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  • 151.
    Engel, Fabian
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Drakare, Stina
    Swedish Univ Agr Sci SLU, Dept Aquat Sci & Assessment, POB 7050, S-75007 Uppsala, Sweden.
    Weyhenmeyer, Gesa A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Environmental conditions for phytoplankton influenced carbon dynamics in boreal lakes2019Inngår i: Aquatic Sciences, ISSN 1015-1621, E-ISSN 1420-9055, Vol. 81, nr 2, artikkel-id 35Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The partial pressure of CO2 (pCO(2)) in lake water, and thus CO2 emissions from lakes are controlled by hydrologic inorganic carbon inputs into lakes, and in-lake carbon transformation (mainly organic carbon mineralization and CO2 uptake by primary producers). In boreal lakes, CO2 uptake by phytoplankton is often considered to be of minor importance. At present, however, it is not known in which and how many boreal lakes phytoplankton CO2 uptake has a sizeable influence on the lake water pCO(2). Using water physico-chemical and phytoplankton data from 126 widely spread Swedish lakes from 1992 to 2012, we found that pCO(2) was negatively related to phytoplankton carbon in lakes in which the phytoplankton share in TOC (C-phyto:TOC ratio) exceeded 5%. Total phosphorus concentration (TP) was the strongest predictor of spatial variation in the C-phyto:TOC ratio, where C-phyto:TOC ratios>5% occurred in lakes with TP>30 mu gl(-1). These lakes were located in the hemi-boreal zone of central and southern Sweden. We conclude that during summer, phytoplankton CO2 uptake can reduce the pCO(2) not only in warm eutrophic lakes, but also in relatively nutrient poor hemi-boreal lakes.

  • 152.
    Engel, Fabian
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Farrell, Kaitlin J.
    McCullough, Ian M.
    Scordo, Facundo
    Denfeld, Blaize A.
    Dugan, Hilary A.
    de Eyto, Elvira
    Hanson, Paul C.
    McClure, Ryan P.
    Nõges, Peeter
    Nõges, Tiina
    Ryder, Elizabeth
    Weathers, Kathleen C.
    Weyhenmeyer, Gesa A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    A lake classification concept for a more accurate global estimate of the dissolved inorganic carbon export from terrestrial ecosystems to inland waters2018Inngår i: The Science of Nature: Naturwissenschaften, ISSN 0028-1042, E-ISSN 1432-1904, Vol. 105, nr 3, artikkel-id 25Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The magnitude of lateral dissolved inorganic carbon (DIC) export from terrestrial ecosystems to inland waters strongly influences the estimate of the global terrestrial carbon dioxide (CO2) sink. At present, no reliable number of this export is available, and the few studies estimating the lateral DIC export assume that all lakes on Earth function similarly. However, lakes can function along a continuum from passive carbon transporters (passive open channels) to highly active carbon transformers with efficient in-lake CO2 production and loss. We developed and applied a conceptual model to demonstrate how the assumed function of lakes in carbon cycling can affect calculations of the global lateral DIC export from terrestrial ecosystems to inland waters. Using global data on in-lake CO2 production by mineralization as well as CO2 loss by emission, primary production, and carbonate precipitation in lakes, we estimated that the global lateral DIC export can lie within the range of 0.70(-0.31)(+0.27) 1.52(-0.90)(+1.09) Pg C yr(-1) depending on the assumed function of lakes. Thus, the considered lake function has a large effect on the calculated lateral DIC export from terrestrial ecosystems to inland waters. We conclude that more robust estimates of CO2 sinks and sources will require the classification of lakes into their predominant function. This functional lake classification concept becomes particularly important for the estimation of future CO2 sinks and sources, since in-lake carbon transformation is predicted to be altered with climate change.

  • 153.
    Englund, David
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution.
    Brunberg, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Jacks, Gunnar
    A Case Study of a Freshwater Pearl Mussel (Margaritifera margaritifera) Population in Central Sweden2008Inngår i: Geografiska Annaler. Series A, Physical Geography, ISSN 0435-3676, E-ISSN 1468-0459, Vol. 90A, nr 4, s. 251-258Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Most of the Margaritifera margaritifera populations in Sweden are not reproducing. Land use such as forestry, eutrophication and water regulation for hydropower are commonly reported causes for the absence of reproduction. A brook with a very dense population of pearl mussels has been investigated with regard to the age distribution of the population and their habitat, in order to discover the reason for the absence of reproduction. The population consisted almost entirely of old mussels with very few young ones. The water flow and chemistry of the water are very stable and well buffered, due to a large glacifluvial deposit in the catchment area. The substrate in the stream is favourable and well aerated to a depth of at least 15 cm. Forestry has been practised with care for at least the last 15 years to avoid siltation of the stream sediments. The most likely reason for the lack of reproduction seems to be the water regulation of the main stream introduced 60 years ago, which has left the main stream dry seasonally. This is likely to have affected the population of brown trout which is the host for the first life-stage of the mussels, the glochidia.

  • 154.
    Erlandsson, Martin
    et al.
    University of Reading, UK.
    Cory, Neil
    SLU.
    Fölster, Jens
    SLU Department of Aquatic Sciences and Assessment.
    Köhler, Stephan
    SLU Department of Aquatic Sciences and Assessment.
    Laudon, Hjalmar
    SLU Department of Forest Ecology and Management.
    Weyhenmeyer, Gesa A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper, Luft-, vatten och landskapslära. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bishop, Kevin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper, Luft-, vatten och landskapslära.
    Increasing Dissolved Organic Carbon Redefines the Extent of Surface Water Acidification and Helps Resolve a Classic Controversy2011Inngår i: BioScience, ISSN 0006-3568, E-ISSN 1525-3244, Vol. 61, nr 8, s. 614-618Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Concentrations of organic acids in freshwaters have increased significantly during recent decades across large parts of Europe and North America. Different theories of the causes (e.g., recovery from acidification, climate change, land use) have different implications for defining the preindustrial levels for dissolved organic carbon (DOC), which are crucial for assessing acidification and other aspects of water quality. We demonstrate this by classifying the acidification status of 66 lakes with long-term observations, representative of about 12,700 acid-sensitive lakes in nemoral and boreal Sweden. Of these lakes, 47% are classified as significantly acidified (Delta pH >= 0.4), assuming preindustrial DOC levels were equal to those observed in 1990. But if instead, the higher DOC levels observed in 2009 define preindustrial conditions, half as many lakes are acidified (24%). This emphasizes the need to establish reference levels for DOC and casts new light on the classic controversy about natural versus anthropogenic acidification.

  • 155. Erlandsson, Martin
    et al.
    Futter, Martyn N.
    Kothawala, Dolly N.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Kohler, Stephan J.
    Variability in spectral absorbance metrics across boreal lake waters2012Inngår i: Journal of Environmental Monitoring, ISSN 1464-0325, E-ISSN 1464-0333, Vol. 14, nr 10, s. 2643-2652Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ultraviolet/visible (UV/Vis) absorbance spectroscopy is a commonly used technique for characterizing dissolved organic matter (DOM). We present an analysis of UV/Vis absorbance spectra from 983 lakes throughout Sweden, sampled during autumn 2009. Metrics included both specific absorbances (i.e. absorbance per mass unit of organic carbon), and descriptions of spectral shape. Overall, we found three factors to which all spectral metrics were similarly related: acidity, retention-time, and latitude. In general, alkaline lakes with a long retention time in northern Sweden have lower specific absorbance and steeper spectral slope than acidic lakes with a short retention time in southern Sweden. Relative to the specific absorbance measured at 254 nm (SUVA), commonly used as a measure of DOM aromaticity, the specific absorbance at longer wavelengths and metrics of spectral shape were more sensitive to acidity and less sensitive to latitude. Although different spectral metrics are hypothesized to reflect different properties of DOM, UV/Vis absorbance spectroscopy may not be useful for more refined characterization of organic matter because of the strong inter-correlation between metrics. Nevertheless, it remains useful as a quick, cheap and reliable method of estimating DOM quantity and describing quality. We suggest that the most informative range to measure absorbance is between approximately 250 and 360 nm, where the between-lake variability is largest and absorbance can, in general, be precisely measured.

  • 156.
    Eugster, W.
    et al.
    ETH Zurich, Institute of Agricultural Sciences.
    DelSontro, T.
    Eawag, Swiss Federal Institute of Aquatic Science and Technology.
    Sobek, Sebastian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Eddy covariance flux measurements confirm extreme CH(4) emissions from a Swiss hydropower reservoir and resolve their short-term variability2011Inngår i: Biogeosciences, ISSN 1726-4170, E-ISSN 1726-4189, Vol. 8, nr 9, s. 2815-2831Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Greenhouse gas budgets quantified via land-surface eddy covariance (EC) flux sites differ significantly from those obtained via inverse modeling. A possible reason for the discrepancy between methods may be our gap in quantitative knowledge of methane (CH(4)) fluxes. In this study we carried out EC flux measurements during two intensive campaigns in summer 2008 to quantify methane flux from a hydropower reservoir and link its temporal variability to environmental driving forces: water temperature and pressure changes (atmospheric and due to changes in lake level). Methane fluxes were extremely high and highly variable, but consistently showed gas efflux from the lake when the wind was approaching the EC sensors across the open water, as confirmed by floating chamber flux measurements. The average flux was 3.8 +/- 0.4 mu g C m(-2) s(-1) (mean +/- SE) with a median of 1.4 mu g C m(-2) s(-1), which is quite high even compared to tropical reservoirs. Floating chamber fluxes from four selected days confirmed such high fluxes with 7.4 +/- 1.3 mu g C m(-2) s(-1). Fluxes increased exponentially with increasing temperatures, but were decreasing exponentially with increasing atmospheric and/or lake level pressure. A multiple regression using lake surface temperatures (0.1 m depth), temperature at depth (10 m deep in front of the dam), atmospheric pressure, and lake level was able to explain 35.4% of the overall variance. This best fit included each variable averaged over a 9-h moving window, plus the respective short-term residuals thereof. We estimate that an annual average of 3% of the particulate organic matter (POM) input via the river is sufficient to sustain these large CH(4) fluxes. To compensate the global warming potential associated with the CH(4) effluxes from this hydropower reservoir a 1.3 to 3.7 times larger terrestrial area with net carbon dioxide uptake is needed if a European-scale compilation of grass-lands, croplands and forests is taken as reference. This indicates the potential relevance of temperate reservoirs and lakes in local and regional greenhouse gas budgets.

  • 157.
    Evans, Chris D.
    et al.
    Ctr Ecol & Hydrol, Deiniol Rd, Bangor LL57 2UW, Gwynedd, Wales.; Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Lennart Hjalms Vag 9, S-75007 Uppsala, Sweden.
    Futter, Martyn N.
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Lennart Hjalms Vag 9, S-75007 Uppsala, Sweden.
    Moldan, Filip
    IVL Swedish Environm Res Inst, POB 5302, S-40014 Gothenburg, Sweden.
    Valinia, Salar
    Norwegian Inst Water Res, Gaustadalleen 21, N-0349 Oslo, Norway.; Swedish Environm Protect Agcy, Valhallavagen 195, S-10648 Stockholm, Sweden.
    Frogbrook, Zoe
    Scottish Water, 55 Buckstone Terrace, Edinburgh EH10 6XH, Midlothian, Scotland.
    Kothawala, Dolly
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Variability in organic carbon reactivity across lake residence time and trophic gradients2017Inngår i: Nature Geoscience, ISSN 1752-0894, E-ISSN 1752-0908, Vol. 10, nr 11, s. 832-835Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The transport of dissolved organic carbon from land to ocean is a large dynamic component of the global carbon cycle. Inland waters are hotspots for organic matter turnover, via both biological and photochemical processes, and mediate carbon transfer between land, oceans and atmosphere. However, predicting dissolved organic carbon reactivity remains problematic. Here we present in situ dissolved organic carbon budget data from 82 predominantly European and North American water bodies with varying nutrient concentrations and water residence times ranging from one week to 700 years. We find that trophic status strongly regulates whether water bodies act as net dissolved organic carbon sources or sinks, and that rates of both dissolved organic carbon production and consumption can be predicted from water residence time. Our results suggest a dominant role of rapid light-driven removal in water bodies with a short water residence time, whereas in water bodies with longer residence times, slower biotic production and consumption processes are dominant and counterbalance one another. Eutrophication caused lakes to transition from sinks to sources of dissolved organic carbon. We conclude that rates and locations of dissolved organic carbon processing and associated CO2 emissions in inland waters may be misrepresented in global carbon budgets if temporal and spatial reactivity gradients are not accounted for.

  • 158. Farkas, Julia
    et al.
    Peter, Hannes
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Christian, Paul
    Urrea, Julian Alberto Gallego
    Hassellov, Martin
    Tuoriniemi, Jani
    Gustafsson, Stefan
    Olsson, Eva
    Hylland, Ketil
    Thomas, Kevin Victor
    Characterization of the effluent from a nanosilver producing washing machine2011Inngår i: Environment International, ISSN 0160-4120, E-ISSN 1873-6750, Vol. 37, nr 6, s. 1057-1062Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The increasing number of nanomaterial based consumer products raises concerns about their possible impact on the environment. This study provides an assessment of the effluent from a commercially available silver nanowashing machine. The washing machine released silver in its effluent at an average concentration of 11 mu g L(-1), as determined by inductive coupled mass spectrometry (ICP-MS). The presence of silver nanoparticles (AgNPs) was confirmed by single particle ICP-MS as well as ion selective electrode measurements and filtration techniques. Size measurements showed particles to be in the defined nanosize range, with an average size of 10 nm measured with transmission electron microscopy (TEM) and 60-100 nm determined with nanoparticle tracking analysis (NTA). The effluent was shown to have negative effects on a natural bacterial community as its abundance was clearly reduced when exposed to the nanowash water. If washing machines capable of producing AgNPs become a common feature of households in the future, wastewater will contain significant loadings of AgNPs which might be released into the environment.

  • 159.
    Farkas, Julia
    et al.
    Norwegian Univ Sci & Technol, Dept Biol, N-7491 Trondheim, Norway..
    Peter, Hannes
    Univ Innsbruck, Inst Ecol, A-6020 Innsbruck, Austria..
    Ciesielski, Tomasz M.
    Norwegian Univ Sci & Technol, Dept Biol, N-7491 Trondheim, Norway..
    Thomas, Kevin V.
    Norwegian Inst Water Res, N-0349 Oslo, Norway..
    Sommaruga, Ruben
    Univ Innsbruck, Inst Ecol, A-6020 Innsbruck, Austria..
    Salvenmoser, Willi
    Univ Innsbruck, Inst Zool, A-6020 Innsbruck, Austria..
    Weyhenmeyer, Gesa A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Tranvik, Lars J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Jenssen, Bjorn M.
    Norwegian Univ Sci & Technol, Dept Biol, N-7491 Trondheim, Norway..
    Impact of TiO2 nanoparticles on freshwater bacteria from three Swedish lakes2015Inngår i: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 535, s. 85-93Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Due to the rapidly rising production and usage of nano-enabled products, aquatic environments are increasingly exposed to engineered nanoparticles (ENPs), causing concerns about their potential negative effects. In this study we assessed the effects of uncoated titanium dioxide nanoparticles (TiO(2)NPs) on the growth and activity of bacterial communities of three Swedish lakes featuring different chemical characteristics such as dissolved organic carbon (DOC) concentration, pH and elemental composition. TiO2NP exposure concentrations were 15, 100, and 1000 mu g L-1, and experiments were performed in situ under three light regimes: darkness, photosynthetically active radiation (PAR), and ambient sunlight including UV radiation (UVR). The nanoparticles were most stable in lake water with high DOC and low chemical element concentrations. At the highest exposure concentration (1000 mu g L-1 TiO2NP) the bacterial abundance was significantly reduced in all lake waters. In the medium and high DOC lake waters, exposure concentrations of 100 mu g L-1 TiO2NP caused significant reductions in bacterial abundance. The cell-specific bacterial activity was significantly enhanced at high TiO2NP exposure concentrations, indicating the loss of nanoparticle-sensitive bacteria and a subsequent increased activity by tolerant ones. No UV-induced phototoxic effect of TiO2NP was found in this study. We conclude that in freshwater lakes with high DOC and low chemical element concentrations, uncoated TiO(2)NPs show an enhanced stability and can significantly reduce bacterial abundance at relatively low exposure concentrations.

  • 160. Farnelid, Hanna
    et al.
    Andersson, Anders F.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Abu Al-Soud, Waleed
    Hansen, Lars H.
    Sorensen, Sören
    Steward, Grieg F.
    Hagström, Åke
    Riemann, Lasse
    Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria2011Inngår i: PLoS ONE, ISSN 1932-6203, Vol. 6, nr 4, s. e19223-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cyanobacteria are thought to be the main N-2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations worldwide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N-2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.

  • 161. Farnelid, Hanna
    et al.
    Bentzon-Tilia, Mikkel
    Andersson, Anders F.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Jost, Guenter
    Labrenz, Matthias
    Juergens, Klaus
    Riemann, Lasse
    Active nitrogen-fixing heterotrophic bacteria at and below the chemocline of the central Baltic Sea2013Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, nr 7, s. 1413-1423Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Baltic Sea receives large nitrogen inputs by diazotrophic (N-2-fixing) heterocystous cyanobacteria but the significance of heterotrophic N-2 fixation has not been studied. Here, the diversity, abundance and transcription of the nifH fragment of the nitrogenase enzyme in two basins of the Baltic Sea proper was examined. N-2 fixation was measured at the surface (5 m) and in anoxic water (200 m). Vertical sampling profiles of >10 and <10 mu m size fractions were collected in 2007, 2008 and 2011 at the Gotland Deep and in 2011 in the Bornholm Basin. Both of these stations are characterized by permanently anoxic bottom water. The 454-pyrosequencing nifH analysis revealed a diverse assemblage of nifH genes related to alpha-, beta- and gammaproteobacteria (nifH cluster I) and anaerobic bacteria (nifH cluster III) at and below the chemocline. Abundances of genes and transcripts of seven diazotrophic phylotypes were investigated using quantitative polymerase chain reaction revealing abundances of heterotrophic nifH phylotypes of up to 2.1 x 10(7) nifH copies l(-1). Abundant nifH transcripts (up to 3.2 x 10(4) transcripts l(-1)) within nifH cluster III and co-occurring N-2 fixation (0.44 +/- 0.26 nmol l(-1) day(-1)) in deep water suggests that heterotrophic diazotrophs are fixing N2 in anoxic ammonium-rich waters. Our results reveal that N-2 fixation in the Baltic Sea is not limited to illuminated N-deplete surface waters and suggest that N-2 fixation could also be of importance in other suboxic regions of the world's oceans.

  • 162.
    Faulks, Leanne
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Svanbäck, Richard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Eklöv, Peter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Östman, Örjan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Genetic and morphological divergence along the littoral–pelagic axis in two common and sympatric fishes: perch, Perca fluviatilis (Percidae) and roach, Rutilus rutilus (Cyprinidae)2015Inngår i: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 114, nr 4, s. 929-940Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Individuals are constantly in competition with one another and, on both ecological and evolutionary timescales, processes act to reduce this competition and promote the gain of fitness advantages via diversification. Here we have investigated the genetic (AFLP) and morphological (geometric morphometrics) aspects of the littoral–pelagic axis, a commonly observed resource polymorphism in freshwater fishes of postglacial lakes. We found a large degree of variation in the genetic and morphological divergence between littoral and pelagic perch and roach across Swedish lakes. Although there was evidence of assortative mating (elevated kinship values) in both species, we could not find any significant coupling of morphology and genetic divergence. Instead, there was evidence that the extent of resource polymorphism may be largely caused by phenotypic plasticity. These results suggest that assortative mating, which can lead to genetically determined adaptive divergence, does occur in these species, particularly perch, but not according to genetically fixed morphological traits. The behavioural mechanisms facilitating associative mating need to be investigated to explore the interaction between phenotypic plasticity and adaptive genetic divergence and their roles in diversification.

  • 163.
    Faulks, Leanne
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Svanbäck, Richard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Ragnarsson-Stabo, Henrik
    Eklöv, Peter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Östman, Örjan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Intraspecific Niche Variation Drives Abundance-Occupancy Relationships in Freshwater Fish Communities2015Inngår i: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 186, nr 2, s. 272-283Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A positive relationship between occupancy and average local abundance of species is found in a variety of taxa, yet the mechanisms driving this association between abundance and occupancy are still enigmatic. Here we show that freshwater fishes exhibit a positive abundance-occupancy relationship across 125 Swedish lakes. For a subset of 9 species from 11 lakes, we estimated species-specific diet breadth from stable isotopes, within-lake habitat breadth from catch data for littoral and pelagic nets, adaptive potential from genetic diversity, abiotic niche position, and dispersal capacity. Average local abundance was mainly positively associated with both within-lake habitat and diet breadth, that is, species with larger intraspecific variation in niche space had higher abundances. No measure was a good predictor of occupancy, indicating that occupancy may be more directly related to abundance or abiotic conditions than to niche breadth per se. This study suggests a link between intraspecific niche variation and a positive abundance-occupancy relationship and implies that management of freshwater fish communities, whether to conserve threatened or control invasive species, should initially be aimed at niche processes.

  • 164.
    Feng, Xin Mei
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Karlsson, Anna
    Svensson, Bo H.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Impact of trace element addition on biogas production from food industrial waste - linking process to microbial communities2010Inngår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 74, nr 1, s. 226-240Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Laboratory-scale reactors treating food industry waste were used to investigate the effects of additions of cobalt (Co), nickel/molybdenum/boron (Ni/Mo/B) and selenium/tungsten (Se/W) on the biogas process and the associated microbial community. The highest methane production (predicted value: 860 mL g-1 VS) was linked to high Se/W concentrations in combination with a low level of Co. A combination of quantitative real-time PCR of 16S rRNA genes, terminal restriction fragment length polymorphism (T-RFLP) and clone library sequencing was used for the community analysis. The T-RFLP data show a higher diversity for bacteria than for archaea in all the treatments. The most abundant bacterial population (31-55% of the total T-RFLP fragments' intensity) was most closely related to Actinomyces europaeus (94% homology). Two dominant archaeal populations shared 98-99% sequence homology with Methanosarcina siciliae and Methanoculleus bourgensis, respectively. Only limited influence of the trace metal additions was found on the bacterial community composition, with two bacterial populations responding to the addition of a combination of Ni/Mo/B, while the dominant archaeal populations were influenced by the addition of Ni/Mo/B and/or Se/W. The maintenance of methanogenic activity was largely independent of archaeal community composition, suggesting a high degree of functional redundancy in the methanogens of the biogas reactors.

  • 165.
    Fernandez Vidal, Leyden
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    High bacterial abundances and aggregation in humic lakes enhance nitrogen fixation potential via non-cyanobacterial diazotrophsManuskript (preprint) (Annet vitenskapelig)
  • 166.
    Fernandez Vidal, Leyden
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Uncoupled diazotrophy and oxygenic photosynthesis inferred from freshwater metagenomes collected from hypolimnetic dark-waterManuskript (preprint) (Annet vitenskapelig)
  • 167.
    Fernandez-Vidal, Leyden
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Non-cyanobacterial nitrogen fixation insights in humic freshwater lakes and ponds2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The biological basis of nitrogen fixation beyond the canonical role of Cyanobacteria is not well understood in freshwater ecosystems. To address this gap in knowledge, the main objective of this thesis is to study non-cyanobacterial nitrogen fixation in freshwater lakes and ponds.

    Microbial communities and diazotrophic potential were characterized by direct metagenome sequencing from seasonally stratified lakes and permafrost thaw ponds, both of which are systems featuring strong redox gradients. To quantify the nitrogen fixation process, we also adopted and applied a 15N tracer method to estimate realized diazotrophic activity in five of the studied lakes. Chemical characteristics were also measured concomitantly to link diazotroph distribution patterns to chemical features and metabolic traits in the studied freshwaters.

    Exploring a 3-year metagenomic time series of a humic lake (Trout Bog), widespread and stable occurrence of nifH genes were detected. This marker gene for nitrogen fixation appeared with accessory genes, validating the marker. The diazotrophic community was diverse and dynamic with contributions from Geobacter, Desulfobacterales, Methylococcales, Acidobacteria, Verrucomicrobia and Chlorobi. Accordingly, nitrogen fixation may be fueled by a variety of metabolic processes (heterotrophic sulfate/iron reducers, methylotrophs and photolithotrophs) in oxygen depleted dark waters. Interestingly the photolithotrophic Chlorobi also carried a Fe-only nitrogenase (anfH) recently implicated in alternative methane production. Overall, we demonstrated widespread potential for nitrogen fixation within hypolimnia in stratified humic lakes, and analyses of depth profiles also confirmed the presence of active diazotrophic communities in boreal lakes. These active nitrogen fixing communities were characterized by overall higher bacterial abundances, cellular aggregation and increased phosphorus availability as compared to communities where nitrogen fixation was not detected.

    Expanding our work to include recently formed freshwater ecosystems, we characterized microbial communities in arctic thaw ponds at different ontogenetic stages. We also investigated the possible role of anfH in methane production, but the abundance of this gene was not correlated with high methane concentration in the water column. NifH was detected in all systems, and interestingly the hypolimnetic waters in the more established systems emerged as suitable niche for diazotrophs with nifH abundances positively correlated to elevated methane concentrations. Based on this observation, we propose that nitrogen-fixing microorganisms may be important partners in complex syntrophic networks established between bacteria and archaeal methanogens.  

    In conclusion, the results presented across the different types of terrestrially influenced freshwater systems revealed widespread potential for nitrogen fixation within hypolimnia of humic lakes and permafrost thaw ponds. Furthermore, nitrogen fixation was confirmed at and below the redoxcline in five Finnish humic lakes. This implies that we need to look beyond phototrophic cyanobacteria to more fully understand the role of nitrogen fixation and overall nitrogen cycling in freshwater ecosystems.

    Delarbeid
    1. Nitrogenase gene seasonal dynamics reveal diazotrophic potential in a humic bog lake
    Åpne denne publikasjonen i ny fane eller vindu >>Nitrogenase gene seasonal dynamics reveal diazotrophic potential in a humic bog lake
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-395054 (URN)
    Tilgjengelig fra: 2019-10-11 Laget: 2019-10-11 Sist oppdatert: 2019-10-15
    2. Uncoupled diazotrophy and oxygenic photosynthesis inferred from freshwater metagenomes collected from hypolimnetic dark-water
    Åpne denne publikasjonen i ny fane eller vindu >>Uncoupled diazotrophy and oxygenic photosynthesis inferred from freshwater metagenomes collected from hypolimnetic dark-water
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-395055 (URN)
    Tilgjengelig fra: 2019-10-11 Laget: 2019-10-11 Sist oppdatert: 2019-10-15
    3. High bacterial abundances and aggregation in humic lakes enhance nitrogen fixation potential via non-cyanobacterial diazotrophs
    Åpne denne publikasjonen i ny fane eller vindu >>High bacterial abundances and aggregation in humic lakes enhance nitrogen fixation potential via non-cyanobacterial diazotrophs
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-395056 (URN)
    Tilgjengelig fra: 2019-10-11 Laget: 2019-10-11 Sist oppdatert: 2019-10-15
    4. Non‐cyanobacterial diazotrophs dominate nitrogen‐fixing communities in permafrost thaw ponds
    Åpne denne publikasjonen i ny fane eller vindu >>Non‐cyanobacterial diazotrophs dominate nitrogen‐fixing communities in permafrost thaw ponds
    2019 (engelsk)Inngår i: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590Artikkel i tidsskrift (Fagfellevurdert) Published
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-395051 (URN)
    Tilgjengelig fra: 2019-10-11 Laget: 2019-10-11 Sist oppdatert: 2019-10-15
  • 168. Finn, Maureen
    et al.
    Lönnstedt, Oona M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Rizzari, Justin
    Jones, Geoffrey
    Frisch, Ashley
    Experimental bleaching of a tropical sea anemone in situ2016Inngår i: Marine Ecolocy, ISSN 0173-9565, E-ISSN 1439-0485, Vol. 37, nr 3, s. 691-696Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bleaching (whitening) of cnidarians such as corals and sea anemones has caused widespread degradation of coral reefs around the world and is therefore an urgent issue for coral reef science and conservation. Although cnidarians often bleach in aquaria, methods for experimental induction of bleaching in wild cnidarians are lacking, which impedes scientists’ ability to understand the ultimate effects of bleaching on the broader ecosystem. In this study, we investigated the utility of an in situ method for experimental induction of bleaching in the tropical sea anemone Heteractis crispa. Healthy, wild anemones were covered with opaque black plastic sheets, mesh cages or left undisturbed (controls) and tentacle colour and body size were monitored with a colour reference card and flexible tape, respectively, every 1–3 days for 15 days. Caged and control anemones remained unchanged for the duration of the experiment, but covered anemones commenced whitening after 4–6 days and were completely white after 7–14 days (mean time to bleaching SE = 10.1 0.7 days). Experimental bleaching occurred without reduction in anemone body size and was visibly similar to natural bleaching seen previously in H. crispa. We hypothesize that light-deprivation, reduced water flow, physical contact or some combination of these factors caused the bleaching. This study provides the basis for a simple and rapid method of inducing bleaching in situ, which releases scientists’ dependence on sporadic natural bleaching events or artificial aquarium experiments, and provides a means to investigate the effects of bleaching on other ecosystem components such as fishes.

  • 169.
    Flaviani, Flavia
    et al.
    Univ Cape Town, Biopharming Res Unit, Dept Mol & Cell Biol, Cape Town, South Africa;Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Schroeder, Declan C.
    Univ Reading, Sch Biol Sci, Reading, Berks, England;Univ Minnesota Twin Cities, Coll Vet Med, Minneapolis, MN 55455 USA;Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Lebret, Karen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Balestreri, Cecilia
    Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Highfield, Andrea C.
    Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Schroeder, Joanna L.
    Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England.
    Thorpe, Sally E.
    NERC, British Antarctic Survey, Cambridge, England.
    Moore, Karen
    Univ Exeter, Exeter Sequencing Serv, Biosci, Exeter, Devon, England.
    Pasckiewicz, Konrad
    Univ Exeter, Exeter Sequencing Serv, Biosci, Exeter, Devon, England.
    Pfaff, Maya C.
    Oceans & Coasts, Dept Environm Affairs, Cape Town, South Africa.
    Rybicki, Edward P.
    Univ Cape Town, Biopharming Res Unit, Dept Mol & Cell Biol, Cape Town, South Africa.
    Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current2018Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikkel-id 1474Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while gamma-Proteobacteria dominated the South-East Indian Ocean. A combination of gamma- and alpha-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order Caudovirales across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity.

  • 170.
    Florenza, Javier
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Tamminen, Manu
    Univ Turku, Dept Biol, FI-20014 Turku, Finland.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Uncovering microbial inter-domain interactions in complex communities2019Inngår i: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 374, nr 1786, artikkel-id 20190087Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Interactions between unicellular eukaryotes and bacteria are difficult to characterize in the environment owing to their large number and inherently microscopic scale. Although particular co-occurrences can be recovered through targeted approaches, e.g. single-cell sequencing or fluorescence in situ hybridization, the vast majority of the interactions remain unseen. Here, we discuss Emulsion, Paired Isolation and Concatenation polymerase chain reaction (epicPCR) as a tool to uncover these interactions in very high throughput. Originally developed for taxonomy-to-function linkage in bacterial communities, epicPCR has the potential to recover the complete interaction network in a given environment at single-cell resolution. This approach relies on the encapsulation of protistan single cells in emulsion droplets that can subsequently be gelified into beads. In this way, encapsulated cells can be exposed to lysis reagents and further phylogenetic paired marker amplification. A bacterium that physically co-occurs with the eukaryote will be jointly trapped, and the amplification will generate a concatenated PCR product containing physically coupled taxonomic markers from both partners, creating a link. Further amplification and sequencing enable the construction of an association pattern with statistically verified physical co-occurrences. Here, we discuss the potential, challenges and limitations of epicPCR. We argue that the microscopic scale at which epicPCR operates, the high throughput it delivers and its exploratory nature make it an unparalleled approach to unravel associations between microbes directly from environmental samples.

    This article is part of a discussion meeting issue 'Single cell ecology'.

  • 171. Florin, Ann-Britt
    et al.
    Sundblad, Göran
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bergström, Ulf
    Characterisation of juvenile flatfish habitats in the Baltic Sea2009Inngår i: Estuarine, Coastal and Shelf Science, ISSN 0272-7714, E-ISSN 1096-0015, Vol. 82, nr 2, s. 294-300Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Survival and growth of the earliest life-stages is considered a key factor in determining the abundance of many marine fish species. For flatfishes, the availability of high quality nursery areas is essential for successful recruitment. Regarding the Baltic Sea, there are large gaps in knowledge on factors that influence the distribution of flatfishes during this sensitive stage. To identify the characteristics of important nursery areas in the Baltic for flounder (Platichthys flesus) and turbot (Psetta maxima), a field survey with push net sampling was conducted in the northern Baltic proper during autumn 2006. The sampling stations were stratified to cover several different habitat types defined by substrate and wave exposure. Apart from density of young-of-the-year (YOY) flatfishes, a number of ecological characteristics of the habitat were recorded. Physical habitat variables included substrate type, salinity, depth, turbidity, vegetation and habitat structure. Variables describing biotic processes, such as prey availability and abundance of competitors, were also sampled. The relationships between the spatial distribution of species and these ecological characteristics were fitted to presence/absence data of juvenile flatfish using generalized additive models (GAM). The best habitat descriptors for flounder in order of contribution were: substrate, habitat structure, salinity, wave exposure and occurrence of filamentous algae. Positive effects of increasing wave exposure, salinity and structure were detected while a high cover of filamentous algae had a negative effect. Sand and gravel were preferred over soft and stony substrates. For turbot the best habitat descriptors in order of contribution were: occurrence of filamentous algae, substrate and turbidity. Turbot showed a preference for areas with a low cover of filamentous algae, high turbidity and sandy substrate. Prey availability and abundance of competitors were not included in the models, indicating that the distribution of flatfishes at the scales studied (tens of kilometres) is mainly governed by physical habitat properties. These results constitute the basis for future efforts on mapping of essential flatfish habitats in the Baltic Sea.

  • 172.
    Fortunato, Caroline S.
    et al.
    University of Maryland Center for Environmental Science.
    Eiler, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Herfort, Lydie
    Oregon Health & Sciences University.
    Needoba, Joseph A.
    Oregon Health & Sciences University.
    Peterson, Tawnya D.
    Oregon Health & Sciences University.
    Crump, Byron C.
    University of Maryland Center for Environmental Science.
    Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin2013Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, nr 10, s. 1899-1911Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=−0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, andProchlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.

  • 173. Frassl, Marieke A.
    et al.
    Hamilton, David P.
    Denfeld, Blaize A.
    de Eyto, Elvira
    Hampton, Stephanie E.
    Keller, Philipp S.
    Sharma, Sapna
    Lewis, Abigail S. L.
    Weyhenmeyer, Gesa A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    O'Reilly, Catherine M.
    Lofton, Mary E.
    Catalán, Núria
    Ten simple rules for collaboratively writing a multi-authored paper2018Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 14, nr 11, artikkel-id e1006508Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Science is increasingly done in large teams, making it more likely that papers will be written by several authors from different institutes, disciplines, and cultural backgrounds. A small number of “Ten simple rules” papers have been written on collaboration and on writing but not on combining the two. Collaborative writing with multiple authors has additional challenges, including varied levels of engagement of coauthors, provision of fair credit through authorship or acknowledgements, acceptance of a diversity of work styles, and the need for clear communication. Miscommunication, a lack of leadership, and inappropriate tools or writing approaches can lead to frustration, delay of publication, or even the termination of a project.

    To provide insight into collaborative writing, we use our experience from the Global Lake Ecological Observatory Network (GLEON) to frame 10 simple rules for collaboratively writing a multi-authored paper. We consider a collaborative multi-authored paper to have three or more people from at least two different institutions. A multi-authored paper can be a result of a single discrete research project or the outcome of a larger research program that includes other papers based on common data or methods. The writing of a multi-authored paper is embedded within a broader context of planning and collaboration among team members. Our recommended rules include elements of both the planning and writing of a paper, and they can be iterative, although we have listed them in numerical order. It will help to revisit the rules frequently throughout the writing process. With the 10 rules outlined below, we aim to provide a foundation for writing multi-authored papers and conducting exciting and influential science.

  • 174. Frieler, K
    et al.
    Lange, S
    Piontek, F
    Reyer, C P O
    Schewe, J
    Warszawski, Lila
    Zhao, Fang
    Chini, Louise
    Denvil, Sebastien
    Emanuel, Kerry
    Geiger, Tobias
    Halladay, Kate
    Hurtt, George
    Mengel, Matthias
    Murakami, Daisuke
    Ostberg, Sebastian
    Popp, Alexander
    Riva, Riccardo
    Stevanovic, Miodrag
    Ts, Tatsuo Suzuki
    Volkholz, Jan
    Burke, Eleanor
    Ciais, Philippe
    Ebi, Kristie
    Pierson, Don
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Assessing the impacts of 1.5° C global warming - simulation protocol of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP2b)2017Inngår i: Geoscientific Model Development, ISSN 1991-959X, E-ISSN 1991-9603, Vol. 10, s. 4321-4345Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In Paris, France, December 2015, the Conference of the Parties (COP) to the United Nations Framework Con- vention on Climate Change (UNFCCC) invited the Inter- governmental Panel on Climate Change (IPCC) to provide a “special report in 2018 on the impacts of global warming of 1.5 ◩C above pre-industrial levels and related global green- house gas emission pathways”. In Nairobi, Kenya, April 2016, the IPCC panel accepted the invitation. Here we de- scribe the response devised within the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) to provide tailored, cross-sectorally consistent impact projections to broaden the scientific basis for the report. The simulation protocol is de- signed to allow for (1) separation of the impacts of histori- cal warming starting from pre-industrial conditions from im- pacts of other drivers such as historical land-use changes (based on pre-industrial and historical impact model simula- tions); (2) quantification of the impacts of additional warm- ing up to 1.5 ◩C, including a potential overshoot and long- term impacts up to 2299, and comparison to higher lev- els of global mean temperature change (based on the low- emissions Representative Concentration Pathway RCP2.6 and a no-mitigation pathway RCP6.0) with socio-economic conditions fixed at 2005 levels; and (3) assessment of the cli- mate effects based on the same climate scenarios while ac- counting for simultaneous changes in socio-economic con- ditions following the middle-of-the-road Shared Socioeco- nomic Pathway (SSP2, Fricko et al., 2016) and in particu- lar differential bioenergy requirements associated with the transformation of the energy system to comply with RCP2.6 compared to RCP6.0.With the aim of providing the scientific basis for an aggregation of impacts across sectors and anal- ysis of cross-sectoral interactions that may dampen or am- plify sectoral impacts, the protocol is designed to facilitate consistent impact projections from a range of impact mod- els across different sectors (global and regional hydrology, lakes, global crops, global vegetation, regional forests, global and regional marine ecosystems and fisheries, global and regional coastal infrastructure, energy supply and demand, temperature-related mortality, and global terrestrial biodiver- sity).

  • 175.
    Frisch, Ashley J.
    et al.
    James Cook Univ, Australian Res Council Ctr Excellence Coral Reef, Townsville, Qld 4811, Australia..
    Ireland, Matthew
    James Cook Univ, Coll Marine & Environm Sci, Townsville, Qld 4811, Australia..
    Rizzari, Justin R.
    James Cook Univ, Australian Res Council Ctr Excellence Coral Reef, Townsville, Qld 4811, Australia.;James Cook Univ, Coll Marine & Environm Sci, Townsville, Qld 4811, Australia..
    Lönnstedt, Oona M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. James Cook Univ, Coll Marine & Environm Sci, Townsville, Qld 4811, Australia.
    Magnenat, Katalin A.
    James Cook Univ, Coll Marine & Environm Sci, Townsville, Qld 4811, Australia..
    Mirbach, Christopher E.
    James Cook Univ, Coll Marine & Environm Sci, Townsville, Qld 4811, Australia..
    Hobbs, Jean-Paul A.
    Curtin Univ, Dept Environm & Agr, Perth, WA 6845, Australia..
    Reassessing the trophic role of reef sharks as apex predators on coral reefs2016Inngår i: Coral reefs (Print), ISSN 0722-4028, E-ISSN 1432-0975, Vol. 35, nr 2, s. 459-472Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Apex predators often have strong top-down effects on ecosystem components and are therefore a priority for conservation and management. Due to their large size and conspicuous predatory behaviour, reef sharks are typically assumed to be apex predators, but their functional role is yet to be confirmed. In this study, we used stomach contents and stable isotopes to estimate diet, trophic position and carbon sources for three common species of reef shark (Triaenodon obesus, Carcharhinus melanopterus and C. amblyrhynchos) from the Great Barrier Reef (Australia) and evaluated their assumed functional role as apex predators by qualitative and quantitative comparisons with other sharks and large predatory fishes. We found that reef sharks do not occupy the apex of coral reef food chains, but instead have functional roles similar to those of large predatory fishes such as snappers, emperors and groupers, which are typically regarded as high-level mesopredators. We hypothesise that a degree of functional redundancy exists within this guild of predators, potentially explaining why shark-induced trophic cascades are rare or subtle in coral reef ecosystems. We also found that reef sharks participate in multiple food webs (pelagic and benthic) and are sustained by multiple sources of primary production. We conclude that large conspicuous predators, be they elasmobranchs or any other taxon, should not axiomatically be regarded as apex predators without thorough analysis of their diet. In the case of reef sharks, our dietary analyses suggest they should be reassigned to an alternative trophic group such as high-level mesopredators. This change will facilitate improved understanding of how reef communities function and how removal of predators (e.g., via fishing) might affect ecosystem properties.

  • 176.
    Galand, Pierre E.
    et al.
    Centre d’Estudis Avançats de Blanes-Consejo Superior de Investigaciones Científicas.
    Alonso-Sáez, Laura
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Lovejoy, Connie
    Université Laval.
    Casamayor, Emilio O.
    Centre d’Estudis Avançats de Blanes-Consejo Superior de Investigaciones Científicas.
    Contrasting activity patterns determined by BrdU incorporation in bacterial ribotypes from the Arctic Ocean in winter2013Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 4, s. 118-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The winter Arctic Ocean is one of the most unexplored marine environments from a microbiological perspective. Heterotrophic bacteria maintain their activity at a baseline level during the extremely low-energy conditions of the winter, but little is known about the specific phylotypes that have the potential to survive and grow in such harsh environment. In this study, we aimed at identifying actively growing ribotypes in winter Arctic Ocean seawater cultures by experimental incubations with the thymidine analog bromodeoxyuridine (BrdU), followed by immunocapturing, terminal restriction fragment length polymorphism fingerprinting, cloning, and sequencing the 16S rRNA gene. We incubated water collected at different months over the Arctic winter and showed that the actively growing bacterial fraction, taking up BrdU, represented only a subset of the total community. Among the BrdU-labeled bacterial taxa we identified the Flavobacteria Polaribacter, theAlphaproteobacteria SAR11, the Gammaproteobacteria Arctic 96B-16 cluster and, predominately, members of Colwellia spp. Interestingly,Colwellia sequences formed three clusters (93 and 97% pairwise 16S rRNA identity) that contributed in contrasting ways to the active communities in the incubations. Polaribacter, Arctic 96B-16 and one cluster of Colwellia were more abundant in the active community represented by the BrdU-labeled DNA. In contrast, SAR11 and two otherColwellia clusters were underrepresented in the BrdU-labeled community compared to total communities. Despite the limitation of the long incubations needed to label slow growing arctic communities, the BrdU approach revealed the potential for active growth in low-energy conditions in some relevant groups of polar bacteria, includingPolaribacter and Arctic 96B-16. Moreover, under similar incubation conditions, the growth of different Colwellia ribotypes varied, suggesting that related clusters of Colwellia may have distinct metabolic features.

  • 177. Galloway, Aaron W. E.
    et al.
    Brett, Michael T.
    Holtgrieve, Gordon W.
    Ward, Eric J.
    Ballantyne, Ashley P.
    Burns, Carolyn W.
    Kainz, Martin J.
    Mueller-Navarra, Doerthe C.
    Persson, Jonas
    Ravet, Joseph L.
    Strandberg, Ursula
    Taipale, Sami J.
    Alhgren, Gunnel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    A Fatty Acid Based Bayesian Approach for Inferring Diet in Aquatic Consumers2015Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 6, artikkel-id e0129723Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We modified the stable isotope mixing model MixSIR to infer primary producer contributions to consumer diets based on their fatty acid composition. To parameterize the algorithm, we generated a 'consumer-resource library' of FA signatures of Daphnia fed different algal diets, using 34 feeding trials representing diverse phytoplankton lineages. This library corresponds to the resource or producer file in classic Bayesian mixing models such as MixSIR or SIAR. Because this library is based on the FA profiles of zooplankton consuming known diets, and not the FA profiles of algae directly, trophic modification of consumer lipids is directly accounted for. To test the model, we simulated hypothetical Daphnia comprised of 80% diatoms, 10% green algae, and 10% cryptophytes and compared the FA signatures of these known pseudo-mixtures to outputs generated by the mixing model. The algorithm inferred these simulated consumers were comprised of 82% (63-92%) [median (2.5th to 97.5th percentile credible interval)] diatoms, 11% (4-22%) green algae, and 6% (0-25%) cryptophytes. We used the same model with published phytoplankton stable isotope (SI) data for delta C-13 and delta N-15 to examine how a SI based approach resolved a similar scenario. With SI, the algorithm inferred that the simulated consumer assimilated 52% (4-91%) diatoms, 23% (1-78%) green algae, and 18% (1-73%) cyanobacteria. The accuracy and precision of SI based estimates was extremely sensitive to both resource and consumer uncertainty, as well as the trophic fractionation assumption. These results indicate that when using only two tracers with substantial uncertainty for the putative resources, as is often the case in this class of analyses, the underdetermined constraint in consumer-resource SI analyses may be intractable. The FA based approach alleviated the underdetermined constraint because many more FA biomarkers were utilized (n < 20), different primary producers (e.g., diatoms, green algae, and cryptophytes) have very characteristic FA compositions, and the FA profiles of many aquatic primary consumers are strongly influenced by their diets.

  • 178.
    Gantner, Stephan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Andersson, Anders F.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Alonso-Saez, Laura
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Novel primers for 16S rRNA-based archaeal community analyses in environmental samples2011Inngår i: Journal of Microbiological Methods, ISSN 0167-7012, E-ISSN 1872-8359, Vol. 84, nr 1, s. 12-18Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Next generation sequencing technologies for in depth analyses of complex microbial communities rely on rational primer design based on up-to-date reference databases. Most of the 16S rRNA-gene based analyses of environmental Archaea community composition use PCR primers developed from small data sets several years ago, making an update long overdue. Here we present a new set of archaeal primers targeting the 165 rRNA gene designed from 8500 aligned archaeal sequences in the SILVA database. The primers 340E-1000R showed a high archaeal specificity (<1% bacteria amplification) covering 93 and 97% of available sequences for Crenarchaeota and Euryarchaeota respectively. In silico tests of the primers revealed at least 38% higher coverage for Archaea compared to other commonly used primers. Empirical tests with clone libraries confirmed the high specificity of the primer pair to Archaea in three biomes: surface waters in the Arctic Ocean, the pelagic zone of a temperate lake and a methanogenic bioreactor. The clone libraries featured both Euryarchaeota and Crenarchaeota in variable proportions and revealed dramatic differences in the archaeal community composition and minimal phylogenetic overlap between samples.

  • 179.
    Garcia Bravo, Andrea
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Cosio, Claudia
    Amouroux, David
    Zopfi, Jakob
    Chevalley, Pierre-Alain
    Spangenberg, Jorge E.
    Ungureanu, Viorel-Gheorghe
    Dominik, Janusz
    Extremely elevated methyl mercury levels in water, sediment and organisms in a Romanian reservoir affected by release of mercury from a chlor-alkali plant2014Inngår i: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 49, s. 391-405Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We examined mercury (Hg) biogeochemistry and biomagnification in the Babeni Reservoir, a system strongly affected by the release of Hg from a chlor-alkali plant. Total mercury (THg) concentrations in river water reached 88 ng L−1 but decreased rapidly in the reservoir (to 9 ng L−1). In contrast, monomethylmercury (MMHg) concentrations increased from the upstream part of the reservoir to the central part (0.7 ng L−1), suggesting high methylation within the reservoir. Moreover, vertical water column profiles of THg and MMHg indicated that Hg methylation mainly occurred deep in the water column and at the sediment–water interface. The discharge of Hg from a chlor-alkali plant in Valcea region caused the highest MMHg concentrations ever found in non-piscivorous fish worldwide. MMHg concentrations and bioconcentration factors (BCF) of plankton and macrophytes revealed that the highest biomagnification of MMHg takes place in primary producers.

  • 180.
    Garcia Bravo, Andrea
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    LeFaucheur, S.
    Monperrus, M.
    Slaveykova, V.
    Species-specific isotope tracers to study the accumulation and biotransformation of mixtures of inorganic and methyl mercury by the microalga Chlamydomonas reinhardtii2014Inngår i: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 192, s. 212-215Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The present study demonstrates that species-specific isotope tracing is an useful tool to precisely measure Hg accumulation and transformations capabilities of living organisms at concentrations naturally encountered in the environment. To that end, a phytoplanktonic green alga Chlamydomonas reinhardtii Dangeard (Chlamydomonadales, Chlorophyceae) was exposed to mixtures of (199)-isotopically enriched inorganic mercury ((IHg)-I-199) and of (201)-isotopically enriched monomethylmercury ((CH3Hg)-C-201) at a concentration range between less than 1 pM to 4 nM. Additionally, one exposure concentration of both mercury species was also studied separately to evaluate possible interactive effects. No difference in the intracellular contents was observed for algae exposed to (IHg)-I-199 and (CH3Hg)-C-201 alone or in their mixture, suggesting similar accumulation capacity for both species at the studied concentrations. Demethylation of (CH3Hg)-C-201 was observed at the highest exposure concentrations, whereas no methylation was detected.

  • 181.
    Garcia, Sarahi L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Mixed cultures as model communities: hunting for ubiquitous microorganisms, their partners, and interactions2016Inngår i: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 77, nr 2, s. 79-85Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Even though thousands of microbial strains have now been successfully cultivated and described, these only represent a small fraction of global microbial diversity. Moreover, many of the ubiquitous and abundant environmental microorganisms still defy axenic cultivation. Here, I present mixed cultures as a powerful tool to cultivate and study ubiquitous but hard-to-cultivate microorganisms. A mixed culture is a subsample from a complex natural community that contains 2 or more microbial strains. When cultivated together with their metabolic partners, these ubiquitous microorganisms can mutually satisfy metabolic dependencies just as they do in the environment. By reducing the complexity while keeping some diversity, mixed cultures can then be used as model communities. Furthermore, by combining the relative simplicity of these model communities with molecular and bioinformatics tools, the complex natural interactions could be deciphered one model community at a time. Ultimately, mixed cultures can be used to generate a working hypothesis to explore the microbial ecology and genetic population structures of the unseen vast majority of microorganisms.

  • 182.
    Garcia, Sarahi L
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA.
    Buck, Moritz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Hamilton, Joshua J.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Goteborg, Germany.
    Grossart, Hans-Peter
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany;Potsdam Univ, Inst Biochem & Biol, Potsdam, Germany.
    McMahon, Katherine D.
    Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA;Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.
    Eiler, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Univ Oslo, Dept Biosci, Sect Aquat Biol & Toxicol, Oslo, Norway.
    Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria2018Inngår i: MSPHERE, ISSN 2379-5042, Vol. 3, nr 3, artikkel-id e00202-18Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.

  • 183.
    Garcia, Sarahi L.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Buck, Moritz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    McMahon, Katherine D.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.;Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA..
    Grossart, Hans-Peter
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, D-16775 Ot Neuglobsow, Stechlin, Germany.;Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany..
    Eiler, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Warnecke, Falk
    Univ Jena, Jena Sch Microbial Commun, D-07743 Jena, Germany..
    Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community2015Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, nr 17, s. 4449-4459Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.

  • 184.
    Garcia, Sarahi L
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. University of Wisconsin-Madison, Madison, USA.
    Stevens, Sarah L R
    University of Wisconsin-Madison, Madison, USA.
    Crary, Benjamin
    University of Wisconsin-Madison, Madison, USA.
    Martinez-Garcia, Manuel
    University of Alicante, Alicante, Spain.
    Stepanauskas, Ramunas
    Bigelow Laboratory for Ocean Sciences, East Boothbay, USA.
    Woyke, Tanja
    DOE Joint Genome Institute, Walnut Creek, USA.
    Tringe, Susannah G
    DOE Joint Genome Institute, Walnut Creek, USA.
    Andersson, Siv G E
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Malmstrom, Rex R
    DOE Joint Genome Institute, Walnut Creek, USA.
    McMahon, Katherine D
    University of Wisconsin-Madison, Madison, USA.
    Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations2018Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, nr 3, s. 742-755Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.

  • 185.
    Garcia, Sarahi L
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Szekely, Anna J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bergvall, Christoffer
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Schattenhofer, Martha
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Peura, S.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Swedish Univ Agr Sci, Sci Life Lab, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden;Uppsala Univ, Dept Cell & Mol Biol, Uppsala, Sweden.
    Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity2019Inngår i: MSPHERE, ISSN 2379-5042, Vol. 4, nr 1, artikkel-id e00626-18Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Climate change scenarios anticipate decreased spring snow cover in boreal and subarctic regions. Forest lakes are abundant in these regions and substantial contributors of methane emissions. To investigate the effect of reduced snow cover, we experimentally removed snow from an anoxic frozen lake. We observed that the removal of snow increased light penetration through the ice, increasing water temperature and modifying microbial composition in the different depths. Chlorophyll a and b concentrations increased in the upper water column, suggesting activation of algal primary producers. At the same time, Chlorobiaceae, one of the key photosynthetic bacterial families in anoxic lakes, shifted to lower depths. Moreover, a decrease in the relative abundance of methanotrophs within the bacterial family Methylococcaceae was detected, concurrent with an increase in methane concentration in the water column. These results indicate that decreased snow cover impacts both primary production and methane production and/or consumption, which may ultimately lead to increased methane emissions after spring ice off. IMPORTANCE Small lakes are an important source of greenhouse gases in the boreal zone. These lakes are severely impacted by the winter season, when ice and snow cover obstruct gas exchange between the lake and the atmosphere and diminish light availability in the water column. Currently, climate change is resulting in reduced spring snow cover. A short-term removal of the snow from the ice stimulated algal primary producers and subsequently heterotrophic bacteria. Concurrently, the relative abundance of methanotrophic bacteria decreased and methane concentrations increased. Our results increase the general knowledge of microbial life under ice and, specifically, the understanding of the potential impact of climate change on boreal lakes.

  • 186. Gascon Diez, Elena
    et al.
    Garcia Bravo, Andrea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    à Porta, Natacha
    Masson, Matthieu
    Graham, Neil D.
    Stoll, Serge
    Akhtman, Yosef
    Amouroux, David
    Loizeau, Jean-Luc
    Influence of a wastewater treatment plant on mercury contamination and sediment characteristics in Vidy Bay (Lake Geneva, Switzerland)2014Inngår i: Aquatic Sciences, ISSN 1015-1621, E-ISSN 1420-9055, Vol. 76, nr S1, s. S21-S32Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Previous direct observations of the sediment surface in Vidy Bay, Lake Geneva (Switzerland), revealed a range of sediment characteristics in terms of colour, texture and morphology. Dives with the MIR submersibles during the éLEMO project permitted the exploration of a large portion of Vidy Bay. It is the most contaminated part of Lake Geneva, due to inputs of treated and untreated waters from a large wastewater treatment plant (WWTP). To evaluate the influence of WWTP effluent on mercury contamination and sediment characteristics, 14 sediment cores were retrieved in the vicinity of the wastewater treatment plant effluent. Total mercury concentrations in sediments ranged between 0.32 and 10.1 mg/kg. Inorganic mercury and monomethylmercury concentrations in overlying and pore waters were also measured. The total partition coefficients of mercury (logK d) ranged from 3.6 to 5.8. The monomethylmercury concentration in pore waters of surface sediments was a large proportion of the total mercury concentration (44 ± 25 %). A Spearman test showed a negative correlation between the distance to the wastewater treatment plant outlet and the concentrations of total mercury in sediments and pore waters. Visual observations from the submersible allowed recognizing six different types of sediment. The areal distribution of these different sediment types clearly showed the influence of the wastewater treatment plant outlet on the sediment surface patterns. However, no relationship with mercury concentrations could be established.

  • 187.
    Gascon Diez, Elena
    et al.
    Univ Geneva, Dept FA Forel Environm & Water Sci, Blvd Carl Vogt 66, CH-1211 Geneva 4, Switzerland.
    Loizeau, Jean-Luc
    Univ Geneva, Dept FA Forel Environm & Water Sci, Blvd Carl Vogt 66, CH-1211 Geneva 4, Switzerland.
    Cosio, Claudia
    Univ Geneva, Dept FA Forel Environm & Water Sci, Blvd Carl Vogt 66, CH-1211 Geneva 4, Switzerland.
    Bouchet, Sylvain
    Univ Pau & Pays Adour, Lab Chim Analyt Bioinorgan & Environm, Inst Sci Analyt & Physicochim Environm & Mat, CNRS,UMR 5254, Helioparc, F-64053 Pau, France.
    Adatte, Thierry
    Univ Lausanne, Inst Earth Sci ISTE, CH-1015 Lausanne, Switzerland.
    Amouroux, David
    Univ Pau & Pays Adour, Lab Chim Analyt Bioinorgan & Environm, Inst Sci Analyt & Physicochim Environm & Mat, CNRS,UMR 5254, Helioparc, F-64053 Pau, France.
    Bravo, Andrea G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Role of settling particles on mercury methylation in the oxic water 1 column of freshwater systems2016Inngår i: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 50, nr 21, s. 11672-11679Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    As the methylation of inorganic divalent mercury (HgII) to neurotoxic methylmercury (MeHg) has been attributed to the activity of anaerobic bacteria, the formation of MeHg in the oxic water column of marine ecosystems has puzzled scientists over the past years. Here we show for the first time that MeHg can be produced in particles sinking through oxygenated water column of lakes. Total mercury (THg) and MeHg concentrations were measured in settling particles and in surface sediments of the largest freshwater lake in Western Europe (Lake Geneva). Whilst THg concentration differences between sediments and settling particles were not significant, MeHg concentrations were up to ten-fold greater in settling particles. MeHg demethylation rate constants (kd) were of similar magnitude in both compartments. In contrast, Hg methylation rate constants (km) were one order of magnitude greater in settling particles. The net potential for MeHg formation, assessed by the ratio between the two rate constants (km kd-1), was therefore up to ten times higher in settling particles, denoting that in situ transformations likely contributed to the high MeHg concentrations found in settling particles. Hg methylation was inhibited ( 80 %) in settling particles amended with molybdate, demonstrating the prominent role of biological sulfate-reduction in the process.

  • 188. Ghiglione, J. -F
    et al.
    Galand, P. E.
    Pommier, T.
    Pedrós-Alió, C.
    Maas, E. W.
    Bakker, K.
    Bertilson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Kirchman, D. L.
    Lovejoy, C.
    Yager, P. L.
    Murray, A. E.
    Pole-to-pole biogeography of surface and deep marine bacterial communities2012Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, nr 43, s. 17633-17638Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately fromeach other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.

  • 189. Ghylin, Trevor W
    et al.
    Garcia, Sarahi L
    Moya, Francisco
    Oyserman, Ben O
    Schwientek, Patrick
    Forest, Katrina T
    Mutschler, James
    Dwulit-Smith, Jeffrey
    Chan, Leong-Keat
    Martinez-Garcia, Manuel
    Sczyrba, Alexander
    Stepanauskas, Ramunas
    Grossart, Hans-Peter
    Woyke, Tanja
    Warnecke, Falk
    Malmstrom, Rex
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    McMahon, Katherine D
    Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage2014Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 8, nr 12, s. 2503-2516Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.

  • 190.
    Gomez-Gener, Lluis
    et al.
    Univ Barcelona, Dept Ecol, Av Diagonal 643, E-08028 Barcelona, Spain..
    Obrador, Biel
    Univ Barcelona, Dept Ecol, Av Diagonal 643, E-08028 Barcelona, Spain..
    Marce, Rafael
    Univ Girona, Catalan Inst Water Res Sci & Technol Pk, Carrer Emili Grahit 101, Girona 17003, Spain..
    Acuna, Vicenc
    Univ Girona, Catalan Inst Water Res Sci & Technol Pk, Carrer Emili Grahit 101, Girona 17003, Spain..
    Catalan, Nuria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Pere Casas-Ruiz, Joan
    Univ Girona, Catalan Inst Water Res Sci & Technol Pk, Carrer Emili Grahit 101, Girona 17003, Spain..
    Sabater, Sergi
    Univ Girona, Catalan Inst Water Res Sci & Technol Pk, Carrer Emili Grahit 101, Girona 17003, Spain..
    Munoz, Isabel
    Univ Barcelona, Dept Ecol, Av Diagonal 643, E-08028 Barcelona, Spain..
    von Schiller, Daniel
    Univ Basque Country, Fac Sci & Technol, Dept Plant Biol & Ecol, Apdo 644, Bilbao 48080, Spain..
    When Water Vanishes: Magnitude and Regulation of Carbon Dioxide Emissions from Dry Temporary Streams2016Inngår i: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 19, nr 4, s. 710-723Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Most fluvial networks worldwide include watercourses that recurrently cease to flow and run dry. The spatial and temporal extent of the dry phase of these temporary watercourses is increasing as a result of global change. Yet, current estimates of carbon emissions from fluvial networks do not consider temporary watercourses when they are dry. We characterized the magnitude and variability of carbon emissions from dry watercourses by measuring the carbon dioxide (CO2) flux from 10 dry streambeds of a fluvial network during the dry period and comparing it to the CO2 flux from the same streambeds during the flowing period and to the CO2 flux from their adjacent upland soils. We also looked for potential drivers regulating the CO2 emissions by examining the main physical and chemical properties of dry streambed sediments and adjacent upland soils. The CO2 efflux from dry streambeds (mean +/- A SD = 781.4 +/- A 390.2 mmol m(-2) day(-1)) doubled the CO2 efflux from flowing streambeds (305.6 +/- A 206.1 mmol m(-2) day(-1)) and was comparable to the CO2 efflux from upland soils (896.1 +/- A 263.2 mmol m(-2) day(-1)). However, dry streambed sediments and upland soils were physicochemically distinct and differed in the variables regulating their CO2 efflux. Overall, our results indicate that dry streambeds constitute a unique and biogeochemically active habitat that can emit significant amounts of CO2 to the atmosphere. Thus, omitting CO2 emissions from temporary streams when they are dry may overlook the role of a key component of the carbon balance of fluvial networks.

  • 191.
    Graham, Emily B.
    et al.
    Univ Colorado, Inst Arctic & Alpine Res, Boulder, CO 80309 USA.;Pacific NW Natl Lab, Div Biol Sci, Richland, WA 99352 USA..
    Knelman, Joseph E.
    Univ Colorado, Inst Arctic & Alpine Res, Boulder, CO 80309 USA.;Joint Genome Inst, US Dept Energy, Walnut Creek, CA USA..
    Schindlbacher, Andreas
    Bundesforsch & Ausblldungszentrum VVald, Fed Res & Tr 3Thing Ctr Forests, Dept Forest Ecol, Vienna, Austria..
    Siciliano, Steven
    Univ Saskatchewan, Dept Soil Sci, Saskatoon, SK, Canada..
    Breulmann, Marc
    Helmholtz Ctr Environm Res, Ctr Environm Biotechnol, Leipzig, Germany..
    Yannarell, Anthony
    Univ Illinois, Dept Nat Resources & Environm Sci, Urbana, IL USA..
    Bemans, J. M.
    Univ Calif Merced, Life & Environm Sci & Sierra Nevada Res Inst, Merced, CA USA..
    Abell, Guy
    Flinders Univ S Australia, Sch Med, Adelaide, SA 5001, Australia..
    Philippot, Laurent
    Inst Natl Rech Agron Agroecol, Dijon, France..
    Prosser, James
    Univ Aberdeen, Inst Biol & Environm Sci, Aberdeen, Scotland..
    Foulquier, Arnaud
    UR MALY, Irstea, Ctr Lyon Villeurbanne, Villeurbanne, France..
    Yuste, Jorge C.
    CSIC, Museo Nacl Ciencias Nat, Dept Biogeog & Global Change, Madrid, Spain..
    Glanville, Helen C.
    Bangor Univ, Environm Ctr Wales, Gwynedd, England..
    Jones, Davey L.
    Bangor Univ, Environm Ctr Wales, Gwynedd, England..
    Angel, Foey
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Vienna, Austria..
    Salminen, Janne
    Hame Univ Appl Sci, Hameenlinna, Finland..
    Newton, Ryan J.
    Univ Wisconsin, Sch Freshwater Sci, Milwaukee, WI 53201 USA..
    Buergmann, Helmut
    Eawag Swiss Fed Inst Aquat Sci & Technol, Dept Surface Waters, Kastanienbaum, Switzerland..
    Ingram, Lachlan J.
    Univ Sydney, Ctr Carbon Water & Food, Sydney, NSW 2006, Australia..
    Hamer, Ute
    Univ Munster, Inst Landscape Ecol, D-48149 Munster, Germany..
    Siljanen, Henri M. P.
    Univ Eastern Finland, Dept Environm & Biol Sci, Kuopio, Finland..
    Peltoniemi, Krista
    Nat Resources Inst, Vantaa, Finland..
    Potthast, Karin
    Tech Univ Dresden, Inst Soil Sci & Site Ecol, D-01062 Dresden, Germany..
    Baneras, Lluis
    Univ Girona, Fac Ciencies, Inst Aquat Ecol, Girona, Spain..
    Hartmann, Martin
    Inst Sustainabil Sci Agroscope, Zurich, Switzerland..
    Banerjee, Samiran
    CSIRO Agr Flagship, Crace, ACT, Australia..
    Yu, Ri-Qing
    Univ Texas Tyler, Dept Biol, Tyler, TX 75799 USA..
    Nogaro, Geraldine
    EDF R&D, Alat Hydraul & Environm Lab, Chatou, France..
    Richter, Andreas
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Vienna, Austria..
    Koranda, Marianne
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Div Terr Ecosyst Res, Vienna, Austria..
    Castle, Sarah C.
    Univ Montana, Dept Ecosyst & Conservat Sci, Missoula, MT 59812 USA..
    Goberna, Marta
    CSIC, Ctr Invest & Docencia Econ, Valencia, Spain..
    Song, Bongkeun
    Virginia Inst Marine Sci, Dept Biol Sci, Gloucester Point, VA USA..
    Chatterjee, Amitava
    N Dakota State Univ, AES Sch Nat Resources Sci, Fargo, ND 58105 USA..
    Nunes, Olga C.
    Lopes, Ana R.
    Univ Porto, Fac Engn, Lab Proc Engn Environm Biotechnol & Energy, LEPABE, Rua Campo Alegre 823, P-4100 Oporto, Portugal..
    Cao, Yiping
    Southern Calif Coastal Water Res Project Author, Costa Mesa, CA USA..
    Kaisermann, Aurore
    INRA Bordeaux, Interact Sol Plante Atmosphere, UMR, Villenave Dornon, France..
    Hallin, Sara
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden..
    Strickland, Michael S.
    State Univ, Virginia Polytech Inst, Dept Biol Sci, Blacksburg, VA USA..
    Garcia-Pausas, Jordi
    Ctr Tecnol Forestal Catalunya, Solsona, Spain..
    Barba, Josep
    Ctr Recerca Ecol & Aplicac Forestals, Barcelona, Spain..
    Kang, Hojeong
    Yonsei Univ, Sch Civil & Environm Engn, Seoul 120749, South Korea..
    Isobe, Kazuo
    Univ Tokyo, Dept Appl Biol Chem, Tokyo, Japan..
    Papaspyrou, Sokratis
    Univ Cadiz, Dept Biomed Biotechnol & Publ Hlth, Puerto Real, Spain..
    Pastorelli, Roberta
    Res Ctr Agrobiol & Pedol, Florence, Italy..
    Lagomarsino, Alessandra
    Res Ctr Agrobiol & Pedol, Florence, Italy..
    Lindström, Eva S.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Basiliko, Nathan
    Laurentian Univ, Vale Living Lakes Ctr, Sudbury, ON P3E 2C6, Canada.;Laurentian Univ, Dept Biol, Sudbury, ON P3E 2C6, Canada..
    Nemergut, Diana R.
    Univ Colorado, Inst Arctic & Alpine Res, Boulder, CO 80309 USA.;Duke Univ, Dept Biol, Durham, NC USA..
    Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?2016Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, artikkel-id 214Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

  • 192.
    Grasset, C.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Levrey, L. H.
    Delolme, C.
    Arthaud, F.
    Bornette, G.
    The interaction between wetland nutrient content and plant quality controls aquatic plant decomposition2017Inngår i: Wetlands Ecology and Management, ISSN 0923-4861, E-ISSN 1572-9834, Vol. 25, nr 2, s. 211-219Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We conducted an in situ decomposition experiment to better understand how habitat nutrient content controls aquatic plant decomposition and, more precisely, to determine the relative importance of the wetland conditions in decomposition, and the intrinsic degradability of plant tissues. We collected the green leaves of three aquatic plant species with contrasting plant strategies from three wetlands of differing nutrient contents, and allowed them to decompose in seven wetlands along a nutrient gradient. The plant mass loss was higher for competitive and ruderal species collected in nutrient richer wetlands as well as when they were led to decompose in nutrient richer wetlands. Plant water content correlated with mass loss for the competitive and ruderal species, which may explain the increase in mass loss with increasing nutrient content in the collection wetlands. Litter decomposition rate may be enhanced by wetland eutrophication, because of both the modification of wetland decomposition conditions and by changes in plant tissue quality.

  • 193.
    Grasset, Charlotte
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Abril, Gwenaël
    Guillard, Ludovic
    Delolme, Cécile
    Bornette, Gudrun
    Carbon emission along a eutrophication gradient in temperate riverine wetlands: effect of primary productivity and plant community composition2016Inngår i: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 61, s. 1405-1420Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Eutrophication increases primary productivity and favours the predominance of floating vegetation in wetlands. Carbon (C) fluxes in wetlands are strongly driven by primary productivity and can differ by vegetation type. However, to the best of our knowledge, the role of eutrophication in C fluxes has rarely been assessed. Consequently, we aimed to measure the seasonal variation in carbon dioxide (CO2) and methane (CH4) fluxes at six aquatic sites in four temperate wetlands, ranging along a gradient of sediment total phosphorus content, and determine whether C fluxes correlate with above-ground net primary productivity (ANPP) and plant community composition along this eutrophication gradient. Daytime CO2 emissions were significantly and negatively correlated with wetland net primary productivity as a result of the greater C fixation by photosynthesis during the peak of production. Conversely, CH4 emissions were significantly and positively correlated with wetland ANPP, possibly due to higher litter production and anaerobic decomposition. The highest CH4 emissions were observed above floating vegetation, which favoured hypoxic conditions in the water column. CH4 emissions including ebullition were higher above macroalgal belts than above vascular plants with floating leaves. CH4 emissions without ebullition (i.e. resulting from plant transport and diffusion) better correlated with the abundance of macroalgae than with the abundance of vascular plants with floating leaves. Our results suggest that eutrophication may greatly modify CO2 and CH4 emissions from wetlands through changes in vegetation type and productivity.

  • 194.
    Grasset, Charlotte
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Laboratory of Aquatic Ecology, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil.
    Abril, Gwenaël
    Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum National d'Histoire Naturelle, Paris cedex 05, France; Programa de Geoquímica, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil.
    Mendonca, Raquel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Laboratory of Aquatic Ecology, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil.
    Roland, Fabio
    Laboratory of Aquatic Ecology, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil.
    Sobek, Sebastian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    The transformation of macrophyte-derived organic matter to methane relates to plant water and nutrient contents2019Inngår i: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 64, nr 4, s. 1737-1749Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Macrophyte detritus is one of the main sources of organic carbon (OC) in inland waters, and it is potentially available for methane (CH4) production in anoxic bottom waters and sediments. However, the transformation of macrophyte‐derived OC into CH4 has not been studied systematically, thus its extent and relationship with macrophyte characteristics remains uncertain. We performed decomposition experiments of macrophyte detritus from 10 different species at anoxic conditions, in presence and absence of a freshwater sediment, in order to relate the extent and rate of CH4 production to the detritus water content, C/N and C/P ratios. A significant fraction of the macrophyte OC was transformed to CH4 (mean = 7.9%; range = 0–15.0%) during the 59‐d incubation, and the mean total C loss to CO2 and CH4 was 17.3% (range = 1.3–32.7%). The transformation efficiency of macrophyte OC to CH4 was significantly and positively related to the macrophyte water content, and negatively to its C/N and C/P ratios. The presence of sediment increased the transformation efficiency to CH4 from an average of 4.0% (without sediment) to 11.8%, possibly due to physicochemical conditions favorable for CH4 production (low redox potential, buffered pH) or because sediment particles facilitate biofilm formation. The relationship between macrophyte characteristics and CH4 production can be used by future studies to model CH4 emission in systems colonized by macrophytes. Furthermore, this study highlights that the extent to which macrophyte detritus is mixed with sediment also affects CH4 production.

  • 195.
    Grasset, Charlotte
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Delolme, Cécile
    Arthaud, Florent
    Bornette, Gudrun
    Carbon allocation in aquatic plants with contrasting strategies: The role of habitat nutrient content2015Inngår i: Journal of Vegetation Science, ISSN 1100-9233, E-ISSN 1654-1103, Vol. 26, s. 946-955Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Questions: The link between the carbon composition of aquatic plants and (1) plant strategies and (2) habitat nutrient availability has received little attention. We tested whether three aquatic species belonging to the three adaptive strategies defined by Grime (ruderal, stress tolerant and competitive) had contrasting carbon allocation patterns, and if these patterns varied in the same way between populations distributed along a gradient of habitat nutrient content. Location: Wetlands in the northern Rhône River Basin, France. Methods: The three species were sampled in 17 wetlands along a gradient of nutrient content in the northern Rhône River Basin. In each population sampled, we measured plant water content, C/N ratio, structural compounds (lignin and structural polysaccharides) and storage compounds (free sugars and starch) in two seasons (spring and autumn 2012). Results: The stress-tolerant species had higher content of structural compounds than the competitive and ruderal species. The content of storage compounds was higher in the competitive and stress-tolerant species compared to the ruderal species. Allocation of carbon compounds varied with habitat nutrient content in different ways for the three species, suggesting contrasting plasticities, possibly linked to plant strategy. Conclusion: Plant strategies and habitat nutrient content are likely key drivers in plant carbon allocation and should be taken into account when studying interactions between habitat and plant quality.

  • 196.
    Grasset, Charlotte
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Laboratory of Aquatic Ecology, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Brazil.
    Mendonça, Raquel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Federal University of Juiz de Fora, Juiz de Fora, Brazil.
    Villamor Saucedo, Gabriella
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Federal University of Juiz de Fora, Juiz de Fora, Brazil.
    Bastviken, David
    Department of Thematic Studies – Environmental Change, Linköping University, Linköping, Sweden.
    Roland, Fabio
    Federal University of Juiz de Fora, Juiz de Fora, Brazil.
    Sobek, Sebastian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Large but variable methane production in anoxic freshwater sediment upon addition of allochthonous and autochthonous organic matter2018Inngår i: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 63, nr 4, s. 1488-1501Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An important question in the context of climate change is to understand how CH4 production is regulated in anoxic sediments of lakes and reservoirs. The type of organic carbon (OC) present in lakes is a key factor controlling CH4 production at anoxic conditions, but the studies investigating the methanogenic potential of the main OC types are fragmented. We incubated different types of allochthonous OC (alloOC; terrestrial plant leaves) and autochthonous OC (autoOC; phytoplankton and two aquatic plants species) in an anoxic sediment during 130 d. We tested if (1) the supply of fresh alloOC and autoOC to an anoxic refractory sediment would fuel CH4 production and if (2) autoOC would decompose faster than alloOC. The addition of fresh OC greatly increased CH4 production and the δ13C-CH4 partitioning indicated that CH4 originated exclusively from the fresh OC. The large CH4 production in an anoxic sediment fueled by alloOC is a new finding which indicates that all systems with anoxic conditions and high sedimentation rates have the potential to be CH4 emitters. The autoOC decomposed faster than alloOC, but the total CH4 production was not higher for all autoOC types, one aquatic plant species having values as low as the terrestrial leaves, and the other one having values as high as phytoplankton. Our study is the first to report such variability, suggesting that the extent to which C fixed by aquatic plants is emitted as greenhouse gases or buried as OC in sediment could more generally differ between aquatic vegetation types.

  • 197.
    Grasset, Charlotte
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Rodriguez, Célia
    Delolme, Cécile
    Marmonier, Pierre
    Bornette, Gudrun
    Can Soil Organic Carbon Fractions Be Used as Functional Indicators of Wetlands?2017Inngår i: Wetlands (Wilmington, N.C.), ISSN 0277-5212, E-ISSN 1943-6246, Vol. 37, nr 6, s. 1195-1205Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This work aimed to determine whether the organic carbon in wetland soils correlated with physico-chemical characteristics of wetlands (e.g. nutrient content, pH) and differentiated wetlands according to their plant community composition definied by the CORINE Biotope nomenclature. 96 wetlands were sampled in southeastern France, belonging to 14 CORINE habitats grouped into 3 CORINE hydrological categories: wet meadows, peatlands and aquatic wetlands. The total organic carbon content, the carbon content of humic fractions (humic acid (CHA), fulvic acid (CFA) and Chumin), and water extractable organic carbon were measured in samples collected in the upper 20 cm soil layer. These soil organic carbon fractions correlated with pH and soil nutrient content but differed slightly among the 14 CORINE habitats. In contrast, soil organic carbon fractions greatly differed among the 3 CORINE hydrological categories. The CFA/CHA ratio was significantly lower for wet meadows and peatlands and the proportion of CHumin was significantly higher for peatlands and aquatic wetlands. These soil organic carbon fractions inform on the hydrological status of wetlands and may consequently be used as functional indicator in addition to a plant-based classification as the CORINE Biotope nomenclature.

  • 198.
    Groeneveld, Marloes M.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Tranvik, Lars J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Natchimuthu, Sivakiruthika
    Linkoping Univ, Dept Themat Studies Environm Change, S-58183 Linkoping, Sweden.
    Koehler, Birgit
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Photochemical mineralisation in a boreal brown water lake: considerable temporal variability and minor contribution to carbon dioxide production2016Inngår i: Biogeosciences Discussions, ISSN 1810-6277, E-ISSN 1810-6285, Vol. 13, nr 13, s. 3931-3943Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sunlight induces photochemical mineralisation of chromophoric dissolved organic matter (CDOM) to dissolved inorganic carbon (DIC) in inland waters, resulting in carbon dioxide (CO2) emissions to the atmosphere. Photochemical rate modelling is used to determine sunlight-induced CO2 emissions on large spatial and temporal scales. A sensitive model parameter is the wavelength-specific photochemical CDOM reactivity, the apparent quantum yield (AQY). The modelling studies so far assume that AQY spectra determined for single lakes and on single occasions represent larger spatial and temporal scales. Here, we studied a humic boreal lake in Sweden. We measured AQY spectra for photochemical DIC production monthly between June and November 2014 and parameterised a photochemical rate model. Photochemical reactivity increased slightly during the open water period, likely due to a high rainfall event with consecutive mixing in autumn that increased availability of highly photoreactive CDOM. However, the variability in AQY spectra over time was much smaller than previously reported variability in AQY spectra across lakes. Yet, using either the AQY spectrum from the least or from the most photoreactive water sample resulted in a 5-fold difference in simulated annual DIC photoproduction (2.0 ± 0.1 and 10.3 ± 0.7 g C m−2 yr−1, respectively). Using the monthly measured AQY spectrum to simulate DIC photoproduction for month-long time periods resulted in an apparent time lag between irradiance and DIC photoproduction. This suggested that temporal variability in AQY spectra occurs on shorter time scales. Therefore, we parameterised the model with the pooled AQY spectrum of six monthly measurements. Simulated DIC photoproduction for three years (2012–2014) averaged 4.5 ± 0.2 g C m−2 yr−1, which represented 3 % of the mean CO2 emissions from this lake. We conclude that (1) it may be recommendable to conduct repeated AQY measurements across the season for more accurate simulation of annual photochemical DIC production in lakes and (2), in agreement with previous studies, direct CDOM photomineralisation makes only a minor contribution to mean CO2 emissions from Swedish humic lakes.

  • 199.
    Grubisic, Lorena M.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Eiler, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Heinrich, Friederike
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Brutemark, Andreas
    Tvarminne Zool Stn, Hango, Finland.;Novia Univ Appl Sci, ARONIA Coastal Zone Res Team, Ekenas, Finland.;Abo Akad Univ, Ekenas, Finland..
    Alonso-Sáez, Laura
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. KTH Royal Inst Technol & Sci Life Lab, Sch Biotechnol, Stockholm, Sweden.
    Gantner, Stephan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Leibniz Inst Sci & Math Educ, Dept Educ Sci Biol, Kiel, Germany..
    Riemann, Lasse
    Univ Copenhagen, Dept Biol, Marine Biol Sect, Helsingor, Denmark..
    Beier, Sara
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Leibniz Inst Balt Sea Res Warnemunde IOW, Rostock, Germany..
    Lake bacterioplankton dynamics over diurnal timescales2017Inngår i: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 62, nr 1, s. 191-204Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    1. Planktonic bacterial community dynamics over short timescales can be of great importance for food webs and ecosystem functioning but are rarely described when microbial community and composition are assessed. To study the significance of such dynamics we sampled the surface water at the deepest point of a mesotrophic lake (Lake Erken, Sweden) every third hour over two days. 2. By combining 454 pyrosequencing of 16S rRNA genes with bromodeoxyuridine immunocapturing of DNA, replicating populations were identified and compared to the community retrieved from total DNA samples. This comparison revealed a significant difference between the actively replicating and total community. 3. The high-frequency diurnal sampling was compared to a year-long survey conducted in the same lake in order to compare the diurnal and seasonal variation in bacterioplankton community composition. At the diurnal-scale, the variation was significantly higher in the replicating than in the total community. However, variation in both active and total diurnal community was significantly lower than the variation in the seasonal total community. 4. Our analysis revealed pronounced short-term dynamics of individual bacterial populations uncoupled from the diurnal light cycle. For example, the proliferating fraction of the most abundant bacterial tribe (LD12) followed a cyclic pattern that covaried with viral abundance. This implies that environmental factors other than light may act as important drivers of microbial community composition, at least in mesotrophic Lake Erken.

  • 200.
    Grubisic, Lorena M.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Brutemark, Andreas
    Weyhenmeyer, Gesa A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Wikner, Johan
    Bamstedt, Ulf
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Effects of stratification depth and dissolved organic matter on brackish bacterioplankton communities2012Inngår i: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 453, s. 37-48Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacterioplankton growth is often directly or indirectly controlled by external energy subsidies via organic matter inputs or solar radiation. We carried out a mesocosm experiment to assess how bacterioplankton communities responded to elevated levels of dissolved organic matter (DOM) and experimentally controlled stratification depth. The month-long experiment consisted of 2500 l mesocosms subjected to 4 experimental manipulations in triplicate: the stratification depth was set to either 1.5 or 3.5 m, with or without experimental addition of ambient levels of chromophoric DOM. DOM addition had a significant effect on bacterial community composition as assessed by terminal restriction fragment length polymorphism of amplified 16S rRNA genes. In contrast, there were no effects of the DOM amendment on bacterial biomass or production. Mixing depth and the coupled effective light climate in the photic zone also had a significant effect on bacterial community composition. Furthermore, shallow mixing depth was associated with enhanced primary production, whereas DOM addition had a negative effect on phyto plankton biomass and productivity. Our results suggest that bacterial community composition is coupled to primary production under the studied coastal nutrient regime, and point to a key role of DOM quality in controlling bacterioplankton communities.

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