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Eiler, Alexander
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Publications (10 of 51) Show all publications
Garcia, S. L., Buck, M., Hamilton, J. J., Wurzbacher, C., Grossart, H.-P., McMahon, K. D. & Eiler, A. (2018). Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria. MSPHERE, 3(3), Article ID e00202-18.
Open this publication in new window or tab >>Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria
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2018 (English)In: MSPHERE, ISSN 2379-5042, Vol. 3, no 3, article id e00202-18Article in journal (Refereed) Published
Abstract [en]

Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.

Place, publisher, year, edition, pages
AMER SOC MICROBIOLOGY, 2018
Keywords
community, interactions, metagenomics, microbial ecology, mixed cultures, promiscuous
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:uu:diva-360993 (URN)10.1128/mSphere.00202-18 (DOI)000437234900021 ()29848762 (PubMedID)
Funder
Swedish Research Council, 2012-4592The Royal Swedish Academy of Sciences, BS2017-0044
Available from: 2018-09-26 Created: 2018-09-26 Last updated: 2018-09-26Bibliographically approved
Peura, S., Buck, M., Aalto, S. L., Morales, S. E., Nykanen, H. & Eiler, A. (2018). Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake. mBio, 9(4), Article ID e00916-18.
Open this publication in new window or tab >>Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake
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2018 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 9, no 4, article id e00916-18Article in journal (Refereed) Published
Abstract [en]

Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate changeassociated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community. IMPORTANCE Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.

Place, publisher, year, edition, pages
AMER SOC MICROBIOLOGY, 2018
Keywords
chemoautotrophy, greenhouse gas emissions, iron oxidizers, metagenomics, redox gradient
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-364476 (URN)10.1128/mBio.00916-18 (DOI)000443884300017 ()30108167 (PubMedID)
Funder
Swedish Research Council, 2012-4592Swedish Foundation for Strategic Research , ICA10-0015Carl Tryggers foundation
Available from: 2018-10-31 Created: 2018-10-31 Last updated: 2018-10-31Bibliographically approved
Corcoll, N., Osterlund, T., Sinclair, L., Eiler, A., Kristiansson, E., Backhaus, T. & Eriksson, K. M. (2017). Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing. FEMS Microbiology Letters, 364(14), Article ID fnx139.
Open this publication in new window or tab >>Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing
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2017 (English)In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 364, no 14, article id fnx139Article in journal (Refereed) Published
Abstract [en]

High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterisation of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol (R) Reagent (PlantDNAzol) and the FastDNA (R) SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77-130 mu g g wet wt(-1)). Lower amounts of DNA were obtained (<37 mu g g wet wt(-1)) with the Power Plant (R) Pro DNA Isolation Kit (PowerPlant) and the Power Biofilm (R) DNA Isolation Kit (PowerBiofilm) methods, but integrity and purity of the extracted DNA were higher. Results from 16S rRNA amplicon sequencing demonstrate that the choice of a DNA extraction method significantly influences the bacterial community profiles generated. A higher number of bacterial OTUs were detected when DNA was extracted with the PowerBiofilm and the PlantDNAzol methods. Overall, this study demonstrates the potential bias in metagenomic diversity estimates associated with different DNA extraction methods.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
Keywords
DNA, extraction methods, bacteria, 16S amplicon sequencing, biofilms, metagenomics
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-335678 (URN)10.1093/femsle/fnx139 (DOI)000410348600002 ()
Funder
Swedish Research Council Formas, 2011-1733Swedish Research Council Formas, 2015-1464
Available from: 2017-12-20 Created: 2017-12-20 Last updated: 2017-12-20Bibliographically approved
Juottonen, H., Eiler, A., Biasi, C., Tuittila, E.-S., Yrjälä, K. & Fritzec, H. (2017). Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios. Applied and Environmental Microbiology, 83(4), Article ID e02533-16.
Open this publication in new window or tab >>Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios
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2017 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 83, no 4, article id e02533-16Article in journal (Refereed) Published
Abstract [en]

Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [C-13] cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2. The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4. RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria. The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia. Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands. IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.

Keywords
anaerobic degradation, greenhouse gas, methane, microbial communities, peat, stable-isotope probing, wetland
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-317592 (URN)10.1128/AEM.02533-16 (DOI)000393482200005 ()
Funder
Carl Tryggers foundation
Available from: 2017-03-22 Created: 2017-03-22 Last updated: 2017-11-29Bibliographically approved
Grubisic, L. M., Bertilsson, S., Eiler, A., Heinrich, F., Brutemark, A., Alonso-Sáez, L., . . . Beier, S. (2017). Lake bacterioplankton dynamics over diurnal timescales. Freshwater Biology, 62(1), 191-204
Open this publication in new window or tab >>Lake bacterioplankton dynamics over diurnal timescales
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2017 (English)In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 62, no 1, p. 191-204Article in journal (Refereed) Published
Abstract [en]

1. Planktonic bacterial community dynamics over short timescales can be of great importance for food webs and ecosystem functioning but are rarely described when microbial community and composition are assessed. To study the significance of such dynamics we sampled the surface water at the deepest point of a mesotrophic lake (Lake Erken, Sweden) every third hour over two days. 2. By combining 454 pyrosequencing of 16S rRNA genes with bromodeoxyuridine immunocapturing of DNA, replicating populations were identified and compared to the community retrieved from total DNA samples. This comparison revealed a significant difference between the actively replicating and total community. 3. The high-frequency diurnal sampling was compared to a year-long survey conducted in the same lake in order to compare the diurnal and seasonal variation in bacterioplankton community composition. At the diurnal-scale, the variation was significantly higher in the replicating than in the total community. However, variation in both active and total diurnal community was significantly lower than the variation in the seasonal total community. 4. Our analysis revealed pronounced short-term dynamics of individual bacterial populations uncoupled from the diurnal light cycle. For example, the proliferating fraction of the most abundant bacterial tribe (LD12) followed a cyclic pattern that covaried with viral abundance. This implies that environmental factors other than light may act as important drivers of microbial community composition, at least in mesotrophic Lake Erken.

Keywords
community, microbes, molecular, pelagic, population
National Category
Ecology Microbiology
Identifiers
urn:nbn:se:uu:diva-313513 (URN)10.1111/fwb.12861 (DOI)000390146000016 ()
Funder
Swedish Research Council Formas
Available from: 2017-02-07 Created: 2017-01-20 Last updated: 2017-11-29Bibliographically approved
Hubalek, V., Buck, M., Tan, B., Foght, J., Wendeberg, A., Berry, D., . . . Eiler, A. (2017). Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions. mSystems, 2(5), Article ID e00038-17.
Open this publication in new window or tab >>Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions
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2017 (English)In: mSystems, E-ISSN 2379-5077, Vol. 2, no 5, article id e00038-17Article in journal (Refereed) Published
Abstract [en]

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

Keywords
Black Queen hypothesis, metagenomics, petroleum, syntrophy M
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-339039 (URN)10.1128/mSystems.00038-17 (DOI)000414004100006 ()
Funder
Swedish Research Council, 2012-4592; 2012-3892Swedish Foundation for Strategic Research , ICA010-015Swedish Research Council Formas, 2012-986Swedish National Infrastructure for Computing (SNIC), b2013274; b2011032
Available from: 2018-01-16 Created: 2018-01-16 Last updated: 2018-02-01Bibliographically approved
Ricão Canelhas, M., Eiler, A. & Bertilsson, S. (2016). Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?. FEMS Microbiology Ecology, 92(2), Article ID UNSP fiw005.
Open this publication in new window or tab >>Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?
2016 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 92, no 2, article id UNSP fiw005Article in journal (Refereed) Published
Abstract [en]

A wide range of carbon compounds sustain bacterial activity and growth in freshwater ecosystems and the amount and quality of these substrates influence bacterial diversity and metabolic function. Biologically labile low-molecular-weight compounds, such as dissolved free amino acids, are particularly important substrates and can fuel as much as 20% of the total heterotrophic production. In this study, we show that extensive laboratory incubations with variable amino acids as substrates caused only minimal differences in bacterial growth rate, growth yield, quantitative amino acid usage, community composition and diversity. This was in marked contrast to incubations under dark or light regimes, where significant responses were observed in bacterial community composition and with higher diversity in the dark incubations. While a few individual taxa still responded to amendment with specific amino acids, our results suggest that compositional shifts in the specific supply of amino acids and possibly also other labile organic substrates have a minor impact on heterotrophic bacterioplankton communities, at least in nutrient rich lakes and compared to other prevailing environmental factors.

Keywords
freshwater bacteria; amino acid substrates; light regime; community composition; substrate specialization
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-275179 (URN)10.1093/femsec/fiw005 (DOI)000371249600019 ()
Funder
Swedish Research CouncilSwedish Research Council Formas
Available from: 2016-02-01 Created: 2016-02-01 Last updated: 2017-11-30Bibliographically approved
Hubalek, V., Wu, X., Eiler, A., Buck, M., Heim, C., Dopson, M., . . . Ionescu, D. (2016). Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield. The ISME Journal, 10(10), 2447-2458
Open this publication in new window or tab >>Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield
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2016 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 10, p. 2447-2458Article in journal (Refereed) Published
Abstract [en]

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

National Category
Ecology Microbiology Oceanography, Hydrology and Water Resources
Identifiers
urn:nbn:se:uu:diva-294186 (URN)10.1038/ismej.2016.36 (DOI)000387035400009 ()
Funder
Swedish Research Council, 621-2014-4398 2012-3892The Crafoord Foundation, 20130557
Note

Supplementary information available for this article at http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej201636s1.html

Available from: 2016-05-18 Created: 2016-05-18 Last updated: 2018-01-10Bibliographically approved
Langenheder, S., Comte, J., Zha, Y., Samad, M. S., Sinclair, L., Eiler, A. & Lindström, E. S. (2016). Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin. Environmental Microbiology Reports, 8(4), 479-485
Open this publication in new window or tab >>Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin
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2016 (English)In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 8, no 4, p. 479-485Article in journal (Refereed) Published
Abstract [en]

Some bacteria can be preserved over time in deep sediments where they persist either in dormant or slow-growing vegetative stages. Here, we hypothesized that such cells can be revived when exposed to environmental conditions similar to those before they were buried in the sediments. To test this hypothesis, we collected bacteria from sediment samples of different ages (140–8500 calibrated years before present, cal BP) from three lakes that differed in the timing of their physical isolation from the Baltic Sea following postglacial uplift. After these bacterial communities were grown in sterile water from the Baltic Sea, we determined the proportion of 16S rRNA sequence reads associated with marine habitats by extracting the environment descriptive terms of homologous sequences retrieved from public databases. We found that the proportion of reads associated with marine descriptive term was significantly higher in cultures inoculated with sediment layers formed under Baltic conditions and where salinities were expected to be similar to current levels. Moreover, a similar pattern was found in the original sediment layers. Our study, therefore, suggests that remnants of marine bacterial communities can be preserved in sediments over thousands of years and can be revived from deep sediments in lakes of marine origin.

National Category
Ecology Microbiology
Research subject
Biology with specialization in Limnology; Biology with specialization in Microbiology
Identifiers
urn:nbn:se:uu:diva-295751 (URN)10.1111/1758-2229.12392 (DOI)000379938900007 ()26929161 (PubMedID)
Funder
Swedish Research Council, 2009-5172Wenner-Gren FoundationsSwedish Institute of Computer Science, SICS, b2011032
Available from: 2016-06-09 Created: 2016-06-09 Last updated: 2017-11-30Bibliographically approved
Sinclair, L., Ijaz, U. Z., Jensen, L. J., Coolen, M. J. L., Gubry-Rangin, C., Chronakova, A., . . . Pafilis, E. (2016). Seqenv: linking sequences to environments through text mining. PeerJ, 4, Article ID e2690.
Open this publication in new window or tab >>Seqenv: linking sequences to environments through text mining
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2016 (English)In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e2690Article in journal (Refereed) Published
Abstract [en]

Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the "nt" nucleotide database provided by NCBI and, out of every hit, extracts if it is available the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, n turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and s of microbial biogeography.

Keywords
Bioinformatics, Ecology, Microbiology, Genomics, Sequence analysis, Text processing, Statistics, Pipeline, Open source software
National Category
Bioinformatics and Systems Biology Computer Sciences
Identifiers
urn:nbn:se:uu:diva-313528 (URN)10.7717/peerj.2690 (DOI)000390057600002 ()
Funder
Swedish Foundation for Strategic Research , ICA10-0015NERC - the Natural Environment Research Council, NE/L011956/1Novo Nordisk, NNF14CC0001EU, FP7, Seventh Framework Programme, 264089
Available from: 2017-02-02 Created: 2017-01-20 Last updated: 2018-01-13Bibliographically approved
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