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  • 1. Abrahamsson, K.
    et al.
    Pakhomovc,, E.A.
    Loréna, A.
    Fronemanc,, P.W.
    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.
    Chiericia,, M.
    Franssona, A.
    Variations of biochemical parameters along a transect in the Southern Ocean, with special emphasis on volatile halogenated organic compounds2004In: Deep Sea Research Part II:: Topical Studies in Oceanography, Vol. 51,, no 22-24, p. 2745-2756Article in journal (Refereed)
    Abstract [en]

    A number of parameters of biogeochemical interest were monitored along a north–southerly transect (S 43–S 63°) in the Atlantic Sector of the Southern Ocean from the 8th to the 20th of December 1997. Changes in total dissolved inorganic carbon (CT) and total alkalinity (AT) were mostly dependent on temperature and salinity until the ice edge was reached. After this point only a weak correlation was seen between these. Highest mean values of CT and AT were observed in the Winter Ice Edge (WIE) (2195 and 2319 μmol kg−1, respectively). Lowest mean AT (2277 μmol kg−1) was observed in the Sub-Antarctic Front (SAF), whereas lowest mean CT concentration (2068 μmol kg−1) was associated with the Sub-Tropical Front (STF). The pH in situ varied between 8.060 and 8.156 where the highest values were observed in the southern part of the Antarctic Polar Front (APF) and in the Summer Ice Edge (SIE) Region . These peaks were associated with areas of high chlorophyll a (chl a) and tribromomethane values. In the other areas the pH in situ was mainly dependent on hydrography. Bacterial abundance decreased more than one order of magnitude when going from north to south. The decrease appeared to be strongly related to water temperature and there were no elevated abundances at frontal zones. Microphytoplankton dominated in the SAF and APF, whereas the nano- and picoplankton dominated outside these regions.

    Volatile halogenated compounds were found to vary both with regions, and with daylight. For the iodinated compounds, the highest concentrations were found north of the STF. Brominated hydrocarbons had high concentrations in the STF, but elevated concentrations were also found in the APF and SIE regions. No obvious correlation could be found between the occurrence of individual halocarbons and chl a. On some occasions trichloroethene and tribromomethane related to the presence of nano- and microplankton, respectively.

  • 2.
    Ahmed Osman, Omneya
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Beier, Sara
    Leibniz Inst Balt Sea Res, Warnemunde, Germany..
    Grabherr, Manfred
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Interactions of Freshwater Cyanobacteria with Bacterial Antagonists2017In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 83, no 7, article id UNSP e02634Article in journal (Refereed)
    Abstract [en]

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

  • 3.
    Alneberg, Johannes
    et al.
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden.
    Karlsson, Christofer M. G.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden.
    Divne, Anna-Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bergin, Claudia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Homa, Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lindh, Markus V.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden;Lund Univ, Dept Biol, Lund, Sweden.
    Hugerth, Luisa W.
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden;Karolinska Inst, Ctr Translat Microbiome Res, Dept Mol Tumour & Cell Biol, Sci Life Lab, Solna, Sweden.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. 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.
    Andersson, Anders F.
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden.
    Pinhassi, Jarone
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden.
    Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes2018In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 6, article id 173Article in journal (Refereed)
    Abstract [en]

    Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.

    Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.

    Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

  • 4.
    Alonso-Saez, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Galand, Pierre E.
    Casamayor, Emilio O.
    Pedros-Alio, Carlos
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    High bicarbonate assimilation in the dark by Arctic bacteria2010In: ISME Journal, ISSN 1751-7362, Vol. 4, no 12, p. 1581-1590Article in journal (Refereed)
    Abstract [en]

    Although both autotrophic and heterotrophic microorganisms incorporate CO2 in the dark through different metabolic pathways, this process has usually been disregarded in oxic marine environments. We studied the significance and mediators of dark bicarbonate assimilation in dilution cultures inoculated with winter Arctic seawater. At stationary phase, bicarbonate incorporation rates were high (0.5-2.5 mu gC L-1 d(-1)) and correlated with rates of bacterial heterotrophic production, suggesting that most of the incorporation was due to heterotrophs. Accordingly, very few typically chemoautotrophic bacteria were detected by 16S rRNA gene cloning. The genetic analysis of the biotin carboxylase gene accC putatively involved in archaeal CO2 fixation did not yield any archaeal sequence, but amplified a variety of bacterial carboxylases involved in fatty acids biosynthesis, anaplerotic pathways and leucine catabolism. Gammaproteobacteria dominated the seawater cultures (40-70% of cell counts), followed by Betaproteobacteria and Flavobacteria as shown by catalyzed reporter deposition fluorescence in situ hybridization (CARDFISH). Both Beta-and Gammaproteobacteria were active in leucine and bicarbonate uptake, while Flavobacteria did not take up bicarbonate, as measured by microautoradiography combined with CARDFISH. Within Gammaproteobacteria, Pseudoalteromonas-Colwellia and Oleispira were very active in bicarbonate uptake (ca. 30 and 70% of active cells, respectively), while the group Arctic96B-16 did not take up bicarbonate. Our results suggest that, potentially, the incorporation of CO2 can be relevant for the metabolism of specific Arctic heterotrophic phylotypes, promoting the maintenance of their cell activity and/or longer survival under resource depleted conditions.

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

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

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

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

  • 7.
    Alonso-Sáez, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Waller, A. S.
    Mende, D. R.
    Bakker, K.
    Farnelid, H.
    Yager, P. L.
    Lovejoy, C.
    Tremblay, J. -E
    Potvin, M.
    Heinrich, Friederike
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Estrada, M.
    Riemann, L.
    Bork, P.
    Pedrós-Alió, C.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Role for urea in nitrification by polar marine Archaea2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 44, p. 17989-17994Article in journal (Refereed)
    Abstract [en]

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

  • 8.
    Andersson, Anders F
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Riemann, Lasse
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities2010In: ISME J, ISSN 1751-7362, Vol. 4, no 2, p. 171-181Article in journal (Refereed)
    Abstract [en]

    Variation in traits causes bacterial populations to respond in contrasting ways to environmental drivers. Learning about this will help us understand the ecology of individual populations in complex ecosystems. We used 454 pyrosequencing of the hypervariable region V6 of the 16S rRNA gene to study seasonal dynamics in Baltic Sea bacterioplankton communities, and link community and population changes to biological and chemical factors. Surface samples were collected from May to October 2003 and in May 2004 at the Landsort Deep in the central Baltic Sea Proper. The analysis rendered, on average, 20 200 sequence reads for each of the eight samples analyzed, providing the first detailed description of Baltic Sea bacterial communities. Community composition varied dramatically over time, supporting the idea of strong temporal shifts in bacterioplankton assemblages, and clustered according to season (including two May samples from consecutive years), suggesting repeatable seasonal succession. Overall, community change was most highly correlated with change in phosphorus concentration and temperature. Individual bacterial populations were also identified that tightly co-varied with different Cyanobacteria populations. Comparing the abundance profiles of operational taxonomic units at different phylogenetic distances revealed a weak but significant negative correlation between abundance profile similarity and genetic distance, potentially reflecting habitat filtering of evolutionarily conserved functional traits in the studied bacterioplankton.

  • 9. Bagatini, Inessa Lacativa
    et al.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Klaveness, Dag
    Tessarolli, Leticia Piton
    Henriques Vieira, Armando Augusto
    Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 1, p. e85950-Article in journal (Refereed)
    Abstract [en]

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

  • 10.
    Beier, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bacterial chitin degradation: mechanisms and ecophysiological strategies2013In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 4, p. 149-Article, review/survey (Refereed)
    Abstract [en]

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

  • 11.
    Beier, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Uncoupling of chitinase activity and uptake of hydrolyses products in freshwater bacterioplankton2011In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 56, no 4, p. 1179-1188Article in journal (Refereed)
    Abstract [en]

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

  • 12.
    Beier, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Jones, Christopher M.
    Mohit, Vani
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Hallin, Sara
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Global Phylogeography of Chitinase Genes in Aquatic Metagenomes2011In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 77, no 3, p. 1101-1106Article in journal (Refereed)
    Abstract [en]

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

  • 13.
    Beier, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Kim, Ok-Sun
    Junier, Pilar
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Witzel, Karl-Paul
    Betaproteobacterial ammonia oxidizers in root zones of aquatic macrophytes2010In: Fundamental and Applied Limnology, ISSN 1863-9135, Vol. 177, no 4, p. 241-255Article in journal (Refereed)
    Abstract [en]

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

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

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

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

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

  • 16.
    Bertilsson, S
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Ecology and Evolution, Limnology. Limnologi.
    Jones, J B Jr
    Supply of dissolved organic matter to aquatic ecosystems: autochthonous sources2003In: Aquatic Ecosystems, Interactivity of Dissolved Organic Matter,, Elsevier Science, USA , 2003Chapter in book (Refereed)
    Abstract [en]

    1. Trophic polymorphism is a common phenomenon in many species. Trade-offs in foraging efficiency on different resources are thought to be a primary cause of such polymorphism.

    2. To test for a trade-off in foraging efficiency perch (Perca fluviatilis L.) were used from a population that differs in morphology between the littoral and pelagic habitat of a lake. Indoor aquarium experiments were performed with three different prey types in two different environments. It was predicted that the morphology of the individual would affect foraging efficiency in the different environments and on the different prey types through search and attack behaviour.

    3. Overall the foraging efficiency of perch was found to be related to individual morphology. A connection was also found between individual morphology and search and attack behaviour. Search behaviour but not attack behaviour was affected by the structure in the aquaria. Furthermore our results show that there are relations between search behaviour and detection rates and between attack behaviour and attack success.

    4. Our results give a mechanistic explanation for the differences in foraging efficiency between littoral and pelagic perch. These differences are probably driven by a functional trade-off between foraging performance and general body form.

  • 17.
    Bertilsson, S
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Widenfalk, A
    Photochemical degradation of PAHs in freshwaters and their impact on bacterial growth -influence of water chemistry.2002In: Hydrobiologia, Vol. 469, p. 23-32Article in journal (Refereed)
  • 18.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    How to see more: double hybridization to reveal ecological differentiation among close bacterial relatives2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2110-2111Article in journal (Other academic)
  • 19.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Sjöns mikroskopiska liv: en myllrande mångfald2016In: Biodiverse, ISSN 1401-5064, no 4, p. 10-10Article in journal (Other (popular science, discussion, etc.))
  • 20.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Strategies to Map the Microbiome of Freshwater Lakes: Sampling and Context2017In: Hydrocarbon and lipid microbiology protocols, Springer Berlin/Heidelberg, 2017, p. 199-217Chapter in book (Refereed)
    Abstract [en]

    Freshwater lakes are indispensible resources for humankind and as such also exposed to significant pressure from anthropogenic activities and environmental change. Organic matter holds a central role in these ecosystems, both in providing energy for the food web and in modifying water quality. The transformation, degradation, and internal production of organic matter is largely mediated by microorganisms and there is hence great interest in learning more about the ecology and function of these microscopic but abundant key players in lake ecosystems. The focus of this chapter is thus on strategies to study the spatial and temporal organization of the freshwater lake microbiome, with special attention to representative and rational sampling of freshwater lakes for subsequent analyses of microbial process or community features. Within-system heterogeneity across spatial and temporal scales will be presented and linkages between the physical structure, chemical gradients, and microbial distribution patterns will be discussed. Useful practical considerations to sample water for experiments or cells for biomolecular analyses will be presented along with recommendations regarding how to collect and compile basic but critically important contextual information. It is evident that the long-standing myth of freshwater lakes as homogenous systems delimited by defined shoreline boundaries is incorrect and that heterogeneity should be considered already in designing sampling strategies.

  • 21.
    Bertilsson, Stefan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Berglund, Olof
    Karl, David M.
    Chisholm, Sallie W
    Elemental composition of marine Prochlorococcus and Syncehococcus: Implications for the ecological stoichiometry of the sea2003In: Limnology and Oceanography, Vol. 48, no 5, p. 1721-1731.Article in journal (Refereed)
  • 22.
    Bertilsson, Stefan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Berglund, Olof
    Pullin, Michael J
    Chisholm, Sallie W
    Release of dissolved organic matter by Prochlorococcus2005In: Vie et Milieu: Life and Environment, Vol. 55, no 3-4, p. 225-231Article in journal (Refereed)
  • 23.
    Bertilsson, Stefan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Burgin, A.
    Carey, C.C.
    Fey, S.B.
    Grossart, H.P.
    Grubisic, L.M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Jones, I.D.
    Kirillin, G.
    Lennon, J.T.
    Shade, A.
    Smith, R.L.
    The under-ice microbiome of seasonally frozen lakes2013In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 58, no 6, p. 1998-2012Article, review/survey (Refereed)
    Abstract [en]

    Compared to the well-studied open water of the ‘‘growing’’ season, under-ice conditions in lakes are characterized by low and rather constant temperature, slow water movements, limited light availability, and reduced exchange with the surrounding landscape. These conditions interact with ice-cover duration to shape microbial processes in temperate lakes and ultimately influence the phenology of community and ecosystem processes. We review the current knowledge on microorganisms in seasonally frozen lakes. Specifically, we highlight how under-ice conditions alter lake physics and the ways that this can affect the distribution and metabolism of auto- and heterotrophic microorganisms. We identify functional traits that we hypothesize are important for understanding under-ice dynamics and discuss how these traits influence species interactions. As ice coverage duration has already been seen to reduce as air temperatures have warmed, the dynamics of the under- ice microbiome are important for understanding and predicting the dynamics and functioning of seasonally frozen lakes in the near future.

  • 24.
    Bertilsson, Stefan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Carlsson, Per
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Granéli, Wilhelm
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Influence of solar radiation on the availability of dissolved organic matter to bacteria in the Southern Ocean2004In: Deep-Sea Research II: Topical Studies in Oceanography, Vol. 51, p. 2557-2568Article in journal (Refereed)
    Abstract [en]

    The influence of solar radiation on the ability of dissolved organic matter (DOM) to support bacterial growth, was studied in the eastern Atlantic sector of the Southern Ocean during the SWEDARP 1997/1998 cruise with SA Agulhas December 1997–February 1998. Vertical profiles of water samples (2–3000 m) were obtained from the Spring Ice Edge (SIE, 60°S, high chlorophyll-a) and from the Winter Ice Edge (WIE, 56°S, low chlorophyll-a) areas. Filter-sterilized water from each area and depth was incubated under natural solar radiation and in the dark for comparison. Photobleaching of humic substance fluorescence occurred in all studied water samples. The bleaching was typically larger in the initially more fluorescent deep waters, compared to the low-fluorescent surface waters. Both the irradiated water and the dark controls were re-inoculated with a mixed bacterial inoculum from the initially sampled water. Bacterial growth (accumulating cells) and bacterial production (protein synthesis) were monitored during a 16–19 day incubation of these cultures at near in situ temperature (2 °C). Bacterial growth in cultures prepared from SIE water was largest at the surface (2–25 m), while the growth in corresponding cultures from the WIE did not vary much over depth. In contrast to the observed photobleaching, no clear effects of the irradiation on the ability of the DOM to support bacterial growth could be observed in either of the experiments. Hence, the degradation of fluorescent structures and other photochemical alterations of the organic matter did not have a major effect on the total pool of biodegradable organic substrates. The lack of effects of photoreactions on bacterial growth potential in the present study disagrees with the short-term bacterial growth response observed in other oceanic environments. This could be due to the different experimental approaches employed (short-vs. long-term incubations) or may indicate that the impact of photoreactions on bacterial growth in the Southern Ocean differ substantially from aquatic systems that are more influenced by terrestrial environments, as well as the warmer oligotrophic oceanic environments.

  • 25.
    Bertilsson, Stefan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Cavanaugh, C M
    Polz, M F
    A sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with detachable primers.2002In: Appl. Environ. Microbiol., Vol. 68, no 12, p. 6077-6086Article in journal (Refereed)
  • 26.
    Bertilsson, Stefan
    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.
    Nordqvist, Anneli
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Jørgensen, Niels O.G.
    Links between bacterial production, amino acid utilization and community composition in productive lakes2007In: ISME Journal, ISSN 1751-7362, Vol. 1, no 6, p. 532-544Article in journal (Refereed)
    Abstract [en]

    Influence of distribution and abundance of bacterial taxa on ecosystem function are poorly understood for natural microbial communities. We related 16S rRNA-based terminal restriction fragment length polymorphism to bacterial production and arginine uptake kinetics to test if functional features of bacterioplankton in four lakes could be predicted from community composition. Maximum arginine uptake rate (arginine Vmax) ranged from 10% to 100% of bacterial production. Owing to high growth efficiencies on arginine (63–77%), the bacterial community could potentially saturate its carbon demand using this single organic substrate, for example, during sudden surges of free amino acids. However, due to low in situ concentrations of arginine in these lakes (<0.9 g l-1), actual uptake rates at ambient concentrations rarely exceeded 10% of Vmax. Bacterial production and arginine Vmax could be predicted from a subset of bacterial ribotypes, tentatively affiliated with several bacterial divisions (Cyanobacteria, Actinobacteria, Bacteroidetes and Proteobacteria). Multivariate statistical analysis indicates that there were both highly important and less important ribotypes for the prediction of bacterial production and arginine Vmax. These populations were either negatively or positively related to the respective functional feature, indicating contrasting ecological roles. Our study provides a statistically robust demonstration that, apart from environmental conditions, patterns in bacterial community composition can also be used to predict lake ecosystem function.

  • 27.
    Bertilsson, Stefan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Hansson, Lars-Anders
    Graneli, Wilhelm
    Philibert, Aline
    Size-selective predation on pelagic microorganisms in arctic freshwaters2003In: Journal of Plankton Research, Vol. 25, no 6, p. 621-631Article in journal (Refereed)
  • 28.
    Bertilsson, Stefan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Stepanauskas, Ramunas
    Cuadros-Hansson, Rocio
    Graneli, Wilhelm
    Wikner, Johan
    Tranvik, Lars
    Photochemically induced changes in bioavailable carbon and nitrogen pools in a boreal watershed1999In: AQUATIC MICROBIAL ECOLOGY, ISSN 0948-3055, Vol. 19, no 1, p. 47-56Article in journal (Refereed)
    Abstract [en]

    In several recent studies, a net stimulation of bacterial growth has been demonstrated after exposing humic surface waters to solar radiation or artificial ultraviolet radiation. This stimulation has been attributed to a photochemical release of bioavaila

  • 29.
    Bertilsson, Stefan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Tranvik, Lars
    Photochemical transformation of dissolved organic matter in lakes2000In: Limnology and Oceanography, ISSN 0024-3590, Vol. 45, p. 753-762Article in journal (Refereed)
    Abstract [en]

    In a survey of photochemical transformation of dissolved organic matter (DOM) in lake water, we found photochemical production of dissolved inorganic carbon (DIC) and low molecular weight carboxylic acids (oxalic, malonic, formic, and acetic acid), upon s

  • 30.
    Bravo, Andrea G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bouchet, Sylvain
    Umea Univ, Dept Chem, SE-90187 Umea, Sweden..
    Tolu, Julie
    Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden..
    Bjorn, Erik
    Umea Univ, Dept Chem, SE-90187 Umea, Sweden..
    Mateos-Rivera, Alejandro
    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.
    Molecular composition of organic matter controls methylmercury formation in boreal lakes2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 14255Article in journal (Refereed)
    Abstract [en]

    A detailed understanding of the formation of the potent neurotoxic methylmercury is needed to explain the large observed variability in methylmercury levels in aquatic systems. While it is known that organic matter interacts strongly with mercury, the role of organic matter composition in the formation of methylmercury in aquatic systems remains poorly understood. Here we show that phytoplankton-derived organic compounds enhance mercury methylation rates in boreal lake sediments through an overall increase of bacterial activity. Accordingly, in situ mercury methylation defines methylmercury levels in lake sediments strongly influenced by planktonic blooms. In contrast, sediments dominated by terrigenous organic matter inputs have far lower methylation rates but higher concentrations of methylmercury, suggesting that methylmercury was formed in the catchment and imported into lakes. Our findings demonstrate that the origin and molecular composition of organic matter are critical parameters to understand and predict methylmercury formation and accumulation in boreal lake sediments.

  • 31.
    Bravo, Andrea Garcia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia, Spain.
    Peura, Sari
    Uppsala University, Science for Life Laboratory, SciLifeLab. 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. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Osman, Omneya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mateos-Rivera, Alejandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Herrero Ortega, Sonia
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Schaefer, Jeffra K.
    Bouchet, Sylvain
    Tolu, Julie
    Björn, Erik
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes2018In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 84, no 23, article id e01774-18Article in journal (Refereed)
    Abstract [en]

    Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the di- versity of these mercury-methylating microbial communities remains largely unex- plored. Previous studies have implicated sulfate-reducing bacteria as the main mer- cury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments us- ing high-throughput sequencing of 16S rRNA and hgcA genes. Our results show that in the lake sediments, Methanomicrobiales and Geobacteraceae also represent abun- dant members of the mercury-methylating communities. In fact, incubation experi- ments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These re- sults suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes.

  • 32.
    Bravo, Andrea Garcia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Zopfi, J
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Xu, J
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Schaefer, J. K.
    Poté, J.
    Cosio, C.
    Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by wastewater releasesIn: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370Article in journal (Refereed)
  • 33.
    Bravo, Andrea Garcia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zopfi, Jakob
    Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel CH-4056, Switzerland.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jingying, Xu
    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.
    Schaefer, Jeffra K.
    Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA.
    Poté, John
    Environmental Biogeochemistry and Ecotoxicology, University of Geneva, Geneva CH-1205, Switzerland.
    Cosio, Claudia
    Environmental Biogeochemistry and Ecotoxicology, University of Geneva, Geneva CH-1205, Switzerland.;Unité Stress Environnementaux et BIOSurveillance des Milieux Aquatiques UMR-I 02 (SEBIO), Université de Reims Champagne Ardenne, Reims F-51687, France.
    Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, p. 802-812Article in journal (Refereed)
    Abstract [en]

    Microbial mercury (Hg) methylation in sediments can result in bioaccumulation of the neurotoxin methylmercury (MMHg) in aquatic food webs. Recently, the discovery of the gene hgcA, required for Hg methylation, revealed that the diversity of Hg methylators is much broader than previously thought. However, little is known about the identity of Hg-methylating microbial organisms and the environmental factors controlling their activity and distribution in lakes. Here, we combined high-throughput sequencing of 16S rRNA and hgcA genes with the chemical characterization of sediments impacted by a waste water treatment plant that releases significant amounts of organic matter and iron. Our results highlight that the ferruginous geochemical conditions prevailing at 1–2 cm depth are conducive to MMHg formation and that the Hgmethylating guild is composed of iron and sulfur-transforming bacteria, syntrophs, and methanogens. Deltaproteobacteria, notably Geobacteraceae, dominated the hgcA carrying communities, while sulfate reducers constituted only a minor component, despite being considered the main Hg methylators in many anoxic aquatic environments. Because iron is widely applied in waste water treatment, the importance of Geobacteraceae for Hg methylation and the complexity of Hgmethylating communities reported here are likely to occur worldwide in sediments impacted by waste water treatment plant discharges and in iron-rich sediments in general.

  • 34.
    Catalán, Núria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Herrero Ortega, S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Gröntoft, H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Hilmarsson, T. G.
    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. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wu, Pianpian
    Levanoni, Oded
    Bishop, K.
    Garcia Bravo, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Effects of beaver impoundments on dissolved organic matter quality and biodegradability in boreal riverine systems2017In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 793, no 1, p. 135-148Article in journal (Refereed)
    Abstract [en]

    Beaver impoundments modify the structure of river reaches and lead to changes in ecosystem function and biogeochemical processes. Here, we assessed the changes in dissolved organic matter (DOM) quality and the biodegradation patterns in a set of beaver systems across Sweden. As the effect of beaver impoundments might be transient and local, we compared DOM quality and biodegradability of both pond and upstream sections of differentially aged beaver systems. Newly established dams shifted the sources and DOM biodegradability patterns. In particular, humic-like DOM, most likely leached from surrounding soils, characterized upstream sections of new beaver impoundments. In contrast, autochthonous and processed compounds, with both higher biodegradation rates and a broader spectrum of reactivities, differentiated DOM in ponds. DOM in recently established ponds seemed to be more humic and less processed compared to older ponds, but system idiosyncrasies determined by catchment particularities influenced this ageing effect.

  • 35.
    de Melo, Michaela L
    et al.
    Departamento de Hidrobiologia, Universidade Federal de São Carlos, São Carlos, Brazil.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Amaral, João Henrique F
    Coordenação de Dinâmica Ambiental, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.
    Barbosa, Pedro M
    Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
    Forsberg, Bruce R
    Coordenação de Dinâmica Ambiental, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.
    Sarmento, Hugo
    Departamento de Hidrobiologia, Universidade Federal de São Carlos, São Carlos, Brazil.
    Flood pulse regulation of bacterioplankton community composition in an Amazonian floodplain lake2019In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 64, no 1, p. 108-120Article in journal (Refereed)
    Abstract [en]

    Understanding spatial and temporal dynamics of microbial communities is a central challenge in microbial ecology since microorganisms play a key role in ecosystem functioning and biogeochemical cycles. Amazonian aquatic systems comprise a dynamic mosaic of heterogeneous habits but are understudied and there is limited information about the mechanisms that shape bacterial community composition (BCC). There is a consensus that environmental selection (species sorting) and dispersal processes (source?sink dynamics) act in concert to shape the composition of these communities, but the relative importance of each mechanism may vary dramatically through time and between systems. Applying 16S rRNA gene amplicon high-throughput sequencing, we studied factors and processes that modulate BCC in an Amazonian floodplain lake and used source-tracking models to trace the main dispersal sources of microorganisms in the whole floodplain system during a full hydrological cycle. Our source-tracking models indicated that dispersal processes were predominant, explaining most of the BCC variability throughout the study period. We observed more sources contributing to the sink community during the falling water than rising water period, when contributions from the Solim?es River dominated. There was a clear seasonal pattern in BCC, closely related to environmental variables, suggesting that the successful establishment of dispersing bacteria also depends on environmental filtering that is linked to water flow. In summary, source?sink dynamics and species sorting were strongly affected by water exchange and connectivity with the main river that varied throughout the flood pulse cycle. Our results demonstrated the influence of lateral transport and temporal dynamics on BCC in Amazonian floodplain lakes that could ultimately impact regional carbon budgets and biogeochemical cycles.

  • 36.
    Dinasquet, Julie
    et al.
    Linnaeus Univ, Dept Nat Sci, Kalmar, Sweden.;Univ Copenhagen, Marine Biol Sect, Helsingor, Denmark.;Scripps Inst Oceanog, Div Marine Biol Res, La Jolla, CA 92093 USA..
    Richert, Inga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. UFZ Helmholtz Ctr Environm Res, Microbial Ecosyst Serv Grp, Dept Environm Microbiol, Leipzig, Germany..
    Logares, Ramiro
    CSIC, Inst Marine Sci, Barcelona, Spain..
    Yager, Patricia
    Univ Georgia, Dept Marine Sci, Athens, GA 30602 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.
    Riemann, Lasse
    Univ Copenhagen, Marine Biol Sect, Helsingor, Denmark..
    Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2453-2467Article in journal (Refereed)
    Abstract [en]

    The number of icebergs produced from ice-shelf disintegration has increased over the past decade in Antarctica. These drifting icebergs mix the water column, influence stratification and nutrient condition, and can affect local productivity and food web composition. Data on whether icebergs affect bacterioplankton function and composition are scarce, however. We assessed the influence of iceberg drift on bacterial community composition and on their ability to exploit carbon substrates during summer in the coastal Southern Ocean. An elevated bacterial production and a different community composition were observed in iceberg-influenced waters relative to the undisturbed water column nearby. These major differences were confirmed in short-term incubations with bromodeoxyuridine followed by CARD-FISH. Furthermore, one-week bottle incubations amended with inorganic nutrients and carbon substrates (a mix of substrates, glutamine, Nacetylglucosamine, or pyruvate) revealed contrasting capacity of bacterioplankton to utilize specific carbon substrates in the iceberg-influenced waters compared with the undisturbed site. Our study demonstrates that the hydrographical perturbations introduced by a drifting iceberg can affect activity, composition, and substrate utilization capability of marine bacterioplankton. Consequently, in a context of global warming, increased frequency of drifting icebergs in polar regions holds the potential to affect carbon and nutrient biogeochemistry at local and possibly regional scales.

  • 37.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Beier, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Säwström, Christin
    Karlsson, Jan
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    High Ratio of Bacteriochlorophyll Biosynthesis Genes to Chlorophyll Biosynthesis Genes in Bacteria of Humic Lakes2009In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 75, no 22, p. 7221-7228Article in journal (Refereed)
    Abstract [en]

    Recent studies highlight the diversity and significance of marinephototrophic microorganisms such as picocyanobacteria, phototrophicpicoeukaryotes, and bacteriochlorophyll- and rhodopsin-holdingphototrophic bacteria. To assess if freshwater ecosystems alsoharbor similar phototroph diversity, genes involved in the biosynthesisof bacteriochlorophyll and chlorophyll were targeted to exploreoxygenic and aerobic anoxygenic phototroph composition in awide range of lakes. Partial dark-operative protochlorophyllideoxidoreductase (DPOR) and chlorophyllide oxidoreductase (COR)genes in bacteria of seven lakes with contrasting trophic statuseswere PCR amplified, cloned, and sequenced. Out of 61 sequencesencoding the L subunit of DPOR (L-DPOR), 22 clustered with aerobicanoxygenic photosynthetic bacteria, whereas 39 L-DPOR sequencesrelated to oxygenic phototrophs, like cyanobacteria, were observed.Phylogenetic analysis revealed clear separation of these freshwaterL-DPOR genes as well as 11 COR gene sequences from their marinecounterparts. Terminal restriction fragment length analysisof L-DPOR genes was used to characterize oxygenic aerobic andanoxygenic photosynthesizing populations in 20 lakes differingin physical and chemical characteristics. Significant differencesin L-DPOR community composition were observed between dystrophiclakes and all other systems, where a higher proportion of genesaffiliated with aerobic anoxygenic photosynthetic bacteria wasobserved than in other systems. Our results reveal a significantdiversity of phototrophic microorganisms in lakes and suggestniche partitioning of oxygenic and aerobic anoxygenic phototrophsin these systems in response to trophic status and coupled differencesin light regime.

  • 38.
    Eiler, Alexander
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes2004In: Environmental Microbiology, Vol. 6, p. 1228-1243Article in journal (Refereed)
    Abstract [en]

    The diversity of freshwater bacterioplankton communities has not been extensively studied despite their key role in foodwebs and the cycling of carbon and associated major elements. In order to explore and characterize the composition of bacterioplankton associated with cyanobacterial blooms, large 16S rRNA clone libraries from four lakes experiencing such blooms were analysed. The four libraries contained 1461 clones, of which 559 were prokaryotic sequences of non-cyanobacterial origin. These clones were classified into 158 operational taxonomic units affiliated mainly with bacterial divisions commonly found in freshwater systems, e.g. Proteobacteria, Bacteriodetes, Actinobacteria, Verrucomicrobia and Planctomycetes. Richness and evenness of non-cyanobacterial clones were similar to other clone libraries obtained for freshwater bacterioplankton, suggesting that bacterial communities accompanying cyanobacterial blooms are as diverse as non-bloom communities. Many of the identified operational taxonomic units grouped with known freshwater clusters but the libraries also contained novel clusters of bacterial sequences that may be characteristic for cyanobacterial blooms. About 25% of the operational taxonomic units were detected in more than one lake. Even so, 16S rRNA heterogeneity analysis demonstrated large differences in community composition between lakes regardless of their similar characteristics and close proximity. Hence even the similar environmental conditions created by different cyanobacterial blooms may foster very dissimilar bacterial communities, which could indicate that the genetic diversity in lake bacteria have been underestimated in the past.

  • 39.
    Eiler, Alexander
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Bertilsson, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Detection and quantification of Vibrio populations using denaturant gradient gel electrophoresis2006In: Journal of Microbiological Methods, Vol. 67, p. 339-348Article in journal (Refereed)
  • 40.
    Eiler, Alexander
    et al.
    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.
    Flavobacteria blooms in four eutrophic lakes: Linking population dynamics of freshwater bacterioplankton to resource availability2007In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 73, no 11, p. 3511-3518Article in journal (Refereed)
    Abstract [en]

    Heterotrophic bacteria are major contributors to biogeochemical cycles and influence water quality. Still, the lack of representative isolates and the few quantitative surveys leave the ecological role and significance of single bacterial populations to be revealed. Here we analyzed the diversity and dynamics of freshwater Flavobacteria populations in four eutrophic temperate lakes. From each lake, clone libraries were constructed using primers specific for either the class Flavobacteria or Bacteria. Sequencing of 194 Flavobacteria clones from 8 libraries revealed a diverse freshwater Flavobacteria community and distinct differences among lakes. Abundance and seasonal dynamics of Flavobacteria were assessed by quantitative PCR with class-specific primers. In parallel, the dynamics of individual populations within the Flavobacteria community were assessed with terminal restriction fragment length polymorphism analysis using identical primers. The contribution of Flavobacteria to the total bacterioplankton community ranged from 0.4 to almost 100% (average, 24%). Blooms where Flavobacteria represented more than 30% of the bacterioplankton were observed at different times in the four lakes. In general, high proportions of Flavobacteria appeared during episodes of high bacterial production. Phylogenetic analyses combined with Flavobacteria community fingerprints suggested dominance of two Flavobacteria lineages. Both drastic alterations in total Flavobacteria and in community composition of this class significantly correlated with bacterial production, emphasizing that resource availability is an important driver of heterotrophic bacterial succession in eutrophic lakes.

  • 41.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Drakare, S.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Pernthaler, J.
    Peura, S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Rofner, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Simek, K.
    Yang, Yang
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Znachor, P.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 1, p. e53516-Article in journal (Refereed)
    Abstract [en]

    The recognition and discrimination of phytoplankton species is one of the foundations of freshwater biodiversity research and environmental monitoring. This step is frequently a bottleneck in the analytical chain from sampling to data analysis and subsequent environmental status evaluation. Here we present phytoplankton diversity data from 49 lakes including three seasonal surveys assessed by next generation sequencing (NGS) of 16S ribosomal RNA chloroplast and cyanobacterial gene amplicons and also compare part of these datasets with identification based on morphology. Direct comparison of NGS to microscopic data from three time-series showed that NGS was able to capture the seasonality in phytoplankton succession as observed by microscopy. Still, the PCR-based approach was only semi-quantitative, and detailed NGS and microscopy taxa lists had only low taxonomic correspondence. This is probably due to, both, methodological constraints and current discrepancies in taxonomic frameworks. Discrepancies included Euglenophyta and Heterokonta that were scarce in the NGS but frequently detected by microscopy and Cyanobacteria that were in general more abundant and classified with high resolution by NGS. A deep-branching taxonomically unclassified cluster was frequently detected by NGS but could not be linked to any group identified by microscopy. NGS derived phytoplankton composition differed significantly among lakes with different trophic status, showing that our approach can resolve phytoplankton communities at a level relevant for ecosystem management. The high reproducibility and potential for standardization and parallelization makes our NGS approach an excellent candidate for simultaneous monitoring of prokaryotic and eukaryotic phytoplankton in inland waters.

  • 42.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Gonzalez-Rey, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Allen, Sophie
    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.
    Growth response of Vibrio cholerae and other Vibrio spp. to cyanobacterial dissolved organic matter and temperature in Brackish Water2007In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 60, no 3, p. 411-418Article in journal (Refereed)
    Abstract [en]

    Environmental control of growth and persistence of vibrios in aquatic environments is poorly understood even though members of the genus Vibrio are globally important pathogens. To study how algal-derived organic matter and temperature influenced the abundance of different Vibrio spp., Baltic Sea microcosms inoculated with Vibrio cholerae, Vibrio vulnificus, Vibrio parahaemolyticus, Vibrio alginolyticus and native bacterioplankton, were exposed to different temperatures (12–25°C) and amended with dissolved organic matter from Nodularia spumigena (0–4.2 mg C L−1). Vibrio abundance was monitored by culture-dependent and molecular methods. Results suggested that Vibrio populations entered a viable but nonculturable state during the incubations. Abundance of Vibrio spp. and total bacterioplankton were orders of magnitude higher in microcosms amended with organic matter compared with reference microcosms. Vibrio cholerae abundances ranged from 0.9 to 1.9 × 105 cells mL−1 in treatments amended with 4.2 mg C L−1. Vibrio cholerae abundance relative to total bacterioplankton and other Vibrio spp. also increased >10-fold. In addition, V. vulnificus abundance increased in mesocosms with the highest organic matter addition (0.9–1.8 × 104 cells mL−1). Temperature alone did not significantly affect abundances of total bacterioplankton, total Vibrio spp. or individual Vibrio populations. By contrast, cyanobacterial-derived organic matter represented an important factor regulating growth and abundance of V. cholerae and V. vulnificus in brackish waters.

  • 43.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Heinrich, Friederike
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Coherent dynamics and association networks among lake bacterioplankton taxa2012In: The ISME Journal: multidisciplinary journal of microbial ecology, ISSN 1751-7362, Vol. 6, no 2, p. 330-342Article in journal (Refereed)
    Abstract [en]

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

  • 44.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Johansson, Mona
    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.
    Environmental influences on Vibrio populations in northern temperate and boreal coastal waters (Baltic and Skagerrak Seas)2006In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 72, no 9, p. 6004-6011Article in journal (Refereed)
    Abstract [en]

    Even if many Vibrio spp. are endemic to coastal waters, their distribution in northern temperate and boreal waters is poorly studied. To identify environmental factors regulating Vibrio populations in a salinity gradient along the Swedish coastline, we combined Vibrio-specific quantitative competitive PCR with denaturant gradient gel electrophoresis-based genotyping. The total Vibrio abundance ranged from 4 X 10(3) to 9.6 X 10(4) cells liter(-1), with the highest abundances in the more saline waters of the Skagerrak Sea. Several Vibrio populations were present throughout the salinity gradient, with abundances of single populations ranging from 5 X 10(4) to 7 X 10(4) cells liter(-1). Clear differences were observed along the salinity gradient, where three populations dominated the more saline waters of the Skagerrak Sea and two populations containing mainly representatives of V anguillarum and V. aestuarianus genotypes were abundant in the brackish waters of the Baltic Sea. Our results suggest that this apparent niche separation within the genus Vibrio may also be influenced by alternate factors such as nutrient levels and high abundances of dinoflagellates. A V. choleraelV. mimicus population was detected in more than 50% of the samples, with abundances exceeding 10(3) cells liter(-1), even in the cold (annual average water temperature of around 5 degrees C) and low-salinity (2 to 4 parts per thousand) samples from the Bothnian Bay (latitude, 65 degrees N). The unsuspected and widespread occurrence of this population in temperate and boreal coastal waters suggests that potential Vibrio pathogens may also be endemic to cold and brackish waters and hence may represent a previously overlooked health hazard.

  • 45.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. limnologi.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. limnologi.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. limnologi.
    Tranvik, Lars J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. limnologi.
    Heterotrophic bacterial growth efficiency and community structure at different natural organic carbon concentrations.2003In: Appl Environ Microbiol, ISSN 0099-2240, Vol. 69, no 7, p. 3701-9Article in journal (Refereed)
  • 46.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mondav, Rhiannon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sinclair, Lucas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Fernandez-Vidal, Leyden
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schwientek, Patrick
    Martinez-Garcia, Manuel
    Torrents, David
    McMahon, Katherine D.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stepanauskas, Ramunas
    Woyke, Tanja
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 8, p. 1902-1914Article in journal (Refereed)
  • 47.
    Eiler, Alexander
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. Limnologi.
    Olsson, Jan
    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.
    Dirunal variations in the auto- and heterotrophic activity of cyanobacterial phycospheres (Gloeotrichia echinulata) and the identity of attached bacteria2006In: Freshwater Biology, Vol. 51, p. 298-311Article in journal (Refereed)
  • 48.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Zaremba-Niedzwiedzka, Katarzyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Martinez Garcia, Manuel
    McMahon, Katherine
    Stepanauskas, Ramunas
    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.
    Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics2014In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 16, no 9, p. 2682-2698Article in journal (Refereed)
    Abstract [en]

    Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared to freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.

  • 49.
    Eklöf, Karin
    et al.
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, SE-75007 Uppsala, Sweden.
    Bishop, Kevin
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, SE-75007 Uppsala, Swede.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Björn, Erik
    Umea Univ, Dept Chem, SE-90187 Umea, Sweden.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Umea Univ, Dept Chem, SE-90187 Umea, Sweden.; National Bioinformatics Infrastructure Sweden, Uppsala SE-75236, Sweden.
    Skyllberg, Ulf
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
    Osman, Omneya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kronberg, Rose Marie
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
    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.
    Formation of mercury methylation hotspots as a consequence of forestry operations2018In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 613-614, p. 1069-1078Article in journal (Refereed)
    Abstract [en]

    Earlier studies have shown that boreal forest logging can increase the concentration and export of methylmercury (MeHg) in stream runoff. Here we test whether forestry operations create soil environments of high MeHg net formation associated with distinct microbial communities. Furthermore, we test the hypothesis that Hg methylation hotspots are more prone to form after stump harvest than stem-only harvest, because of more severe soil compaction and soil disturbance. Concentrations of MeHg, percent MeHg of total Hg (THg), and bacterial community composition were determined at 200 soil sampling positions distributed across eight catchments. Each catchment was either stem-only harvested (n = 3), stem- and stump-harvested (n = 2) or left undisturbed (n = 3). In support of our hypothesis, higher MeHg to THg ratios was observed in one of the stump-harvested catchments. While the effects of natural variation could not be ruled out, we noted that most of the highest % MeHg was observed in water-filled cavities created by stump removal or driving damage. This catchment also featured the highest bacterial diversity and highest relative abundance of bacterial families known to include Hg methylators. We propose that water-logged and disturbed soil environments associated with stump harvest can favor methylating microorganisms, which also enhance MeHg formation.

  • 50. Enwall, Karin
    et al.
    Nyberg, Karin
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Stenström, John
    Hallin, Sara
    Long-Term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil2007In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 39, no 1, p. 106-115Article in journal (Refereed)
    Abstract [en]

    To explore long-term impact of organic and inorganic fertilizers on microbial communities, we targeted both the total bacterial community and the autotrophic ammonia oxidizing bacteria (AOB) in soil from six treatments at an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, unfertilized and unfertilized without crops. All plots, except the bare fallows, were cropped with maize. Effects on activity were assessed by measuring the basal respiration and substrate induced respiration (SIR) rates, and the potential activity of the AOB. To determine the bacterial community composition, 16S rRNA genes were used to fingerprint total soil communities by terminal restriction fragment length polymorphism analysis and AOB communities by denaturing gradient gel electrophoresis. The fertilization regimes had clear effects on both activity and composition of the soil communities. Basal respiration and r, which was kinetically derived as the exponentially growing fraction of the SIR-response, correlated well with the soil organic C content (r=0.93 and 0.66, respectively). Soil pH ranged from 3.97 to 6.26 in the treatments and was found to be an important factor influencing all microbial activities. pH correlated negatively with the ratio between basal respiration and SIR (r=0.90), indicating a decreased efficiency of heterotrophic microorganisms to convert organic carbon into microbial biomass in the most acid soils with pH 3.97 and 4.68 ((NH4)2SO4 and sewage sludge fertilized plots, respectively). The lowest SIR and ammonia oxidation rates were also found in these treatments. In addition, these treatments exhibited individually different community fingerprints, showing that pH affected the composition of AOB and total bacterial communities. The manure fertilized plots harbored the most diverse AOB community and the pattern was linked to a high potential ammonia oxidation activity. Thus, the AOB community composition appeared to be more strongly linked to the activity than the total bacterial communities were, likely explained by physiological differences in the populations present.

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