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  • 1.
    Barouillet, Cécilia
    et al.
    INRAE, Université Savoie Mont Blanc, CARRTEL, Thonon les Bains, France; UMR CARRTEL, Pôle R&D ECLA, Thonon les Bains, France.
    Monchamp, Marie‐Eve
    Department of Biology, McGill University, Québec, Canada; Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Québec, Canada.
    Bertilsson, Stefan
    Department of Aquatic Sciences Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Swedennd Assessment Swedish University of Agricultural Sciences Uppsala Sweden.
    Brasell, Katie
    Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
    Domaizon, Isabelle
    INRAE, Université Savoie Mont Blanc, CARRTEL, Thonon les Bains, France; UMR CARRTEL, Pôle R&D ECLA, Thonon les Bains, France.
    Epp, Laura S.
    Department of Biology, Limnological Institute, University of Konstanz, Constance, Germany.
    Ibrahim, Anan
    Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie -Hans-Knöll-Institut, Jena, Germany.
    Mejbel, Hebah
    Centre for Advanced Research In Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada.
    Nwosu, Ebuka Canisius
    GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany.
    Pearman, John K.
    Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
    Picard, Maïlys
    Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
    Thomson‐Laing, Georgia
    Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
    Tsugeki, Narumi
    Faculty of Law, Matsuyama University, Matsuyama, Japan.
    Von Eggers, Jordan
    Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA.
    Gregory‐Eaves, Irene
    Department of Biology, McGill University, Québec, Canada; Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Québec, Canada.
    Pick, Frances
    Centre for Advanced Research In Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada.
    Wood, Susanna A.
    Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Investigating the effects of anthropogenic stressors on lake biota using sedimentary DNA2022Ingår i: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 68, nr 11, s. 1799-1817Artikel i tidskrift (Refereegranskat)
    Abstract [en]
    1. Analyses of sedimentary DNA (sedDNA) have increased exponentially over the last decade and hold great potential to study the effects of anthropogenic stressors on lake biota over time.
    2. Herein, we synthesise the literature that has applied a sedDNA approach to track historical changes in lake biodiversity in response to anthropogenic impacts, with an emphasis on the past c. 200 years.
    3. We identified the following research themes that are of particular relevance: (1) eutrophication and climate change as key drivers of limnetic communities; (2) increasing homogenisation of limnetic communities across large spatial scales; and (3) the dynamics and effects of invasive species as traced in lake sediment archives.
    4. Altogether, this review highlights the potential of sedDNA to draw a more comprehensive picture of the response of lake biota to anthropogenic stressors, opening up new avenues in the field of paleoecology by unrevealing a hidden historical biodiversity, building new paleo-indicators, and reflecting either taxonomic or functional attributes.
    5. Broadly, sedDNA analyses provide new perspectives that can inform ecosystem management, conservation, and restoration by offering an approach to measure ecological integrity and vulnerability, as well as ecosystem functioning.
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  • 2.
    Cabrol, Léa
    et al.
    Aix Marseille University, Univ. Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France; Institute of Ecology and Biodiversity (IEB), University of Chile, Santiago, Chile.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    van Vliet, Daan M.
    Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands; Wageningen Food and Biobased Research, Wageningen, Netherlands.
    Bastiaan von Meijenfeldt, F.A.
    Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands.
    Bertilsson, Stefan
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Villanueva, Laura
    Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, Netherlands.
    Sánchez-Andrea, Irene
    Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands.
    Björn, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bravo, Andrea G.
    Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain.
    Boavida, Lars-Eric Heimburger
    Aix Marseille University, Univ. Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France.
    Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea2023Ingår i: mSystems, E-ISSN 2379-5077, Vol. 8, nr 4Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc+) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc+ microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc+ microorganisms belonged to a unique assemblage of diverse—previously underappreciated—anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc+) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc+ microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.

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  • 3.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Barouillet, CéciliaINRAE, Université Savoie Mont Blanc CARRTEL, Thonon-les-Bains, France.Smol, John P.Paleoecological Environmental Assessment and Research Lab (PEARL) Department of Biology, Queen’s University, Kingston, Canada.
    Tracking environmental change using lake sediments: volume 6: sedimentary DNA2023Samlingsverk (redaktörskap) (Refereegranskat)
    Abstract [en]

    This book, entitled Tracking Environmental Change Using Lake Sediments: Volume 6 – Sedimentary DNA, provides an overview of the applications of sedimentary DNA-based approaches to paleolimnological studies. These approaches have shown considerable potential in providing information about the long-term changes of overall biodiversity in lakes and their watersheds in response to natural and anthropogenic changes, as well as tracking human migrations over the last thousands of years.

    Although the first studies investigating the preservation of these molecular proxies in sediments originate from the late-1990s, the number of scientific publications on this topic has increased greatly over the last five years. Alongside numerous ecological findings, several sedimentary DNA studies have been dedicated to understanding the reliability of this approach to reconstruct past ecosystem changes.  Despite the major surge of interest, a comprehensive compilation of sedimentary DNA approaches and applications has yet to be attempted. The overall aim of this DPER volume is to fill this knowledge gap. 

  • 4.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Bravo, Andrea G.
    Soerensen, Anne L.
    Bertilsson, Stefan
    Pinhassi, Jarone
    Feng, Caiyan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Andersson, Anders F.
    Buck, Moritz
    Björn, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Deltaproteobacteria and Spirochaetes-Like Bacteria Are Abundant Putative Mercury Methylators in Oxygen-Deficient Water and Marine Particles in the Baltic Sea2020Ingår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 11, artikel-id 574080Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the composition and distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this knowledge gap, we used the Baltic Sea Reference Metagenome (BARM) dataset to study the abundance and distribution of the genes involved in Hg methylation (thehgcABgene cluster). We determined the relative abundance of thehgcABgenes and their taxonomic identity in 81 brackish metagenomes that cover spatial, seasonal and redox variability in the Baltic Sea water column. ThehgcABgenes were predominantly detected in anoxic water, but somehgcABgenes were also detected in hypoxic and normoxic waters. Phylogenetic analysis identified putative Hg methylators within Deltaproteobacteria, in oxygen-deficient water layers, but also Spirochaetes-like and Kiritimatiellaeota-like bacteria. Higher relative quantities ofhgcABgenes were found in metagenomes from marine particles compared to free-living communities in anoxic water, suggesting that such particles are hotspot habitats for Hg methylators in oxygen-depleted seawater. Altogether, our work unveils the diversity of the microorganisms with the potential to mediate MeHg production in the Baltic Sea and pinpoint the important ecological niches for these microorganisms within the marine water column.

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  • 5.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Aquatic Sciences and Assessment, SLU Uppsala, Uppsala, Sweden.
    Broman, Elias
    Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Baltic Sea Centre, Stockholm University, Stockholm, Sweden.
    Bonaglia, Stefano
    Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
    Bravo, Andrea G.
    Department of Marine Biology and Oceanography, Institute of Marine Sciences, Spanish National Research Council (CSIC), Barcelona, Spain.
    Bertilsson, Stefan
    Department of Aquatic Sciences and Assessment, SLU Uppsala, Uppsala, Sweden.
    Soerensen, Anne L.
    Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Stockholm, Sweden.
    Pinhassi, Jarone
    Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden.
    Lundin, Daniel
    Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden.
    Buck, Moritz
    Department of Aquatic Sciences and Assessment, SLU Uppsala, Uppsala, Sweden.
    Hall, Per O. J.
    Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
    Nascimento, Francisco J. A.
    Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Baltic Sea Centre, Stockholm University, Stockholm, Sweden.
    Björn, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Oxygen-deficient water zones in the Baltic Sea promote uncharacterized Hg methylating microorganisms in underlying sediments2022Ingår i: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 67, nr 1, s. 135-146Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Human-induced expansion of oxygen-deficient zones can have dramatic impacts on marine systems and its resident biota. One example is the formation of the potent neurotoxic methylmercury (MeHg) that is mediated by microbial methylation of inorganic divalent Hg (HgII) under oxygen-deficient conditions. A negative consequence of the expansion of oxygen-deficient zones could be an increase in MeHg production due to shifts in microbial communities in favor of microorganisms methylating Hg. There is, however, limited knowledge about Hg-methylating microbes, i.e., those carrying hgc genes critical for mediating the process, from marine sediments. Here, we aim to study the presence of hgc genes and transcripts in metagenomes and metatranscriptomes from four surface sediments with contrasting concentrations of oxygen and sulfide in the Baltic Sea. We show that potential Hg methylators differed among sediments depending on redox conditions. Sediments with an oxygenated surface featured hgc-like genes and transcripts predominantly associated with uncultured Desulfobacterota (OalgD group) and Desulfobacterales (including Desulfobacula sp.) while sediments with a hypoxic-anoxic surface included hgc-carrying Verrucomicrobia, unclassified Desulfobacterales, Desulfatiglandales, and uncharacterized microbes. Our data suggest that the expansion of oxygen-deficient zones in marine systems may lead to a compositional change of Hg-methylating microbial groups in the sediments, where Hg methylators whose metabolism and biology have not yet been characterized will be promoted and expand.

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  • 6.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Cosio, Claudia
    Université de Reims Champagne-Ardenne, Reims, France.
    Gascón Díez, Elena
    Department F.-A. Forel for Environmental and Aquatic Sciences, and Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland; Direction générale de la santé, Secteur des produits chimiques, République et Canton de Genève, Switzerland.
    Loizeau, Jean-Luc
    Department F.-A. Forel for Environmental and Aquatic Sciences, and Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland.
    Mendes, Elsa
    Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Adatte, Thierry
    ISTE, Institut des Sciences de la Terre, Universit´e de Lausanne, GEOPOLIS, Lausanne, Switzerland.
    Franzenburg, Sören
    Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany.
    Bravo, Andrea G.
    Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Anaerobic mercury methylators inhabit sinking particles of oxic water columns2023Ingår i: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 229, artikel-id 119368Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Increased concentration of mercury, particularly methylmercury, in the environment is a worldwide concern because of its toxicity in severely exposed humans. Although the formation of methylmercury in oxic water columns has been previously suggested, there is no evidence of the presence of microorganisms able to perform this process, using the hgcAB gene pair (hgc+ microorganisms), in such environments. Here we show the prevalence of hgc+ microorganisms in sinking particles of the oxic water column of Lake Geneva (Switzerland and France) and its anoxic bottom sediments. Compared to anoxic sediments, sinking particles found in oxic waters exhibited relatively high proportion of hgc+genes taxonomically assigned to Firmicutes. In contrast hgc+members from Nitrospirae, Chloroflexota and PVC superphylum were prevalent in anoxic sediment while hgc+ Desulfobacterota were found in both environments. Altogether, the description of the diversity of putative mercury methylators in the oxic water column expand our understanding on MeHg formation in aquatic environments and at a global scale.

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  • 7.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Domaizon, Isabelle
    Maier, Dominique
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Debroas, Didier
    Bigler, Christian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    To what extent is the DNA of microbial eukaryotes modified during burying into lake sediments?: A repeat-coring approach on annually laminated sediments2017Ingår i: Journal of Paleolimnology, ISSN 0921-2728, E-ISSN 1573-0417, Vol. 58, nr 4, s. 479-495Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Paleogenetics provides a powerful framework to reconstruct the long-term temporal dynamics of various biological groups from aquatic sediments. However, validations are still required to ensure the authenticity of the molecular signal obtained from sedimentary DNA. Here, we investigated the effects of early diagenesis on the DNA signal from micro-eukaryotes preserved in sediments by comparing metabarcoding inventories obtained for two sediment cores sampled in 2007 and 2013 respectively. High-throughput sequencing (Illumina MiSeq) of sedimentary DNA was utilized to reconstruct the composition of microbial eukaryotic communities by targeting the V7 region of the 18S rDNA gene. No significant difference was detected between the molecular inventories obtained for the two cores both for total richness and diversity indices. Moreover, community structures obtained for the two cores were congruent as revealed by procrustean analysis. Though most of the eukaryotic groups showed no significant difference in terms of richness and relative proportion according to the core, the group of fungi was found to differ both in terms of richness and relative proportion (possibly due to their spatial heterogeneity and potential activity in sediments). Considering the OTUs level (i.e. Operational Taxonomic Units as a proxy of ecological species), our results showed that, for the older analyzed strata (age: 15-40 years), the composition and structure of communities were very similar for the two cores (except for fungi) and the DNA signal was considered stable. However, for the uppermost strata (age < 15 years), changes of moderate magnitude were detected in the relative abundance of few OTUs. Overall, this study points out that, in Nylandssjon sediments, early diagenesis did not induce marked modifications in the micro-eukaryotic DNA signal, thus opening new perspectives based on the analysis of eukaryotic sedimentary DNA to address scientific issues both in the domains of paleolimnology and microbial ecology. Because this study site is ideal for DNA preservation in sediment (quick sedimentation processes, no sediment resuspension, anoxic conditions at sediment-water interface), the generalization of our conclusions, in particular for less favorable sites, must be considered cautiously.

  • 8.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Feng, Caiyan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bravo, Andrea G.
    Department of Marine Biology and Oceanography, Institute of Marine Sciences, Spanish National Research Council (CSIC), Barcelona, Spain.
    Bertilsson, Stefan
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Soerensen, Anne L.
    Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Stockholm, Sweden.
    Pinhassi, Jarone
    Centre for Ecology and Evolution in Microbial Model Systems-EEMiS, Linnaeus University, Kalmar, Sweden.
    Buck, Moritz
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Karlsson, Camilla
    Centre for Ecology and Evolution in Microbial Model Systems-EEMiS, Linnaeus University, Kalmar, Sweden.
    Hawkes, Jeffrey
    Department of Chemistry, Uppsala University, Uppsala, Sweden.
    Björn, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters2022Ingår i: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 56, nr 18, s. 13119-13130Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved HgII-sulfide species were strong predictors of both the HgII methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc+ microorganisms by reconstructing their genomes from metagenomes (i.e., hgc+ MAGs), which highlighted the versatility of putative HgII methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the HgII methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficient zones.

  • 9.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Giguet-Covex, Charline
    Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204, CNRS, University Savoie Mont Blanc, Le Bourget du Lac, France.
    Rouillard, Alexandra
    Department of Geosciences, UiT the Arctic University of Norway, Tromsø, Norway; Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
    Nota, Kevin
    Department of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Heintzman, Peter D.
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway.
    Vuillemin, Aurèle
    Department of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany; GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany.
    Ariztegui, Daniel
    Department of Earth Sciences, University of Geneva, Geneva, Switzerland.
    Arnaud, Fabien
    Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204, CNRS, University Savoie Mont Blanc, Le Bourget du Lac, France.
    Belle, Simon
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Bertilsson, Stefan
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Bigler, Christian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Bindler, Richard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Brown, Antony G.
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway; School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom.
    Clarke, Charlotte L.
    School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom.
    Crump, Sarah E.
    Institute of Arctic and Alpine Research, University of Colorado Boulder, CO, Boulder, United States.
    Debroas, Didier
    LMGE, UMR CNRS 6023, University Clermont Auvergne, Clermont-Ferrand, France.
    Englund, Göran
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Ficetola, Gentile Francesco
    Department of Environmental Science and Policy, University of Milan, Milan, Italy; Laboratoire d’Écologie Alpine (LECA), University Grenoble Alpes, CNRS, Grenoble, France.
    Garner, Rebecca E.
    Department of Biology, Concordia University, QC, Montréal, Canada; Groupe de Recherche Interuniversitaire en Limnologie, QC, Montréa, Canada.
    Gauthier, Joanna
    Groupe de Recherche Interuniversitaire en Limnologie, QC, Montréa, Canada; Department of Biology, University McGill, QC, Montréal, Canada.
    Gregory-Eaves, Irene
    Groupe de Recherche Interuniversitaire en Limnologie, QC, Montréa, Canada; Department of Biology, University McGill, QC, Montréal, Canada.
    Heinecke, Liv
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany; Institute for Mathematics, University of Potsdam, Potsdam, Germany.
    Herzschuh, Ulrike
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany; Institute for Environmental Sciences and Geography, University of Potsdam, Potsdam, Germany.
    Ibrahim, Anan
    Department of Biology, University of Konstanz, Konstanz, Germany.
    Kisand, Veljo
    Institute of Technology, University of Tartu, Tartu, Estonia.
    Kjær, Kurt H.
    Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
    Lammers, Youri
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway.
    Littlefair, Joanne
    School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
    Messager, Erwan
    Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204, CNRS, University Savoie Mont Blanc, Le Bourget du Lac, France.
    Monchamp, Marie-Eve
    Groupe de Recherche Interuniversitaire en Limnologie, QC, Montréa, Canada; Department of Biology, University McGill, QC, Montréal, Canada.
    Olajos, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Orsi, William
    Department of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany; GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany.
    Pedersen, Mikkel W.
    Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
    Rijal, Dilli P.
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway.
    Rydberg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Spanbauer, Trisha
    Department of Environmental Sciences and Lake Erie Center, University of Toledo, OH, Toledo, United States.
    Stoof-Leichsenring, Kathleen R.
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany.
    Taberlet, Pierre
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway; Laboratoire d’Écologie Alpine (LECA), University Grenoble Alpes, CNRS, Grenoble, France.
    Talas, Liisi
    Institute of Technology, University of Tartu, Tartu, Estonia.
    Thomas, Camille
    Department of Earth Sciences, University of Geneva, Geneva, Switzerland.
    Walsh, David A.
    Department of Biology, Concordia University, QC, Montréal, Canada.
    Wang, Yucheng
    Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
    Willerslev, Eske
    Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
    van Woerkom, Anne
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Zimmermann, Heike H.
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany.
    Coolen, Marco J. L.
    Western Australia Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, the Institute for Geoscience Research (TIGeR), Curtin University, Bentley, Australia.
    Epp, Laura S.
    Limnological Institute, Department of Biology, University of Konstanz, Konstanz, Germany.
    Domaizon, Isabelle
    INRAE, University Savoie Mont Blanc, CARRTEL, Thonon les bains, France; UMR CARRTEL, Pôle R&D ECLA, Thonon les bains, France.
    Alsos, Inger G.
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway.
    Parducci, Laura
    Department of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden; Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
    Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations2021Ingår i: Quaternary, E-ISSN 2571-550X, Vol. 4, nr 1, artikel-id 6Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

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  • 10.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Ninnes, Sofia
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Domaizon, Isabelle
    INRAE, UMR CARRTEL, Université Savoie Mont Blanc, Thonon les Bains, France.
    Bigler, Christian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Wang, Xiao-Ru
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Bindler, Richard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Rydberg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Landscape setting drives the microbial eukaryotic community structure in four Swedish mountain lakes over the holocene2021Ingår i: Microorganisms, E-ISSN 2076-2607, Vol. 9, nr 2, artikel-id 355Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. How-ever, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co‐located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock‐dominated lakes—where the oldest DNA samples are dated to only a few hundred years after the lake formation—certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.

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  • 11.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Rydberg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Tolu, Julie
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.
    Domaizon, Isabelle
    Debroas, Didier
    Bindler, Richard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Bigler, Christian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    How Does Environmental Inter-annual Variability Shape Aquatic Microbial Communities?: A 40-Year Annual Record of Sedimentary DNA From a Boreal Lake (Nylandssjon, Sweden)2019Ingår i: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 7, artikel-id 245Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To assess the sensitivity of lakes to anthropogenically-driven environmental changes (e.g., nutrient supply, climate change), it is necessary to first isolate the effects of between-year variability in weather conditions. This variability can strongly impact a lake's biological community especially in boreal and arctic areas where snow phenology play an important role in controlling the input of terrestrial matter to the lake. Identifying the importance of this inherent variability is difficult without time series that span at least several decades. Here, we applied a molecular approach (metabarcoding on eukaryotic 18S rRNA genes and qPCR on cyanobacterial 16S rRNA genes) to sedimentary DNA (sed-DNA) to unravel the annual variability of microbial community in 40 years' sediment record from the boreal lake Nylandssjon which preserve annually-laminated sediments. Our comparison between seasonal meteorological data, sediment inorganic geochemistry (X-ray fluorescence analyses) and organic biomarkers (pyrolysis-gas chromatography/mass spectrometry analyses), demonstrated that inter-annual variability strongly influence the sediment composition in Nylandssjon. Spring temperature, snow and ice phenology (e.g., the percentage of snow loss in spring, the timing of lake ice-off) were identified as important drivers for the inputs of terrestrial material to the lake, and were therefore also important for shaping the aquatic biological community. Main changes were detected in the late-80s/mid-90s and mid-2000s associated with increases in algal productivity, in total richness of the protistan community and in relative abundances of Chlorophyta, Dinophyceae as well as Cyanobacteria abundance. These changes could be linked to a decline in terrestrial inputs to the lake during the snow melt and run-off period, which in turn was driven by warmer winter temperatures. Even if our data shows that meteorological factors do affect the sediment composition and microbial communities, they only explain part of the variability. This is most likely a consequence of the high inter-annual variability in abiotic and biotic parameters highlighting the difficulty to draw firm conclusions concerning drivers of biological changes at an annual or sub-annual resolution even with the 40-year varved sediment record from Nylandssjon. Hence, it is necessary to have an even longer time perspective in order to reveal the full implications of climate change.

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  • 12.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Spong, Goran
    Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden.
    Norman, Sven
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Königsson, Helena
    Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden.
    Bartels, Pia
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Byström, Pär
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes2019Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 14, nr 12, artikel-id e0226638Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Classical methods for estimating the abundance of fish populations are often both expensive, time-consuming and destructive. Analyses of the environmental DNA (eDNA) present in water samples could alleviate such constraints. Here, we developed protocols to detect and quantify brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) populations by applying the droplet digital PCR (ddPCR) method to eDNA molecules extracted from water samples collected in 28 Swedish mountain lakes. Overall, contemporary fish CPUE (catch per unit effort) estimates from standardized survey gill nettings were not correlated to eDNA concentrations for either of the species. In addition, the measured environmental variables (e.g. dissolved organic carbon concentrations, temperature, and pH) appear to not influence water eDNA concentrations of the studied fish species. Detection probabilities via eDNA analysis showed moderate success (less than 70% for both species) while the presence of eDNA from Arctic char (in six lakes) and brown trout (in one lake) was also indicated in lakes where the species were not detected with the gillnetting method. Such findings highlight the limits of one or both methods to reliably detect fish species presence in natural systems. Additional analysis showed that the filtration of water samples through 1.2 mu m glass fiber filters and 0.45 mu m mixed cellulose ester filters was more efficient in recovering DNA than using 0.22 mu m enclosed polyethersulfone filters, probably due to differential efficiencies of DNA extraction. Altogether, this work showed the potentials and limits of the approach for the detection and the quantification of fish abundance in natural systems while providing new insights in the application of the ddPCR method applied to environmental DNA.

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  • 13.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden.
    Spong, Göran
    Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden; Fisheries, Wildlife and Conservation Biology Program, Department of Forestry and Environmental Resources, North Carolina State University, NC, Raleigh, United States.
    Koizumi, Shuntaro
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Puts, Isolde
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Olajos, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Königsson, Helena
    Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden.
    Karlsson, Jan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Byström, Pär
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Droplet digital PCR applied to environmental DNA, a promising method to estimate fish population abundance from humic-rich aquatic ecosystems2021Ingår i: Environmental DNA, E-ISSN 2637-4943, Vol. 3, nr 2, s. 343-352Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Measures of environmental DNA (eDNA) concentrations in water samples have the potential to be both a cost-efficient and a nondestructive method to estimate fish population abundance. However, the inherent temporal and spatial variability in abiotic and biotic conditions in aquatic systems have been suggested to be a major obstacle to determine relationships between fish eDNA concentrations and fish population abundance. Moreover, once water samples are collected, methodological biases are common, which introduces additional sources of variation to potential relationships between eDNA concentrations and fish population abundance. Here, we evaluate the performance of applying the droplet digital PCR (ddPCR) method to estimate fish population abundance in experimental enclosures. Using large-scale enclosure ecosystems that contain populations of nine-spined stickleback (Pungitius pungitius), we compared the concentrations of fish eDNA (COI mitochondrial region, 134 bp) obtained with the ddPCR method with high precision estimates of fish population abundance (i.e., number of individuals) and biomass. To evaluate the effects of contrasted concentrations of humic substances (potential PCR inhibitors) on the performance of ddPCR assays, we manipulated natural dissolved organic carbon (DOC) concentrations (range 4–11 mg/L) in the enclosures. Additionally, water temperature (+2°C) was manipulated in half of the enclosures. Results showed positive relationships between eDNA concentration and fish abundance and biomass estimates although unexplained variation remained. Still and importantly, fish eDNA estimates from high DOC enclosures were not lowered by potential inhibitory effects with our procedure. Finally, water temperature (although only 2°C difference) was neither detected as a significant factor influencing fish eDNA estimates. Altogether, our work highlights that ddPCR-based eDNA is a promising method for future quantification of fish population abundance in natural systems.

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  • 14.
    Capo, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden.
    Spong, Göran
    Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden; Fisheries, Wildlife and Conservation Biology Program, Department of Forestry and Environmental Resources, North Carolina State University, NC, Raleigh, United States.
    Königsson, Helena
    Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden.
    Byström, Pär
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Effects of filtration methods and water volume on the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) eDNA concentrations via droplet digital PCR2020Ingår i: Environmental DNA, E-ISSN 2637-4943, Vol. 2, nr 2, s. 152-160Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The quantification of the abundance of aquatic organisms via the use of environmental DNA (eDNA) molecules present in water is potentially a useful tool for efficient and noninvasive population monitoring. However, questions remain about the reliability of molecular methods. Among the factors that can hamper the reliability of the eDNA quantification, we investigated the influence of five filtration methods (filter pore size, filter type) and filtered water volume (1 and 2 L) on the total eDNA and the fish eDNA concentrations of two species, brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from tanks with known number of individuals and biomass. We applied a droplet digital PCR (ddPCR) approach to DNA extracted from water samples collected from two cultivation tanks (each of them containing one of the targeted species). Results showed that the quantification of fish eDNA concentrations of both species varies with filtration methods. More specifically, the 0.45-µm Sterivex enclosed filters were identified to recover the highest eDNA concentrations. Difficulties to filter 2 L water samples were present for small pore size filters (≤0.45 µm) and likely caused by filter clogging. To overcome issues related to filter clogging, common in studies aiming to quantify fish eDNA molecules from water samples, we recommend a procedure involving filtration of multiple 1 L water samples with 0.45-µm enclosed filters, to recover both high quality and high concentrations of eDNA from targeted species, and subsequent processing of independent DNA extracts with the ddPCR method.

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  • 15.
    Figueroa, Daniela
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF).
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Lindh, Markus V.
    Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar, Sweden.
    Rowe, Owen F.
    Baltic Marine Environment Protection Commission HELCOM, Helsinki, Finland.
    Paczkowska, Joanna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF).
    Pinhassi, Jarone
    Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar, Sweden.
    Andersson, Agneta
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF).
    Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea)2021Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 23, nr 8, s. 4200-4213Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may thus be affected. We studied the responses of bacterial community to inflow of terrestrial dissolved organic matter in a subarctic estuary in the northern Baltic Sea, using a 16S rRNA gene metabarcoding approach. Betaproteobacteria dominated during the spring river flush, constituting ~ 60% of the bacterial community. Bacterial diversity increased as the runoff decreased during summer, when Verrucomicrobia, Betaproteobacteria, Bacteroidetes, Gammaproteobacteria and Planctomycetes dominated the community. Network analysis revealed that a larger number of associations between bacterial populations occurred during the summer than in spring. Betaproteobacteria and Bacteroidetes populations appeared to display similar correlations to environmental factors. In spring, freshly discharged organic matter favoured specialists, while in summer a mix of autochthonous and terrestrial organic matter promoted the development of generalists. Our study indicates that increased inflows of terrestrial organic matter-loaded freshwater to coastal areas would promote specialist bacteria, which in turn might enhance the transformation of terrestrial organic matter in estuarine environments.

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  • 16.
    Huston, Grayson P.
    et al.
    School of Biology and Ecology, University of Maine, ME, Orono, United States; Maine Center for Genetics in the Environment, University of Maine, ME, Orono, United States.
    Lopez, Mark Louie D.
    Department of Biochemistry & Microbiology, University of Victoria, BC, Victoria, Canada.
    Cheng, Yuanyu
    Department of Biology, McGill University, QC, Montreal, Canada; Groupe de recherche interuniversitaire en limnologie (GRIL), Canada.
    King, Leighton
    Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland; Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
    Duxbury, Lucinda C.
    School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, Australia; ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), The University of Adelaide, Adelaide, Australia.
    Picard, Maïlys
    Cawthron Institute, Nelson, New Zealand; Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, New Zealand.
    Thomson-Laing, Georgia
    Cawthron Institute, Nelson, New Zealand; School of Geography, Environment, and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand.
    Myler, Erika
    Department of Integrative Biology, College of Biological Science, University of Guelph, ON, Guelph, Canada.
    Helbing, Caren C.
    Department of Biochemistry & Microbiology, University of Victoria, BC, Victoria, Canada.
    Kinnison, Michael T.
    School of Biology and Ecology, University of Maine, ME, Orono, United States; Maine Center for Genetics in the Environment, University of Maine, ME, Orono, United States.
    Saros, Jasmine E.
    School of Biology and Ecology, University of Maine, ME, Orono, United States; Climate Change Institute, University of Maine, ME, Orono, United States.
    Gregory-Eaves, Irene
    Department of Biology, McGill University, QC, Montreal, Canada; Groupe de recherche interuniversitaire en limnologie (GRIL), Canada.
    Monchamp, Marie-Eve
    Department of Biology, McGill University, QC, Montreal, Canada; Groupe de recherche interuniversitaire en limnologie (GRIL), Canada.
    Wood, Susanna A.
    Cawthron Institute, Nelson, New Zealand.
    Armbrecht, Linda
    Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Battery Point, Australia.
    Ficetola, Gentile Francesco
    Department of Environmental Sciences and Policy, University of Milan, Milan, Italy; Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes and Université Savoie Mont Blanc, Grenoble, France.
    Kurte, Lenka
    Núcleo Milenio INVASAL, University of Concepción, Concepción, Chile.
    Von Eggers, Jordan
    Department of Geology and Geophysics, University of Wyoming, WY, Laramie, United States.
    Brahney, Janice
    Watershed Sciences and Ecology Center, Utah State University, UT, Logan, United States.
    Parent, Genevieve
    Laboratory of Genomics, Maurice Lamontagne Institute, Fisheries and Oceans Canada, QC, Mont-Joli, Canada.
    Sakata, Masayuki K.
    Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan.
    Doi, Hideyuki
    Graduate School of Informatics, Kyoto University, Kyoto, Japan.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities2023Ingår i: Environmental DNA, E-ISSN 2637-4943, Vol. 5, nr 6, s. 1449-1472Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short- and long-term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro-organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.

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  • 17. Ibrahim, Anan
    et al.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Wessels, Martin
    Martin, Isabel
    Meyer, Axel
    Schleheck, David
    Epp, Laura S.
    Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment-core environmental DNA2021Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, nr 13, s. 3040-3056Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    During the 20th century, many lakes in the Northern Hemisphere were affected by increasing human population and urbanization along their shorelines and catchment, resulting in aquatic eutrophication. Ecosystem monitoring commenced only after the changes became apparent, precluding any examination of timing and dynamics of initial community change in the past and comparison of pre- and postimpact communities. Peri-Alpine Lake Constance (Germany) underwent a mid-century period of eutrophication followed by re-oligotrophication since the 1980s and is now experiencing warm temperatures. We extended the period for which monitoring data of indicator organisms exist by analysing historical environmental DNA (eDNA) from a sediment core dating back some 110 years. Using three metabarcoding markers-for microbial eukaryotes, diatoms and cyanobacteria-we revealed two major breakpoints of community change, in the 1930s and the mid-1990s. In our core, the latest response was exhibited by diatoms, which are classically used as palaeo-bioindicators for the trophic state of lakes. Following re-oligotrophication, overall diversity values reverted to similar ones of the early 20th century, but multivariate analysis indicated that the present community is substantially dissimilar. Community changes of all three groups were strongly correlated to phosphorus concentration changes, whereas significant relationships to temperature were only observed when we did not account for temporal autocorrelation. Our results indicate that each microbial group analysed exhibited a unique response, highlighting the particular strength of multimarker analysis of eDNA, which is not limited to organisms with visible remains and can therefore discover yet unknown responses and abiotic-biotic relationships.

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  • 18.
    Lin, Qi
    et al.
    State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
    Zhang, Ke
    State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
    McGowan, Suzanne
    School of Geography, University of Nottingham, Nottingham, United Kingdom.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Shen, Ji
    School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, China.
    Synergistic impacts of nutrient enrichment and climate change on long-term water quality and ecological dynamics in contrasting shallow-lake zones2021Ingår i: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 66, nr 9, s. 3271-3286Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Anthropogenic and climatic stressors on freshwater ecosystems are of global concern. However, the interactions and effects of multiple stressors (e.g., nutrient enrichment, climate warming, altered wind and precipitation) acting over different spatial and temporal scales are often complex and remain controversial. Here, we reconstructed one-century dynamics of eutrophication and primary producer communities in algal-dominated and macrophyte-dominated zones of a large shallow lake (Taihu, China), by integrating sedimentary photosynthetic pigments and geochemical records with water monitoring and historical archives. We aimed to explore the long-term underlying mechanisms of the responses of water quality and lake biota to multiple environmental perturbations. We found that water quality degradation and algal community modification showed similar trends but distinct timings and trajectories in contrasting ecological zones. Onset and intensity of eutrophication in north Meiliang Bay (since the 1950s) exceeded far beyond that of macrophyte-dominated Eastern Taihu (~1990s). Anthropogenic nutrients overtook past climatic control on production and composition of phototrophic assemblages. More importantly, lake phytoplankton responded markedly to climate warming, decreasing wind speed, and extreme weathers after cultural eutrophication. Synergistic interactions of nutrients and climate on lake ecosystems became increasingly significant in promoting harmful algal blooms (HABs) dominated by Microcystis, close to the hyper-eutrophic north lake zones. The asynchronous limnological and ecological responses also indicated the modulating roles of lake ecological regime and catchment hydrogeomorphic characteristic. Collectively, our findings suggest that mitigation of eutrophication and HABs calls for a triple management strategy integrating anthropogenic nutrients, climate change, and lake-catchment setting.

  • 19.
    Lin, Qi
    et al.
    State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
    Zhang, Ke
    State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
    McGowan, Suzanne
    Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.
    Huang, Shixin
    State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
    Xue, Qingju
    State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Zhang, Can
    State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
    Zhao, Cheng
    School of Geography and Oceanography Sciences, Nanjing University, Nanjing, China.
    Shen, Ji
    State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; School of Geography and Oceanography Sciences, Nanjing University, Nanjing, China.
    Characterization of lacustrine harmful algal blooms using multiple biomarkers: historical processes, driving synergy, and ecological shifts2023Ingår i: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 235, artikel-id 119916Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Harmful algal blooms (HABs) producing toxic metabolites are increasingly threatening environmental and human health worldwide. Unfortunately, long-term process and mechanism triggering HABs remain largely unclear due to the scarcity of temporal monitoring. Retrospective analysis of sedimentary biomarkers using up-to-date chromatography and mass spectrometry techniques provide a potential means to reconstruct the past occurrence of HABs. By combining aliphatic hydrocarbons, photosynthetic pigments, and cyanotoxins, we quantified herein century-long changes in abundance, composition, and variability of phototrophs, particularly toxigenic algal blooms, in China's third largest freshwater Lake Taihu. Our multi-proxy limnological reconstruction revealed an abrupt ecological shift in the 1980s characterized by elevated primary production, Microcystis-dominated cyanobacterial blooms, and exponential microcystin production, in response to nutrient enrichment, climate change, and trophic cascades. The empirical results from ordination analysis and generalized additive models support climate warming and eutrophication synergy through nutrient recycling and their feedback through buoyant cyanobacterial proliferation, which sustain bloom-forming potential and further promote the occurrence of increasingly-toxic cyanotoxins (e.g., microcystin-LR) in Lake Taihu. Moreover, temporal variability of the lake ecosystem quantified using variance and rate of change metrics rose continuously after state change, indicating increased ecological vulnerability and declined resilience following blooms and warming. With the persistent legacy effects of lake eutrophication, nutrient reduction efforts mitigating toxic HABs probably be overwhelmed by climate change effects, emphasizing the need for more aggressive and integrated environmental strategies.

  • 20.
    Mattsson, Lina
    et al.
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Sörenson, Eva
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Farnelid, Hanna Maria
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Hirwa, Maurice
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden; Axis Communications, Lund, Sweden.
    Olofsson, Martin
    BioResM, Maroc Sarl, Safi, Morocco.
    Svensson, Fredrik
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Lindehoff, Elin
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Legrand, Catherine
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System2021Ingår i: Frontiers in Bioengineering and Biotechnology, E-ISSN 2296-4185, Vol. 9, artikel-id 651895Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Functionally uniform monocultures have remained the paradigm in microalgal cultivation despite the apparent challenges to avoid invasions by other microorganisms. A mixed microbial consortium approach has the potential to optimize and maintain biomass production despite of seasonal changes and to be more resilient toward contaminations. Here we present a 3-year outdoor production of mixed consortia of locally adapted microalgae and bacteria in cold temperate latitude. Microalgal consortia were cultivated in flat panel photobioreactors using brackish Baltic Sea water and CO2 from a cement factory (Degerhamn, Cementa AB, Heidelberg Cement Group) as a sustainable CO2 source. To evaluate the ability of the microbial consortia to maintain stable biomass production while exposed to seasonal changes in both light and temperature, we tracked changes in the microbial community using molecular methods (16S and 18S rDNA amplicon sequencing) and monitored the biomass production and quality (lipid, protein, and carbohydrate content) over 3 years. Despite changes in environmental conditions, the mixed consortia maintained stable biomass production by alternating between two different predominant green microalgae (Monoraphidium and Mychonastes) with complementary tolerance to temperature. The bacterial population was few taxa co-occured over time and the composition did not have any connection to the shifts in microalgal taxa. We propose that a locally adapted and mixed microalgal consortia, with complementary traits, can be useful for optimizing yield of commercial scale microalgal cultivation.

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  • 21.
    Rincón-Tomás, Blanca
    et al.
    AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain; Grupo Inv. Geología Aplicada a Recursos Marinos y Ambientes Extremos, Instituto Geológico y Minero de España (IGME-CSIC), Madrid, Spain.
    Lanzén, Anders
    AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
    Sánchez, Pablo
    Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.
    Estupiñán, Mónica
    AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain.
    Sanz-Sáez, Isabel
    Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.
    Bilbao, M. Elisabete
    AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain.
    Rojo, Diana
    AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain.
    Mendibil, Iñaki
    AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain.
    Pérez-Cruz, Carla
    AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain.
    Ferri, Marta
    Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Abad-Recio, Ion L.
    AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain.
    Amouroux, David
    Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux (IPREM), Pau, France.
    Bertilsson, Stefan
    Dep. Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Sánchez, Olga
    Dep. Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
    Acinas, Silvia G.
    Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.
    Alonso-Sáez, Laura
    AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain.
    Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota2024Ingår i: Journal of Hazardous Materials, ISSN 0304-3894, E-ISSN 1873-3336, Vol. 465, artikel-id 133120Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments.

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  • 22.
    Sörenson, Eva
    et al.
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Farnelid, Hanna
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Lindehoff, Elin
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Legrand, Catherine
    Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community: Enabling Continuous Production of Microalgal Biomass2021Ingår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 12, artikel-id 607601Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To better predict the consequences of environmental change on aquatic microbial ecosystems it is important to understand what enables community resilience. The mechanisms by which a microbial community maintain its overall function, for example, the cycling of carbon, when exposed to a stressor, can be explored by considering three concepts: biotic interactions, functional adaptations, and community structure. Interactions between species are traditionally considered as, e.g., mutualistic, parasitic, or neutral but are here broadly defined as either coexistence or competition, while functions relate to their metabolism (e.g., autotrophy or heterotrophy) and roles in ecosystem functioning (e.g., oxygen production, organic matter degradation). The term structure here align with species richness and diversity, where a more diverse community is though to exhibit a broader functional capacity than a less diverse community. These concepts have here been combined with ecological theories commonly used in resilience studies, i.e., adaptive cycles, panarchy, and cross-scale resilience, that describe how the status and behavior at one trophic level impact that of surrounding levels. This allows us to explore the resilience of a marine microbial community, cultivated in an outdoor photobioreactor, when exposed to a naturally occurring seasonal stress. The culture was monitored for 6weeks during which it was exposed to two different temperature regimes (21 ± 2 and 11 ± 1°C). Samples were taken for metatranscriptomic analysis, in order to assess the regulation of carbon uptake and utilization, and for amplicon (18S and 16S rRNA gene) sequencing, to characterize the community structure of both autotrophs (dominated by the green microalgae Mychonastes) and heterotrophs (associated bacterioplankton). Differential gene expression analyses suggested that community function at warm temperatures was based on concomitant utilization of inorganic and organic carbon assigned to autotrophs and heterotrophs, while at colder temperatures, the uptake of organic carbon was performed primarily by autotrophs. Upon the shift from high to low temperature, community interactions shifted from coexistence to competition for organic carbon. Network analysis indicated that the community structure showed opposite trends for autotrophs and heterotrophs in having either high or low diversity. Despite an abrupt change of temperature, the microbial community as a whole responded in a way that maintained the overall level of diversity and function within and across autotrophic and heterotrophic levels. This is in line with cross-scale resilience theory describing how ecosystems may balance functional overlaps within and functional redundancy between levels in order to be resilient to environmental change (such as temperature).

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  • 23.
    Vandewalle-Capo, Marine
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Rehamnia, Baraa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Microbial Biotechnology, Université Frères Mentouri.
    Sheldrake, Merlin
    Lee, Natuschka M.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    The biotechnological potential of yeast under extreme conditions2020Ingår i: Biotechnological applications of extremophilic microorganisms / [ed] Natuschka M. Lee, Walter de Gruyter, 2020, s. 313-356Kapitel i bok, del av antologi (Refereegranskat)
  • 24.
    Von Eggers, Jordan M.
    et al.
    Department of Geology and Geophysics, University of Wyoming, WY, Laramie, United States; Program in Ecology and Evolution, University of Wyoming, WY, Laramie, United States.
    Wisnoski, Nathan I.
    Wyoming Geographic Information Science Center, University of Wyoming, WY, Laramie, United States; Department of Biological Sciences, Mississippi State University, MS, Mississippi State, United States.
    Calder, John W.
    Department of Botany, University of Wyoming, WY, Laramie, United States.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Groff, Dulcinea V.
    Department of Geology and Geophysics, University of Wyoming, WY, Laramie, United States.
    Krist, Amy C.
    Program in Ecology and Evolution, University of Wyoming, WY, Laramie, United States; Department of Zoology and Physiology, University of Wyoming, WY, Laramie, United States.
    Shuman, Bryan
    Department of Geology and Geophysics, University of Wyoming, WY, Laramie, United States; Program in Ecology and Evolution, University of Wyoming, WY, Laramie, United States.
    Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes2024Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 26, nr 3, artikel-id e16607Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low-energy adapted taxa in deeper zones. Stochastic processes—like dispersal limitation—contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.

  • 25.
    Williams, John W.
    et al.
    Department of Geography, University of Wisconsin-Madison, WI, Madison, United States.
    Spanbauer, Trisha L.
    Department of Environmental Science and Lake Erie Center, University of Toledo, OH, Toledo, United States.
    Heintzman, Peter D.
    The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway; Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, Sweden; Department of Geological Sciences, Stockholm University, Stockholm, Sweden.
    Blois, Jessica
    Department of Life and Environmental Sciences, University of California -Merced, CA, Merced, United States.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Goring, Simon J.
    Department of Geography, University of Wisconsin-Madison, WI, Madison, United States.
    Monchamp, Marie-Eve
    Department of Biology, McGill University, QC, Montreal, Canada.
    Parducci, Laura
    Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, Sweden.
    Von Eggers, Jordan M.
    Department of Geology and Geophysics, University of Wyoming, WY, Laramie, United States.
    Strengthening global-change science by integrating aeDNA with paleoecoinformatics2023Ingår i: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.

  • 26.
    Yan, Dongna
    et al.
    Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China.
    An, Zhisheng
    Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Organic matter content and source is associated with the depth-dependent distribution of prokaryotes in lake sediments2024Ingår i: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 69, s. 496-508Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Aquatic sediments harbour a diverse array of microorganisms that drive organic matter recycling, carbon sequestration and greenhouse gases (e.g., CO2, CH4, N2O) emissions. Although largely studied in water columns, vertical profiles of the diversity and composition of prokaryotic communities (i.e., Bacteria and Archaea) in aquatic sediments are still rare. More specifically, much remains to be learnt about their vertical distribution in lake sediments and how environmental conditions at the time of burial have impacted their diversity and composition.

    We investigated the vertical distribution of prokaryotic community with 16S rRNA gene quantitative (q)PCR and metabarcoding approaches applied to 93 sediment layers collected in a 2-m-long sediment core from the eutrophic alkaline Lake Chenghai in subtropical China. We aimed to study the diversity, composition and structure distribution of the prokaryotic community as well as environmental factors influencing it.

    Bacterial abundance was found to decrease with sediment depth although the richness of both bacterial and archaeal assemblages slightly increased with sediment depth. In terms of composition, a strongly stratified sediment–depth pattern was observed in which Proteobacteria, Desulfobacterota, Bacteroidota and Verrucomicrobiota dominated the inventories in the surface sediment layers, whereas Chloroflexi, Spirochaetota, Planctomycetota, Crenarchaeota were more abundant in the deep sediment layers. Organic matter contents and sources were identified as major factors shaping the structure of the prokaryotic community.

    Overall, our study provides new evidence about how lake sediment's prokaryotic community are linked to external sources of energy. This complement existing data from other lake systems towards a better understanding of sediment prokaryotic community's contribution to biogeochemical cycle in lakes.

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  • 27.
    Yan, Dongna
    et al.
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China.
    Han, Yongming
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China; National Observation and Research Station of Regional Ecological Environment Change and Comprehensive Management in the Guanzhong Plain, Shaanxi, Xi'an, China.
    An, Zhisheng
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China.
    Lei, Dewen
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China; University of Chinese Academy of Sciences, Beijing, China.
    Zhao, Xue
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China.
    Zhao, Haiyan
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China; Xi'an Institute for Innovative Earth Environment Research, Xi'an, China.
    Liu, Jinzhao
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Anthropogenic drivers accelerate the changes of lake microbial eukaryotic communities over the past 160 years2024Ingår i: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 327, artikel-id 108535Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Human impacts on Earth's atmosphere, hydrosphere, litosphere and biosphere are so significant as to naming a new geological epoch, the Anthropocene. Lakes and their biota are highly sensitive to environmental changes. Among aquatic organisms, microbial eukaryotes play fundamental roles associated with lake ecosystem functioning, food webs, nutrient cycling, and pollutant degradation. However, the response of lake microbial eukaryotic community during the Anthropocene to changes in environmental conditions remain poorly understood. Here, we applied a 18S metabarcoding approach to sedimentary DNA to reconstruct the temporal dynamics of microbial eukaryotic community over the past 160 years. We investigated the influence of environmental conditions and of biotic interactions on the microbial eukaryotes in Sihailongwan Maar Lake, one of the candidate sites of Global boundary Stratotype Section and Point (GSSP) for demarcation of the Anthropocene. Microbial eukaryotes were dominated by dinoflagellates, chlorophytes, ciliates, pirsoniales, rotifers, ochrophytes, apicomplexans and cercozoans that were divided into four functional groups that are photoautotrophs, mixotrophs, consumers and parasites. The predominance of phototrophs and their strong associations with organisms from other trophic levels, confirmed their crucial roles in nutrient cycling, energy flows and ecosystem services in freshwater ecosystems. Abrupt changes in the 1950s in microbial eukaryotic diversity and composition were consistent with changes observed in the pollutants emissions i.e., heavy metals, combustion indices (spheroidal carbonaceous particles, polycyclic aromatic hydrocarbon, Soot F14C), radioactivity indicators (239,240Pu, 129I/127I), nutrients (total organic carbon, total nitrogen, phosphorus), and temperature. Statistical analysis revealed that anthropogenic drivers controlled the temporal dynamic of microbial eukaryotic community. Our findings provide additional biostratigraphy evidence of the impact of environmental change on this lake biota, which further supports the value of this system to characterize the Anthropocene.

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  • 28.
    Yan, Dongna
    et al.
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China.
    Han, Yongming
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China; National Observation and Research Station of Regional Ecological Environment Change and Comprehensive Management in the Guanzhong Plain, Shaanxi, Xi'an, China.
    Zhong, Meifang
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Wen, Hanfeng
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China; University of Chinese Academy of Sciences, Beijing, China.
    An, Zhisheng
    State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Shaanxi, Xi'an, China.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Historical trajectories of antibiotics resistance genes assessed through sedimentary DNA analysis of a subtropical eutrophic lake2024Ingår i: Environment International, ISSN 0160-4120, E-ISSN 1873-6750, Vol. 186, artikel-id 108654Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Investigating the occurrence of antibiotic-resistance genes (ARGs) in sedimentary archives provides opportunities for reconstructing the distribution and dissemination of historical (i.e., non-anthropogenic origin) ARGs. Although ARGs in freshwater environments have attracted great attention, historical variations in the diversity and abundance of ARGs over centuries to millennia remain largely unknown. In this study, we investigated the vertical change patterns of bacterial communities, ARGs and mobile genetic elements (MGEs) found in sediments of Lake Chenghai spanning the past 600 years. Within resistome preserved in sediments, 177 ARGs subtypes were found with aminoglycosides and multidrug resistance being the most abundant. The ARG abundance in the upper sediment layers (equivalent to the post-antibiotic era since the 1940s) was lower than those during the pre-antibiotic era, whereas the ARG diversity was higher during the post-antibiotic era, possibly because human-induced lake eutrophication over the recent decades facilitated the spread and proliferation of drug-resistant bacteria. Statistical analysis suggested that MGEs abundance and the bacterial community structure were significantly correlated with the abundance and diversity of ARGs, suggesting that the occurrence and distribution of ARGs may be transferred between different bacteria by MGEs. Our results provide new perspectives on the natural history of ARGs in freshwater environments and are essential for understanding the temporal dynamics and dissemination of ARGs.

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  • 29.
    Yan, Dongna
    et al.
    State key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an Shaanxi, China.
    Picard, Mailys
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Han, Yongming
    State key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an Shaanxi, China; National Observation and Research Station of Regional Ecological Environment Change and Comprehensive Management in the Guanzhong Plain, Shaanxi, China.
    An, Zhisheng
    State key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an Shaanxi, China.
    Lei, Dewen
    State key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an Shaanxi, China; University of Chinese Academy of Sciences, Beijing, China.
    Zhao, Xue
    State key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an Shaanxi, China.
    Zhang, Luyuan
    State key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an Shaanxi, China.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Sedimentary DNA reveals phytoplankton diversity loss in a deep maar lake during the Anthropocene2024Ingår i: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Anthropogenic-driven environmental change, including current climate warming, has influenced lake ecosystems globally during the Anthropocene. Phytoplankton are important indicators of environmental changes in lakes and play a fundamental role in maintaining the functioning and stability of these ecosystems. However, the extent to which lake phytoplankton were affected by anthropogenic or climatic forces during the Anthropocene remains unclear. Here, we investigated the 160-yr-long dynamics of the phytoplankton community (cyanobacteria and eukaryotic microalgae) in response to anthropogenic forcing in Sihailongwan Maar Lake—a candidate for a Global boundary Stratotype Section and Point for demarcation of the Anthropocene—using DNA metabarcoding and traditional paleolimnological approaches. Our results show a significant decline in phytoplankton diversity and an abrupt shift in community composition around the 1950s, corresponding to the beginning of the “Great Acceleration” period. Specifically, phytoplankton taxa coexistence patterns, niche differentiation, and assembly mechanisms changed significantly after the 1950s. Overall, increases in air temperature and anthropogenic forcing appear to be the dominant controls for community reorganization and diversity decline of the phytoplankton from this deep maar lake. A neutral community model suggests that phytoplankton community composition was mainly controlled by stochastic processes before the 1950s; however, as time progressed, deterministic effects driven by anthropogenic global warming increased. The results of this study imply that anthropogenic perturbations have led to a loss of phytoplankton diversity and a further decline in ecological resilience in deep lakes, with likely knock-on effects on the productivity and function of lake ecosystems.

  • 30.
    Zhong, Meifang
    et al.
    Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, China.
    Capo, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Aquatic Sciences and Assessment, SLU, Uppsala, Sweden.
    Zhang, Huayong
    Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, China.
    Hu, Haiyan
    Department of Aquatic Sciences and Assessment, SLU, Uppsala, Sweden; State key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China.
    Wang, Zhongyu
    Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, China.
    Tian, Wang
    Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, China.
    Huang, Tousheng
    Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, China.
    Bertilsson, Stefan
    Department of Aquatic Sciences and Assessment, SLU, Uppsala, Sweden.
    Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe, China)2023Ingår i: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 68, nr 1, s. 155-171Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Planktonic and benthic bacterial communities hold central roles in the functioning of freshwater ecosystems and mediate key ecosystem services such as primary production and nutrient remineralisation. Although it is clear that such communities vary in composition both within and between lakes, the environmental factors and processes shaping the diversity and composition of freshwater bacteria are still not fully understood. In order to assess seasonal and spatial variability in lake bacterial communities and identify environmental factors underpinning biogeographical patterns, we performed a large-scale sampling campaign with paired water and sediment sample collection at 18 locations during four seasons in Lake Balihe, a subtropical shallow fish-farming lake in mid-eastern China. Pelagic and benthic bacterial communities were distinctly different in terms of diversity, taxonomic composition and community structure, with Actinobacteria, Bacteroidetes, Cyanobacteria and Alphaproteobacteria dominating lake water, and Acidobacteria, Bacteroidetes, Chloroflexi, Gammaproteobacteria and Deltaproteobacteria dominating sediment. Nevertheless, these two communities had stronger spatial concordance and overlap in taxa during spring and autumn seasons. Together, the main drivers of both the spatial and temporal variations in Lake Balihe bacterial communities were identified as water temperature, turbidity, nitrogen and phosphorus availability, and thermal stratification controlled by wind-mixing and activity of the dense farmed fish populations. Notably, populations affiliated with Firmicutes, known to be abundant in fish gut microbiome, were especially abundant in the summer season and locations where high fish biomass was found, suggesting a potential link between fish gut microbiome and the pelagic bacterial communities. Our findings demonstrated seasonal homogenisation of pelagic and benthic bacterial communities linked to marked shifts in a set of seasonally-driven environmental variables including water temperature and nutrient availability. 

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