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  • 1.
    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.

  • 2.
    Buck, Moritz
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Nilsson, Louise K. J.
    Swedish Univ Agr Sci SLU, Dept Ecol, S-75007 Uppsala, Sweden..
    Brunius, Carl
    Swedish Univ Agr Sci SLU, Dept Food Sci, S-75007 Uppsala, Sweden..
    Dabire, Roch K.
    Inst Rech Sci Sante, Ctr Muraz, O1 BP 390, Bobo Dioulasso 01, Burkina Faso..
    Hopkins, Richard
    Swedish Univ Agr Sci SLU, Dept Ecol, S-75007 Uppsala, Sweden.;Univ Greenwich, Nat Resources Inst, Cent Ave, Chatham ME4 4TB, Kent, England..
    Terenius, Olle
    Swedish Univ Agr Sci SLU, Dept Ecol, S-75007 Uppsala, Sweden..
    Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 22806Article in journal (Refereed)
    Abstract [en]

    The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21st century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world.

  • 3.
    Buck, Moritz
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Nilsson, Louise K. J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology. Swedish Univ Agr Sci SLU, Dept Ecol, S-75007 Uppsala, Sweden..
    Brunius, Carl
    Swedish Univ Agr Sci SLU, Dept Food Sci, S-75007 Uppsala, Sweden..
    Dabire, Roch K.
    Inst Rech Sci Sante, Ctr Muraz, O1 BP 390, Bobo Dioulasso 01, Burkina Faso..
    Hopkins, Richard
    Swedish Univ Agr Sci SLU, Dept Ecol, S-75007 Uppsala, Sweden.;Univ Greenwich, Nat Resources Inst, Cent Ave, Chatham ME4 4TB, Kent, England..
    Terenius, Olle
    Swedish Univ Agr Sci SLU, Dept Ecol, S-75007 Uppsala, Sweden..
    Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 22806Article in journal (Refereed)
    Abstract [en]

    The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21st century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world.

  • 4.
    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.

  • 5.
    Garcia, Sarahi L.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    McMahon, Katherine D.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.;Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA..
    Grossart, Hans-Peter
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, D-16775 Ot Neuglobsow, Stechlin, Germany.;Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany..
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Warnecke, Falk
    Univ Jena, Jena Sch Microbial Commun, D-07743 Jena, Germany..
    Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 17, p. 4449-4459Article in journal (Refereed)
    Abstract [en]

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

  • 6.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tan, BoonFei
    University of Alberta, Edmonton, Canada; Singapore-MIT Alliance for Research and Technology, Leipzig, Germany.
    Foght, Julia
    University of Alberta, Edmonton, Canada.
    Wendeberg, Annelie
    Centre for Environmental Research, Leipzig, Germany.
    Berry, David
    University of Vienna, Vienna, Austria.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. eDNA Solutions AB, Mölndal, Sweden.
    Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions2017In: mSystems, E-ISSN 2379-5077, Vol. 2, no 5, article id e00038-17Article in journal (Refereed)
    Abstract [en]

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

  • 7.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wu, Xiaofen
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Heim, Christine
    Univ Gottingen, GZG Geobiol, Gottingen, Germany.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ionescu, Danny
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Neuglobsow, Germany.
    Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 10, p. 2447-2458Article in journal (Refereed)
    Abstract [en]

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

  • 8. Jingying, Xu
    et al.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Eklöf, Karin
    Osman, Omneya
    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.
    Bishop, Kevin
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Uppsala Centre for Sustainable Development, CSD Uppsala, Centre for Environment and Development Studies.
    Björn, Erik
    Skyllberg, Ulf
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bravo, Andrea Garcia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Present address: Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish National Research Council (CSIC), C/Jordi Girona, 18-26 - E-08034 Barcelona – Spain.
    Mercury methylating microbial communities of boreal forest soilsManuscript (preprint) (Other academic)
    Abstract [en]

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

  • 9.
    Jingying, Xu
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Liem-Nguyen, Van
    School of Science and Technology, Örebro University, Örebro, Sweden.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Björn, Erik
    Faculty of Science and Technology, Department of Chemistry, Umeå University, Sweden.
    Bravo, Andrea Garcia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish National Research Council (CSIC), Barcelona, Spain.
    Mercury methylating microbial communities in boreal wetlandsManuscript (preprint) (Other academic)
    Abstract [en]

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

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