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  • 51. Farnelid, Hanna
    et al.
    Andersson, Anders F.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    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-Cyanobacteria2011In: PLoS ONE, ISSN 1932-6203, Vol. 6, no 4, p. e19223-Article in journal (Refereed)
    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.

  • 52. Farnelid, Hanna
    et al.
    Bentzon-Tilia, Mikkel
    Andersson, Anders F.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Jost, Guenter
    Labrenz, Matthias
    Juergens, Klaus
    Riemann, Lasse
    Active nitrogen-fixing heterotrophic bacteria at and below the chemocline of the central Baltic Sea2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 7, p. 1413-1423Article in journal (Refereed)
    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.

  • 53.
    Feng, Xin Mei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Karlsson, Anna
    Svensson, Bo H.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Impact of trace element addition on biogas production from food industrial waste - linking process to microbial communities2010In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 74, no 1, p. 226-240Article in journal (Refereed)
    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.

  • 54.
    Galand, Pierre E.
    et al.
    Centre d’Estudis Avançats de Blanes-Consejo Superior de Investigaciones Científicas.
    Alonso-Sáez, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    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 winter2013In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 4, p. 118-Article in journal (Refereed)
    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.

  • 55.
    Gantner, Stephan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Andersson, Anders F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Alonso-Saez, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Novel primers for 16S rRNA-based archaeal community analyses in environmental samples2011In: Journal of Microbiological Methods, ISSN 0167-7012, E-ISSN 1872-8359, Vol. 84, no 1, p. 12-18Article in journal (Refereed)
    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.

  • 56.
    Garcia, Sarahi L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, 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 University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Malmstrom, Rex R
    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 populations2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, no 3, p. 742-755Article in journal (Refereed)
    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.

  • 57. Ghiglione, J. -F
    et al.
    Galand, P. E.
    Pommier, T.
    Pedrós-Alió, C.
    Maas, E. W.
    Bakker, K.
    Bertilson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Kirchman, D. L.
    Lovejoy, C.
    Yager, P. L.
    Murray, A. E.
    Pole-to-pole biogeography of surface and deep marine bacterial communities2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 43, p. 17633-17638Article in journal (Refereed)
    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.

  • 58. 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 University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    McMahon, Katherine D
    Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage2014In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 8, no 12, p. 2503-2516Article in journal (Refereed)
    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.

  • 59. Goedkoop,, W.
    et al.
    Widenfalk,, A.
    Haglund,, A-L.,
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Microbial characterization of artificial sediment and comparisons with natural sediment-Implications for toxicity testing.2005In: Environmental Toxicology and Chemistry., no 24:, p. 2725-2733.Article in journal (Refereed)
  • 60. Goldstone, J V
    et al.
    Pullin, M J
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Voelker, B M
    Reactions of hydroxyl radical with humic substances: bleaching, mineralization, and production of bioavailable carbon substrates.2002In: Environ Sci Technol, ISSN 0013-936X, Vol. 36, no 3, p. 364-72Article in journal (Refereed)
  • 61.
    Granéli, Wilhelm
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Philibert, A
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Phosphorus limitation of bacterial growth in high Arctic lakes and ponds2004In: Aquatic Sciences, Vol. 66, p. 430-439Article in journal (Refereed)
  • 62.
    Granéli, Wilhelm
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Carlsson, Per
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bacterial abundance, production and organic carbon limitation in the Southern Ocean (39-62°S, 4-14°E) during the austral summer 1997/19982004In: Deep-Sea Research II: Topical Studies in Oceanography, Vol. 51, p. 2569-2582Article in journal (Refereed)
  • 63.
    Grubisic, Lorena M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Heinrich, Friederike
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, 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 University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. KTH Royal Inst Technol & Sci Life Lab, Sch Biotechnol, Stockholm, Sweden.
    Gantner, Stephan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, 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 University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Leibniz Inst Balt Sea Res Warnemunde IOW, Rostock, Germany..
    Lake bacterioplankton dynamics over diurnal timescales2017In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 62, no 1, p. 191-204Article in journal (Refereed)
    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.

  • 64.
    Grubisic, Lorena M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Brutemark, Andreas
    Weyhenmeyer, Gesa A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wikner, Johan
    Bamstedt, Ulf
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Effects of stratification depth and dissolved organic matter on brackish bacterioplankton communities2012In: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 453, p. 37-48Article in journal (Refereed)
    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.

  • 65.
    Hamilton, Joshua J.
    et al.
    University of Wisconsin—Madison, Madison, USA.
    Garcia, Sarahi L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Brown, Brittany S.
    University of Wisconsin—Madison, Madison, USA.
    Oyserman, Ben O.
    University of Wisconsin—Madison, Madison, USA.
    Moya-Flores, Francisco
    University of Wisconsin—Madison, Madison, USA.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Malmstrom, Rex R.
    United States Department of Energy Joint Genome Institute, Walnut Creek, USA.
    Forest, Katrina T.
    University of Wisconsin—Madison, Madison, USA.
    McMahon, Katherine D.
    University of Wisconsin—Madison, Madison, USA.
    Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI2017In: mSystems, E-ISSN 2379-5077, Vol. 2, no 4, article id e00091-17Article in journal (Refereed)
    Abstract [en]

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

  • 66.
    He, Shaomei
    et al.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.;Univ Wisconsin, Dept Geosci, Madison, WI USA..
    Stevens, Sarah L. R.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA..
    Chan, Leong-Keat
    DOE Joint Genome Inst, Walnut Creek, CA USA..
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    del Rio, Tijana Glavina
    DOE Joint Genome Inst, Walnut Creek, CA USA..
    Tringe, Susannah G.
    DOE Joint Genome Inst, Walnut Creek, CA USA..
    Malmstrom, Rex R.
    DOE Joint Genome Inst, Walnut Creek, CA USA..
    McMahon, Katherine D.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.;Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA..
    Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes2017In: MSPHERE, ISSN 2379-5042, Vol. 2, no 5, article id e00277-17Article in journal (Refereed)
    Abstract [en]

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

  • 67.
    Heinrich, Friederike
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Seasonality and environmental control of freshwater SAR11 (LD12) in a temperate lake (Lake Erken, Sweden)2013In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 70, no 1, p. 33-44Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 69.
    Herrero Ortega, Sonia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. Leibniz Inst Freshwater Ecol & Inland Fisheries I, Dept Expt Limnol, Stechlin, Germany.
    Catalán, Núria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. Catalan Inst Water Res ICRA, Girona, Spain.
    Björn, Erik
    Gröntoft, Hannes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Hilmarsson, Torfi Geir
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wu, Pianpian
    Bishop, Kevin
    Levanoni, Oded
    Bravo, Andrea Garcia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    High methylmercury formation in ponds fueled by fresh humic and algal derived organic matter2018In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 63, no S1, p. S44-S53Article in journal (Refereed)
    Abstract [en]

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

  • 70.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tan, BoonFei
    University of Alberta, Edmonton, Canada; Singapore-MIT Alliance for Research and Technology, Leipzig, Germany.
    Foght, Julia
    University of Alberta, Edmonton, Canada.
    Wendeberg, Annelie
    Centre for Environmental Research, Leipzig, Germany.
    Berry, David
    University of Vienna, Vienna, Austria.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. eDNA Solutions AB, Mölndal, Sweden.
    Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions2017In: mSystems, E-ISSN 2379-5077, Vol. 2, no 5, article id e00038-17Article in journal (Refereed)
    Abstract [en]

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

  • 71.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wu, Xiaofen
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Heim, Christine
    Univ Gottingen, GZG Geobiol, Gottingen, Germany.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ionescu, Danny
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Neuglobsow, Germany.
    Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 10, p. 2447-2458Article in journal (Refereed)
    Abstract [en]

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

  • 72. Hunt, Dana E
    et al.
    Klepac-Ceraj, Vanja
    Acinas, Silvia G
    Gautier, Clement
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Polz, Martin F
    Evaluation of 23S rRNA PCR Primers for Use in Phylogenetic Studies of Bacterial Diversity.2006In: Applied and Environmental Microbiology, ISSN 0099-2240, Vol. 72, no 3, p. 2221-2225Article in journal (Refereed)
  • 73. Jacobsen, Carsten Suhr
    et al.
    Nielsen, Tue Kjærgaard
    Vester, Jan Kjølhede
    Stougaard, Peter
    Nielsen, Jeppe Lund
    Voriskova, Jana
    Winding, Anne
    Baldrian, Petr
    Liu, Binbin
    Frostegård, Åsa
    Pedersen, Dorthe
    Tveit, Alexander Tøsdal
    Svenning, Mette Marianne
    Tebbe, Christoph C.
    Øvreås, Lise
    Jakobsen, Pia Bach
    Blazewicz, Steven J.
    Hubablek, Valerie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Hansen, Lars Hestbjerg
    Cary, S. Craig
    Holben, William E.
    Ekelund, Flemming
    Bælum, Jacob
    Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 5711Article in journal (Refereed)
    Abstract [en]

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

  • 74.
    Jarvius, Jonas
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Melin, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Göransson, Jenny
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Stenberg, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Fredriksson, Simon
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Gonzalez-Rey, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Nilsson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Digital Quantification using Amplified Single-Molecule Detection2006In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 3, no 9, p. 725-727Article in journal (Refereed)
    Abstract [en]

    We describe a scheme for biomolecule enumeration by converting nanometer-scale specific molecular recognition events mediated by rolling-circle amplification to fluorescent micrometer-sized DNA molecules amenable to discrete optical detection. Our amplified single-molecule detection (SMD) approach preserves the discrete nature of the molecular population, allowing multiplex detection and highly precise quantification of molecules over a dynamic range of seven orders of magnitude. We apply the method for sensitive detection and quantification of the bacterial pathogen Vibrio cholerae.

  • 75.
    Jeske, Jan Torsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Helmholtz Ctr Environm Res, Dept Environm Microbiol, Leipzig, Germany.
    Müller, Roger Andre
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wendeberg, Annelie
    Helmholtz Ctr Environm Res, Dept Environm Microbiol, Leipzig, Germany.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Microscale decoupling of sediment oxygen consumption and microbial biomass in an oligotrophic lake2016In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 61, no 9, p. 1477-1491Article in journal (Refereed)
    Abstract [en]

    Sediments of aquatic ecosystems are hotspots for biological activity. Here, we address the question if, within surface sediments, oxygen consumption is linearly related to cell abundance. In addition, we identify habitat-specific factors influencing underlying microbial processes. Sediment microcosms were established from three sites within oligotrophic Lake angstrom nnsjon, Sweden, to use microsensors for measuring oxygen profiles and estimate spatially resolved oxygen consumption rates at the water-sediment interfaces. To evaluate differences between habitats, we measured sediment carbon content and C:N:P as a proxy for diagenetic state and organic matter bioavailability. Epifluorescence microscopy was used to assess the microscale distribution and size of surface-colonising microorganisms. There was no linear correlation between oxygen consumption rates and microbial cell abundances. Cell-specific respiration rates were highest in the profundal compared to the littoral- and inflow-sediment microcosms, whereas vertical variability in all these parameters was highest at the inflow, intermediate in the littoral and least variable in profundal sediments. Illumina sequencing of spatially resolved 16SrRNA genes was used to test for possible influence of bacterial diversity on spatially resolved oxygen consumption rates. Bacterial -diversity decreased over depth at each site, but was also lower in sediments from the most active profundal zones of the lake compared to the inflow. We suggest that bacteria in profundal sediments mainly use highly oxidised organic compounds, resulting in overall low growth yield despite high metabolic activity. In the lake inflow and the littoral, more reduced organic substrates of terrestrial origin are used at lower rates but with higher yield.

  • 76.
    Jeske, Jan Torsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Osman Ahmed, Omneya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Centler, Florian
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wendeberg, Annelie
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Population-linkages in freshwater bacterial communities associated with individual diatoms and particlesManuscript (preprint) (Other academic)
  • 77.
    Jeske, Jan Torsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wendeberg, Annelie
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bacterial communities shaping the redox environment in top-layer sediments of an oligotrophic high latitude lakeManuscript (preprint) (Other academic)
  • 78.
    Jingying, Xu
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eklöf, Karin
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden.
    Ahmed Osman, Omneya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Schaefer, Jeffra K.
    Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey 08901, USA.
    Bishop, Kevin
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Skyllberg, Ulf
    Department of Forest Ecology and Management, Swedish University of Agricultural Science, Umeå, Sweden.
    Björn, Erik
    epartment of Forest Ecology and Management, Swedish University of Agricultural Science, Umeå, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bravo, Andrea Garcia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Catalunya, Spain.
    Mercury methylating microbial communities of boreal forest soils2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 518Article in journal (Refereed)
    Abstract [en]

    The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase, hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. The hgcA sequences obtained were distributed among diverse clades, including Proteobacteria, Firmicutes, and Methanomicrobia, with Deltaproteobacteria, particularly Geobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is linked to the composition of also non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for the hgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.

  • 79.
    Jingying, Xu
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Liem-Nguyen, Van
    School of Science and Technology, Örebro University, Örebro, Sweden.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Björn, Erik
    Faculty of Science and Technology, Department of Chemistry, Umeå University, Sweden.
    Bravo, Andrea Garcia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish National Research Council (CSIC), Barcelona, Spain.
    Mercury methylating microbial communities in boreal wetlandsManuscript (preprint) (Other academic)
    Abstract [en]

    Understanding the formation of the potent neurotoxic methylmercury (MeHg) is a major concern due to its threats to wildlife and human health. As boreal wetlands play a crucial role for Hg cycling on a global scale, it is crucial to understand the biogeochemical processes involved in MeHg formation in this landscape. A strategy combining high-throughput hgcA amplicon sequencing with molecular barcoding was used to revealed diverse clades of Hg(II) methylators in a wide range of wetland soils. Our results confirms a predominant role of Deltaproteobacteria, and in particular Geobacteraceae, as important Hg(II) methylators in boreal wetland soils. Firmicutes, and in particular Ruminococcaceae, were also abundant members of the Hg(II) methylating microbial communities. Our survey highlight the importance of nutrient status for the shaping of Hg(II) methylating communities across the four wetlands and reveal that water content and prevailing redox states are key factors determining the local variation in Hg(II) methylating community composition within individual wetlands. Also, our study suggests that high nutrient levels linked to low redox potential seemed to favour Hg(II) methylating methanogens within the Methanoregulaceae. Our findings expand the current knowledge on the Hg(II) methylating microbial community composition in wetland soils and the geochemical factors underpinning spatial heterogeity in such communities.  

  • 80.
    Johansson, Mona
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Distribution of the Dinoflagellate parasite Parvilucifera infectans (Parkinsozoa) along the Swedish coast2006In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 43, no 3, p. 289-302Article in journal (Refereed)
    Abstract [en]

    Dinoflagellate parasites, e.g. Parvilucifera infectans Noren et Moestrup, 1996 can potentially control dinoflagellate blooms and thereby modify plankton communities and nutrient fluxes. Parvilucifera infectans has been detected in Swedish waters, but its distribution is largely unknown. Based on 18S rRNA sequences of 2 P. infectans isolates of different geographic origin (Sweden and Tasmania), we designed 2 primer pairs for specific PCR amplification of rRNA fragments from these parasites. We screened for presence of F infectans in a salinity gradient along the Swedish coastline (2 to 30 parts per thousand, 13 stations) from June to August 2004. Parasites were only detected in July and August at 3 stations in the region with highest salinity (Skagerrak). Presence of parasites was correlated with high abundances of dinoflagellate hosts (Prorocentrum spp., Ceratium spp.) but was also restricted to warm and saline waters. In addition, these stations were characterized by low bacterial abundances, low chl a and low nutrient levels. Parasites were not detected in this region in June, when temperatures were lower (< 15 degrees C) and microzooplankton predators were most abundant. Hence, our study reveals both temporal and spatial patchiness of P. infectans in coastal waters.

  • 81. Kara, Emily L.
    et al.
    Hanson, Paul
    Hamilton, David
    Hipsey, Matthew R.
    McMahon, Katherine D.
    Read, Jordan S.
    Winslow, Luke
    Dedrick, John
    Rose, Kevin
    Carey, Cayelan C.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Marques, David da Motta
    Beversdorf, Lucas
    Miller, Todd
    Wu, Chin
    Hsieh, Yi-Fang
    Gaiser, Evelyn
    Kratz, Tim
    Time-scale dependence in numerical simulations: Assessment of physical, chemical, and biological predictions in a stratified lake at temporal scales of hours to months2012In: Environmental Modelling & Software, ISSN 1364-8152, E-ISSN 1873-6726, Vol. 35, p. 104-121Article in journal (Refereed)
    Abstract [en]

    We evaluated the predictive ability of a one-dimensional coupled hydrodynamic-biogeochemical model across multiple temporal scales using wavelet analysis and traditional goodness-of-fit metrics. High-frequency in situ automated sensor data and long-term manual observational data from Lake Mendota, Wisconsin, USA, were used to parameterize, calibrate, and evaluate model predictions. We focused specifically on short-term predictions of temperature, dissolved oxygen, and phytoplankton biomass over one season. Traditional goodness-of-fit metrics indicated more accurate prediction of physics than chemical or biological variables in the time domain. This was confirmed by wavelet analysis in both the time and frequency domains. For temperature, predicted and observed global wavelet spectra were closely related, while observed dissolved oxygen and chlorophyll fluorescence spectral characteristics were not reproduced by the model for key time scales, indicating that processes not modeled may be important drivers of the observed signal. Although the magnitude and timing of physical and biological changes were simulated adequately at the seasonal time scale through calibration, time scale-specific dynamics, for example short-term cycles, were difficult to reproduce, and were relatively insensitive to the effects of varying parameters. The use of wavelet analysis is novel to aquatic ecosystem modeling, is complementary to traditional goodness-of-fit metrics, and allows for assessment of variability at specific temporal scales. In this way, the effect of processes operating at distinct temporal scales can be isolated and better understood, both in situ and in silico. Wavelet transforms are particularly well suited for assessment of temporal and spatial heterogeneity when coupled to high-frequency data from automated in situ or remote sensing platforms.

  • 82. Keller, Andreas Hardy
    et al.
    Schleinitz, Kathleen M.
    Starke, Robert
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Vogt, Carsten
    Kleinsteuber, Sabine
    Metagenome-based metabolic reconstruction reveals the ecophysiological function of Epsilonproteobacteria in a hydrocarbon-contaminated sulfidic aquifer2015In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, article id 1396Article in journal (Refereed)
    Abstract [en]

    The population genome of an uncultured bacterium assigned to the Campylobacterales (Epsilonproteobacteria) was reconstructed from a metagenome dataset obtained by whole-genome shotgun pyrosequencing. Genomic DNA was extracted from a sulfate-reducing, m-xylene-mineralizing enrichment culture isolated from groundwater of a benzene-contaminated sulfidic aquifer. The identical epsilonproteobacterial phylotype has previously been detected in toluene- or benzene-mineralizing, sulfate-reducing consortia enriched from the same site. Previous stable isotope probing (SIP) experiments with 13C6-labeled benzene suggested that this phylotype assimilates benzene-derived carbon in a syntrophic benzene-mineralizing consortium that uses sulfate as terminal electron acceptor. However, the type of energy metabolism and the ecophysiological function of this epsilonproteobacterium within aromatic hydrocarbon-degrading consortia and in the sulfidic aquifer are poorly understood. Annotation of the epsilonproteobacterial population genome suggests that the bacterium plays a key role in sulfur cycling as indicated by the presence of an sqr gene encoding a sulfide quinone oxidoreductase and psr genes encoding a polysulfide reductase. It may gain energy by using sulfide or hydrogen/formate as electron donors. Polysulfide, fumarate, as well as oxygen are potential electron acceptors. Auto- or mixotrophic carbon metabolism seems plausible since a complete reductive citric acid cycle was detected. Thus the bacterium can thrive in pristine groundwater as well as in hydrocarbon-contaminated aquifers. In hydrocarbon-contaminated sulfidic habitats, the epsilonproteobacterium may generate energy by coupling the oxidation of hydrogen or formate and highly abundant sulfide with the reduction of fumarate and/or polysulfide, accompanied by efficient assimilation of acetate produced during fermentation or incomplete oxidation of hydrocarbons. The highly efficient assimilation of acetate was recently demonstrated by a pulsed 13C2-acetate protein SIP experiment. The capability of nitrogen fixation as indicated by the presence of nif genes may provide a selective advantage in nitrogen-depleted habitats. Based on this metabolic reconstruction, we propose acetate capture and sulfur cycling as key functions of Epsilonproteobacteria within the intermediary ecosystem metabolism of hydrocarbon-rich sulfidic sediments.

  • 83. Krause, Sascha
    et al.
    Le Roux, Xavier
    Niklaus, Pascal A.
    Van Bodegom, Peter M.
    Lennon, Jay T.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Grossart, Hans-Peter
    Philippot, Laurent
    Bodelier, Paul L. E.
    Trait-based approaches for understanding microbial biodiversity and ecosystem functioning2014In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 5, p. 251-Article, review/survey (Refereed)
    Abstract [en]

    In ecology, biodiversity-ecosystem functioning (BEE) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEE of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEE using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEE studies are often inadequate to unravel BEE relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEE relationships and thus generating systematic principles in microbial ecology and more generally ecology.

  • 84.
    Krizsan, Sophie J
    et al.
    Swedish University of Agricultural Sciences, Umeå, Sweden.
    Mateos-Rivera, Alejandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Felton, Annika
    Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Anttila, Anne
    Helsinki University, Helsinki, Finland.
    Ramin, Mohammad
    Swedish University of Agricultural Sciences, Umeå, Sweden.
    Vaga, Merko
    Swedish University of Agricultural Sciences, Umeå, Sweden.
    Gidlund, Helena
    Swedish University of Agricultural Sciences, Umeå, Sweden.
    Huhtanen, Pekka
    Swedish University of Agricultural Sciences, Umeå, Sweden.
    An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods2018In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, p. 4183-4196Article in journal (Refereed)
    Abstract [en]

    Evolutionary morphological and physiological differences between browsers and grazers contribute to species- specific digestion efficiency of food resources. Rumen microbial community structure of browsers is supposedly adapted to characteristic nutrient composition of the diet source. If this assumption is correct, domesticated ruminants, or grazers, are poor model animals for assessing the nutritional value of food consumed by browsing game species. In this study, typical spring and summer foods of the European moose (Alces alces) were combined with rumen fluid collected from both dairy cows (Bos taurus) and from moose, with the aim of comparing fer- mentation efficiency and microbial community composition. The nutritional value of the food resources was characterized by chemical analysis and advanced in vitro measurements. The study also addressed whether or not feed evaluation based on in vitro techniques with cattle rumen fluid as inoculum could be a practical alternative when evaluating the nutritional value of plants consumed by wild browsers. Our re- sults suggest that the fermentation characteristics of moose spring and summer food are partly host- specific and related to the contribution of the bacterial phyla Firmicutes and Bacteriodetes to the rumen microbial community. Host- specific adaptations of the ruminal microbial community structure could be explained from the evolutionary adaptations related to feeding habitats and morphophysiological differences be- tween browsers and grazers. However, the observed overall differences in microbial community structure could not be related to ruminal digestion parameters measured in vitro. The in vitro evaluation of digestion efficiency reveals that equal amounts of methane were produced across all feed samples regardless of whether the ruminal fluid was from moose or dairy cow. The results of this study suggested that the nutri- tional value of browsers’ spring and summer food can be predicted using rumen fluid from domesticated grazers as inoculum in in vitro assessments of extent of digestion when excluding samples of the white water lily root, but not of fermentation characteristics as indicated by the proportions of individual fermentation fatty acids to the total of volatile fatty acids.

  • 85.
    Lindström, Eva S.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Drakare, Stina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Ragnarsson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Does ecosystem size determine aquatic bacterial richness? Comment2007In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 88, no 1, p. 252-253Article in journal (Refereed)
  • 86.
    Linz, Alexandra M.
    et al.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.
    He, Shaomei
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA;Univ Wisconsin, Dept Geosci, Madison, WI USA.
    Stevens, Sarah L. R.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.
    Anantharaman, Karthik
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.
    Rohwer, Robin R.
    Univ Wisconsin, Environm Chem & Technol Program, Madison, WI USA.
    Malmstrom, Rex R.
    Joint Genome Inst, Dept Energy, Walnut Creek, CA USA.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    McMahon, Katherine D.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA;Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA.
    Freshwater carbon and nutrient cycles revealed through reconstructed population genomes2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e6075Article in journal (Refereed)
    Abstract [en]

    Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.

  • 87.
    Liu, Haoyu
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Waldén, Tomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology, Integrative Physiology.
    Cai, Demin
    Univ Calif Davis, Dept Biochem & Mol Med, Sacramento, CA 95817 USA.
    Ahl, David
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology, Integrative Physiology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Phillipson, Mia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology, Integrative Physiology.
    Nyman, Margareta
    Lund Univ, Dept Food Technol Engn & Nutr, S-22100 Lund, Sweden.
    Holm, Lena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology, Integrative Physiology.
    Dietary Fiber in Bilberry Ameliorates Pre-Obesity Events in Rats by Regulating Lipid Depot, Cecal Short-Chain Fatty Acid Formation and Microbiota Composition2019In: Nutrients, ISSN 2072-6643, E-ISSN 2072-6643, Vol. 11, no 6, article id 1350Article in journal (Refereed)
    Abstract [en]

    Obesity is linked to non-alcoholic fatty liver disease and risk factors associated to metabolic syndrome. Bilberry (Vaccinium myrtillus) that contains easily fermentable fiber may strengthen the intestinal barrier function, attenuate inflammation and modulate gut microbiota composition, thereby prevent obesity development. In the current study, liver lipid metabolism, fat depot, cecal and serum short-chain fatty acids (SCFAs) and gut microbiome were evaluated in rats fed bilberries in a high-fat (HFD + BB) or low-fat (LFD + BB) setting for 8 weeks and compared with diets containing equal amount of fiber resistant to fermentation (cellulose, HFD and LFD). HFD fed rats did not obtain an obese phenotype but underwent pre-obesity events including increased liver index, lipid accumulation and increased serum cholesterol levels. This was linked to shifts of cecal bacterial community and reduction of major SCFAs. Bilberry inclusion improved liver metabolism and serum lipid levels. Bilberry inclusion under either LFD or HFD, maintained microbiota homeostasis, stimulated interscapular-brown adipose tissue depot associated with increased mRNA expression of uncoupling protein-1; enhanced SCFAs in the cecum and circulation; and promoted butyric acid and butyrate-producing bacteria. These findings suggest that bilberry may serve as a preventative dietary measure to optimize microbiome and associated lipid metabolism during or prior to HFD.

  • 88.
    Logares, Ramiro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Brate, Jon
    Heinrich, Friederike
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Shalchian-Tabrizi, Kamran
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11)2010In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, no 2, p. 347-357Article in journal (Refereed)
    Abstract [en]

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

  • 89.
    Logares, Ramiro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Bråte, Jon
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Clasen, Jessica L.
    Shalchian-Tabrizi, Kamran
    Rengefors, Karin
    Infrequent marine-freshwater transitions in the microbial world2009In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 17, no 9, p. 414-422Article, review/survey (Refereed)
    Abstract [en]

    Until recently, the evolutionary relationships between marine and freshwater microbes were unclear, but the use of molecular phylogenies is beginning to shed light on this subject. An increasing amount of studies are showing that marine and freshwater microbes (including viruses) are usually not closely related, often grouping into distinct marine and freshwater phylogenetic clusters, similar to what has been reported before for macroorganisms. These studies indicate that marine–freshwater transitions have been infrequent events during the diversification of microbes and that most of these transitions occurred a long time ago in evolutionary terms. Here we discuss the significance of recent studies addressing this question and consider possible avenues for future research.

  • 90.
    Logares, Ramiro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Paterson, Harriet
    Laybourn-Parry, Johanna
    Rengefors, Karin
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Biogeography of bacterial communities exposed to progressive long-term environmental change2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 5, p. 937-948Article in journal (Refereed)
    Abstract [en]

    The response of microbial communities to long-term environmental change is poorly understood. Here, we study bacterioplankton communities in a unique system of coastal Antarctic lakes that were exposed to progressive long-term environmental change, using 454 pyrosequencing of the 16S rDNA gene (V3-V4 regions). At the time of formation, most of the studied lakes harbored marine-coastal microbial communities, as they were connected to the sea. During the past 20 000 years, most lakes isolated from the sea, and subsequently they experienced a gradual, but strong, salinity change that eventually developed into a gradient ranging from freshwater (salinity 0) to hypersaline (salinity 100). Our results indicated that present bacterioplankton community composition was strongly correlated with salinity and weakly correlated with geographical distance between lakes. A few abundant taxa were shared between some lakes and coastal marine communities. Nevertheless, lakes contained a large number of taxa that were not detected in the adjacent sea. Abundant and rare taxa within saline communities presented similar biogeography, suggesting that these groups have comparable environmental sensitivity. Habitat specialists and generalists were detected among abundant and rare taxa, with specialists being relatively more abundant at the extremes of the salinity gradient. Altogether, progressive long-term salinity change appears to have promoted the diversification of bacterioplankton communities by modifying the composition of ancestral communities and by allowing the establishment of new taxa. The ISME Journal (2013) 7, 937-948; doi:10.1038/ismej.2012.168; published online 20 December 2012

  • 91.
    Logue, Jürg Brendan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Andersson, Anders F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Drakare, Stina
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU).
    Lanzén, Anders
    Centre for Geobiology and Department of Biology, University of Bergen.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships2012In: The ISME Journal, ISSN 1751-7362, Vol. 6, no 6, p. 1127-1136Article in journal (Refereed)
    Abstract [en]

    A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22 669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species-area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few “laws” in ecology.

  • 92.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden;Helmholtz Zentrum Dresden Rossendorf, Inst Resource Ecol, Dresden, Germany.
    Broman, Elias
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden;Stockholm Univ, Dept Ecol Environm & Plant Sci, Stockholm, Sweden.
    Simone, Domenico
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden;Swedish Univ Agr Sci, SLU Bioinformat Infrastruct, Uppsala, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala Univ, Limnol & Sci Life Lab, Dept Ecol & Genet, Uppsala, Sweden;Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters2019In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 4, article id e01470-19Article in journal (Refereed)
    Abstract [en]

    Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two "modern marine" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic "thoroughly mixed" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H-2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or "geogases." IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omits studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.

  • 93.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Barlastgatan 11, Kalmar, Sweden.;Helmholtz Zentrum Dresden Rossendorf, Inst Resource Ecol, Bautzner Landstr 400, D-01328 Dresden, Germany..
    Broman, Elias
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Barlastgatan 11, Kalmar, Sweden..
    Turner, Stephanie
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Barlastgatan 11, Kalmar, Sweden..
    Wu, Xiaofen
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Barlastgatan 11, Kalmar, Sweden.;Univ Copenhagen, Dept Biol, Copenhagen, Denmark..
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Barlastgatan 11, Kalmar, Sweden..
    Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling2018In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 94, no 8, article id fiy121Article in journal (Refereed)
    Abstract [en]

    The deep biosphere is the largest 'bioreactor' on earth, and microbes inhabiting this biome profoundly influence global nutrient and energy cycles. An important question for deep biosphere microbiology is whether or not specific populations are viable. To address this, we used quantitative PCR and high throughput 16S rRNA gene sequencing of total and viable cells (i.e. with an intact cellular membrane) from three groundwaters with different ages and chemical constituents. There were no statistically significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities. This suggests that populations were adapted to prevailing oligo trophic conditions and that non-viable cells are rapidly degraded and recycled into new biomass. With higher concentrations of organic carbon, the modem marine and undefined mixed waters hosted a community with a larger range of predicted growth strategies than the ultra-oligo trophic old saline water. These strategies included fermentative and potentially symbiotic lifestyles by candidate phyla that typically have streamlined genomes. In contrast, the old saline waters had more 16S rRNA gene sequences in previously cultured lineages able to oxidize hydrogen and fix carbon dioxide. This matches the paradigm of a hydrogen and carbon dioxide-fed chemolithoauto trophic deep biosphere.

  • 94. Lopez-Fernandez, Margarita
    et al.
    Simone, Domenico
    Wu, Xiaofen
    Soler, Lucile
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Nilsson, Emelie
    Holmfeldt, Karin
    Lantz, Henrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Dopson, Mark
    Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere2018In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 9, no 6, article id e01792-18Article in journal (Refereed)
    Abstract [en]

    The continental subsurface is suggested to contain a significant part of the earth's total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the Äspö Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20 years, defined as "modern marine," and an "old saline" groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available.IMPORTANCE A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the Äspö Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbon-fed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 16S rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes.

  • 95.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
    Åström, Mats
    Linnaeus Univ, Dept Biol & Environm Sci, Kalmar, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
    Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 2880Article in journal (Refereed)
    Abstract [en]

    The continental deep biosphere is suggested to contain a substantial fraction of the earth’s total biomass and microorganisms inhabiting this environment likely have a substantial impact on biogeochemical cycles. However, the deep microbial community is still largely unknown and can be influenced by parameters such as temperature, pressure, water residence times, and chemistry of the waters. In this study, 21 boreholes representing a range of deep continental groundwaters from the Äspö Hard Rock Laboratory were subjected to high-throughput 16S rRNA gene sequencing to characterize how the different water types influence the microbial communities. Geochemical parameters showed the stability of the waters and allowed their classification into three groups. These were (i) waters influenced by infiltration from the Baltic Sea with a “modern marine (MM)” signature, (ii) a “thoroughly mixed (TM)” water containing groundwaters of several origins, and (iii) deep “old saline (OS)” waters. Decreasing microbial cell numbers positively correlated with depth. In addition, there was a stronger positive correlation between increased cell numbers and dissolved organic carbon for the MM compared to the OS waters. This supported that the MM waters depend on organic carbon infiltration from the Baltic Sea while the ancient saline waters were fed by “geogases” such as carbon dioxide and hydrogen. The 16S rRNA gene relative abundance of the studied groundwaters revealed different microbial community compositions. Interestingly, the TM water showed the highest dissimilarity compared to the other two water types, potentially due to the several contrasting water types contributing to this groundwater. The main identified microbial phyla in the groundwaters were Gammaproteobacteria, unclassified sequences, Campylobacterota (formerly Epsilonproteobacteria), Patescibacteria, Deltaproteobacteria, and Alphaproteobacteria. Many of these taxa are suggested to mediate ferric iron and nitrate reduction, especially in the MM waters. This indicated that nitrate reduction may be a neglected but important process in the deep continental biosphere. In addition to the high number of unclassified sequences, almost 50% of the identified phyla were archaeal or bacterial candidate phyla. The percentage of unknown and candidate phyla increased with depth, pointing to the importance and necessity of further studies to characterize deep biosphere microbial populations.

  • 96. Lundqvist, Anna
    et al.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Goedkoop, Willem
    Effects of extracellular polymeric and humic substances on chlorpyrifos bioavailability to Chironomus riparius2010In: Ecotoxicology, ISSN 0963-9292, E-ISSN 1573-3017, Vol. 19, no 4, p. 614-622Article in journal (Refereed)
    Abstract [en]

    The role of sediment organic matter quality and quantity for chlorpyrifos bioavailability was studied in experiments with Chironomus riparius larvae and with four types of organic matter; (1) commercially available extracellular polymeric substances (EPS), (2) EPS produced by sediment microbes, (3) commercially available humic substances and, (4) humic substances extracted from a boreal lake. The effects of each type of organic matter were assessed at three concentrations. We used a C-14-tracer approach to quantify uptake of chlorpyrifos in the larvae, and the partitioning of the insecticide within the microcosm. Carbon-normalised larval uptake was reduced both by EPS and humic substances. However, the reduction in uptake was much greater for EPS than for humic substances: uptake was reduced by 94 and 88% for commercial and complex EPS, and by 59 and 57% for commercial and complex humic substances, respectively. We also found differences in chlorpyrifos uptake, and sediment concentrations between treatments with commercially available and complex polymers, suggesting that minor differences in the quality of relatively simple organic molecules can affect contaminant behaviour in ecotoxicological studies. Passive uptake in dead controls was 40% of that in living larvae. Therefore, both passive and digestive uptake were important processes for chlorpyrifos uptake by larvae. Our results show that both EPS and humic substances affect chlorpyrifos bioavailability to sediment biota negatively and contribute to the understanding of the processes that regulate organic contaminant bioavailability in aquatic environments.

  • 97. Lundqvist, Anna
    et al.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Goedkoop, Willem
    Interactions with DOM and biofilms affect the fate and bioavailability of insecticides to invertebrate grazers2012In: Ecotoxicology, ISSN 0963-9292, E-ISSN 1573-3017, Vol. 21, no 8, p. 2398-2408Article in journal (Refereed)
    Abstract [en]

    We studied the fate and bioavailability of insecticides in short-term experiments (48 h) with different hydrophobicity (3.8 pM carbofuran, 3.0 pM lindane, and 5.3 pM chlorpyrifos) across gradients in dissolved organic matter (low-, medium-, and high-DOM) in freshwater microcosms, mimicking runoff events of pesticides. The effects of biofilms were studied by including treatments with biofilms cultivated under different DOM-concentrations. The presence of biofilms negatively affected chlorpyrifos water concentrations, indicating rapid sorption of this hydrophobic pesticide, while lindane concentrations instead increased and carbofuran concentrations were unaffected. Associations of lindane and chlorpyrifos with biofilms were 1.6-2.0 times higher in low- and high-DOM than in medium-DOM treatments, indicating that sorption was affected not only by the quantity, but also by the quality of DOM. Although the proportion of pesticides recovered in biofilms was consistently less than 1 % of added pesticide, pesticide concentrations in biofilms were on average more than 75- (carbofuran) and 382-times (lindane) higher than those in water. Snail accumulation of all three pesticides was significantly affected by DOMconcentrations and correlated to pesticide hydrophobicity, but the relationships were not straightforward. For example, carbofuran uptake in treatments without biofilms was higher in low-DOM than in medium- and high-DOM treatments, while chlorpyrifos uptake instead increased across the DOM-gradient. Biofilms played a role only for the uptake of chlorpyrifos, which decreased markedly in the presence of biofilms. Bioconcentration factors (BCF) calculated for snails and biofilms differed for the three pesticides and were related to their sorption behaviour (i.e., hydrophobicity). The relative proportion of pesticide uptake through biofilm consumption was consistently less than 2 %, showing that passive uptake was by far the predominant uptake pathway for all three pesticides.

  • 98.
    Monard, C.
    et al.
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala BioCtr, POB 7026, SE-75007 Uppsala, Sweden; Univ Rennes 1, UMR ECOBIO 6553, OSUR, CNRS, F-35042 Rennes, France.
    Gantner, Stephan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala BioCtr, POB 7026, SE-75007 Uppsala, Sweden; Rhein Akad Koln, Vogelsanger Str 295, D-50825 Cologne, Germany.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Hallin, S.
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala BioCtr, POB 7026, SE-75007 Uppsala, Sweden.
    Stenlid, J.
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala BioCtr, POB 7026, SE-75007 Uppsala, Sweden.
    Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 37719Article in journal (Refereed)
    Abstract [en]

    Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of ActinobacteriaSordariomycetesAgaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum.

  • 99. Newton, Ryan J.
    et al.
    Jones, Stuart E.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    McMahon, Katherine D.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    A Guide to the Natural History of Freshwater Lake Bacteria2011In: Microbiology and molecular biology reviews, ISSN 1092-2172, E-ISSN 1098-5557, Vol. 75, no 1, p. 14-49Article, review/survey (Refereed)
    Abstract [en]

    Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.

  • 100.
    Nilsson, Anna
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Johansson, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Skarp, Astrid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Kaden, Rene
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Bertilsson, Stefan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Rautelin, Hilpi
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Survival of Campylobacter jejuni and C. coli water isolates in lake and well water2018In: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS), ISSN 0903-4641, E-ISSN 1600-0463, Vol. 126, no 9, p. 762-770Article in journal (Refereed)
    Abstract [en]

    The role of water for transmission of Campylobacter jejuni and C. coli to humans might be underestimated, as factors important for bacterial viability in water are largely unknown. We have studied water survival of seven C. jejuni and eight C. coli isolates originally isolated from Swedish waters, together with selected reference strains, over eight days at 4 °C in the dark in untreated water collected from a local lake and a private well. To study seasonality, lake water samples were collected during spring and autumn. Samples for culturable bacterial counts were taken on days 2, 4, 6, and 8 and compared to the start inoculum. For C. jejuni, a significantly better survival was observed in autumn than in spring lake water. Furthermore, C. jejuni had a significantly better survival than C. coli in autumn lake and well water samples; the rate of culturability loss was almost double for C. coli in autumn lake water. These findings contribute to a better understanding on the seasonality of waterborne Campylobacter infections and the general predominance of C. jejuni.

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