acted as a population bottleneck. My work shows that bacterial populations can respond in very different ways to environmental drivers, highlight the importance of highly resolved temporal and spatial scales as well as the need for high phylogenetic resolutions to target ecologically coherent populations.

    List of papers
    1. Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11)
    Open this publication in new window or tab >>Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11)
    Show others...
    2010 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, no 2, p. 347-357Article in journal (Refereed) Published
    Abstract [en]

    The aquatic bacterial group SAR11 is one of the most abundant organisms on Earth, with an estimated global population size of 2.4 x 10(28) cells in the oceans. Members of SAR11 have also been detected in brackish and fresh waters, but the evolutionary relationships between the species present in the different environments have been ambiguous. In particular, it was not clear how frequently this lineage has crossed the saline-freshwater boundary during its evolutionary diversification. Due to the huge population size of SAR11 and the potential of microbes for long-distance dispersal, we hypothesized that environmental transitions could have occurred repeatedly during the evolutionary diversification of this group. Here, we have constructed extensive 16S rDNA-based molecular phylogenies and undertaken metagenomic data analyses to assess the frequency of saline-freshwater transitions in SAR11 and to investigate the evolutionary implications of this process. Our analyses indicated that very few saline-freshwater transitions occurred during the evolutionary diversification of SAR11, generating genetically distinct saline and freshwater lineages that do not appear to exchange genes extensively via horizontal gene transfer. In contrast to lineages from saline environments, extant freshwater taxa from diverse, and sometimes distant, geographic locations were very closely related. This points to a rapid diversification and dispersal in fresh waters or to slower evolutionary rates in fresh water SAR11 when compared with marine counterparts. In addition, the colonization of both saline and fresh waters appears to have occurred early in the evolution of SAR11. We conclude that the different biogeochemical conditions that prevail in saline and fresh waters have likely prevented the environmental transitions in SAR11, promoting the evolution of clearly distinct lineages in each environment.

    Keywords
    environmental transitions, prokaryotes, saline, freshwater, SAR11, 16S rDNA
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-137815 (URN)10.1093/molbev/msp239 (DOI)000273704400013 ()
    Available from: 2010-12-17 Created: 2010-12-16 Last updated: 2017-12-11Bibliographically approved
    2. Abundance and diveristy of Alphaproteobacteria in the Southern Ocean: the dark side of SAR11
    Open this publication in new window or tab >>Abundance and diveristy of Alphaproteobacteria in the Southern Ocean: the dark side of SAR11
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Alphaproteobacteria represented by lineages such as SAR11 and Roseobacter are ubiquitous and often dominant in marine bacterioplankton communities. The Southern Ocean is no exception even if annual extremes in light regime and autochthonous inputs of organic substrates present an environment that are in many ways very different from other oceanic regions. Using population mapping and community analysis of bacterioplankton during the highly dynamic summer season within the Ross and Amundsen Seas, in combination with experimental incubations under contrasting light regimes, we studied the impact of solar radiation and other environmental factors on individual lineages and populations within class Alphaproteobacteria. Quantitative population tracking by fluorescence in-situ hybridization was combined with pyrosequencing-derived 16S rRNA gene inventories to resolve the community beyond class and abundant lineages. Both experiments and depth-resolved distribution patterns confirm SAR11 as a major component of the bacterial community regardless of water mass and depth. However, the experiments revealed that SAR11 as a lineage was less competitive under solar-exposed conditions whereas the opposite response was observed for Roseobacter. Resolving the SAR11 linage into subclades, clear partitioning of groups between the different water masses and light regimes was observed. Also the diversity within the SAR11 lineage varied with significantly higher richness in the deeper, permanently dark water masses. Using this abundant marine bacterial lineage as a model, we could demonstrate clear separation of closely related bacterial populations between water masses and along environmental gradients of light exposure, oxygen availability, phytoplankton and nutrients. It is evident that such ecologically coherent populations can only be tracked at high phylogenetic resolution and that ecological and evolutionary mechanisms underpinning the observed phylogeographic patterns differ between water masses in the Southern Ocean. 

    Keywords
    Southern Ocean, Alphaproteobacteria, SAR11, Roseobacter, community composition, solar radiation
    National Category
    Ecology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-245066 (URN)
    Available from: 2015-02-24 Created: 2015-02-24 Last updated: 2015-04-17
    3. Seasonality and environmental control of freshwater SAR11 (LD12) in a temperate lake (Lake Erken, Sweden)
    Open this publication in new window or tab >>Seasonality and environmental control of freshwater SAR11 (LD12) in a temperate lake (Lake Erken, Sweden)
    2013 (English)In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 70, no 1, p. 33-44Article in journal (Refereed) Published
    Abstract [en]

    THE SAR11 clade is ubiquitous and abundant in planktonic environments. In freshwater lakes, the clade is represented by tribe LD12 which is phylogenetically distinct from the marine SAR11. We studied the ecology of LD12 in a temperate dimictic lake (Lake Erken, Sweden), by analyzing its seasonal dynamics with quantitative PCR, CARD-FISH and 454 pyrosequencing of the 16S rRNA gene. Results showed that LD12 can be as numerous in freshwater bacterioplankton as their marine SAR11 siblings. They exhibited strong seasonality and made up from 1.8 to 40% of the total bacterial 16S rRNA pool (mean 14%) with pronounced peaks in summer and late fall. Except in spring, LD12 was the dominant Alphaproteobacteria, contributing on average 72% of the 16S rRNA within this class. The LD12 population was dominated by a single persistent ribotype, suggesting low local divergence, at least at the phylogenetic resolution accessed with rRNA genes. The relative abundance of LD12 was positively correlated to nutrient concentrations (phosphate, ammonia, nitrate, and silica) and water transparency whereas the relative abundance was lower during periods characterized by high phytoplankton biomass. Based on these observations we propose that LD12 are poor competitors during periods of high phytoplankton productivity and associated release of labile organic compounds, but thrive when availability of inorganic nutrients is high. Similar to the marine SAR11 sibling group, local LD12 populations appear to respond in contrasting ways to nutrient availability in different lakes, pointing to either ecological divergence within the tribe or variations in the interplay between environmental driver variables.

    Keywords
    LD12, Freshwater SAR11, Alphaproteobacteria, Seasonal dynamics, Quantitative PCR, 454 Pyrosequencing, CARD-FISH, 16S rRNA
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-207118 (URN)10.3354/ame01637 (DOI)000322999500003 ()
    Available from: 2013-09-10 Created: 2013-09-09 Last updated: 2017-12-06Bibliographically approved
    4. Alteration of lake bacterioplankton diversity and community composition during lake stratification and gradual oxygen depletion
    Open this publication in new window or tab >>Alteration of lake bacterioplankton diversity and community composition during lake stratification and gradual oxygen depletion
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Hypolimnetic waters of many stratifying lakes experience gradual oxygen depletion and seasonal hypoxia as organic matter is degraded with oxygen as terminal electron acceptor. Such changes are known to have dramatic effects on larger organisms, but also resident microbiota are likely to be affected by altered availability of oxygen, nutrients and other chemical constituents. We explored how such seasonal shifts in water mass characteristics influenced the resident bacterioplankton in a mesotrophic temperate lake by tracing the temporal dynamics of bacterial communities and populations at different phylogenetic resolution across the entire period of summer stratification. Compared to the epilimnion, bacterial richness was significantly higher in the hypolimnion where varying hypoxia was also reflected in higher beta diversity. Many abundant groups of freshwater bacteria, such as Actinobacteria acI, Polynucleobacter and freshwater SAR11 (LD12), were abundant in both the epi- and hypolimnion, with distinct temporal and vertical population shifts observed at the 97% population identity level. The mechanisms that lead to closely related populations partitioning into ecotypes are not well understood, but are probably due to fine-tuned physiological adaptions towards oxygen and nutrient concentrations in the lake. The existence of ecotypes partitioned by oxygen availability and the seasonal succession in hypolimnetic bacteria driven by gradual oxygen depletion and associated changes in water chemistry merits further studies on their implications for biogeochemical cycles.

    Keywords
    hypolimnion, Bacteria, Community Composition, Diversity, Hypoxia, Dynamics, Indicator, Habitat
    National Category
    Ecology
    Research subject
    Biology with specialization in Evolutionary Genetics; Biology with specialization in Limnology
    Identifiers
    urn:nbn:se:uu:diva-245068 (URN)
    Available from: 2015-02-24 Created: 2015-02-24 Last updated: 2015-04-17
    5. Coherent dynamics and association networks among lake bacterioplankton taxa
    Open this publication in new window or tab >>Coherent dynamics and association networks among lake bacterioplankton taxa
    2012 (English)In: The ISME Journal: multidisciplinary journal of microbial ecology, ISSN 1751-7362, Vol. 6, no 2, p. 330-342Article in journal (Refereed) Published
    Abstract [en]

    Bacteria have important roles in freshwater food webs and in the cycling of elements in the ecosystem. Yet specific ecological features of individual phylogenetic groups and interactions among these are largely unknown. We used 454 pyrosequencing of 16S rRNA genes to study associations of different bacterioplankton groups to environmental characteristics and their co-occurrence patterns over an annual cycle in a dimictic lake. Clear seasonal succession of the bacterioplankton community was observed. After binning of sequences into previously described and highly resolved phylogenetic groups (tribes), their temporal dynamics revealed extensive synchrony and associations with seasonal events such as ice coverage, ice-off, mixing and phytoplankton blooms. Coupling between closely and distantly related tribes was resolved by time-dependent rank correlations, suggesting ecological coherence that was often dependent on taxonomic relatedness. Association networks with the abundant freshwater Actinobacteria and Proteobacteria in focus revealed complex interdependencies within bacterioplankton communities and contrasting linkages to environmental conditions. Accordingly, unique ecological features can be inferred for each tribe and reveal the natural history of abundant cultured and uncultured freshwater bacteria.

    Keywords
    freshwater, 454 pyrosequencing, 16S rRNA, phylogenetic tribes, bacteria
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-171679 (URN)10.1038/ismej.2011.113 (DOI)000300984200011 ()
    Available from: 2012-03-26 Created: 2012-03-25 Last updated: 2016-04-22Bibliographically approved
  • 223.
    Heinrich, Friederike
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Seasonality and environmental control of freshwater SAR11 (LD12) in a temperate lake (Lake Erken, Sweden)2013In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 70, no 1, p. 33-44Article in journal (Refereed)
    Abstract [en]

    THE SAR11 clade is ubiquitous and abundant in planktonic environments. In freshwater lakes, the clade is represented by tribe LD12 which is phylogenetically distinct from the marine SAR11. We studied the ecology of LD12 in a temperate dimictic lake (Lake Erken, Sweden), by analyzing its seasonal dynamics with quantitative PCR, CARD-FISH and 454 pyrosequencing of the 16S rRNA gene. Results showed that LD12 can be as numerous in freshwater bacterioplankton as their marine SAR11 siblings. They exhibited strong seasonality and made up from 1.8 to 40% of the total bacterial 16S rRNA pool (mean 14%) with pronounced peaks in summer and late fall. Except in spring, LD12 was the dominant Alphaproteobacteria, contributing on average 72% of the 16S rRNA within this class. The LD12 population was dominated by a single persistent ribotype, suggesting low local divergence, at least at the phylogenetic resolution accessed with rRNA genes. The relative abundance of LD12 was positively correlated to nutrient concentrations (phosphate, ammonia, nitrate, and silica) and water transparency whereas the relative abundance was lower during periods characterized by high phytoplankton biomass. Based on these observations we propose that LD12 are poor competitors during periods of high phytoplankton productivity and associated release of labile organic compounds, but thrive when availability of inorganic nutrients is high. Similar to the marine SAR11 sibling group, local LD12 populations appear to respond in contrasting ways to nutrient availability in different lakes, pointing to either ecological divergence within the tribe or variations in the interplay between environmental driver variables.

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

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

  • 225. Herlemann, Daniel P. R.
    et al.
    Labrenz, Matthias
    Juergens, Klaus
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Waniek, Joanna J.
    Andersson, Anders F.
    Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea2011In: The ISME Journal, ISSN 1751-7362, Vol. 5, no 10, p. 1571-1579Article in journal (Refereed)
    Abstract [en]

    Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater-freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche.

  • 226.
    Herrero Ortega, Sonia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. Leibniz Inst Freshwater Ecol & Inland Fisheries I, Dept Expt Limnol, Stechlin, Germany.
    Catalán, Núria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. Catalan Inst Water Res ICRA, Girona, Spain.
    Björn, Erik
    Gröntoft, Hannes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Hilmarsson, Torfi Geir
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wu, Pianpian
    Bishop, Kevin
    Levanoni, Oded
    Bravo, Andrea Garcia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    High methylmercury formation in ponds fueled by fresh humic and algal derived organic matter2018In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 63, no S1, p. S44-S53Article in journal (Refereed)
    Abstract [en]

    Neurotoxic methylmercury causes adverse effects to ecosystem viability and human health. Previous studies have revealed that ponding alters natural organic matter (NOM) composition and increase methylmercury concentrations in rivers, especially in the first years after flooding. Here, we investigate the influence of NOM composition (i.e., sources and degradation status) on mercury methylation rate constants in nine boreal beaver ponds of different ages across Sweden.We show that increased methylmercury concentrations in surface waters is a consequence of enhanced mercury methylation in the pond sediments. Moreover, our results reveal that during the first years after the initial flooding, mercury methylation rates are fueled by the amount of fresh humic substances released from the flooded soils and by an increased production of algal-derived NOM triggered by enhanced nutrient availability. Our findings indicate that impoundment-induced changes in NOM composition control mercury methylation processes, causing the raise in MeHg levels in ponds.

  • 227. Hillebrand, Helmut
    et al.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lebret, Karen
    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.
    Östman, Örjan
    Striebel, Maren
    Decomposing multiple dimensions of stability in global change experiments2018In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 21, no 1, p. 21-30Article in journal (Refereed)
    Abstract [en]

    Ecological stability is the central framework to understand an ecosystem's ability to absorb or recover from environmental change. Recent modelling and conceptual work suggests that stability is a multidimensional construct comprising different response aspects. Using two freshwater mesocosm experiments as case studies, we show how the response to single perturbations can be decomposed in different stability aspects (resistance, resilience, recovery, temporal stability) for both ecosystem functions and community composition. We find that extended community recovery is tightly connected to a nearly complete recovery of the function (biomass production), whereas systems with incomplete recovery of the species composition ranged widely in their biomass compared to controls. Moreover, recovery was most complete when either resistance or resilience was high, the latter associated with low temporal stability around the recovery trend. In summary, no single aspect of stability was sufficient to reflect the overall stability of the system.

  • 228. Hilt, Sabine
    et al.
    Wanke, Thomas
    Scharnweber, Kristin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Brauns, Mario
    Syväranta, Jari
    Brothers, Soren
    Gaedke, Ursula
    Köhler, Jan
    Lischke, Betty
    Mehner, Thomas
    Contrasting response of two shallow eutrophic cold temperate lakes to a partial winterkill of fish2015In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 749, no 1, p. 31-42Article in journal (Refereed)
    Abstract [en]

    Food-web effects of winterkill are difficult to predict as the enhanced mortality of planktivorous fish may be counterbalanced by an even higher mortality of piscivores. We hypothesised that a winterkill in a clear and a turbid shallow lake would equalise their fish community composition, but seasonal plankton successions would differ between lakes. After a partial winterkill, we observed a reduction of fish biomass by 16 and 43% in a clear-water and a turbid small temperate lake, respectively. Fish biomass and piscivore shares (5% of fish biomass) were similar in both lakes after this winterkill, but young-of-the-year (YOY) abundances were higher in the turbid lake. Top-down control by crustaceans was only partly responsible for low phytoplankton biomass at the end of May following the winterkill in both lakes. Summer phytoplankton biomass remained low in the clear-water lake despite high abundances of YOY fish (mainly roach). In contrast, the crustacean biomass of the turbid lake was reduced in summer by a high YOY abundance (sunbleak and roach), leading to a strong increase in phytoplankton biomass. The YOY abundance of fish in shallow eutrophic lakes may thus be more important for their summer phytoplankton development after winterkill than the relative abundance of piscivores.

  • 229. Hinrichsen, H. -H
    et al.
    Petereit, C
    von Dewitz, B
    Haslob, H
    Ustups, D
    Florin, A. -B
    Nissling, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Biophysical modeling of survival and dispersal of Central and Eastern Baltic Sea flounder (Platichthys flesus) larvae2018In: Journal of Sea Research, ISSN 1385-1101, Vol. 142, p. 11-20Article in journal (Refereed)
    Abstract [en]

    The period of larval drift into a suitable nursery area is considered to be of great significance for recruitment variability in flatfish. Here, a hydrodynamic model coupled with a Lagrangian particle tracking technique was utilized to study the drift from the first feeding larval stage until time of settlement of Central and Eastern Baltic flounder (Platichthys flesus), originating from spawning in the Baltic Sea deep basins, the Arkona- and Bornholm basin (central Baltic Sea), and the Gdansk deep and Gotland basin (eastern Baltic Sea). We examined the spatio-temporal dynamics of the probability to settle in preferred nursery habitat by detailed drift model simulations. The study suggests that the majority of larvae (89% and 74% for Central- and Eastern Baltic flounder, respectively) drift towards coastal areas and settle at metamorphosis ≤20 km from a sandy habitat enabling further migration to a preferred nursery area, i.e. larval drift seems not to be a major bottleneck in recruitment of flounder spawning in the Baltic Sea deep basins. The drift model results suggest that Central Baltic flounder utilize nursery areas mainly in the central and western Baltic, and in the Kattegat, whereas Eastern Baltic flounder mainly utilize the coast in the central and eastern Baltic. Thus, the two stock components seem to use different nursery areas following settlement. Further, in accordance with the “nursery size hypothesis”, the model demonstrates that larvae from the Bornholm basin, utilizing areas with extensive distribution of preferred nursery habitat, display the highest relative successful transport to nursery grounds until settling (72% of successfully settled larvae), suggesting that spawning in the Bornholm Basin is of great importance for stock recruitment of deep basin spawning Baltic flounder.

  • 230.
    Hinrichsen, Hans-Harald
    et al.
    GEOMAR Helmholtz Ctr Ocean Res Kiel, Dusternbrooker Weg 20, D-24105 Kiel, Germany..
    Petereit, Christoph
    GEOMAR Helmholtz Ctr Ocean Res Kiel, Dusternbrooker Weg 20, D-24105 Kiel, Germany..
    Nissling, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wallin, Isa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Ustups, Didzis
    Inst Food Safety Anim Hlth & Environm BIOR, Daugavgrivas Str 8, LV-1048 Riga, Latvia..
    Florin, Ann-Britt
    Swedish Univ Agr Sci, Dept Aquat Resources, Inst Coastal Res, Skolgatan 6, S-74242 Oregrund, Sweden..
    Survival and dispersal variability of pelagic eggs and yolk-sac larvae of central and eastern baltic flounder (Platichthys flesus): application of biophysical models2017In: ICES Journal of Marine Science, ISSN 1054-3139, E-ISSN 1095-9289, Vol. 74, no 1, p. 41-55Article in journal (Refereed)
    Abstract [en]

    A hydrodynamic model coupled with a Lagrangian particle tracking technique was utilized to simulate spatially and temporally resolved long-term environmentally related (i) size of habitat suitable for reproduction, (ii) egg/yolk-sac larval survival, (iii) separation of causes of mortality, and (iv) connectivity between spawning areas of Baltic flounder with pelagiceggs. Information on reproduction habitat requirements and mortality sources were obtained from field or laboratory studies. In our modelling study we only quantified physical processes generating heterogeneity in spatial distribution of eggs and yolk-sac larvae, as e.g. predation is not accounted for. The spatial extent of eggs and larvae represented as modelled particles is primarily determined by oxygen and salinity conditions. The reproduction habitat most suitable was determined for the Gdansk Deep, followed by the Bornholm Basin. Relatively low habitat suitability was obtained for the Arkona Basin and the Gotland Basin. The model runs also showed yolk-sac larval survival to be to a large extent affected by sedimentation. Eggs initially released in the Arkona Basin and Bornholm Basin are strongly affected by sedimentation compared with those released in the Gdansk Deep and Gotland Basin. Highest relative survival of eggs occurred in the Gdansk Deep and in the Bornholm Basin. Relatively low survival rates in the Gotland Basin were attributable to oxygen-dependent mortality. Oxygen content had almost no impact on survival in the Arkona Basin. For all spawning areas mortality caused by lethally low temperatures was only evident after severe winters. Buoyancy of eggs and yolk-sac larvae in relation to topographic features appear as a barrier for the transport of eggs and yolk-sac larvae and potentially limits the connectivity of early life stages between the different spawning areas.

  • 231.
    Hirsch, Philipp E
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Phenotypic Processes Triggered by Biological Invasions2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Individuals within a single population can vary widely in their phenotype e.g. in their body shape. These differences are an important source of biodiversity and they can precede evolutionary divergence within a population.

    In this thesis we use the biological invasion of the zebra mussels into Swedish lakes to investigate which processes create or maintain phenotypic diversity within populations of the two native fish species perch and roach and the mussel itself. Both fishes have specially adapted body shapes that depend on whether they feed in the near-shore or open-water habitat of lakes. This habitat-specific divergence was more pronounced in lakes with zebra mussels, probably because resources in both habitats were in higher supply due to the mussels’ effects on the lakes. Divergence in perch body shapes between habitats was also higher in lakes with a higher water clarity, suggesting that visual conditions can affect the resource use and thus also the expression of a habitat-specific body shape.

    When investigating the diversity of body shapes in the mussel itself we found that mussels from one lake changed their shell shape when exposed to different predators: fish predators induced a more elongated shell shape while crayfish predators induced a rounder shell. These specific shell shapes probably serve as two alternative predator defenses protecting the mussel from predation.

    We conclude that the availability and use of distinct resources is an important source of diversity within populations. Abiotic conditions can play a previously underappreciated role by promoting or impairing the use of the distinct resources thus affecting the divergence. The diversity of shell shapes we found in the zebra mussels complements our study by demonstrating that not only consumer responses to resources but also resources’ responses to predators can generate phenotypic diversity.

    List of papers
    1. Different venues, different menus: causes and consequences of disruptive selection in natural populations
    Open this publication in new window or tab >>Different venues, different menus: causes and consequences of disruptive selection in natural populations
    2011 (English)Manuscript (preprint) (Other academic)
    National Category
    Biological Sciences
    Research subject
    Biology
    Identifiers
    urn:nbn:se:uu:diva-158670 (URN)
    Available from: 2011-09-13 Created: 2011-09-13 Last updated: 2013-06-12
    2. Indirect trophic interactions with an invasive species affect phenotypic divergence in a top consumer
    Open this publication in new window or tab >>Indirect trophic interactions with an invasive species affect phenotypic divergence in a top consumer
    2013 (English)In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 172, no 1, p. 245-256Article in journal (Refereed) Published
    Abstract [en]

    While phenotypic responses to direct species interactions are well studied, we know little about the consequences of indirect interactions for phenotypic divergence.In this study we used lakes with and without the zebra mussel to investigate effects ofindirect trophic interactions on phenotypic divergence between littoral and pelagic perch. We found a greater phenotypic divergence between littoral and pelagic individuals inlakes with zebra mussels and propose a mussel-mediated increase in pelagic and benthic resource availability as a major factor underlying this divergence. Lakes withzebra mussels contained higher densities of large plankton taxa and large invertebrates. We suggest that this augmented resource availability improved perch foraging opportunities in both the littoral and pelagic zones. Perch in both habitats could hence express a more specialized foraging morphology, leading to an increased divergence of perch forms in lakes with zebra mussels. As perch do not prey on mussels directly, we conclude that the increased divergence results from indirect interactions with the mussels. Our results hence suggest that species at lower food web levels can indirectlyaffect phenotypic divergence in species at the top of the food chain.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-158687 (URN)10.1007/s00442-013-2611-1 (DOI)000317686800022 ()
    Available from: 2011-09-13 Created: 2011-09-13 Last updated: 2017-12-08Bibliographically approved
    3. Replicated divergence in two consumer species affected by resource availability
    Open this publication in new window or tab >>Replicated divergence in two consumer species affected by resource availability
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    food web, resource polymorphisms, adaptive foraging, morphological divergence, Rutilus rutilus, Perca fluviatilis
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-158685 (URN)
    Available from: 2011-09-13 Created: 2011-09-13 Last updated: 2013-02-11
    4. 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
    5. Plastic Responses of a Sessile Prey to Multiple Predators: A Field and Experimental Study
    Open this publication in new window or tab >>Plastic Responses of a Sessile Prey to Multiple Predators: A Field and Experimental Study
    2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 12, p. e115192-Article in journal (Refereed) Published
    Abstract [en]

    Background: Theory predicts that prey facing a combination of predators with different feeding modes have two options: to express a response against the feeding mode of the most dangerous predator, or to express an intermediate response. Intermediate phenotypes protect equally well against several feeding modes, rather than providing specific protection against a single predator. Anti-predator traits that protect against a common feeding mode displayed by all predators should be expressed regardless of predator combination, as there is no need for trade-offs. Principal Findings: We studied phenotypic anti-predator responses of zebra mussels to predation threat from a handling-time-limited (crayfish) and a gape-size-limited (roach) predator. Both predators dislodge mussels from the substrate but diverge in their further feeding modes. Mussels increased expression of a nonspecific defense trait (attachment strength) against all combinations of predators relative to a control. In response to roach alone, mussels showed a tendency to develop a weaker and more elongated shell. In response to crayfish, mussels developed a harder and rounder shell. When exposed to either a combination of predators or no predator, mussels developed an intermediate phenotype. Mussel growth rate was positively correlated with an elongated weaker shell and negatively correlated with a round strong shell, indicating a trade-off between anti-predator responses. Field observations of prey phenotypes revealed the presence of both anti-predator phenotypes and the trade-off with growth, but intra-specific population density and bottom substrate had a greater influence than predator density. Conclusions: Our results show that two different predators can exert both functionally equivalent and inverse selection pressures on a single prey. Our field study suggests that abiotic factors and prey population density should be considered when attempting to explain phenotypic diversity in the wild.

    Keywords
    trade-off, multiple predators, inducible defenses, Dreissena polymorpha, Rutilus rutilus, Pacifastacus leniusculus
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-158690 (URN)10.1371/journal.pone.0115192 (DOI)000347215600054 ()
    Available from: 2011-09-13 Created: 2011-09-13 Last updated: 2017-12-08Bibliographically approved
  • 232.
    Hirsch, Philipp E
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Cayon, Diaz
    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.
    Plastic Responses of a Sessile Prey to Multiple Predators: A Field and Experimental Study2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 12, p. e115192-Article in journal (Refereed)
    Abstract [en]

    Background: Theory predicts that prey facing a combination of predators with different feeding modes have two options: to express a response against the feeding mode of the most dangerous predator, or to express an intermediate response. Intermediate phenotypes protect equally well against several feeding modes, rather than providing specific protection against a single predator. Anti-predator traits that protect against a common feeding mode displayed by all predators should be expressed regardless of predator combination, as there is no need for trade-offs. Principal Findings: We studied phenotypic anti-predator responses of zebra mussels to predation threat from a handling-time-limited (crayfish) and a gape-size-limited (roach) predator. Both predators dislodge mussels from the substrate but diverge in their further feeding modes. Mussels increased expression of a nonspecific defense trait (attachment strength) against all combinations of predators relative to a control. In response to roach alone, mussels showed a tendency to develop a weaker and more elongated shell. In response to crayfish, mussels developed a harder and rounder shell. When exposed to either a combination of predators or no predator, mussels developed an intermediate phenotype. Mussel growth rate was positively correlated with an elongated weaker shell and negatively correlated with a round strong shell, indicating a trade-off between anti-predator responses. Field observations of prey phenotypes revealed the presence of both anti-predator phenotypes and the trade-off with growth, but intra-specific population density and bottom substrate had a greater influence than predator density. Conclusions: Our results show that two different predators can exert both functionally equivalent and inverse selection pressures on a single prey. Our field study suggests that abiotic factors and prey population density should be considered when attempting to explain phenotypic diversity in the wild.

  • 233.
    Hirsch, Philipp E
    et al.
    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.
    Reyes, Martha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Quevedo, Mario
    Cantabrian Institute of Biodiversity (ICAB), Oviedo University, Departmento Biología Organismos y Sistemas, Campus del Cristo, 33006 Oviedo, Spain.
    Fransson, Rebecca
    Svanbäck, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Replicated divergence in two consumer species affected by resource availabilityManuscript (preprint) (Other academic)
  • 234.
    Hirsch, Philipp E
    et al.
    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.
    Svanbäck, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Indirect trophic interactions with an invasive species affect phenotypic divergence in a top consumer2013In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 172, no 1, p. 245-256Article in journal (Refereed)
    Abstract [en]

    While phenotypic responses to direct species interactions are well studied, we know little about the consequences of indirect interactions for phenotypic divergence.In this study we used lakes with and without the zebra mussel to investigate effects ofindirect trophic interactions on phenotypic divergence between littoral and pelagic perch. We found a greater phenotypic divergence between littoral and pelagic individuals inlakes with zebra mussels and propose a mussel-mediated increase in pelagic and benthic resource availability as a major factor underlying this divergence. Lakes withzebra mussels contained higher densities of large plankton taxa and large invertebrates. We suggest that this augmented resource availability improved perch foraging opportunities in both the littoral and pelagic zones. Perch in both habitats could hence express a more specialized foraging morphology, leading to an increased divergence of perch forms in lakes with zebra mussels. As perch do not prey on mussels directly, we conclude that the increased divergence results from indirect interactions with the mussels. Our results hence suggest that species at lower food web levels can indirectlyaffect phenotypic divergence in species at the top of the food chain.

  • 235. Ho, Lionel
    et al.
    Hoefel, Daniel
    Grasset, Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Palazot, Sebastien
    Newcombe, Gayle
    Saint, Christopher P.
    Brookes, Justin D.
    Removal of cyanobacterial metabolites through wastewater treatment plant filters2012In: Water Science and Technology, ISSN 0273-1223, E-ISSN 1996-9732, Vol. 65, no 7, p. 1244-1251Article in journal (Refereed)
    Abstract [en]

    Wastewaters have the potential to proliferate excessive numbers of cyanobacteria due to high nutrient levels. This could translate to the production of metabolites, such as the saxitoxins, geosmin and 2-methylisoborneol (MIB), which can impair the quality of wastewater destined for re-use. Biological sand filtration was assessed for its ability to remove these metabolites from a wastewater. Results indicated that the sand filter was incapable of effectively removing the saxitoxins and in some instances, the effluent of the sand filter displayed greater toxicity than the influent. Conversely, the sand filter was able to effectively remove geosmin and MIB, with removal attributed to biodegradation. Granular activated carbon was employed as an alternative filter medium to remove the saxitoxins. Results showed similar removals to previous drinking water studies, where efficient removals were initially observed, followed by a decrease in the removal; a consequence of the presence of competing organics which reduced adsorption of the saxitoxins.

  • 236.
    Hoarfrost, Adrienne
    et al.
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27515 USA;Rutgers State Univ, Dept Biochem & Microbiol, New Brunswick, NJ 08901 USA.
    Balmonte, John Paul
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27515 USA.
    Ghobrial, Sherif
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27515 USA.
    Ziervogel, Kai
    Univ New Hampshire, Inst Study Earth Oceans & Space, Durham, NH 03824 USA.
    Bane, John
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27515 USA.
    Gawarkiewicz, Glen
    Woods Hole Oceanog Inst, Dept Phys Oceanog, Woods Hole, MA 02543 USA.
    Arnosti, Carol
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27515 USA.
    Gulf Stream Ring Water Intrusion on the Mid-Atlantic Bight Continental Shelf Break Affects Microbially Driven Carbon Cycling2019In: Frontiers in Marine Science, E-ISSN 2296-7745, Vol. 6, article id 394Article in journal (Refereed)
    Abstract [en]

    Warm core, anticyclonic rings that spin off from the Gulf Stream circulate through the region directly offshore of the Mid-Atlantic Bight. If a warm core ring reaches the continental shelf break, its warm, highly saline water may subduct under cooler, fresher continental shelf surface water, resulting in subsurface waters at the shelf break and over the upper continental slope with high temperatures and salinities and distinct physical and chemical properties characteristic of Gulf Stream water. Such intruding water may also have microbial communities with distinct functional capacities, which may in turn affect the rate and nature of carbon cycling in this coastal/shelf environment. However, the functional capabilities of microbial communities within ring intrusion waters relative to surrounding continental shelf waters are largely unexplored. We investigated microbial community capacity to initiate organic matter remineralization by measuring hydrolysis of a suite of polysaccharide, peptide, and glucose substrates along a transect oriented across the Mid-Atlantic Bight shelf, shelf break, and upper slope. At the outermost sampling site, warm and salty water derived from a Gulf Stream warm core ring was present in the lower portion of the water column. This water exhibited hydrolytic capacities distinct from other sampling sites, and exhibited lower heterotrophic bacterial productivity overall. Warm core rings adjacent to the Mid-Atlantic Bight shelf have increased in frequency and duration in recent years. As the influence of warm core rings on the continental shelf and slope increases in the future, the rate and nature of organic matter remineralization on the continental shelf may also shift.

  • 237.
    Hubalek, Valerie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Exposing the Dark Microbial Biosphere2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Dark biosphere research has been widely neglected, although by volume this biome comprises the lion’s share of habitats on our planet. In these systems the main metabolic strategies are of chemotrophic nature, leading to gradual depletion of redox gradients essential for sustaining life. Thus these environments are regarded more or less close to chemical equilibrium.

    Here, we use sequence data of whole community metagenomes and taxonomic marker approaches to study the ecology of environments close to the thermodynamic limit: deep terrestrial aquifers and aphotic systems impacted by petroleum- derived products. We show that these systems select for individuals with reduced genomes and cell sizes, likely as a mode to save energy. Due to genome reduction, these so called “streamlined” cells are reduced in the number of genes and metabolic pathways. This loss has led to community members sharing the metabolic burden of synthesizing in particular energy costly metabolites, creating tight interdependencies between the community members, as a consequence. In addition, we propose that cells scavenging anabolic products derived from detrital biomass and intermediate fermentation products are equally important in these systems. Hence, life at the thermodynamic limit involves a much more complex biological system than previously shown, that goes beyond traditionally described electron- and intermediate metabolite-transfer dependencies.

    This thesis furthermore includes ecological implications, demonstrating how species diversity and community metabolism are shaped by redox gradients and dispersal potential in the deep biosphere and contaminated sediments. This research is also relevant from a practical point of view, as it pinpoints new opportunities for enhanced bioremediation through metabolite additions in order to raise the efficiency of degradation processes.

    List of papers
    1. Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations
    Open this publication in new window or tab >>Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations
    Show others...
    2016 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 5, p. 1192-1203Article in journal (Refereed) Published
    Abstract [en]

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

    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-264125 (URN)10.1038/ismej.2015.185 (DOI)000374377200016 ()26484735 (PubMedID)
    Funder
    Swedish Research Council, 621-2014-4398Swedish Research Council, 2012-3892The Crafoord Foundation, 20130557
    Note

    Supplementary information available for this article at http://www.nature.com/ismej/journal/v10/n5/suppinfo/ismej2015185s1.html

    Available from: 2015-10-06 Created: 2015-10-06 Last updated: 2017-12-01Bibliographically approved
    2. Connectivity driven bacterial diversity patterns and functional potential in three deep aquifers of the Fennoscandian shield
    Open this publication in new window or tab >>Connectivity driven bacterial diversity patterns and functional potential in three deep aquifers of the Fennoscandian shield
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-264126 (URN)
    Available from: 2015-10-06 Created: 2015-10-06 Last updated: 2015-11-10
    3. Metabolic partitioning in an alkane degrading bioreactor operating under methanogenic condition
    Open this publication in new window or tab >>Metabolic partitioning in an alkane degrading bioreactor operating under methanogenic condition
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-264127 (URN)
    Available from: 2015-10-06 Created: 2015-10-06 Last updated: 2015-11-10
    4. Functional potential of microbial communities in freshwater sediments affected by century-long tar-contamination
    Open this publication in new window or tab >>Functional potential of microbial communities in freshwater sediments affected by century-long tar-contamination
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-264128 (URN)
    Available from: 2015-10-06 Created: 2015-10-06 Last updated: 2015-11-10
  • 238.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Buck, Moritz
    Tan, BoonFei
    Foght, Julia
    Wendeberg, Annelie
    Berry, David
    Bertilsson, Stefan
    Eiler, Alexander
    Metabolic partitioning in an alkane degrading bioreactor operating under methanogenic conditionManuscript (preprint) (Other academic)
  • 239.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tan, BoonFei
    University of Alberta, Edmonton, Canada; Singapore-MIT Alliance for Research and Technology, Leipzig, Germany.
    Foght, Julia
    University of Alberta, Edmonton, Canada.
    Wendeberg, Annelie
    Centre for Environmental Research, Leipzig, Germany.
    Berry, David
    University of Vienna, Vienna, Austria.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. eDNA Solutions AB, Mölndal, Sweden.
    Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions2017In: mSystems, E-ISSN 2379-5077, Vol. 2, no 5, article id e00038-17Article in journal (Refereed)
    Abstract [en]

    Syntrophy among Archaea and Bacteria facilitates the anaerobic degra- dation of organic compounds to CH4 and CO2 . Particularly during aliphatic and aro- matic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutu- alistic microbial partners are of central importance. Using micromanipulation com- bined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methano- genic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermenta- tion of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and inter- mediate fermentation products derived from detrital biomass was a common fea- ture. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2 -producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocar- bon transformation. IMPORTANCE

  • 240.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Richert, Inga
    Peura, Sari
    Saw, Jimmy
    Wendeberg, Annelie
    Ettema, Thijs
    Bertilsson, Stefan
    Functional potential of microbial communities in freshwater sediments affected by century-long tar-contaminationManuscript (preprint) (Other academic)
  • 241.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wu, Xiaofen
    Eiler, Alexander
    Buck, Moritz
    Heim, Christine
    Dopson, Mark
    Bertilsson, Stefan
    Ionescu, Danny
    Connectivity driven bacterial diversity patterns and functional potential in three deep aquifers of the Fennoscandian shieldManuscript (preprint) (Other academic)
  • 242.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wu, Xiaofen
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Heim, Christine
    Univ Gottingen, GZG Geobiol, Gottingen, Germany.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ionescu, Danny
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Neuglobsow, Germany.
    Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 10, p. 2447-2458Article in journal (Refereed)
    Abstract [en]

    Little research has been conducted on microbial diversity deep under the Earth/'s surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

  • 243. Humborg, Christoph
    et al.
    Andersen, Hans Estrup
    Blenckner, Thorsten
    Gadegast, Mathias
    Giesler, Reiner
    Hartmann, Jens
    Hugelius, Gustaf
    Hürdler, Jens
    Kortelainen, Pirkko
    Blicher-Mathiesen, Gitte
    Venohr, Markus
    Weyhenmeyer, Gesa A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Environmental Impacts—Freshwater Biogeochemistry2015In: Second Assessment of Climate Change for the Baltic Sea Basin, Cham: Springer, 2015, p. 307-336Chapter in book (Other academic)
  • 244.
    Huser, Brian J.
    et al.
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Box 7050, S-75007 Uppsala, Sweden..
    Egemose, Sara
    Univ Southern Denmark, Dept Biol, Campusvej 55, DK-5230 Odense M, Denmark..
    Harper, Harvey
    ERD Environm Res & Design, 3419 Trentwood Blvd,Suite 102, Orlando, FL USA..
    Hupfer, Michael
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Berlin, Germany..
    Jensen, Henning
    Univ Southern Denmark, Dept Biol, Campusvej 55, DK-5230 Odense M, Denmark..
    Pilgrim, Keith M.
    Barr Engn, 4077 77th St, Minneapolis, MN 55304 USA..
    Reitzel, Kasper
    Univ Southern Denmark, Dept Biol, Campusvej 55, DK-5230 Odense M, Denmark..
    Rydin, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Futter, Martyn
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Box 7050, S-75007 Uppsala, Sweden..
    Longevity and effectiveness of aluminum addition to reduce sediment phosphorus release and restore lake water quality2016In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 97, p. 122-132Article in journal (Refereed)
    Abstract [en]

    114 lakes treated with aluminum (Al) salts to reduce internal phosphorus (P) loading were analyzed to identify factors driving longevity of post-treatment water quality improvements. Lakes varied greatly in morphology, applied Al dose, and other factors that may have affected overall treatment effectiveness. Treatment longevity based on declines in epilimnetic total P (TP) concentration averaged 11 years for all lakes (range of 0-45 years). When longevity estimates were used for lakes with improved conditions through the end of measurements, average longevity increased to 15 years. Significant differences in treatment longevity between deeper, stratified lakes (mean 21 years) and shallow, polymictic lakes (mean 5.7 years) were detected, indicating factors related to lake morphology are important for treatment success. A decision tree developed using a partition model suggested Al dose, Osgood index (01, a morphological index), and watershed to lake area ratio (related to hydraulic residence time, WA:LA) were the most important variables determining treatment longevity. Multiple linear regression showed that Al dose, WA:LA, and 01 explained 47, 32 and 3% respectively of the variation in treatment longevity. Other variables (too data limited to include in the analysis) also appeared to be of importance, including sediment P content to Al dose ratios and the presence of benthic feeding fish in shallow, polymictic lakes.

  • 245.
    Hållén, Joakim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    PCB i Oxundasjön och Rosersbergsviken: Prediktiv modellering av återhämtningsscenarier2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A regional survey of environmentally harmful substances in fish in autumn 2013 revealed elevated levels of polychlorinated biphenyls (PCBs) in perch from Lake Oxundasjön, north of Upplands Väsby in Stockholm County. Follow-up studies have shown that the quantity of PCBs contained in the lake is unique of its kind in Sweden, and that the area of influence also includes downstream Rosersbergsviken, a bay of Lake Mälaren. The elevated concentrations in fish exceed today's market limits and environmental quality standards for PCBs, as of this, responsible authorities discourage from consumption of fish from Lake Oxundasjön and Rosersbergsviken. The aim has been to use statistical analyses and mass-balance modelling to study the current state of the lake system and how it may evolve in the future under different circumstances.

    There is a statistically significant correlation between PCB levels in sediment and perch from 21 different sites in the Stockholm-Mälaren region, including Lake Oxundasjön and Rosersbergsviken, this was demonstrated with a linear regression model. With the multivariate analysis method principal component analysis (PCA), it was illustrated how the contaminant levels in fish from Lake Oxundasjön and Rosersbergsviken differed on contaminant levels in fish from other sites. The difference mainly concerned the size and composition of PCBs.

    Mass-balance modelling of quantities and flows of PCBs in Lake Oxundasjön and Rosersbergsviken was made in the simulation program STELLA®. The modelling indicated that the system currently serves as a secondary distribution source of PCBs to the environment. The recovery of PCB levels is slow in the system, it will take more than 25 years for concentrations in fish to reach today’s market limits and environmental quality standards for PCBs. The model was used to evaluate three different treatment methods for Lake Oxundasjön: dredging, capping and activated carbon treatment. Simulations of these treatments led to a substantial improvement of the PCB situation in Lake Oxundasjön. Moreover, they also had a positive impact on the recovery process in the downstream Rosersbergsviken. Future climate changes, with warmer temperatures and higher run off, led to a slightly faster recovery progress of PCBs in the system. 

  • 246. Ingram, Travis
    et al.
    Svanbäck, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Kraft, Nathan
    Kratina, Pavel
    Southcott, Laura
    Schluter, Dolph
    Intraguild predation drives evolutionary niche shift in threespine stickleback2012In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 66, no 6, p. 1819-1832Article in journal (Refereed)
    Abstract [en]

    Intraguild predation—competition and predation by the same antagonist—is widespread, but its evolutionary consequences are unknown. Intraguild prey may evolve antipredator defenses, superior competitive ability on shared resources, or the ability to use an alternative resource, any of which may alter the structure of the food web. We tested for evolutionary responses by threespine stickleback to a benthic intraguild predator, prickly sculpin. We used a comparative morphometric analysis to show that stickleback sympatric with sculpin are more armored and have more limnetic-like body shapes than allopatric stickleback. To test the ecological implications of this shift, we conducted a mesocosm experiment that varied sculpin presence and stickleback population of origin (from one sympatric and one allopatric lake). Predation by sculpin greatly increased the mortality of allopatric stickleback. In contrast, sculpin presence did not affect the mortality of sympatric stickleback, although they did have lower growth rates suggesting increased nonpredatory effects of sculpin. Consistent with their morphology, sympatric stickleback included more pelagic prey in their diets, leading to depletion of zooplankton in the mesocosms. These findings suggest that intraguild prey evolution has altered food web structure by reducing both predation by the intraguild predator and diet overlap between species

  • 247.
    Isidorova, Anastasija
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bravo, Andrea G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Riise, Gunnhild
    Norwegian Univ Life Sci, Dept Environm Sci, Akershus, Norway..
    Bouchet, Sylvain
    Umea Univ, Dept Chem, Umea, Sweden..
    Björn, Erik
    Umea Univ, Dept Chem, Umea, Sweden..
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    The effect of lake browning and respiration mode on the burial and fate of carbon and mercury in the sediment of two boreal lakes2016In: Journal of Geophysical Research - Biogeosciences, ISSN 2169-8953, E-ISSN 2169-8961, Vol. 121, no 1, p. 233-245Article in journal (Refereed)
    Abstract [en]

    In many northern temperate regions, the water color of lakes has increased over the past decades (lake browning), probably caused by an increased export of dissolved organic matter from soils. We investigated if the increase in water color in two lakes in Norway has resulted in increased burial of organic carbon (OC) and mercury (Hg) in the sediments and if the Hg was prone to methylation. Lake Solbergvann experienced a threefold water color increase, and OC burial increased approximately twofold concomitant to the water color increase. This lake had prolonged periods of anoxic bottom water, and anoxic OC mineralization rates were only about half of the oxic OC mineralization rates (7.7 and 17.5g C m(-2)yr(-1), respectively), contributing to an efficient OC burial. In Lake Elvaga, where water color increase was only approximately twofold and bottom water was oxygenated, no recent increase in OC burial could be observed. Hg burial increased strongly in both lakes (threefold and 1.6-fold in Lake Solbergvann and Lake Elvaga, respectively), again concomitant to the recent water color increase. The proportion of methylated Hg (MeHg) in surficial sediment was 1 order of magnitude higher in Lake Elvaga (up to 6% MeHg) than in Lake Solbergvann (0.2-0.6% MeHg), probably related to the different oxygenation regimes. We conclude that lake browning can result in increased OC and Hg burial in lake sediments, but the extent of browning and the dominating mode of sediment respiration (aerobic or anaerobic) strongly affect burial and fate of OC and Hg in sediments.

  • 248.
    Isidorova, Anastasija
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Grasset, Charlotte
    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.
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Methane formation in tropical reservoirs predicted from sediment age and nitrogen2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 11017Article in journal (Refereed)
    Abstract [en]

    Freshwater reservoirs, in particular tropical ones, are an important source of methane (CH4) to the atmosphere, but current estimates are uncertain. The CH4 emitted from reservoirs is microbially produced in their sediments, but at present, the rate of CH4 formation in reservoir sediments cannot be predicted from sediment characteristics, limiting our understanding of reservoir CH4 emission. Here we show through a long-term incubation experiment that the CH4 formation rate in sediments of widely different tropical reservoirs can be predicted from sediment age and total nitrogen concentration. CH4 formation occurs predominantly in sediment layers younger than 6-12 years and beyond these layers sediment organic carbon may be considered effectively buried. Hence mitigating reservoir CH4 emission via improving nutrient management and thus reducing organic matter supply to sediments is within reach. Our model of sediment CH4 formation represents a first step towards constraining reservoir CH4 emission from sediment characteristics.

  • 249.
    Isidorova, Anastasija
    et al.
    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. Univ Fed Juiz de Fora, Dept Biol, Lab Aquat Ecol, Juiz De Fora, Brazil.
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Reduced Mineralization of Terrestrial OC in Anoxic Sediment Suggests Enhanced Burial Efficiency in Reservoirs Compared to Other Depositional Environments2019In: Journal of Geophysical Research - Biogeosciences, ISSN 2169-8953, E-ISSN 2169-8961, Vol. 124, no 3, p. 678-688Article in journal (Refereed)
    Abstract [en]

    Freshwater reservoirs are important sites of organic carbon (OC) burial, but the extent to which reservoir OC burial is a new anthropogenic carbon sink is currently unclear. While burial of aquatic OC (by, e.g., phytoplankton) in reservoirs may count as a new C sink, the burial of terrestrial OC in reservoirs constitutes a new C sink only if the burial is more efficient in reservoirs than in other depositional environments. We carried out incubation experiments that mimicked the environmental conditions of different depositional environments along the land‐sea continuum (oxic and anoxic freshwater, oxic and anoxic seawater, oxic river bedload, and atmosphere‐exposed floodplain) to investigate whether reservoirs bury OC more efficiently compared to other depositional environments. For sediment OC predominantly of terrestrial origin, OC degradation rates were significantly lower, by a factor of 2, at anoxic freshwater and saltwater conditions compared to oxic freshwater and saltwater, river, and floodplain conditions. However, the transformation of predominantly terrestrial OC to methane was one order of magnitude higher in anoxic freshwater than at other conditions. For sediment OC predominantly of aquatic origin, OC degradation rates were uniformly high at all conditions, implying equally low burial efficiency of aquatic OC (76% C loss in 57 days). Since anoxia is more common in reservoirs than in the coastal ocean, these results suggest that reservoirs are a depositional environment in which terrestrial OC is prone to become buried at higher efficiency than in the ocean but where also the terrestrial OC most efficiently is transformed to methane.

  • 250. Jacobsen, Carsten Suhr
    et al.
    Nielsen, Tue Kjærgaard
    Vester, Jan Kjølhede
    Stougaard, Peter
    Nielsen, Jeppe Lund
    Voriskova, Jana
    Winding, Anne
    Baldrian, Petr
    Liu, Binbin
    Frostegård, Åsa
    Pedersen, Dorthe
    Tveit, Alexander Tøsdal
    Svenning, Mette Marianne
    Tebbe, Christoph C.
    Øvreås, Lise
    Jakobsen, Pia Bach
    Blazewicz, Steven J.
    Hubablek, Valerie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Hansen, Lars Hestbjerg
    Cary, S. Craig
    Holben, William E.
    Ekelund, Flemming
    Bælum, Jacob
    Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 5711Article in journal (Refereed)
    Abstract [en]

    Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. An extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.

2345678 201 - 250 of 654
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