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Dietz R, Sonne C, Jenssen BM, Das K, de Wit CA, Harding KC, Siebert U, Olsen MT. The Baltic Sea: An ecosystem with multiple stressors. Environ Int 2021; 147:106324. [PMID: 33326905 DOI: 10.1016/j.envint.2020.106324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
This introductory chapter to our Environment International VSI does not need an abstract and therefore we just include our recommendations below in order to proceed with the resubmission. Future work should examine waterbirds as food web sentinels of multiple stressors as well as Baltic Sea food web dynamics of hazardous substances and how climate change may modify it. Also, future work should aim at further extending the new frameworks developed within BALTHEALTH for energy and contaminant transfer at the population level (Desforges et al., 2018, Cervin et al., 2020/this issue Silva et al., 2020/this issue) and their long term effects on Baltic Sea top predators, such as harbour porpoises, grey seals ringed seals, and white-tailed eagles. Likewise, the risk evaluation conducted for PCB in connection with mercury on Arctic wildlife (Dietz et al., 2019, not a BONUS BALTHEALTH product) could be planned for Baltic Sea molluscs, fish, bird and marine mammals in the future. Finally, future efforts could include stressors not covered by the BONUS BALTHEALTH project, such as food web fluxes, overexploitation, bycatches, eutrophication and underwater noise.
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Affiliation(s)
- R Dietz
- Department of Bioscience, Arctic Research Centre (ARC), Aarhus University, Faculty of Science and Technology, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark.
| | - C Sonne
- Department of Bioscience, Arctic Research Centre (ARC), Aarhus University, Faculty of Science and Technology, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - B M Jenssen
- Department of Bioscience, Arctic Research Centre (ARC), Aarhus University, Faculty of Science and Technology, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark; Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - K Das
- Freshwater and Oceanic sciences Unit of reSearch (FOCUS), Laboratory of Oceanology, University of Liege, Allée du six Août 11, Bât. B6C, 4000 Liège, Belgium
| | - C A de Wit
- Department of Environmental Science, Stockholm University, Svante Arrheniusvägen 8, SE-10691 Stockholm, Sweden
| | - K C Harding
- Department of Biological and Environmental Sciences, Gothenburg University, Box 461, SE-40530 Gothenburg, Sweden
| | - U Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Büsum, Germany
| | - M T Olsen
- Evolutionary Genomics, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen K, Denmark
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Thiel V, Wood JM, Olsen MT, Tank M, Klatt CG, Ward DM, Bryant DA. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing. Front Microbiol 2016; 7:919. [PMID: 27379049 PMCID: PMC4911352 DOI: 10.3389/fmicb.2016.00919] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/27/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, strongly dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Thermodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arminicenantes (OP8) represented ≥1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. This study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community, particularly for Roseiflexus spp.
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Affiliation(s)
- Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Millie T Olsen
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Marcus Tank
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Christian G Klatt
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA; Agricultural Research Service, United States Department of Agriculture, University of MinnesotaSaint Paul, MN, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA; Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, USA
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Melendrez MC, Becraft ED, Wood JM, Olsen MT, Bryant DA, Heidelberg JF, Rusch DB, Cohan FM, Ward DM. Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat. Front Microbiol 2016; 6:1540. [PMID: 26834710 PMCID: PMC4712262 DOI: 10.3389/fmicb.2015.01540] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022] Open
Abstract
Recent studies of bacterial speciation have claimed to support the biological species concept—that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B') of Synechococcus in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B' lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B' lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.
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Affiliation(s)
- Melanie C Melendrez
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Eric D Becraft
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Millie T Olsen
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, Pennsylvania State University University Park, PA, USA
| | - John F Heidelberg
- Department of Biological Sciences, College of Letters, Arts and Sciences, University of Southern California Los Angeles, CA, USA
| | - Douglas B Rusch
- Informatics Group, J. Craig Venter Institute Rockville, MD, USA
| | | | - David M Ward
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
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Nowack S, Olsen MT, Schaible GA, Becraft ED, Shen G, Klapper I, Bryant DA, Ward DM. The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light. Front Microbiol 2015; 6:626. [PMID: 26175719 PMCID: PMC4484337 DOI: 10.3389/fmicb.2015.00626] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/08/2015] [Indexed: 11/13/2022] Open
Abstract
Closely related strains of thermophilic Synechococcus were cultivated from the microbial mats found in the effluent channels of Mushroom Spring, Yellowstone National Park (YNP). These strains have identical or nearly identical 16S rRNA sequences but are representative of separate, predicted putative ecotype (PE) populations, which were identified by using the more highly resolving psaA locus and which predominate at different vertical positions within the 1-mm-thick upper-green layer of the mat. Pyrosequencing confirmed that each strain contained a single, predominant psaA genotype. Strains differed in growth rate as a function of irradiance. A strain with a psaA genotype corresponding to a predicted PE that predominates near the mat surface grew fastest at high irradiances, whereas strains with psaA genotypes representative of predominant subsurface populations grew faster at low irradiance and exhibited greater sensitivity to abrupt shifts to high light. The high-light-adapted and low-light-adapted strains also exhibited differences in pigment content and the composition of the photosynthetic apparatus (photosystem ratio) when grown under different light intensities. Cells representative of the different strains had similar morphologies under low-light conditions, but under high-light conditions, cells of low-light-adapted strains became elongated and formed short chains of cells. Collectively, the results presented here are consistent with the hypothesis that closely related, but distinct, ecological species of Synechococcus occupy different light niches in the Mushroom Spring microbial mat and acclimate differently to changing light environments.
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Affiliation(s)
- Shane Nowack
- Department of Mathematical Sciences, Montana State University, Bozeman MT, USA ; School of Environmental Sciences, University of Guelph, Guelph ON, Canada
| | - Millie T Olsen
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - George A Schaible
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - Eric D Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park PA, USA
| | - Isaac Klapper
- Department of Mathematical Sciences, Montana State University, Bozeman MT, USA ; Department of Mathematics, Temple University, Philadelphia, PA USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park PA, USA ; Department of Chemistry and Biochemistry, Montana State University, Bozeman MT, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
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Olsen MT, Nowack S, Wood JM, Becraft ED, LaButti K, Lipzen A, Martin J, Schackwitz WS, Rusch DB, Cohan FM, Bryant DA, Ward DM. The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Front Microbiol 2015; 6:604. [PMID: 26157428 PMCID: PMC4477158 DOI: 10.3389/fmicb.2015.00604] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/01/2015] [Indexed: 11/26/2022] Open
Abstract
Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes (PEs) that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related PEs have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.
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Affiliation(s)
- Millie T Olsen
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Shane Nowack
- Department of Mathematical Sciences, Montana State University Bozeman, MT, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Eric D Becraft
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Kurt LaButti
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Joel Martin
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | | | | | | | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA ; Department of Chemistry and Biochemistry, Montana State University Bozeman, MT, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
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Kim YM, Nowack S, Olsen MT, Becraft ED, Wood JM, Thiel V, Klapper I, Kühl M, Fredrickson JK, Bryant DA, Ward DM, Metz TO. Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms. Front Microbiol 2015; 6:209. [PMID: 25941514 PMCID: PMC4400912 DOI: 10.3389/fmicb.2015.00209] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/02/2015] [Indexed: 11/29/2022] Open
Abstract
Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.
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Affiliation(s)
- Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Shane Nowack
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
- Department of Mathematical Sciences, Montana State UniversityBozeman, MT, USA
| | - Millie T. Olsen
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA
| | - Isaac Klapper
- Department of Mathematical Sciences, Montana State UniversityBozeman, MT, USA
- Department of Mathematics, Temple UniversityPhiladelphia, PA, USA
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of CopenhagenHelsingør, Denmark
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneyUltimo, NSW, Australia
| | - James K. Fredrickson
- Biological Sciences Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA
- Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, USA
| | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National LaboratoryRichland, WA, USA
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Klimova A, Phillips CD, Fietz K, Olsen MT, Harwood J, Amos W, Hoffman JI. Global population structure and demographic history of the grey seal. Mol Ecol 2014; 23:3999-4017. [PMID: 25041117 DOI: 10.1111/mec.12850] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/04/2014] [Accepted: 06/25/2014] [Indexed: 02/06/2023]
Abstract
Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habitat availability and anthropogenic exploitation. We therefore analysed samples from over 1500 individuals collected from 22 colonies spanning the Western and Eastern Atlantic and the Baltic Sea regions, represented by 350 bp of the mitochondrial hypervariable region and up to nine microsatellites. Strong population structure was observed at both types of marker, and highly asymmetrical patterns of gene flow were also inferred, with the Orkney Islands being identified as a source of emigrants to other areas in the Eastern Atlantic. The Baltic and Eastern Atlantic regions were estimated to have diverged a little over 10 000 years ago, consistent with the last proposed isolation of the Baltic Sea. Approximate Bayesian computation also identified genetic signals consistent with postglacial population expansion across much of the species range, suggesting that grey seals are highly responsive to changes in habitat availability.
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Affiliation(s)
- A Klimova
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501, Bielefeld, Germany
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Dietz R, Riget F, Born EW, Sonne C, Grandjean P, Kirkegaard M, Olsen MT, Asmund G, Renzoni A, Baagøe H, Andreasen C. Trends in mercury in hair of Greenlandic polar bears (Ursus maritimus) during 1892-2001. Environ Sci Technol 2006; 40:1120-5. [PMID: 16572764 DOI: 10.1021/es051636z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Mercury concentrations in hair from 397 Greenland polar bears (Ursusmaritimus) sampled between 1892 and 2001 were analyzed for temporal trends. In East Greenland the concentrations showed a significant (p < 0.0001, n = 27) increase of 3.1%/year in the period 1892-1973. In Northwest Greenland, a similar (p < 0.0001, n = 69) increase of 2.1%/year was found, which continued until 1991, when the most recent samples were obtained. In East Greenland, a significant (p = 0.009, n = 322) decrease of 0.8%/year was observed after 1973. Two Northwest Greenland samples from 1300 A.D. had a mean value of 0.52 mg/kg of dry weight, which can be considered as a baseline level. The Hg concentration during 1985-1991 from Northwest Greenland (mean value of 7.45 mg/kg of dry weight) was more than 14-fold higher than the assumed baseline level from 1300 A.D. from the same region (i.e., about 93% anthropogenic). Although a decrease was found in East Greenland after 1973, the concentration is still ca. 11-fold higher than the baseline level (i.e., about 90% anthropogenic).
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Affiliation(s)
- R Dietz
- Department of Arctic Environment, National Environmental Research Institute, P.O. Box 358, Frederiksborgvej 399, DK-4000 Roskilde, Denmark.
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