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Hu, H., Wang, B., Bravo, A. G., Björn, E., Skyllberg, U., Amouroux, D., . . . Bertilsson, S. (2020). Shifts in mercury methylation across a peatland chronosequence: From sulfate reduction to methanogenesis and syntrophy. Journal of Hazardous Materials, 387, Article ID 121967.
Open this publication in new window or tab >>Shifts in mercury methylation across a peatland chronosequence: From sulfate reduction to methanogenesis and syntrophy
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2020 (English)In: Journal of Hazardous Materials, ISSN 0304-3894, E-ISSN 1873-3336, Vol. 387, article id 121967Article in journal (Refereed) Published
Abstract [en]

Peatlands are globally important ecosystems where inorganic mercury is converted to bioaccumulating and highly toxic methylmercury, resulting in high risks of methylmercury exposure in adjacent aquatic ecosystems. Although biological mercury methylation has been known for decades, there is still a lack of knowledge about the organisms involved in mercury methylation and the drivers controlling their methylating capacity. In order to investigate the metabolisms responsible for mercury methylation and methylmercury degradation as well as the controls of both processes, we studied a chronosequence of boreal peatlands covering fundamentally different biogeochemical conditions. Potential mercury methylation rates decreased with peatland age, being up to 53 times higher in the youngest peatland compared to the oldest. Methylation in young mires was driven by sulfate reduction, while methanogenic and syntrophic metabolisms became more important in older systems. Demethylation rates were also highest in young wetlands, with a gradual shift from biotic to abiotic methylmercury degradation along the chronosequence. Our findings reveal how metabolic shifts drive mercury methylation and its ratio to demethylation as peatlands age.

Place, publisher, year, edition, pages
ELSEVIER, 2020
Keywords
Mercury, Methylation, Demethylation, Peatland, Chronosequence
National Category
Forest Science
Identifiers
urn:nbn:se:uu:diva-407973 (URN)10.1016/j.jhazmat.2019.121967 (DOI)000514758500003 ()31901845 (PubMedID)
Funder
Swedish Research Council Formas, 2016-00896Wenner-Gren Foundations
Available from: 2020-04-02 Created: 2020-04-02 Last updated: 2020-04-02Bibliographically approved
Liu, H., Waldén, T., Cai, D., Ahl, D., Bertilsson, S., Phillipson, M., . . . Holm, L. (2019). Dietary Fiber in Bilberry Ameliorates Pre-Obesity Events in Rats by Regulating Lipid Depot, Cecal Short-Chain Fatty Acid Formation and Microbiota Composition. Nutrients, 11(6), Article ID 1350.
Open this publication in new window or tab >>Dietary Fiber in Bilberry Ameliorates Pre-Obesity Events in Rats by Regulating Lipid Depot, Cecal Short-Chain Fatty Acid Formation and Microbiota Composition
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2019 (English)In: Nutrients, ISSN 2072-6643, E-ISSN 2072-6643, Vol. 11, no 6, article id 1350Article in journal (Refereed) Published
Abstract [en]

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

Place, publisher, year, edition, pages
MDPI, 2019
Keywords
adipose tissue, bilberry, butyrate-producing bacteria, gut microbiota, hepatic steatosis, lipid metabolism, obesity-resistant, fermentation, prebiotic dietary fiber, short-chain fatty acids
National Category
Nutrition and Dietetics
Identifiers
urn:nbn:se:uu:diva-390634 (URN)10.3390/nu11061350 (DOI)000474936700156 ()31208043 (PubMedID)
Funder
Swedish Research Council Formas, 222-2006-454Swedish Research CouncilSwedish Society for Medical Research (SSMF)
Available from: 2019-08-21 Created: 2019-08-21 Last updated: 2019-08-21Bibliographically approved
de Melo, M. L., Bertilsson, S., Amaral, J. H., Barbosa, P. M., Forsberg, B. R. & Sarmento, H. (2019). Flood pulse regulation of bacterioplankton community composition in an Amazonian floodplain lake. Freshwater Biology, 64(1), 108-120
Open this publication in new window or tab >>Flood pulse regulation of bacterioplankton community composition in an Amazonian floodplain lake
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2019 (English)In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 64, no 1, p. 108-120Article in journal (Refereed) Published
Abstract [en]

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

Keywords
16S rRNA gene, high-throughput sequencing, metacommunity, source–sink dynamics, spatiotemporal dynamics
National Category
Microbiology Ecology
Identifiers
urn:nbn:se:uu:diva-369341 (URN)10.1111/fwb.13198 (DOI)000453853500009 ()
Available from: 2018-12-12 Created: 2018-12-12 Last updated: 2019-01-15Bibliographically approved
Liu, H., Waldén, T., Ahl, D., Nyman, M., Bertilsson, S., Phillipson, M. & Holm, L. (2019). High-Fat Diet Enriched with Bilberry Modifies Colonic Mucus Dynamics and Restores Marked Alterations of Gut Microbiome in Rats. Molecular Nutrition & Food Research, 63(20), Article ID 1900117.
Open this publication in new window or tab >>High-Fat Diet Enriched with Bilberry Modifies Colonic Mucus Dynamics and Restores Marked Alterations of Gut Microbiome in Rats
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2019 (English)In: Molecular Nutrition & Food Research, ISSN 1613-4125, E-ISSN 1613-4133, Vol. 63, no 20, article id 1900117Article in journal (Refereed) Published
Abstract [en]

Scope Emerging evidence suggests that high-fat diet (HFD) is associated with gut microbiome dysbiosis and related disorders. Bilberry is a prebiotic food component with known health benefits. Herein, the dynamics of the colonic mucus layer and microbiome during HFD and bilberry supplementation are addressed. Methods and results The effects on colonic mucus thickness in vivo and gut microbiota composition (Illumina sequencing, quantitative real-time PCR) are investigated in young rats fed a low-fat diet or HFD with or without bilberries for 8 weeks (n = 8). HFD induced significant local colonic effects, despite no observed weight gain or systemic inflammation, as HFD causes epithelial upregulation of inducible nitric oxide synthase, which is counteracted by bilberry. The firmly adherent mucus layer becomes thicker and the mRNA levels of Muc2 and Tff3 are increased by HFD with or without bilberry. In parallel, HFD reduced the colonic abundance of mucolytic bacterial species Akkermansia muciniphila and Bacteroides spp. Finally, bilberry prevents HFD-induced microbiota dysbiosis, including expansion of pathobionts, for example, Enterobacteriaceae. Conclusion HFD expand firmly adherent mucus thickness and reduce mucus-foraging bacteria populations in the colon prior to obesity. Enriching HFD with bilberry protects against intestinal inflammation and marked microbiota encroachment.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
Akkermansia muciniphila, bilberries, gut microbiome, high-fat diet, mucus
National Category
Nutrition and Dietetics
Identifiers
urn:nbn:se:uu:diva-398866 (URN)10.1002/mnfr.201900117 (DOI)000480470800001 ()31336403 (PubMedID)
Funder
Swedish Research CouncilSwedish Research Council Formas, 2006-454Swedish Society for Medical Research (SSMF)Fredrik och Ingrid Thurings Stiftelse
Note

De två första författarna delar förstaförfattarskapet.

Available from: 2019-12-11 Created: 2019-12-11 Last updated: 2019-12-11Bibliographically approved
Jingying, X., Buck, M., Eklöf, K., Ahmed Osman, O., Schaefer, J. K., Bishop, K., . . . Bravo, A. G. (2019). Mercury methylating microbial communities of boreal forest soils. Scientific Reports, 9, Article ID 518.
Open this publication in new window or tab >>Mercury methylating microbial communities of boreal forest soils
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2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 518Article in journal (Refereed) Published
Abstract [en]

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

National Category
Forest Science
Research subject
Biology with specialization in Limnology
Identifiers
urn:nbn:se:uu:diva-346175 (URN)10.1038/s41598-018-37383-z (DOI)000456553400083 ()
Funder
Swedish Research Council, 2011-7192Swedish Research Council, 2012-3892Swedish Research Council, 2013-6978Swedish Energy Agency, 36155-1
Available from: 2018-03-15 Created: 2018-03-15 Last updated: 2019-02-18Bibliographically approved
Segura, J., Nilsson, M. B., Schleucher, J., Haei, M., Sparrman, T., Szekely, A. J., . . . Öquist, M. G. (2019). Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures. Soil Biology and Biochemistry, 135, 438-448
Open this publication in new window or tab >>Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures
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2019 (English)In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 135, p. 438-448Article in journal (Refereed) Published
Abstract [en]

Boreal peatlands are key high-latitude ecosystem types and act as a carbon (C) sink storing an estimated 25% of the world's soil C. These environments are currently seeing the most substantial changing climate, especially during the winter. CO2 emissions during the winter can correspond to 80% of the growing season's net CO2 assimilation. Yet, our conceptual understanding of the controls on microbial metabolic activity in peat soils at temperatures <= 0 degrees C is poor. We used stable isotope probing of peat samples and tracked the fate of C-13-glucose using C-13-NMR. We show that microorganisms in frozen boreal peat soils utilize monomeric C-substrates to sustain both catabolic and anabolic metabolism at temperatures down to -5 degrees C. The C-13-substrate was transformed into C-13-CO2, different metabolites, and incorporated into membrane phospholipid fatty acids. The 16S rRNA-based community analyses revealed the activity at -3 degrees C changes the composition of the bacterial cornmunity over relevant timescales. Below 0 degrees C, small temperature changes have strong effects on process rates and small differences in winter soil temperature may affect C dynamics of northern peatlands. Understanding biological processes at low and below zero temperatures are central for the overall functioning of these systems representing one of the world's major soil C pools.

Place, publisher, year, edition, pages
PERGAMON-ELSEVIER SCIENCE LTD, 2019
Keywords
Frozen peat soils, Microbial activity, Metabolism, C-13-NMR, DNA, Carbon cycling
National Category
Soil Science
Identifiers
urn:nbn:se:uu:diva-392577 (URN)10.1016/j.soilbio.2019.06.006 (DOI)000477689700051 ()
Funder
Swedish Research Council, 621-2011-4874Swedish Research Council Formas, 214-2013- 834Knut and Alice Wallenberg Foundation, 2011.0228The Kempe Foundations, JCK1107Carl Tryggers foundation , 13:536
Available from: 2019-09-09 Created: 2019-09-09 Last updated: 2019-09-09Bibliographically approved
Heinrich, K., Leslie, D. J., Morlock, M., Bertilsson, S. & Jonas, K. (2019). Molecular Basis and Ecological Relevance of Caulobacter Cell Filamentation in Freshwater Habitats. mBio, 10(4), Article ID e01557-19.
Open this publication in new window or tab >>Molecular Basis and Ecological Relevance of Caulobacter Cell Filamentation in Freshwater Habitats
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2019 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 4, article id e01557-19Article in journal (Refereed) Published
Abstract [en]

All living cells are characterized by certain cell shapes and sizes. Many bacteria can change these properties depending on the growth conditions. The underlying mechanisms and the ecological relevance of changing cell shape and size remain unclear in most cases. One bacterium that undergoes extensive shape-shifting in response to changing growth conditions is the freshwater bacterium Caulobacter crescentus. When incubated for an extended time in stationary phase, a subpopulation of C. crescentus forms viable filamentous cells with a helical shape. Here, we demonstrated that this stationary-phase-induced filamentation results from downregulation of most critical cell cycle regulators and a consequent block of DNA replication and cell division while cell growth and metabolism continue. Our data indicate that this response is triggered by a combination of three stresses caused by prolonged growth in complex medium, namely, the depletion of phosphate, alkaline pH, and an excess of ammonium. We found that these conditions are experienced in the summer months during algal blooms near the surface in freshwater lakes, a natural habitat of C. crescentus, suggesting that filamentous growth is a common response of C. crescentus to its environment. Finally, we demonstrate that when grown in a biofilm, the filamentous cells can reach beyond the surface of the biofilm and potentially access nutrients or release progeny. Altogether, our work highlights the ability of bacteria to alter their morphology and suggests how this behavior might enable adaptation to changing environments.

IMPORTANCE Many bacteria drastically change their cell size and morphology in response to changing environmental conditions. Here, we demonstrate that the freshwater bacterium Caulobacter crescentus and related species transform into filamentous cells in response to conditions that commonly occur in their natural habitat as a result of algal blooms during the warm summer months. These filamentous cells may be better able to scavenge nutrients when they grow in biofilms and to escape from protist predation during planktonic growth. Our findings suggest that seasonal changes and variations in the microbial composition of the natural habitat can have profound impact on the cell biology of individual organisms. Furthermore, our work highlights that bacteria exist in morphological and physiological states in nature that can strongly differ from those commonly studied in the laboratory.

Place, publisher, year, edition, pages
AMER SOC MICROBIOLOGY, 2019
Keywords
Caulobacter crescentus, biofilms, cell cycle, cell shape, environmental signals, freshwater habitats, stationary phase
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-397784 (URN)10.1128/mBio.01557-19 (DOI)000493912200004 ()31431551 (PubMedID)
Funder
Swedish Foundation for Strategic Research
Available from: 2019-11-29 Created: 2019-11-29 Last updated: 2019-11-29Bibliographically approved
Kennedy, B., Peura, S., Hammar, U., Vicenzi, S., Hedman, A., Almqvist, C., . . . Fall, T. (2019). Oral Microbiota Development in Early Childhood. Scientific Reports, 9, Article ID 19025.
Open this publication in new window or tab >>Oral Microbiota Development in Early Childhood
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2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 19025Article in journal (Refereed) Published
Abstract [en]

Early life determinants of the oral microbiota have not been thoroughly elucidated. We studied the association of birth and early childhood characteristics with oral microbiota composition using 16 S ribosomal RNA (rRNA) gene sequencing in a population-based Swedish cohort of 59 children sampled at 6, 12 and 24 months of age. Repeated-measurement regression models adjusted for potential confounders confirmed and expanded previous knowledge about the profound shift of oral microbiota composition in early life. These alterations included increased alpha diversity, decreased beta diversity and alteration of bacterial composition with changes in relative abundance of 14 of the 20 most common operational taxonomic units (OTUs). We also found that birth characteristics, breastfeeding and antibiotic use were associated with overall phyla distribution and/or with the relative abundance of specific OTUs. Further, we detected a novel link between morning salivary cortisol level, a physiological marker of neuroendocrine activity and stress, and overall phyla distribution as well as with decreased abundance of the most common OTU mapped to the Streptococcaceae family. In conclusion, a major part of the maturation of the oral microbiome occurs during the first two years of life, and this development may be influenced by early life circumstances.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2019
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-402239 (URN)10.1038/s41598-019-54702-0 (DOI)000503073900001 ()31836727 (PubMedID)
Funder
Swedish National Infrastructure for Computing (SNIC), SNIC sens2018616Swedish Research Council, 2015-03477Swedish Research Council, 2015-02434_3Swedish Research Council, 2018-02640Knut and Alice Wallenberg FoundationStockholm County CouncilSwedish Heart Lung FoundationSwedish Asthma and Allergy AssociationForte, Swedish Research Council for Health, Working Life and Welfare
Available from: 2020-01-16 Created: 2020-01-16 Last updated: 2020-01-22Bibliographically approved
Lopez-Fernandez, M., Broman, E., Simone, D., Bertilsson, S. & Dopson, M. (2019). Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters. mBio, 10(4), Article ID e01470-19.
Open this publication in new window or tab >>Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters
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2019 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 4, article id e01470-19Article in journal (Refereed) Published
Abstract [en]

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

Place, publisher, year, edition, pages
AMER SOC MICROBIOLOGY, 2019
Keywords
deep biosphere, groundwaters, metatranscriptomes, protein-coding RNA, rRNA
National Category
Microbiology Oceanography, Hydrology and Water Resources
Identifiers
urn:nbn:se:uu:diva-393530 (URN)10.1128/mBio.01470-19 (DOI)000481617000077 ()31409677 (PubMedID)
Funder
Swedish Research Council, 2018-04311Swedish Research Council, 2017-04422Swedish Research Council, 2014-4398Swedish Research Council
Available from: 2019-09-24 Created: 2019-09-24 Last updated: 2019-09-24Bibliographically approved
Richert, I., Yager, P. L., Dinasquet, J., Logares, R., Riemann, L., Wendeberg, A., . . . Scofield, D. (2019). Summer comes to the Southern Ocean: How phytoplankton shape bacterioplankton communities far into the deep dark sea. Ecosphere, 10(3), Article ID e02641.
Open this publication in new window or tab >>Summer comes to the Southern Ocean: How phytoplankton shape bacterioplankton communities far into the deep dark sea
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2019 (English)In: Ecosphere, ISSN 2150-8925, E-ISSN 2150-8925, Vol. 10, no 3, article id e02641Article in journal (Refereed) Published
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-382662 (URN)10.1002/ecs2.2641 (DOI)000463977000027 ()
Available from: 2019-03-12 Created: 2019-05-07 Last updated: 2019-05-07Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-4265-1835

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