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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
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
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
Krizsan, S. J., Mateos-Rivera, A., Bertilsson, S., Felton, A., Anttila, A., Ramin, M., . . . Huhtanen, P. (2018). An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods. Ecology and Evolution, 8, 4183-4196
Open this publication in new window or tab >>An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods
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2018 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, p. 4183-4196Article in journal (Refereed) Published
Abstract [en]

Evolutionary morphological and physiological differences between browsers and grazers contribute to species- specific digestion efficiency of food resources. Rumen microbial community structure of browsers is supposedly adapted to characteristic nutrient composition of the diet source. If this assumption is correct, domesticated ruminants, or grazers, are poor model animals for assessing the nutritional value of food consumed by browsing game species. In this study, typical spring and summer foods of the European moose (Alces alces) were combined with rumen fluid collected from both dairy cows (Bos taurus) and from moose, with the aim of comparing fer- mentation efficiency and microbial community composition. The nutritional value of the food resources was characterized by chemical analysis and advanced in vitro measurements. The study also addressed whether or not feed evaluation based on in vitro techniques with cattle rumen fluid as inoculum could be a practical alternative when evaluating the nutritional value of plants consumed by wild browsers. Our re- sults suggest that the fermentation characteristics of moose spring and summer food are partly host- specific and related to the contribution of the bacterial phyla Firmicutes and Bacteriodetes to the rumen microbial community. Host- specific adaptations of the ruminal microbial community structure could be explained from the evolutionary adaptations related to feeding habitats and morphophysiological differences be- tween browsers and grazers. However, the observed overall differences in microbial community structure could not be related to ruminal digestion parameters measured in vitro. The in vitro evaluation of digestion efficiency reveals that equal amounts of methane were produced across all feed samples regardless of whether the ruminal fluid was from moose or dairy cow. The results of this study suggested that the nutri- tional value of browsers’ spring and summer food can be predicted using rumen fluid from domesticated grazers as inoculum in in vitro assessments of extent of digestion when excluding samples of the white water lily root, but not of fermentation characteristics as indicated by the proportions of individual fermentation fatty acids to the total of volatile fatty acids.

Keywords
bacterial community composition, browser, digestion efficiency, feed evaluation, grazer, in vitro system, methane, microbiota
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-351133 (URN)10.1002/ece3.3920 (DOI)000430807200033 ()29721290 (PubMedID)
Funder
The Kempe Foundations
Available from: 2018-05-19 Created: 2018-05-19 Last updated: 2018-07-04Bibliographically approved
Garcia, S. L., Stevens, S. L., Crary, B., Martinez-Garcia, M., Stepanauskas, R., Woyke, T., . . . McMahon, K. D. (2018). Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. The ISME Journal, 12(3), 742-755
Open this publication in new window or tab >>Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
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2018 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, no 3, p. 742-755Article in journal (Refereed) Published
Abstract [en]

To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.

National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-350143 (URN)10.1038/s41396-017-0001-0 (DOI)000427226100010 ()29222442 (PubMedID)
Funder
Wenner-Gren FoundationsSwedish Research Council
Available from: 2018-05-04 Created: 2018-05-04 Last updated: 2018-05-28Bibliographically approved
Lopez-Fernandez, M., Åström, M., Bertilsson, S. & Dopson, M. (2018). Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers. Frontiers in Microbiology, 9, Article ID 2880.
Open this publication in new window or tab >>Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers
2018 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 2880Article in journal (Refereed) Published
Abstract [en]

The continental deep biosphere is suggested to contain a substantial fraction of the earth’s total biomass and microorganisms inhabiting this environment likely have a substantial impact on biogeochemical cycles. However, the deep microbial community is still largely unknown and can be influenced by parameters such as temperature, pressure, water residence times, and chemistry of the waters. In this study, 21 boreholes representing a range of deep continental groundwaters from the Äspö Hard Rock Laboratory were subjected to high-throughput 16S rRNA gene sequencing to characterize how the different water types influence the microbial communities. Geochemical parameters showed the stability of the waters and allowed their classification into three groups. These were (i) waters influenced by infiltration from the Baltic Sea with a “modern marine (MM)” signature, (ii) a “thoroughly mixed (TM)” water containing groundwaters of several origins, and (iii) deep “old saline (OS)” waters. Decreasing microbial cell numbers positively correlated with depth. In addition, there was a stronger positive correlation between increased cell numbers and dissolved organic carbon for the MM compared to the OS waters. This supported that the MM waters depend on organic carbon infiltration from the Baltic Sea while the ancient saline waters were fed by “geogases” such as carbon dioxide and hydrogen. The 16S rRNA gene relative abundance of the studied groundwaters revealed different microbial community compositions. Interestingly, the TM water showed the highest dissimilarity compared to the other two water types, potentially due to the several contrasting water types contributing to this groundwater. The main identified microbial phyla in the groundwaters were Gammaproteobacteria, unclassified sequences, Campylobacterota (formerly Epsilonproteobacteria), Patescibacteria, Deltaproteobacteria, and Alphaproteobacteria. Many of these taxa are suggested to mediate ferric iron and nitrate reduction, especially in the MM waters. This indicated that nitrate reduction may be a neglected but important process in the deep continental biosphere. In addition to the high number of unclassified sequences, almost 50% of the identified phyla were archaeal or bacterial candidate phyla. The percentage of unknown and candidate phyla increased with depth, pointing to the importance and necessity of further studies to characterize deep biosphere microbial populations.

Keywords
16S rRNA gene, amplicon sequencing, deep subsurfac, 16s rrna gene, amplicon sequencing, chemistry, deep subsurface, groundwaters, microbial diversity
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-369343 (URN)10.3389/fmicb.2018.02880 (DOI)000451406100001 ()30538690 (PubMedID)
Funder
Swedish Research Council, 2014-4398Swedish Research Council, 2012-3892Swedish Research Council, 2017-04422
Available from: 2018-12-12 Created: 2018-12-12 Last updated: 2019-03-19Bibliographically approved
Eklöf, K., Bishop, K., Bertilsson, S., Björn, E., Buck, M., Skyllberg, U., . . . Bravo, A. G. (2018). Formation of mercury methylation hotspots as a consequence of forestry operations. Science of the Total Environment, 613-614, 1069-1078
Open this publication in new window or tab >>Formation of mercury methylation hotspots as a consequence of forestry operations
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2018 (English)In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 613-614, p. 1069-1078Article in journal (Refereed) Published
Abstract [en]

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

Keywords
Methylmercury, Microbial communities, Soil disturbance, Stump harvest
National Category
Earth and Related Environmental Sciences Microbiology
Identifiers
urn:nbn:se:uu:diva-334877 (URN)10.1016/j.scitotenv.2017.09.151 (DOI)000414160500109 ()28950669 (PubMedID)
Funder
Swedish Research Council, 2011-7192, 2012-3892, 2013-6978Swedish Energy Agency, 36155-1
Available from: 2017-11-29 Created: 2017-11-29 Last updated: 2018-12-11Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-4265-1835

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