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Job opportunities

The MicroArctic network will train 15 Early Stage Researchers. Information about individual ESR projects can be found below.

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Please note that all positions have now been filled and applications are no longer accepted.

ESR 1: Seasonal nutrient pulses to Arctic ecosystems (WP1)

Objectives:
1. Through chemical analysis of major ions by ion chromatography, Si (as a tracer of water residence time); nutrients (including DON and DOP) and DOC by flow injection analyser and TC/TN analysis, we will determine seasonal changes in nutrient budgets of snow, ice and soil; 2. Through measurements of community respiration, photosynthesis and bacterial production, we will determine seasonal changes in C fluxes of snow, ice and soil; 3. To experimentally demonstrate the impact of external N and C inputs have on microbial growth in the warming Arctic using analyses of carbohydrates and stable isotopes. Expected Results: detailed understanding of (i) the contribution of snow to carbon and nitrogen cycling in Arctic terrestrial habitats; (ii) the downstream contribution of nutrients from glaciers on Arctic terrestrial habitats and (iii) predictions of the impact of increased industrial inputs of nutrients to changes in carbon and nitrogen cycling of Arctic habitats.

Planned secondment(s): UNIS, 4 months, through Year 1 of the project for fieldwork and training and ENOVEO, 2 months, for mesocosm experiments in the middle of Year 2. This links to ESR12 in WP3.
Host Institute: University of Bristol

ESR 2: Population dynamics and functions of terrestrial Arctic microbial communities (WP1)
Objectives:
1. To determine seasonal changes in microbial communities of snow, ice and soil by using next-generation sequencing and community profiling techniques; 2. To determine the function and activity of microbial communities of snow, ice and soil through metagenomic and metatranscriptomic approaches as well as quantitative PCR of functional genes; 3. To determine the contribution of microorganisms to biogeochemical cycling in Arctic ecosystems using meso- and microcosm approaches. Expected Results: detailed understanding of (i) the contribution of snow microorganisms to biogeochemical cycling in Arctic terrestrial habitats; (ii) the identification of key players and genes involved in regulating biogeochemical cycling (iii) baseline information and process rates to improve climate model predictability.

Planned secondment(s): MBI, 3 months for bioinformatics in year 2 for pipeline development and UoB, 1 month during Year 3 for joint bioinformatics approaches to mine specific genes. This links to ESR8 in WP2 and ESR14 in WP4.
Host Institute: Ecole Centrale de Lyon

ESR 3: Microbial biogeography and colonization of terrestrial Arctic ecosystems (WP1)
Objectives:
1. Obtain large scale microbial biodiversity data from across a range of Arctic soils and combine it with in situ productivity measurements through high throughput DNA sequencing, mapping (ArcGIS) and radioisotope incorporation rates; 2. evaluate the presence and movement of microorganisms in the atmosphere over the Arctic using airsamplers and microbial counts with flow cytometry; 3. measure the extent of transfer between different environment types (incl. snow, ice, soil, freshwater, marine) as transition zones are potentially of fundamental importance for colonization and establishment in new environments. Expected Results: (i) A dynamic map of the distribution and transfer of microbial biodiversity across the Arctic, (ii) an understanding of the role of aerobiological transfer of microorganisms across the Arctic region, and (iii) identify source and sink populations for a better understanding of the need to establish reserves or specially protected areas.

Planned secondment(s): Brill, 2 months during Year 1 for sterile sampling techniques, linking with ESR15 in WP4. UoI, 2 months in year 2 for radioisotope work. This links to ESR4 in WP1.
Host Institute: University of Northumbria

ESR 4: Airborne Inoculation Sources of Microbial Communities on Glacial and Terrestrial Environments (WP1)
Objectives:
1. Understanding the atmosphere as living space for microbial communities by investigating the degree of activity by radioactive tracing methods; 2. quantification of cell load and nutrient input originating from airborne organisms by usage of various types of airsamplers for collection, flow cytometry for quantification, molecular biology for sequencing and chemical analysis of cloud water; 3. analysing potential degradation capabilities of contaminants by airborne organisms; Expected Results: (i) understanding the role of the atmosphere not simply as transport corridor for microbes but also as habitat, (ii) solid results of organic carbon deriving from atmospheric cell deposition, (iii) positive proof of active airborne organisms and biodiversity to metabolize contaminants which are transported long- and short term.

Planned secondment(s): UoAb, 3 months, for molecular biology in Year 2, linking to ESR13 in WP4, UoN, 3 months in Year 3, for metagenomic libraries, linking to ESR3 in WP1
Host institute: University of Innsbruck

ESR 5: The role of methanogenic archaea within the carbon cycle in a warming Arctic (WP2)
Objectives:
1. Characterizing the diversity of archaeal communities involved in the carbon cycle and their reaction to changing environmental conditions (present and past) by next generation sequencing; 2. Analysing the functional repertoire of the microbial communities involved in the anaerobic carbon degradation by using quantitative PCR for functional genes and metagenome analyses; 3. Identifying microbial key processes regulating the carbon decomposition and trace gas fluxes from permafrost environments by stable isotope probing and metatranscriptome analyses. Expected Results: (i) understanding the response of microbial communities (diversity and function) to global warming in the Arctic, (ii) identification of microbial key-players within the carbon cycle, (iii) biogeography of methanogenic archaea for Arctic environments.

Planned secondment(s): IoF, 1 month, through Year 1 of the project for fieldwork and training, linking to partner organization 20; and UoLj, 3 months in Year 3, for fungal diversity analyses, linking to ESR9 in WP3.
Host institute: German Research Centre for Geosciences (GFZ)

ESR 6: Weathering and its role in carbon and nutrient cycling in Arctic settings (WP2)

Objectives:
1. Quantify the depth- and age-dependent variations in bulk elemental compositions (digestion and mass spectrometric elemental analyses) and μ-scale mineralogical characteristics (X-ray diffraction and high resolution transmission electron microscopy, spectroscopy and nanodiffraction); 2. derive a budget for carbon (C) and nutrients (P, N and Fe) in the soils via quantitatively assessing their speciation and isotopic signatures; Total N, total, inorganic, organic and black C as well as their respective isotopic (N an C) signatures will be analyzed by mass spectrometry after specific sequential treatments; P and Fe speciation will be analyzed by flow injection and mass spectrometry after sequential extractions; 3. develop a geochemical model to evaluate the bulk and μ-scale framework changes in geochemical and mineralogical parameters linking C and nutrients to glacial and permafrost soil weathering processes Expected Results: (i) a model for soil formation processed in Arctic environments. This model will link high-resolution mineralogical, geochemical and microbiological as well as micro-spectroscopic observations to bulk analyses and gain a better understanding about how nutrient cycling and specifically C cycling is affected by glacier retreat or thawing of permafrost sites.

Planned secondment(s): WSL between 3 months in Year 2 for training linked to soil properties, linking to ESR7 in WP2 and UoB, 2 months for training in biogeochemical and microbial processes linking to ESR1 in WP1
Host institute: German Research Centre for Geosciences (GFZ)

ESR 7: E ffects of warming on the soil microbiome in Arctic soils (WP2)

Objectives:
1. Assess the soil microbiome (bacteria, archaea, fungi) and their reactions to warming by Illumina sequencing of phylogenetic marker genes; 2. identify microbial key-players in the N-cycling processes by using quantitative PCR and Illumina sequencing of functional N cycling genes; 3. analyse ecosystem distribution patterns of these microbial key players in Arctic environments by indicator species and network analysis. Expected Results: (i) a better understanding of the response of the soil microbiome to global warming in the Arctic, (ii) distribution patterns of bacterial and fungal communities in Arctic soils, (iii) identification of microbial key-players in the N-cycling processes.

Planned secondment(s): UoI, 1 month at the end of Year 1 for training in microbial activity analyses linking to ESR4 in WP1; MBI, 2 months in the beginning of Year 2 for bioinformatics linking with ESR8.
Host institute: Swiss Federal Research Institute

ESR 8: In vitro testing of climate change model predictions using microcosms and quantitative analyses of genes involved in geochemical nutrient cycling (WP3)

Objectives:
1. To determine the optimal procedure for sequence error free reverse transcriptase based conversion of total RNA into cDNA; 2. to determine the fastest protocol for BlastN based annotation of rRNA genes in mixed populations of bacteria, fungi, protozoa and virus; 3. to develop a standardized pipeline for full RNA no PCR based analysis of the microbial populations in environmental samples. Expected Results: (i) combined approach to analyse microbial community structure using a no-PCR biased approach. Planned secondment(s): ECL, 3 months during Years 2 and 3 for calibrating bioinformatics procedure, linking to ESR2 in WP1. UoB, 2 months during Year 3 for additional bioinformatics calibration, linking to ESR15 in WP4.
Host institute: mBioInform

ESR 9: Microorganisms from glacial ice: diversity, stress response, and interactions (WP 3)
Objectives:
1. To assess fungal diversity along the glaciers ice core, also identifying pathogenic fungi;
2. To find new antimicrobial compounds from glacial fungal/bacterial strains;
3. To determine the multidrug resistance and virulence factors /mechanisms in fungi from glacial ice;
4. To determine fungal transcriptomic response and survival on freezing/thawing.
Expected Results: Increased knowledge on (i) fungal diversity in glacial ice with the focus on potentially pathogenic fungi and on their possible spreading from the melting glaciers into the surrounding environment and futher; (ii) interactions (both synergistic and antagonistic) between microorganisms inhabiting glacial ice (synthesis of antimicrobial compounds, drug resistance, and virulence factors); (iii) how do microorganisms response to low temperatures and low nutrients in these environments.

Planned secondment(s): UoB, 1 month during Year 1 for geochemical analyses, linking to ESR1 in WP1; Brill, 2 months during Year 2 for comparison of data on pathogens, linking with ESR13 in WP4
Host institute: University of Llubljana

ESR 10: Glacier metatranscriptomic thermal response and cold-adaptation mechanisms of pyrimidine biosynthesis in psychrophilic methanogens (WP3)
Objectives:
1. To determine the active microbiota response to their habitat thermal changes by metatranscriptome sequencing and reconstitution of different Arctic glacier microbioms subjected to increasing temperatures (1°C to 30°C); 2. To investigate the temperature response of pyrimidine biosynthesis gene expression in the psychrophilic methanogen M. burtonii by RT-PCR after incubation at increasing temperatures; 3. to identify cold-adaptation mechanisms of DNA synthesis in psychrophilic methanogens by cloning and characterization of key enzymes of pyrimidine biosynthesis from M. burtonii: thermostability, activity, regulation, protein interactions, and molecular modelling, and X-ray crystallography of individual and interacting enzymes. Expected Results: (i) Functional genomics shift of ice-embedded microbioms in response to Arctic glaciers melting; (ii) advance understanding of cold protection strategies of DNA synthesis in methanogens from Polar environments; (iii) structure-function characterization of pyrimidine biosynthetic enzymes from M. burtonii for understanding the metabolism response of cold-adapted methanogens to environmental changes.

Planned secondment(s): GFZ, 2 months, Years 1 and 2, for X-ray crystallography, linking to ESR6 in WP2; WSL, 2 months, Year 1, training in metagenomic Illumina sequencing, linking to ESR7 in WP2.
Host institute: Institute of Biology Bucharest

ESR 11: Composition, activity and fate of cyanobacterial and betaproteobacterial populations in natural and simulated habitat types in the warming Arctic (WP3)

Objectives:
1. To determine microbiota composition in palsa mires and oroboreal scrubs in three sites in Iceland, Greenland and Siberia by next generation sequencing; 2. to assess viability and activity of selected taxa within these habitats through metaproteomics; 3. to monitor by quantitative PCR the fate and relative abundance of selected bacterial taxa in temperature-controlled mire and scrub mesocosms. Expected Results: (i) identification of microbes characteristic for Arctic palsa mires and oroboreal scrubs, (ii) prediction of the fate of key microbes in different Arctic habitat types due to warming, (iii) identification of bacterial taxa that may be under threat by warming of the studied habitat types.

Planned secondment(s): IBB, 3 months in Year 2 for protein profiling linking with ESR10 and NHM, 2 months in Year 3 for cyanobacteria, linking with Partner Organisation 18
Host institute: University of Akureyri

ESR 12: In vitro testing of climate change model predictions using microcosms and quantitative analyses of genes involved in geochemical nutrient cycling (WP3)
Objectives:
1. Determine which geochemical cycle genes are the most sensitive to simulated climate change by qPCR and metagenomic NGS approach; 2. Determine changes in these critical gene expressions during simulated climate change in laboratory tests by RT-qPCR and metatranscriptomic NGS approach; 3. Determine the potential change in the contribution of microorganisms to biogeochemical cycling in Arctic ecosystems by metagenic and metagenomic NGS comparison. Expected Results: Deliverables will be a detailed understanding of (i) the potential perturbation of the biogeochemical cycling in Arctic terrestrial habitats, (ii) the identification of key genes involved in regulating biogeochemical cycling and (iii) identification of key microorganisms involved in regulating the biogeochemical cycling.

Planned secondment(s): UoB, 3 months during Years 1 and 2 for joint microcosm experiments and field work linking with ESR1 in WP1; GFZ, 1 month in Year 2 for work on soil permafrost material, linking to ESR5 in WP2.
Host institute: ENOVEO

ESR 13: Glacier Ecosystem Services: Investigating the biotechnology potential of the Arctic cryospheric biome (WP4)


Objectives:
1. Investigate the functional diversity of cryospheric microorganisms for utility in economic and environmental services; 2. to generate deep-sequenced metagenomes, both directly sequenced from the environment, and metagenomic gene pools enriched for antimicrobial activity from clone libraries; 3. employ functional metagenomics to identify genes and enzymes in uncultured microbes from a range of arctic cryopsheric field sites that exhibit key functional capabilities for drug discovery. Expected Results: Identification of (i) genes and (ii) enzymes in uncultured microbes from a range of arctic cryospheric field sites that exhibit key functional capabilities for drug discovery

Planned secondment(s): UoAk, 1 month in Year 1 for biotechnology discussions and fieldwork, linking to ESR11 at WP3. DEX, 3 months in Year 2 to develop practical techniques of screening natural samples for bioactivity against model pathogens and develop understanding of commercialisation and up scaling biotechnology linking to Partner Organisation 17.
Host institute: University of Aberystwyth

ESR 14: Developing bioinformatics tools for the discovery of novel metabolic genes (WP4)
Objectives:
1. Perform de novo assembly of existing and newly acquired environmental shotgun DNA sequence datasets to organise short reads into contigs containing whole genes, gene clusters and partial genomes; 2. Locate coding regions in assemblies, both by BLAST to known genes and by ab inito prediction and highlight genetic variants in genes which are non-synonymous (result in amino acid change) and/or fall within known functional domains; 3. Search for novel juxtapositions of protein domains in assembled gene clusters as areas with possible novel anabolic/catabolic pathway coding potential; 4. Validate the above tools in silico by testing their ability to predict known unique metabolic abilities in existing datasets. Expected Results: A suite of publically available tools to process raw shotgun sequence data into a database of candidate novel metabolic genes and pathways.

Planned secondment(s): UoAk, 2 months in Year 1 for biotechnology discussions and fieldwork, linking to ESR11 at WP3. ENO, 2 months in Year 3 for understanding of commercialisation and up scaling biotechnology linking with ESR12 in WP3.
Host institute: University of Bristol

ESR 15: Organisms, associations and bio-mining (WP3)
Objectives:
1. Perform a quantitative and qualitative assessment using selective culturimg of the abundance and diversity of potential pathogenic bacteria in soils/aquifers with special regards to changing environmental conditions (Arctic warming/ thawing); 2. use lab based experiments to understanding of the identified bacterial pathogens response and tolerance to warming; 3. screen anti-microbial compounds against the isolated bacteria, fungi (from other groups) and if applicable bacteriophages and viruses by MIC-testing according to DIN 58940, bactericidal, yeasticidal and fungicidal efficacy testing based on EN 13727, EN 13624. Expected Results: (i) Understanding the activity and response of pathogenic bacteria (diversity and function) to global warming in the arctic region including biogeography of pathogenic bacteria. (ii) Identification of risk factors for humans, animals and environment the future when pathogenic organisms are activated through the artic warming. (iii) Identification of new anti-microbial substances for use as biocides, antibiotics or anti-fungal substances.

Planned secondment(s): UoLj with 3 secondments of 1 month each over the 36 months project duration for exchange of data and strains for anti-microbial screening and microbiological diversity linking to ESR9 in WP3. UoAb, 2 months in year 2 for molecular characterization and identification of isolated pathogenic bacteria linking with ESR13.
Host institute: Brill and University Potsdam

 

Work packages

The Arctic plays a key role in Earth's climate system and is an geographical area of growing strategic importance for European policy. In this ITN, we will train the next generation of Arctic microbiology and biogeochemistry experts who, through their unique understanding of the fast changing Arctic environment and the factors that impact ecosystem and organism response to the warming Arctic, will be able to respond to the need for governance and leadership in various aspects related to public, policy and commercial interests.

The training and research programme of MicroArctic is made up of seven interlinked Work Packages (WP). WP1 to WP4 are research work packages at the cutting-edge of Arctic science and these are linked through three overarching WPs (WP5-7) associated with the training and management of the ITN. WP1 will deliver information about the role and influence of external inputs of nutrients that drive biogeochemical processes through the investigation of annual variation in microbial activity and biogeochemical processes in terrestrial Arctic ecosystems. For the first time, biogeochemical winter processes and their impact on the summer melting microbial dynamics will also be considered. WP2 will explore ecosystem responses to these inputs in the already changing Arctic. The effect of time and season and the warming of the Arctic (melting glaciers and thawing permafrost) on ecosystem functioning and Arctic natural resources, such as soil development, evolutionary ecology and fast adaptation, over time scales of hundreds of years will be quantified through geochemical analyses and next generation multi-omics approaches. Complementing WP2, WP3 will focus on organism response and adaptation (e.g., key fungal species, psychrophiles, methanogens and cyanobacteria) using a range on biochemical, molecular, experimental and culturing approaches. These first three WP will be developed interactively in order to provide synergistic scientific evaluations of the potential effects of managing Arctic warming during Horizon 2020 and beyond. Addressing specific societal issues, such as agricultural practices, colonisation by pathogenic organisms and biotechnological exploitation of Arctic ecosystems, will be the focus of WP4, which will link the research underpinning the first three WP's with local community knowledge and practices. WP4 will also provide, for the first time, information on policy and economic aspects related to the commercial exploitation of microorganisms in the Arctic.

Training on all aspects of research WP1- 3 will give MicroArctic fellows much needed knowledge in state-of-the-are skills to better grasp pressing social, policy and economic issues. These latter themes will be further reinforced through the projects in WP4, which will focus on the relationships between societal needs and fundamental science. Interactions between these four complementary WPs will be achieved in part through cross-sectoral secondments that will also transcend WP boundaries. Annual meetings between the various teams and all Early Stage Researchers (ESRs) will fully explore possible interactions at each collaborative partner scale and target discussions to lead to common crossdisciplinary and cross-team publications that connect the different activities. To achieve this vision, MicroArctic brought together interdisciplinary experts from across Europe into a network of 21 Institutions from 12 countries. MicroArctic encompasses teams with outstanding track records in microbial ecology, biogeochemistry, environmental mineralogy, molecular biology, pathogenic microbes and social sciences. Furthermore, non-academic partners providing services in bioinformatics, bio-sensing, bio-prospecting, biomining and understanding of pathogens boost the inter-sectoral training opportunities for the network's ESRs and thus link the next generation of Arctic microbiologists and biogeochemists with Europe's market needs. This will result in substantial synergy and provide an exciting research and training environment for all ESRs. The research goals of MicroArctic will be implemented by managerial WPs (WP0 and 5). These will deal with recruitment following best practice based on knowhow of network members with extensive previous experience in running EU projects (WP0) and also provide the framework for overall management, functioning and communication within the network and with the European Union (WP5). Finally, WP 6 and 7 will ensure the coordinated delivery of the overall training (WP6) and result dissemination programme (WP7) of MicroArctic.

 

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