The MicroArctic Network
Congratulations to our first PhD students!
On Friday, October 11th, ESR Lucie Malard successfully defended her PhD at Northumbria University in the U.K. Lucie is the first of the MicroArctic ESRs to complete her doctorate degree. Congratulations Lucie!
Next, on October 24th, ESR Muhammad Zohaib Anwar successfully defended his PhD at Aarhus University. Congratulations Zohaib!
Another successful PhD defence!
Congratulations to Antonio Mondini on passing his viva on December 6th with the highest mark.
Final network meeting
The final MicroArctic network event took place in Lyon, France from May 19-24, 2019. This event focussed on career opportunities for ESRs, lectures on bioprospecting and political ecology as well as production of an outreach video. A schedule for the event is available here.
To see recent publications by MicroArctic ESRs, please visit our publications page.
Special issue of Frontiers in Microbiology!
Now open for manuscript submissions. For more information: https://www.frontiersin.org/research-topics/11477/polar-and-alpine-microbiological-and-biogeochemical-processes-in-the-warming-world
To see what MicroArctic ESRs have been doing since the start of their fellowships, please visit our progress report pages
Mid term review
The MicroArctic mid-term review took place in Austria from April 19-24, 2018. An agenda for the mid-term review and subsequent training course can be found here.
Third network event: Bioinformatics
MicroArctic ESRs received hands on training in Bioinformatics through a course offered by MicroArctic beneficiary, mBioinform in Copenhagen. The course took place from June 7-11, 2017.
Second network event
The second MicroArctic event took place in Akureyri, Iceland from April 3-9, 2017. The theme for this training course was "Further skills in Microbial Ecology." The schedule is available here.
A booklet of proceedings from this event is available here.
First network event
The first MicroArctic network took place from November 20-27 in Longyearbyen. A schedule for the meeting is available here.
To view larger group photo (courtesy of Gary Barker), click here.
In collaboration with other MicroArctic ESRs and beneficiaries, ESR Robin Wojcik from GFZ has created a logo for the MicroArctic project. Click here to open up the full size logo
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.
MicroArctic involves 11 different beneficiaries throughout Europe. For more information about the network, please see below.
Prof. Alex Anesio, Project Coordinator
Gary Barker PhD Lecturer
Dr. Catherine Larose
Ecole Centrale de Lyon, Université de Lyon
Prof. David Pearce
Prof. Birgit Sattler
University of Innsbruck
Prof. Dirk Wagner
German Research Centre for Geosciences
Dr. Beat Frey
Swiss Federal Research Institute
Prof. Liane G. Benning
German Research Centre for Geosciences
Dr. Carsten Jacobsen
Department of Environmental Science
Prof. Nina Gunde Cimerman
University of Ljubljana
Dr. Cristina Purcarea
University of Bucharest
Dr. Oddur Vilhelmsson
University of Akureyri
Dr. Cédric Malandain
Dr. Andrew Mitchell
University of Aberystwyth
Dr. Florian H. H. Brill
Dr. Brill + Partner GmbH
Dr. David Pearce
Dr. Anders Priemé
University of Copenhagen
Dr. Elke Dittmann- Thünemann
University of Potsdam
Dr. David Rooke
Dr. Anne Jungblut
Natural History Museum
Dr. Starri Heidmarsson
Icelandic Institute of Natural History
Dr. Svetlana Evgrafova
Siberian Branch of Russian Academy of Sciences
University of Iceland
Dr. Cinzia Verde
Clare Desplats is the project manager for the MicroArctic network.
To contact Clare: firstname.lastname@example.org
MicroArctic final management meeting: Lyon, France May 20, 2019
All beneficiaries were represented at the management meeting. ESRs were also encouraged to attend.
The meeting started with a review of ESR contract start and end dates and anticipated PhD defence dates. All ESRs are on track to defend their PhDs although many will defend after the end of their MSCA employment contracts. Many of the host institutions consider that 36 months is too short to perform research, experiments and writing and expect their ESRs to defend some time in year 4. The group also discussed local administrative requirements for defending a PhD including type and number of publications.
The meeting next moved to a review of secondments. The majority of the ESR group have completed their secondments but there are some anticipated minor changes which will be communicated ASAP to the project officer for approval. Those who have not yet completed their secondments have scheduled when they will take place and all ESRs will have gone on secondment before the end of their MSCA contracts.
After the invoices have been paid for the final network event in Lyon this week, there will still be some money remaining in the network meetings budget which was held back from the research training budget. A proposal for the MicroArctic group to publish in a special issue of Frontiers was put forward and many were interested in collaborating. However, it was agreed that the money would be re-distributed (pro rata participation in network events) and that each institute would pay its own open access costs rather than holding on to the money and making a group payment. Clare will get in touch with the finance office at Aarhus to determine what information is required for re-distribution of the funds and exactly how much is left in this budget once all invoices from Lyon have been processed.
A list of remaining deliverables was presented indicating the lead institutions for each deliverable and the due dates. All beneficiaries were reminded that these deliverables should be uploaded in a timely manner. The training courses promised in the grant agreement will all have been delivered by the end of the project.
Although the ESR MSCA employment contracts will end within the next 6-8 months, ESRs were reminded about remaining contractual obligations such as:
- Informing Clare about any new publications which can then be uploaded to the MicroArctic website and Zenodo repository
- Informing Clare about any outreach activities they have engaged in
- Sending Clare short updates about their activities while on secondment to be posted to the website
- Providing updated career plans before the end of their MSCA employment contracts
Beneficiaries were reminded to check that researcher declarations were correct and up to date. They were also informed about the final periodic and financial report at the close of the project.
Management meeting: Obergurgl, Austria, April 2018
The meeting started with a reminder to all PIs about the first periodic report. Each beneficiary must submit a financial statement at the end of the first reporting period. This statement is automatically filled in on the participant portal based on the start date and end date of the ESRs employment contract. Clare explained where to find the financial statement on the portal and asked all PIs to check that the ”Number of units” correspond to the number of months the ESR(s) have worked on the project, that the total ”Costs of recruited researchers” correspond to the salaries incl. deductions for pension, taxation etc. paid to the ESRs in Reporting Period 1 (01/04/16 – 31/03/18). If the amount paid out to the ESRs is lower, Clare asked the PIs to contact the finance office at their institutes to ensure that any underpayment in Reporting Period 1 will be corrected by the end of Reporting Period 2 which ends on 31/03/2020 at the latest. The project officer recommends making the correction for period 1 at the end of period 1 and then (if necessary) another correction at the end of period 2. In case of any questions, the individual finance offices or PIs should contact Clare.
Once ALL of the financial statements have been received from ALL of the partners, the periodic report will be submitted to the commission. The sooner the financial reports are received, the sooner the sooner the commission will review the report and then make the interim payment. At the very latest, reports must be submitted by May 31st so PIs were asked to check with their finance departments on their return from Obergurgl to make sure that the financial statement gets sent out to Bristol. The interim payment (corresponding to approx. 25% of the total budget for each institute) should be made within 90 days of submission of our report, assuming the project officer does not ask us to correct anything or make any changes. The final 15% payment will only be sent when the entire project is over and final report submitted and approved by the commission (report due 31/03/2020).
Clare reminded the PIs about the consortium agreement and monies held back from the management and overheads budget at Bristol as well as from the Research Training budget. This was an internal agreement which is not reflected on each insitute's financial report. The financial report will simply calculate a flat rate of 1800 euros per month in Research training for each month your ESR has been employed and 1200 euros per month for management. The full flat rate must be declared on each beneficiary financial statement.. Clare also strongly recommend that each PI check with his/her finance department to see how much money has been spent in the research training category and management and overheads category to have a better idea of how much is left.
The meeting next moved to a discussion of the amendment procedure. Prior to the mid-term review, the project officer had asked us to provide a table of changes in secondments for each of the ESRs. Before the review, she was very clear that she would accept changes in locations and timing, but did not want to see the total duration of secondments reduced. After the review, however, she saw how much time ESRs have spent doing fieldwork and away from their host institutes and is now more willing to reduce the total time spent on secondments. Clare is to send the PIs a sheet for each ESR which should be reviewed and modified (if necessary) and then returned to Clare. We will then set up an amendment to incorporate any and all changes, and the project officer has asked us not to make any further changes for the next 12 months. Please remember that the minimum duration for a secondment is four weeks. Anything less is considered to be a visit. A second part of the amendment will deal with the closing down of mBioinform which will be replaced with Aarhus University. If anyone has any objections to the addition of Aarhus as a beneficiary, please let Clar know by May 15th.
After the amendment, Clare introduced a discussion of management costs. Because the mid-term review is a contractual obligation, we can reimburse the costs of transportation to the meeting in Innsbruck for both PIs and ESRs. Bristol has just incorporated a new finance system, so it may take a bit longer than usual to process payments. In order to have better visibility of what is left in both the network meetings budget and management budget, Clare asked PIs to please try to send her all claims by June 1st.
As part of the grant agreement, a network training event in bio prospecting, bio politics and political ecologywas promised. There are a number of experts in this area at the University of Bristol, so this training event will likely take place in Bristol in the autumn of 2018 (September – November) or may be associated with a final network meeting. If PIs wish to attend, they are welcome, but the meeting is more targeted to the ESRs. As regards the final network event, t was agreed that it is too soon to determine when and where that event will take place, so this issue will be revisited later on.
The ESRs are more or less halfway through their projects and it is imperative to have a game plan moving forward for the next 18 months. This is a good time for the PIs to sit down with their ESRs to discuss what they will do in the coming months, what will they publish, when, where, what are the requirements for defending a PhD thesis? When will they defend? Will they be allowed access to labs etc once their employment contracts have ended? What about ESRs with visa issues? The ESRs should be very clear about what is expected of them and should feel that they are getting the support and supervision they need to complete their training programs. ESRs should also continue their outreach activities and when possible do joint activities (ie when ESRs go on secondment to other institutes).
The meeting concluded with a discussion of a potential phase 2 project of MicroArctic.
Management meeting: Nuuk, Greenland, September 11, 2017
The fourth MicroArctic management meeting was held during the PAM Conference in Nuuk, Greenland. The main theme of this management meeting was project finances. The project coordinator started by reminding PIs about the original budget distributions defined in the consortium agreement. He then presented spending in the management category to date and the costs of network events to date. Claims submitted by the PIs for management events were revisited and anticipated future costs were explained. PIs were asked to submit travel claims following attendance at management meetings promptly in order to allow better real time visibility of the budget.
After discussing the management budget, the coordinator next provided information on the costs of network events in Svalbard, Akureyri and Copenhagen. So far, spending is on track and future network events will take place as planned.
The coordinator reminded all PIs about the Mid-term review to take place in April 2018 in Innsbruck, Austria. The costs of travel for PIs and ESRs to attend this event can be covered by the management budget held in Bristol as well as the costs of accommodations during the mid-term review. The MTR will be followed by a network wide training event at the Innsbruck University Research Centre in Obergurgl but the costs of this part of the week will be covered from the Research Training budget held in Bristol. The first financial report to be submitted to the European Commission will be due in May 2017 and the project manager will send information about how to complete the financial forms to all beneficiaries at a later date.
The meeting concluded with a review of work promised in the original grant agreement to ensure that the network is on track to achieve its original goals. ESRs appear to be working very well together and to be invested in their research projects and have already started to produce some interesting results. PIs were reminded to review secondment plans with their ESRs on return home from PAM and to inform the coordinator and project manager promptly in the event of any changes. The coordinator emphasised that all changes must be pre-approved by the project officer.
A photo of the PIs at the management meeting is provided below (courtesy of O. Vilhelmsson, University of Akureyri).
Management meeting: Akureyri, Iceland, April 8, 2017
The third MicroArctic management meeting (open to all PIs and ESRs) was held at University of Akureyri on April 8, 2017. The meeting commenced with a review of finances and more particularly an explanation of how network meeting costs are covered.
As the project manager had received a number of email inquiries about how the costs of secondments should be handled, the meeting next moved to a review of secondment obligations and finances. ESRs were reminded about their obligation to go on secondment and to write a short paragraph about their experiences while on secondment to be posted to the MicroArctic website. Both PIs and ESRs were reminded that any changes to the original secondment plan have to be first approved by the project officer. The project manager also explained that the participant portal now has an option to add information about secondments to the researcher declaration and reminded all PIs that they should complete this information for their ESRs.
Next, the project manager and coordinator presented the first progress report to be submitted to the European Commission by April 30, 2017. The six parts of the progress report were reviewed: general progress of the action, recruitment strategy, career development plans for ESRs, management, communication activities and impact. PIs and ESRs were requested to send the coordinator any updates to their outreach activities and/or publications by April 15, 2017.
The meeting next moved to a discussion of the mid-term review. The project manager explained the typical breakdown of a mid-term review and reminded all ESRs and PIs that their presence is obligatory. Several locations were suggested for the review with the understanding that the dates and location have to be submitted to the project officer for approval. To keep costs down, a management meeting and training event will be associated with the mid-term review.
After this discussion, the group reviewed the originally scheduled network events as defined in the consortium agreement to ensure that all training is on track to be delivered before the end of the project. ESRs were asked to contact the project manager with any additional training needs they might have. The project manager will then contact the PIs to see what is available and to post optional training courses to the project website.
As Outreach is an important component of MSCA ITN projects, all ESRs were reminded about this obligation. So far, all ESRs have completed at least one activity and some have even done three or four. In Akureyri, the project coordinator, PIs and ESRs took part in a large-scale outreach activity open to primary school students. The project manager reminded the ESRs to document these activities on the progress reports they submit to her every six months.
PIs next discussed insurance issues when ESRs are working in the field. It was agreed that the local rules at each institute should be respected and that ESRs MUST always check that they have insurance in please, but that when ESRs from different institutes work together in the field, they must ensure that they are in compliance with the rules of the various institutes.
Both PIs and ESRs were reminded about the open access obligation of H2020 ITNs and the need to acknowledge EC funding. The project manager has created a community in the Zenodo repository and publications will be stored there as they become available.
The meeting concluded with an open forum for discussion.
Management meeting Svalbard, November 21, 2016
The second MicroArctic management meeting was held during the kick off meeting in Svalbard and was attended by a representative from all beneficiaries as well as by the Early Stage Researchers. The meeting commenced with a reminder about various contractual obligations including the submission of researcher declarations on the participant portal and the requirement to provide the ESRs with a copy of the grant agreement. Initially, several host institutes had difficulties submitting the researcher declarations due to problems on the portal but all declarations have now been created. Clare, the project manager, has asked the project officer to re-open the declarations to allow beneficiaries to modify the email addresses provided for the ESRs. As the commission wishes to contact the ESRs 2 years after termination of their employment contracts, it is necessary to provide an email address which will still be valid in the future.
The meeting next moved to a review of project finances. As indicated in the consortium agreement, a portion of the Research Training budget was held back at University of Bristol to cover the costs associated with network wide training events. Because of the location of these events (the Arctic), the costs tend to be quite high for the group, but this was anticipated in the original project description and some of the later network events will be held in continental Europe (i.e the mid-term review) so costs should be lower. Clare next asked if there were any questions about the four budget categories: Living, Mobility, Research Training and Management+Overheads. She reminded all beneficiaries that a first financial report will be submitted to the European Commission after month 24 (April 2018).
Following a question and answer session about finances, the meeting moved to a discussion about Open Access requirements for publications. Under H2020, all peer reviewed publications must be Open Access. One of the beneficiaries raised the question about book chapters and how this would work in terms of Open Access. It was agreed that Clare would contact the project officer to ask her how to proceed. Beneficiaries were also reminded about the contractual obligation to request permits for sampling and transportation of samples outside of EU countries before performing sampling activities.
The Early Stage Researchers were reminded about their contractual obligations to spend time on secondment and to perform public outreach activities. Two ESRs volunteered to create facebook and twitter accounts to be used to post information of interest to the general public. These accounts will be linked to the dedicated MicroArctic website. The ESRs were also reminded about their obligation to fill in a personal career development plan in collaboration with their supervisors. ESRs will also be obliged to fill in semi-annual progress reports which will serve not only as a record of their training experience but will also be used to complete the annual progress reports to be provided to the European Commission. Both PIs and ESRs were reminded that their attendance at the project mid-term review is obligatory.
The meeting concluded with a discussion about upcoming network events and more particularly about the finances behind these events: how to find the most reasonably priced accommodations, how to bring fellows into the field in the most economical manner and how to optimize transportation costs (i.e. bus rentals vs. car rentals).
MicroArctic first management meeting: April 5, 2016: London, United Kingdom
The first MicroArctic management meeting was held at the Hilton Garden Inn near Heathrow Airport to facilitate travel to the event for a maximum number of beneficiaries and administrative and financial staff. After a brief personal introduction from all present and a welcome to everyone by the project coordinator, Alex Anesio, the meeting moved on to a detailed discussion of H2020 MSCA ITN finances.
First, the project manager, Clare Desplats, described the project consortium, the type of project, the number of expected ESRs and the project start and end dates. Next, she presented an explanation of pre-financing and the expected schedule of payments over the course of the project. The presentation then moved on to a description of unit costs as defined by H2020 projects and an explanation of the various cost categories: Living, Mobility, Research Training and Management and Overheads. Clare explained which costs are devoted to recruited researchers and which costs are considered to be institutional costs. Differences in the various cost categories between FP7 and H2020 ITNs were also underscored and an explanation of how to declare non euro costs was provided. All participants were informed about the need to fill in a financial report after month 24 and after month 48 of the project and a schedule of project reports to be submitted to the European Commission was circulated.
Following a question and answer session devoted to project finances, the meeting next moved on to a discussion of the Consortium Agreement and particularly the use of funds from the Research Training Category and from the Management and Overheads category. Participants also discussed intellectual property rights and the need to make fellows aware of IPR, particularly for those working in industry. Beneficiaries were reminded of the need to comply with local and national rules governing ethics in terms of transportation of materials from non EU countries.
After the consortium agreement, the meeting continued with a discussion of Recruitment practices. All beneficiaries were informed about the European Commission's guidelines for OTM-R (Open, Transparent, Merit-based Recruitment) and a checklist of items to consider when recruiting was distributed. Eligibility and mobility criteria were explained. All 15 ESR positions were advertised in a group advertisement placed on the Euraxess website, but beneficiaries were encouraged to advertise widely in other locations to encourage a maximum number of applications. It was agreed that a project website would be developed by Clare and that links to job opportunities at various host institutes would be added once the information was sent to Clare. A list of items to be included on employment contracts was presented and a pdf of the presentation was circulated to all beneficiaries. All partners were reminded about the obligation to fill in an online declaration of conformity within 20 days of the start date of the ESR employment contract. This portion of the meeting concluded with another question and answer session.
The next part of the meeting turned to a review of the obligations of Marie Curie fellows to spend time on secondment and to perform outreach activities targeting the general public. Beneficiaries were asked to remind fellows to acknowledge Marie Curie funding on any and all publications, posters, etc produced during their fellowships. Various opportunities for Outreach actions at the different host institutes were discussed. Next, the meeting moved to a discussion of network events described in Annex 1 to the Grant Agreement. Dates and locations of the anticipated events were reviewed and finally, the entire group reviewed the breakdown of work packages and ESR positions as described in the annex to ensure that no major deviations were anticipated.
The meeting ended with an open forum to encourage the beneficiaries to discuss possible future collaborations and to allow industrial and academic partners to discuss joint recruitment strategies.
Early Stage Researchers (ESRs)
15 Early Stage Researchers will be recruited to the MicroArctic network. As fellows join the network, their photos and contact information will be posted here.
|ESR 1: Alexandra Holland
Home country: USA
School of Geographical Sciences,
University of Bristol,
Bristol BS8 1SS
|Research interests||I am interested in studying the surface chemistry of glaciers and ice sheets in order to identify the different factors that are influencing their decrease in albedo and subsequent increased melting rate. I am specifically interested in supraglacial impurities such as dark snow and cryconite material that have been found to be significantly decreasing the surface reflectivity of the glaciers. My research interests revolve around analyzing these substances and understanding more clearly what they are composed of. By understanding that, we can identify their origin and be able to more accurately include them into our models for predicting the melting rates of glacier and ice sheets.|
|ESR 2: Benoît Bergk Pinto
Home country: Belgium
Environmental Microbial Genomics Group
Laboratoire Ampère UMR CNRS 5005
Ecole Centrale de Lyon
Université de Lyon
36, avenue Guy de Collongue
69134 ECULLY cedex
|Research interests||I’m fascinated by microbiology but also by bioinformatics, this is why I’ve done two masters. For this reason, I’m very glad to have the opportunity to carry out a PHD in the Microarctic Project because it includes both scientific fields. During these three years, I would like to investigate the microbial diversity of arctic ecosystems by means of metagenomic/metatranscriptomic studies in order to characterize the seasonal changes affecting these communities as well as their roles in the biogeochemical cycles. The results of these global studies could also be used to build new hypotheses to test in the field or in microcosm experiments. Finally, if I get the opportunity, the development of a whole new tool (bioinformatics software or experimental method) for the microbiologic field could also be a challenge that I would like to face.|
|ESR 3: Lucie Malard
Home country: France
Faculty of Health and Life Sciences
2 Ellison Place Newcastle-upon-Tyne
|Research interests||My professional experience in biology is very diverse; my main focus has been ecology in marine ecosystems but I have also worked in medical microbiology before moving on to marine chemistry, bioprospecting and coral microbiology. My main research aim is to provide an understanding of biological networks and their interactions by using a wide diversity of tools, from genomics to ecology. Extremophiles are some of the most intriguing organisms mainly due their adaptations to their extreme living environments, which can be surprising and unique. Being fascinated by the Arctic, I am pleased to have the opportunity to work as part of the MicroArctic consortium. I will explore microbial biodiversity in diverse Arctic environments and aim to identify sources and sink populations across the Arctic region.|
|ESR 4: Nora Els
Home country: Germany
University of Innsbruck
Institute of Ecology
Lakes and Glacier Research Group
|Research interests||During both my academic and personal life, I have been fascinated by snow and ice in all their features and the global connections of these systems. Air masses are essential in global and local environmental interlinkage, especially with respect to climate change. My research will focus on investigating the mechanisms and patterns of airborne community inputs on glacial ecosystems and their potential as seed populations to understand biodiversity, biogeography and evolutionary relationships of glacial microbial diversity. In association with this scope I am also interested in the connection of aerial microbiota to anthropogenic neighbourhoods and their potential as cloud and ice condensation nuclei. However, for me it is equally important to think about ways to communicate science to a broader public.
|ESR 5: Stine Holm
Home country: Denmark
Helmholtz Centre Potsdam
GFZ German Research Centre for Geosciences
|Research interests||I am fascinated by the barren, challenging and isolated - Arctic as a microbial habitat, with its low biomass, spatial heterogeneity and growth limiting factors. How do microorganisms survive, encountering stress factors such as desiccation, freeze-thaw and high UV radiation, and how do they respond to environmental changes? I do understand the importance of studying glacial environments in the light of the ongoing warming of our planet, and the potential conversion of the Arctic tundra from a carbon sink to a carbon source, as a result of the melting glaciers. With an offset in the model organism the methanogenic archeon Methanosarcina soligelidi SMA-21 (Wagner D. et al, 2013), isolated from permafrost in the North-east Siberian, my research will focus on mapping archeal communities in circum Arctic and characterizing those members involved in the carbon cycling in permafrost environments by next generation sequencing and laboratory based batch experiments.|
|ESR 6: Robin Wojcik
Home country: France
GFZ, German Research Center for Geosciences
Interface Geochemistry Group
|Research interests||My work within the MicroArctic project will aim to improve our understanding of the glacial forefield ecosystem response to changing environmental conditions in the Arctic. My research interest specifically aims to develop a geochemical model of the bulk and micro-scale changes in geochemical and mineralogical parameters that link C and nutrient cycling to weathering. To this end, my task is to participate in Arctic field work and collect depth- and time-resolved samples; to quantify the bulk elemental and micro-scale geochemical and mineralogical variations to evaluate weathering budgets; determine carbon and nutrient (P, N and Fe) speciation and evaluate links between abiotic and biotic processes affecting weathering.|
|ESR 7: Johanna Donhauser
Home country: Germany
Swiss Federal Research Institute for Forest, Snow and Landscape Research WSL
Forest Soils and Biogeochemistry
|Research interests||I am mainly interested in how soil microorganisms react to warming and other global change related climatic shifts. More precisely, I want to find out how their altered activity is associated with soil formation and with global element cycles, especially the carbon and the nitrogen cycle which in turn will have a feedback on climate change. This is of particular interest in extreme environments such as the Arctic or alpine regions, as those are predicted to be especially susceptible to climatic alterations. I use a suit of molecular tools such as next generation sequencing in order to analyze how the composition of microbial communities shifts in response to warming and other climatic impacts.|
|ESR 8: Muhammad Zohaib Anwar
Home country: Pakistan
Ole Maaloes Vej 3,
|Research interests||My research interests have been very diverse in Bioinformatics. My professional research experience is in developing and using computational techniques to explore the microbial diversity and building a comprehensive database of 16S Microbial Profiles of different environments [Henschel et. al, PLoS Comput Biol, 11(10), e1004468.]. During my PhD in the MicroArctic Project I would like to explore the microbial diversity of arctic environment in addition to formulate standardized pipelines for full RNA based analysis of the microbial communities in Arctic environment. Arctic plays a pivotal role in the Earth’s climate system and with this study we will be able to understand the abundance and functional profile of different Microorganisms in the region.|
|ESR 9: Laura Perini
Home country: Italy
University of Ljubljana
Department of Biology
|Research interests||My research interests are focused on microbial ecology in cold extreme ecosystems with primary interests on: I) biodiversity of extremophilic microorganisms (Bacteria and Fungi) in Arctic glacial ice, including mechanisms of multidrug resistance and pathogenity; II) development and application of metagenomic and transcriptomic approaches to the study of microbial biodiversity with a focus on fungal responses to some environmental driver variables; III) analysis of synergistic and antagonistic interactions between microorganisms inhabiting glacial ice and assessment of a their possible production of new antimicrobial compounds.|
|ESR 10: Antonio Mondini
Home country: Italy
Institute of Biology Bucharest
Department of Microbiology
296 Splaiul Independentei
|Research interests||I am mainly interested in bioprospecting from extreme environments, and in particular from extreme cold environments such us Arctic and Antarctic regions. Extremophilic microorganisms, population dynamics and genetic diversity of Bacteria and Archaea in cold environments. I am especially interested in psychrophilic enzymes isolated from these microorganisms, which have high biotechnological and medical applications. Molecular adaptation mechanisms to extreme environments and external stress factors. In addition, novel methods for microorganisms isolation in order to improve the isolation of bacteria belonging to the so-called “uncultivable fraction of microorganisms|
|ESR 11: Ingeborg Klarenberg
Home country: Netherlands
The University of Akureyri
|Research interests||I have a diverse background in earth science and environmental science and so are my research interests. They range from microbial ecology to biogeochemical cycles to plant and landscape ecology and nature conservation. I am fascinated by the Arctic and interested in understanding the interactions between these topics in relation to global environmental change. High-arctic wetlands are important carbon stores and are threatened by climate change. Many organisms in these systems rely on symbioses with bacteria for instance for nutrient acquisition. In order to understand ongoing changes in microbial communities associated with vegetation in these wetlands, my research will focus on determining the composition, activity and fate of bacterial symbiotic associations with lichens and bryophytes in permafrost-marginal Arctic wetlands, using mesocosms, molecular techniques and culturing techniques.|
|ESR 12: Rose Layton
Home country: United Kingdom
7 Place Antonin Poncet
|Research interests||My research interests are founded in microbiology with a particular emphasis on extremophiles, their adaptations and their fundamental role in biogeochemical cycling. I feel passionately about conservation and minimising the effects of global warming for future generations and to preserve the natural world. As the Arctic plays a pivotal role in the Earth’s climate system, my research seeks to link the molecular changes in Arctic microbial communities with the abiotic changes occurring as a result of global warming. I will be applying climate change simulations, metagenomic and metatranscriptomic approaches to help elucidate microbial community diversity and function and the potential implications of a rapidly warming Arctic. |
|ESR 13: Melanie Claire Hay
Home country: South Africa
Department of Geography & Earth Sciences
|Research interests||I intend to use my background in medical biochemistry and genetics to investigate potential applications for Arctic microorganisms in economic and environmental services. Specifically, I am interested in identifying genes and enzymes for pharmaceutical or biotechnological use, with a focus on drug discovery. Due to global warming, the investigation of these Arctic microorganisms is of urgent importance, as theses extreme environments, and the microbial biodiversity they contain, are under threat. To identify biomolecules of interest, I will generate deep-sequenced metagenomes and employ functional metagenomics to identify genes and enzymes in microbes that exhibit key functional capabilities.|
|ESR 14: Gilda Varliero
Home country: Italy
School of Biological Sciences,
University of Bristol,
24 Tyndall Avenue,
Bristol BS8 1TQ
|Research interests||I have always been fascinated by the stunning complexity possessed by living cells. My main research interest is to unravel it through the development of new bioinformatics tools and pipelines. Having a better quality of genomic and gene data would increase the amount of information that we are now able to extrapolate and would allow us to reveal novel biosynthetic/catalytic pathways and protein variants of interest. I am specifically interested on microbial and fungal communities sampled in extreme environment, such the Arctic.|
|ESR 15: Diana Carolina Mogrovejo Arias
Home country: Ecuador
Dr. Brill + Partner GmbH
Institut für Hygiene und Mikrobiologie
DE - 22339 Hamburg
|Research interests||I am very fond of life sciences in general, particularly Microbiology. I have worked with microorganisms for the most part of my professional life and have grown to become passionate about them. My work will be aimed at sampling and characterizing potentially pathogenic bacteria evaluating their antibiotic resistance in order to determine their abundance, diversity and significance in Arctic environments. My research’s goal is to contribute with clear applications of microbial research to economy and health for I believe microorganisms from extreme environments are the source of a myriad of molecules and could provide a sustainable solution to many problems that industry and academia face nowadays.|
For more information about this position: http://www.brillhygiene.com/en/company/carreer
Abstracts, publications in peer reviewed journals and other outcomes produced by the MicroArctic consortium will be provided here as they become available.
OPEN ACCESS PUBLICATIONS
In compliance with H2020 regulations, any peer reviewed articles will be made available through open access and can be found on the Zenodo repository under the MicroArctic community here.
The following publications are already available:
Complete Genome and Plasmid Sequences of Salmonella enterica subsp. enterica Serovar Enteritidis PT1, Obtained from the Salmonella Reference Laboratory at Public Health England, Colindale, United Kingdom
Muhammad Zohaib Anwar, Athanasios Zervas, Lars Hestbjerg Hansen, Gary Barker, Alexandre Magno Anesio, Carsten Suhr Jacobsen
Microbiology Resource Announcements, ASM Volume - 9, Issue - 2, Date - 09 January, 2020
Fungal and bacterial diversity of Svalbard subglacial ice
Perini L., Gostincar C., Gunde-Cimerman N.
Phenotypes associated with pathogenicity: their expression in arctic fungal isolates.
Perini L., Mogrovejo D.C., Tomazin R., Gostincar C., Brill F.H.H., Gunde-Cimerman N.
Entirely Off-Grid and Solar-Powered DNA Sequencing of Microbial Communities during an Ice Cap Traverse Expedition
Glen-Oliver. F. Gowers, Oliver Vince, John-Henry Charles, Ingeborg Klarenberg, Tom Ellis and Arwyn Edwards
Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow?
Benoît Bergk Pinto, Lorrie Maccario, Aurélien Dommergue, Timothy M. Vogel and Catherine Larose1
Frontiers in Microbiology
Assessment of Artificial and Natural Transport Mechanisms of Ice Nucleating Particles in an Alpine Ski Resort in Obergurgl, Austria
Philipp Baloh, Nora Els, Robert O. David, Catherine Larose, Karin Whitmore, Birgit Sattler and Hinrich Grothe
Frontiers in Microbiology
Biogeographical patterns in soil bacterial communities across the Arctic region
Lucie A Malard, Muhammad Zohaib Anwar, Carsten S Jacobsen, David A Pearce
FEMS Microbiology Ecology, Volume 95, Issue 9; Sept. 2019
Dissolved organic nutrients dominate melting surface ice of the Dark Zone (Greenland Ice Sheet)
Alexandra T. Holland, Christopher J. Williamson, Fotis Sgouridis, Andrew J. Tedstone, Jenine McCutcheon, Joseph M. Cook, Ewa Poniecka, Marian L. Yallop, Martyn Tranter, Alexandre M. Anesio1, and The Black & Bloom Group
Microbial composition in seasonal time series of free tropospheric air and precipitation reveals community separation
Nora Els, Catherine Larose, Kathrin Baumann-Stanzer, Romie Tignat-Perrier, Christoph Keuschnig, Timothy M. Vogel, Birgit Sattler
Total RNA Protocol (extraction, quantification and Illumina library preparation)
Antonio Mondini, Morten Dencker Schostag, Lea Ellegaard-Jensen, Toke Bang-Andreasen, Muhammad Zohaib Anwar, Cristina Purcarea, Carsten Suhr Jacobsen
DOI: protocols.io dx.doi.org/10.17504/protocols.io.457gy9n
To assemble or not to resemble—A validated Comparative Metatranscriptomics Workflow (CoMW) Muhammad Zohaib Anwar, Anders Lanzen, Toke Bang-Andreasen, Carsten Suhr Jacobsen
GigaScience, Volume 8, Issue 8, August 2019, giz096,
Bacterial Dynamics in Supraglacial Habitats of the Greenland Ice Sheet
Miranda Jane Nicholes, Christopher James Williamson, Martyn Tranter, Alexandra Holland, Ewa Poniecka, Marian Louise Yallop, The Black & Bloom Group and Alexandre Anesio
Frontiers in Microbiology (2019)
Land cover and landform-based upscaling of soil organic carbon stocks on the Brøgger Peninsula, Svalbard.
Arctic, Antarctic, and Alpine Research 51 (2019)
Spatial Variability of Antarctic Surface Snow Bacterial Communities
Lucie A. Malard, Marie Šabacká, Iordanis Magiopoulos, Matt Mowlem, Andy Hodson, Martyn Tranter, Martin J. Siegert and David A. Pearce
Frontiers in Microbiology
Darkening of the Greenland Ice Sheet: Fungal Abundance and Diversity Are Associated With Algal Bloom
Laura Perini, Cene Gostincar, Alexandre Magno Anesio, Christopher Williamson,Martyn Tranter and Nina Gunde-Cimerman
Frontiers in Microbiology
Linkages between geochemistry and microbiology in a proglacial terrain in Svalbard.
Wojcik, R., Donhauser, J., Holm, S., Frey, B., Anesio, A., Holland, A., Wagner, D., Pearce, P., and Malard, L. and Benning, L.G.B.
Annals of Glaciology 2019
High-throughput sequencing of fungal communities across the perennial ice block of Scărișoara Ice Cave.
Antonio Mondini, Johanna Donhauser, Corina Itcus, Constantin Marin, Aurel Persoiu,Beat Frey, Cristina Purcarea
Annals of Glaciology 2019
Beyond the Planetary Boundary Layer: Bacterial and Fungal Vertical Biogeography at Mount Sonnblick, Austria
N. Els, K. Baumann-Stanzer, C. Larose, T.M. Vogel, and B. Sattler.
Metagenomic insights into diazotrophic communities across Arctic glacier forefields
Maisie V Nash, Alexandre M Anesio, Gary Barker, Martyn Tranter, Gilda Varliero, Emiley A Eloe-Fadrosh, Torben Nielsen, Thomas Turpin-Jelfs, Liane G Benning, Patricia Sánchez-Baracaldo. 2018.
FEMS Microbiology Ecology .
Alpine soil microbial ecology in a changing world
Donhauser J & Frey B
Fems Microbiol Ecol 2018
Microbial diversity and biogeography in Arctic soils
Lucie A. Malard, D. Pearce
Environmental Microbiology Reports
Ice algal bloom development on the surface of the Greenland Ice Sheet
C J Williamson, A M Anesio, J Cook, A Tedstone, E Poniecka, A Holland, D Fagan, M Tranter, M L Yallop
FEMS Microbiology Ecology, Volume 94, Issue 3, 1 March 2018, fiy025, https://doi.org/10.1093/femsec/fiy025
Characterisation of Arctic Bacterial Communities in the Air above Svalbard
Cuthbertson, Lewis; Amores-Arrocha, Herminia; Malard, Lucie A.; Els, Nora; Sattler, Birgit; Pearce, David A.
Published in Biology, Volume 6, Issue 2, May 2017
Inhibition of anaerobic digestion processes: Applications of molecular tools
Yamrot M.Amha, Muhammad Zohaib Anwar, Andrew Brower,Carsten S.Jacobsen, Lauren B.Stadler, Tara M.Webster, Adam L.Smith
Bioresource Technology Volume 247, January 2018, Pages 999-1014
The microbiome of glaciers and ice sheets
Anesio, Alexandre M.; Lutz, Stefanie; Benning, Liane G.; Christmas, Nathan M. A.
Published in Nature Partner Journals Biofilms and Microbiomes, April 2017
Yeasts in Polar and Subpolar Habitats.
In Yeasts in Natural Ecosystems: Diversity (pp. 331-365)
Buzzini, P., Turk, M., Perini, L., Turchetti, B., & Gunde-Cimerman, N. (2017).
SESS 2018: The State of Environmental Sciencein Svalbard – a technical annual report
ESRs Mohammad Zohaib Anwar (mBio/Aarhus) and Lucie Malard (Northumbria) along with PIs David Pearce (Northumbria) and Catherine Larose (ECL) contributed to chapters 2 and 3 of the report which became available in January 2019.
Microbial activity monitoring by the integrated arctic earth observing system(mamsios)
L. A. Malard, M. Avila-Jimenez, P. Convey, C. Larose, A. Hodson, l. Ovreas, J. Y. Schmale, M. Z. Anwar, D. A. Pearce,
Svalbard Integrated Arctic Earth Observing System (SIOS), Tech. Rep., 2019.
Online Link: https://sios-svalbard.org/sites/sios-svalbard.org/files/common/SESSreport_2018_FullReport.pdf
The novel results of the Institute of Biology Bucharest into fields of ecology, microbiology and citobiology.
Antonio MONDINI and Cristina PURCAREA
Publisher: Ars Docendi, ISBN: 978-606-998-044-6
Cold-active proteins from psychrophilic microorganisms Department of Microbiology, Institute of Biology, Bucharest, Romania (page 116)
PEER REVIEWED SOFTWARE PUBLICATIONS AND COMPUTE CAPSULES
Comparative Metatranscriptomics Workflow (CoMW)
Muhammad Zohaib Anwar, Anders Lanzen, Toke Bang-Andreasen, Carsten Suhr Jacobsen
BioRxiv preprinting is submitted to journals that promote open-access and preprinting with no embargo policy. Nature, Oxford and BMC publishers strongly promote preprinting before submission for quick access to science.
Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in a subarctic alpine heathland
Ingeborg J. Klarenberg, Christoph Keuschnig, Ana J. Russi Colmenares, Anne D. Jungblut, Ingibjörg S. Jónsdóttir, Oddur Vilhelmsson
Development of the DRoplet Ice Nuclei Counter Zürich (DRINCZ): Validation and application to field collected snow samples
Robert O. David, Maria Cascajo Castresana, Killian P. Brennan, Michael Rösch, Nora Els, Julia Werz, Vera Weichlinger, Lin S. Boynton, Sophie Bogler, Nadine Borduas-Dedekind, Claudia Marcolli, and Zamin A. Kanji1 https://doi.org/10.5194/amt-2019-213
Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome
Morten Dencker Schostag, Muhammad Zohaib Anwar, Carsten Suhr Jacobsen, Catherine Larose, Timothy M. Vogel, Lorrie Maccario, Samuel Jacquiod, Samuel Faucherre, Anders Priemé
Total RNA-sequencing reveals multi-level microbial community changes and functional responses to wood ash application in agricultural and forest soil
Toke Bang-Andreasen, Muhammad Zohaib Anwar, Anders Lanzén, Rasmus Kjøller, Regin Rønn, Flemming Ekelund, Carsten Suhr Jacobsen
ABSTRACTS AND POSTERS FROM INTERNATIONAL CONFERENCES and MEETINGS
Abstracts from Goldschmidt 2019, Barcelona, Spain: 18-23 August, 2019
Phosphorus, not the limitation it was thought to be?
Alexandra Holland, Benoit Bergk Pinto, Catherine Larose, Timothy M. Vogel, Rose Layton, Martyn Tranter, Alexandre Anesio
2019 FEMS Congress, July 7-11th, Glasgow, Scotland.
L.A. Malard and D.A.Pearce
Microbial biogeography and colonization of Arctic terrestrial ecosystems.
Abstract O014 (Oral Presentation)
L.A. Malard* and D.A. Pearce.
Multi-scale variability analysis of Arctic soil microbial communities. https://fems2019.org/fileadmin/user_upload/FEMS/fems2019_abstractbook.pdf
Abstract PW212 (Poster Presentation).
2019 Microbiology Society annual conference, April 8-11th, Belfast, Northern Ireland.
L.A. Malard and D.A. Pearce.
Multi-scale variability analysis of Arctic soil microbial communities.
https://doi.org/10.1099/acmi.ac2019.po0330 (Oral Presentation.)
Abstracts from PAM2019, Hamilton, New Zealand: 4-8 February, 2019
A. Mondini, M. Z. Anwar, C. S. Jacobsen, C. Larose, C. Purcarea
Effect of environmental heat-shock stress on glacier microbiome
Abstract Book Link: https://www.confer.nz/pam2019/wp-content/uploads/2019/02/Pam-2019-book-of-abstracts.pdf
Els, N., Larose, C., Baumann-Stanzer, K., Tignat-Perrier, R., Vogel, T., Keuschnig, C., Sattler, B.
Beyond the Boundary Layer – Bacterial and Fungal Diversity along a Vertical Transect at Mount Sonnblick, Austria (3106m asl,)
Els, N., P. David, R., Larose, C., Varliero, G., Sattler, B.
High Diversity and Ice Nucelation Activity in Iceland Air and Snow
Els, N., Baloh2, P. David, R., Larose, C., Sattler, B., Grothe, H.
Ice Nucelation Potential and Microbiology of Natural and Artificial Snow
Spatial variability in Antarctic surface snow bacterial communities
L.A. Malard, M. Sabacka, I. Magiopoulos, A. Hodson, M. Tranter, M.J. Siegert, D. A. Pearce. https://www.confer.nz/pam2019/abstracts/
The diversity and biogeography of the Antarctic surface snow bacteriome
Malard, L.A., Magiopoulos, I., Sabacka, M., Hodson, A., Tranter, M., and Pearce, D.A.
Abstracts from EGU 2019, Vienna, Austria, 7-12 April 2019
Nora Els, Catherine Larose, Kathrin Baumann-Stanzer, Romie Tignat-Perrier, ChristophKeuschnig , Timothy M. Vogel, Birgit SattlerFree Tropospheric Precipitation does not serve as Proxy for Air MicrobialComposition
Robin Wojcik, Johanna Donhauser, Beat Frey, Anja M. Schleicher, Liane G. Benning
Age and geomorphological controls on geo-bio successions in a sub-Arcticglacial forefield.
Abstracts from ISME2018: Leipzig, Germany: 12-17 August 2018
Fabian Horn, Stine Holm, Lars Ganzert, Andre Friese, Julia Boike, Paul Overduin, Dirk Wagner, Susanne Liebner, Matthias Winkel
The core microbiome of permafrost-affected arctic peatlands is stable over decades but sensitive to hydrological differences
Holm S., Gorecki A.,Winkel M., Liebner S., Wagner D, Dziurzynski M., Dziewit L.,Horn F.
Ecological role of plasmids in Arctic permafrost environments
Abstracts from POLAR2018: 15-26 June 2018
Wojcik, R., Donhauser, J., Holm, S., Malard, L., Holland, A., Frey, B., Wagner, D., Pearce, P., Anesio, A. and Benning, L.G.B.
Geochemical and microbiological co-succession in an Arctic glacier forefield.
Oral presentation at the POLAR2018 Conference in the session ‘Functional ecology of polar microbial communities in a changing world’. 2018 Jun 19-26; Davos, Switzerland. http://www.professionalabstracts.com/POLAR2018/iPlanner/#/grid/1529712000
Microbial Biogeography in Arctic Soils
Lucie Malard, David Pearce
Long-term warming effects on bacterial communities associated with Racomitrium moss in lcelandic tundra
Abstract at following link on page 1542
Gilda Varliero, Maisie Nash, Joshua Blacker, Alex Anesio, Liane G. Benning, Gary Barker. 2018
A computational pipeline for taxon, gene and allelic analysis of microbial omics
Abstract at following link on page 86
Nora Els, Birgit Sattler
Snow Does Not Mirrow Air Microbial Communities as Shown on Transects in Iceland
Abstract at following link on page 1469:
Catherine Larose, Benoit Bergk Pinto, Adrien Boniface, Rose Layton, Romie Tignat Perrier, Laura Sanguino, Lorrie Maccario, Aurélien Dommergue, Timothy M. Vogel
Environmental vs Ecological Drivers of Microbial Adaptation to Frozen EcosystemsAbstract at following link on page 1755: https://www.polar2018.org/uploads/2/4/6/0/24605948/polar2018_abstractproceedings.pdf
Stine Holm, Susanne Liebner, Fabian Horn, Christian Knoblauch, Dirk Wagner
Methane Producing Archaea in Siberian Permafrost and their Response to Thaw
Abstract at following link on page 2388
Johanna Donhauser, Pascal Niklaus, Beat Frey
Temperature Sensitivity of the High Alpine Soil icrobiome
Abstract at following link on page 2334 https://www.polar2018.org/uploads/2/4/6/0/24605948/polar2018_abstractproceedings.pdf
Antonio Mondini, Muhammad Zohaib Anwar, Carsten Suhr Jacobsen, Catherine Larose, Cristina Purcarea
Heat shock response of glacier microbiome.
Link to poster
Abstracts from 11th International Mycological Congress, San Juan, Puerto Rico: July 16-21, 2018
Enzymes of halophilic and psychrophilic fungi for a more sustainable world.
GOSTINČAR, Cene, PERINI, Laura, ZALAR, Polona, GUNDE-CIMERMAN, Nina.
Abstract on page 9. http://ut.suagm.edu/sites/default/files/uploads/pdf/IMC-2018-Abstract-Book-071618.pdf.
Bass Becking was right : polar fungi in refrigerators, tropical in dishwashers.
ZALAR, Polona, ZUPANČIČ, Jerneja, NOVAK BABIČ, Monika, GOSTINČAR, Cene, PERINI, Laura, GUNDE-CIMERMAN, Nina.
Abstract on page 107 http://ut.suagm.edu/sites/default/files/uploads/pdf/IMC-2018-Abstract-Book-071618.pdf.
Workshop Black Yeasts, post-congress workshop of 20th Congress of the International Society for Human and Animal Mycology, Amsterdam (The Netherlands), 4-5 July 2018.
Perini L., Zalar P., Gostinčar C., Zupančič J., Gunde -Cimerman N. (2018)
Black and white – Black yeasts in the Arctic.
Link to abtract
15th Conference on Cloud Physics, Vancouver, 11.July 2018
R. Wagner, A. Bertram, N. Els, L.Ickes, V.Irish, O.Möhler, B.J.Murray, G.Porter, M.Salter, N.Umo
Influence of Biogenic Constituents on the Heterogeneous Ice Nucelation Ability of Sea Salt Aerosol Particles at Cirrus Temperatures
3rd Conference on Ecology of Soil Microorganisms 17–21 June 2018, Helsinki, Finland
Adrian Gorecki, Stine Holm, Matthias Winkel, Susanne Liebner, Dirk Wagner, Mikolaj Dziurzynski, Lukasz Dziewit, Fabian Horn
Bacterial plasmids and their ecological role in Arctic permafrost environment
See abstract 77 on page 14 at following link:
Microbe 2018: American Society for Microbiology, Atlanta, GA, USA, June 7-11, 2018
Diana C. Mogrovejo-Arias, Florian H. H. Brill
Pathogens from the Arctic: what is the real risk?
Westerdijk Symposium, Utrecht, Netherlands: Leading women in fungal biology
Perini, L., Frisvad, J.C., Zalar, P., Gostincar, C., Anesio, A., Gunde-Cimerman, N. (2017)
Black and white - Arctic black bloom fungi
Link to abstract
Kongres Slovenskega mikrobiološkega društva, Bled, Slovenija.
Perini, L., Frisvad, J.C., Zalar, P., Gostinčar, C., Anesio, A., Gunde-Cimerman, N. (2017)
˝Črno cvetenje˝ grenlandske ledene plošče - kaj pa glive?
Abstract book 7
Virtual Alpine Observatory Meeting, Grenoble (13-15.3.2018)
Nora Els, Karoline Wiesinger, Christina Schweighofer, Tamara Schober, Birgit Sattler
Seasonal, Daily and Altitudinal Variations of Primary Biological Aerosol Occurences at Mount Sonnblick Observatory, Austria, 3106 masl (Poster presentation)
Microbiology Society Annual Conference 2018: 10-13 April 2018, Birmingham, U.K.
Melanie Hay, Sara Rassner Edwards, Andrew Mitchell, Arwyn Edwards
Metagenomics: revealing the antimicrobial potential of the cryosphere
See PO64 at following link:
International Symposium on Cryosphere and Biosphere (International Glaciological Society), Kyoto, Japan, 14–19 March 2018
Antonio Mondini, Cristina Purcarea
Thermal response of pyrimidine nucleotide genes expression in the psychrophilic bacterium Glaciibactersuperstes
Link to abstract
Perini, L., Anesio, A., Williamson, C., Nicholes, M., Gostinčar, C., Gunde-Cimerman, N. (2018)
Fungal-algal interactions on the Greenland ice sheet surface.
See 10:45 session on Sunday, March 18 at following link:
Holland A, Anesio A, Tranter M, Williamson C (2018)
Nutrient Retention in the Weathering Crust of the Greenland Ice Sheet
Link to presentation
Danish Microbiological Society, Annual Congress 2017
Muhammad Zohaib Anwar, Toke Bang-Andreasen, Anders Lanzen, Carsten Suhr J
Analyzing functional dynamics in environmental total RNA with No PCR bias
Abstract P5, page 25, Danish Microbiological Society Programme Abstract Book
Poster presentation: Swiss Park Research Seminar, Bern, Switzerland, May 2017
Johanna Donhauser, Sonja Wipf, Frank Hagedorn, Beat Frey: The impact of warming on the soil microbiome assessed by soil transfer on alpine summits along an altitudinal gradient
Article in “Cratschla” ( Journal of the Swiss National Parks), May 2017
Johanna Donhauser, Beat Frey: Klein aber wirksam – Alpine Mikroorganismen im Klimawandel (Small but powerful – Alpine microbes and climate change,
Abstracts from PAM 2017 in Nuuk, Greenland, Sept. 2017
Johanna Donhauser, Arwyn Edwards, Thomas Rime, Beat Frey
Structural and Functional Characterization of the Soil Microbiome along a Glacier Forefield Chronosequence including Sources of Colonizers
Abstract 16, page 27: PAM 2017 Programme and Abstract Book
L. Malard,, R. Wojcik, J. Donhauser, S. Holm, A. Holland, B. Frey, D. Wagner, D. Pearce, A. Anesio, L. Benning
Geochemical and microbiological gradients along an Arctic chronosequence
Abstract P13, page 65: PAM 2017 Programme and Abstract Book
Nora Els, Marina Fernandez-Delgado Juarez, Maria Gomez-Brandon, Arwyn Edwards, Birgit Sattler
Optimization of air sampling efficiency at subzero temperatures applying liquid impinging and membrane filtration
Abstract P20, page 37: PAM 2017 Programme and Abstract Book
Melanie Claire Hay, Sara Rassner, Andrew Mitchell, Arwyn Edwards:
Mining the Arctic microbial metagenome for industrially useful cold-active enzymes
Abstract P25, page 77: PAM 2017 Programme and Abstract Book
Holm S., Liebner S., Winkel M. , Mitzscherling J., Lehr C., Fritz M., Obu J., Lantuit H.,Heslop J., Anthony K.W., Horn F. Knoblauch C. and Wagner D.:
The effect of permafrost thaw on circum-Arctic methanogenic communities
Abstract P29, page 81: PAM 2017 Programme and Abstract Book
Antonio Mondini, Cristina Purcarea
Cold-active enzymes from the psychrophilic bacterium Glaciibacter superstes involved in pyrimidine nucleotide biosynthesis
Abstract P37, page 91: PAM 2017 Programme and Abstract Book
B. Bergk Pinto, T. Vogel and C. Larose:
Co-occurrence networks demonstrate microbial community shiftsin arctic snow
Abstract 12, page 23: PAM 2017 Programme and Abstract Book
Diana C. Mogrovejo-Arias, Florian H. H. Brill, Dirk Wagner
Pathogens from the Arctic: What is the real risk
Abstract P17, page 69: PAM 2017 Programme and Abstract Book
Ingeborg Klarenberg and Oddur Vilhemsson
Symbiotic nitrogen fixation in lichens and bryophytes in a warming arctic
Abstract P15, page 66: PAM 2017 Programme and Abstract Book
Alexandra Holland, Christopher Williamson, Fo s Sgouridis, Martyn Tranter, Alexandre Anesio
The Geochemistry of Surface Ice on the Greenland Ice Sheet and its Effect on the Primary Production of Microbes Abstract P22, page 75: PAM 2017 Programme and Abstract Book
Anwar, M.Z., Bang-Andreasen.T., Lanzen, A. and Jacobsen, C.S.
Standardized pipeline for Full RNA No PCR Biased Analysis of the Microbial Populations in Arctic Environment
Abstract P21, page 73: PAM 2017 Programme and Abstract Book
L. Perini, J.C. Frisvad, P. Zalar, C. Gostinčar, N. Gunde-Cimerman.
"Tropical diversity" of Arctic penicillia
Abstract P42, page 94: PAM 2017 Programme and Abstract Book
L. Perini, J.C. Frisvad, P. Zalar, C. Gostinčar, A. Anesio, N. Gunde-Cimerman
"Black bloom" Penicillium sp. on the Greenland Ice Sheet. 7
Abstract 35, page 46: PAM 2017 Programme and Abstract Book
Gilda Varliero, Joshua Blacker, Alex Anesio, Liane Benning, Gary Barker
A computational pipeline for taxon, gene and allelic analysis of microbial metagenome
Abstract P12, page 63: PAM 2017 Programme and Abstract Book
Abstracts from Goldschmidt Conference 2017, Paris France, June 2017
Robin Wojcik, Johanna Donhauser, Stine Holm, Lucie Malard, Alexandra Holland, Beat Frey, Dirk Wagner, David Pearce, Alex Anesio, Hörn Hövelmann and Liane G. Benning:
Geochemical and microbiological gradients in a High-Arctic glacier forefield
(Poster presentation: session 15g ‘Geobiology and Geochemistry of the Cryosphere: Processes, Pathways, and Drivers’)
Alexandra Holland: The Geochemistry of Surface Ice on the Greenland Ice Sheet and its Effect on the Primary Production of Microbes (Poster presentation 15th of August).
All MicroArctic ESRs will receive training on how to communicate to the general public in order to make science approachable as well as understandable. During the project we intend to link national programmes to include the younger generation (from little kids to teenagers) to (a) excite them for natural sciences and (b) to enlarge their horizon for polar regions being tightly coupled to temperate habitats due to globalization.
As MicroArctic fellows and/or PIs engage in Outreach activities, a list of events will be posted here.
June 2019: Creation of an outreach video about the MicroArctic network
During the final MicroArctic network meeting held in Lyon in May 2019, the ESRs created an outreach video about the MicroArctic network. The video has been posted to YouTube and can be viewed here:
May 2019: Photography connecting art, design and arctic science
ESR Ingeborg Klarenberg (Akureyri) participated in a project with long-exposure photography in the Arctic, aiming to connect art, design and arctic science: https://udoprinsen.com/touch-base/. Ingeborg hung six of Udo Prinsen's pinhole cameras in Eyjafjörður valley, close to Akureyri (picture of camera below). These pinhole cameras track the movement of the sun for some time (a month and a half for the cameras that Ingeborg put up). The resulting presentation is aimed to be ready in 2020. Udo has scanned the pinhole photos and will publish some of them via his Facebook page soon.
14 March 2019: University of Aberystwyth
ESR Melanie Hay (Aberystwyth) presented a 50 minute "Hot Topic" seminar on "Drug Discovery and Bioprospecting in the Environment" to Microbiology undergraduates at the University of Aberystwyth. The talk was one of six hot topic seminars that will be presented this semester.
11-12 March 2019: Polar Takeover week at Techniquest, Cardiff, Wales
On 11 and 12 March, MicroArctic ESR Melanie Hay presented at the Polar Takeover Week at Techniquest in Cardiff to speak about Polar Microbiology. Over 400 children between the ages of 6 and 11 years old, from a number of schools around Wales, attended over the two days. It was a wonderful, busy, exciting event. Each school got a turn to be involved in five different talks or activities on a rotation basis. They had a presentation by Richard Parks, a Welsh rugby legend and Antarctic explorer, learnt about ‘wild weather’, about the size of different animals in the Arctic and Antarctic and got to take part in a knock-out quiz which also involved running to select the correct answer. Melanie spoke about just how tiny bacteria are compared to animals and plants, how she was trained to go from a lab-rat to a polar scientist, and also explained how many of the things we use and love, like ice-cream and laundry detergent, are thanks to help from bacteria that live in the cold.
22 February 2019: NERC Open Day, Cambridge
On 22 February, the NERC Arctic Station hosted an Open Day (https://www.arctic.ac.uk/events/nerc-arctic-research-station-open-day ) at the British Antarctic Survey (BAS) headquarters in Cambridge. The event was open to the public, and to people interested in getting involved in research at the Arctic Station.
MicroArctic ESR Melanie Hay and supervisor Dr Arwyn Edwards attended the event, where Arwyn gave a talk about the work they have done in Ny-Ålesund over the last few years, including this latest field season. A brochure was also circulated to all participants, with a few examples of work being undertaken at the station, including the work done by Melanie and Arwyn on the MicroArctic project. The pdf of presentations at the event is also available digitally from the NERC Arctic Station site (https://www.arctic.ac.uk/wp-content/uploads/2019/03/Svalbard-Station-Summaries.pdf )
February 2019: American Association for the Advancement of Science (AAAS), Washington, DC 14-17 February 2019
ESR Alex Holland (Bristol) provided a short video testimonial about her personal experience as a Marie Sklowdowska Curie fellow entitled: Experience Europe while advancing your career. The video can be viewed here: https://ec.europa.eu/info/experience-europe-while-advancing-your-career_en
December 2018: Access to Bristol
ESR Alex Holland (Bristol) co-organized an Access to Bristol event in December 2018, which is where A level students attend an hour-long session and are introduced to the different opportunities available to them if they attend the University. Alex's session focused on the physical geography department, with a special focus on the glaciology centre and the exciting research conducted there. During this 2 hour-long session, students received a short background presentation and participated in three different hands on activities to provide an example of the topics currently being studied about the Arctic.
5 December 2018 : Presentation about fungal abundance and diversity on the Greenland Ice Sheet.
ESR Laura Perini gave a lecture about fungal abundance and diversity on the Greenland Ice Sheet at the University of Ljubljana. More than 70 students of Microbiology attended the event called Mikrobiološka družina. Below is a photo and a program of the event is available here.
9 November 2018: Presentation at Holar University, Iceland
ESR Ingeborg Klarenberg gave a presentation about her work at Hólar University (Sauðárkrókur, Iceland) to approximately 50 students and staff working in ecology and fisheries related fields.
23 October 2018: UK polar network presentation at the International Forum in St Petersburg
ESR Lucie Malard (Northumbria) gave an oral presentation to present the UK Polar Network aims and work + her research and the power of collaboration. The title of the presentation was: ‘The UK polar network and ECR collaboration for large scale projects’. Approximately 30 Russian Uni students/Young researchers attended the event.
Below are some photos from the event
10 October 2018 : Interview with visiting researcher
ESR Muhammad Zohaib Anwar gave an interview to visiting researcher Alex Dauncey-Elwood from Carleton University, Ottawa, Canada about the MicroArctic ITN. The interview covered the different aspects of this Marie Sklodowska-Curie ITN and especially its commitment towards training of Early Career Researchers through mobility, dedicated network events and research support. The interview was part of a larger study funded by the government of Canada to improve the transition of international STEM students to postgrad opportunities by optimizing policies. The interview will be published in a report.
September 2018: Science Festival, Denmark
Prof. Carsten Suhr Jacobsen (Aarhus) delivered 7 lectures in 7 different schools as part of Science Festival 2018 in Denmark. The audience included ~500 high-school students. The talks included the introduction to MicroArctic ITN in general and specifically “The ice sheet melting limits for microbial growth".
September 25, 2018; Tuesday Himmelev School, ollerupvej, Roskilde (45 students)
September 26, 2018; Wednesday Bramdrup School, Møllegårdsvej, Kolding (125 students)
September 26, 2018; Wednesday Kolding Gymnasium, Skovvangen, Kolding (50-60 students)
September 27, 2018; Thursday Roskilde Gymnasium, Roskilde (70 students)
September 27, 2018; Thursday Gefion Gymnasium, Copenhagen (30 students)
September 28, 2018; Friday Fjordbakkeskolen Taulov, Fredericia (120 students)
September 28, 2018; Friday Løsning School, Løsning (120 students)
August 2018: MicroArctic presentation in Siberia
During her secondment in Siberia, ESR Stine Holm (GFZ) gave a presentation entitled “MicroArctic” at the Russian-German field station in the far Northeast Siberia. 25 scientists from German and Russia were present with various scientific backgrounds e.g.; hydrologists, physicists, geologists and biologists. The talk was about the projects within the MicroArctic network and Stine's own project about microorganisms in permafrost and their response to warming conditions.
11 July 2018: Junge Uni Maria Alm
ESR Nora Els (Innsbruck) gave a presentation to approximately 15 young people about aerobiology at theYoung University Upper Austria event in July of 2018.
14 June 2018: Institute of Biology Bucharest. Romania.
ESR Antonio Mondini gave a presentation of the MicroArctic project and his results on microbial thermal response studies to a group of appximately 35 participants composed of researchers and PhD students.
9 June 2018: Langenachtderwissenschaften "Long Night of Science" 2018
The “long night of science” is an event which takes place once a year when large German scientific institutions hold lectures and demonstrations for the general public in order to present themselves and provide a general overview of their research topics. This year, about 2 thousand people visited the Telegrafenberg campus where the GFZ is located. Along with colleagues from the group ‘Interface Geochemistry,’ ESR Robin Wojcik presented mineral synthesis experiments, introduction to microscopy as well as visits of the laboratory.
7 May 2018: Interview with French TV Station ARTE
While in Ny Alesund for sampling for the MicroARctic project, ESRs Benoit Bergk Pinto (ECL), Rose Layton (Enoveo) and Alex Holland (Bristol) were interviewed as part of a documentary on polar bears diffused by French television station ARTE. The documentary can be viewed here:
2-4 May 2018: TACATA Workshop in Radstadt
ESR Nora Els (Innsbruck) participated in the TACATA workshop (Campus for talented kids) with a presentation about aerobiology. The workshop hosted approximately 120 young people and 200 adults over the course of three days.
April 2018: Sonnblick Observatory Project Activities 2018
ESR Nora Els (Innsbruck) contributed to the Sonnlick Observatory Project Acivities Information booklet: https://www.sonnblick.net/de/wissenschaft/aktivitaeten-projekte/
14-16 March, 2018: British Science Week Science Fair
As part of the British Science Week Science Fair, ESR Melanie Hay (Aberystwth) spoke to scholars about climate change. With the young people, she created an interactive display that tested how different glacial surfaces affect melt rate. [Lightbulbs represented the sun; large ice blocks represented glaciers.] "Glaciers" were covered in blue ice packs to represent lakes, polystyrene chips to represent snow, black plastic pieces to represent cryoconite/algae and a control with no cover. The young people asked wonderful questions and budding scientists provided insights. This activity targeted 1500 schoolchildren from across Wales. The theme of the event was: Change is Constant and the title of Melanie's stand was: ALGAE vs ICE SHEET
13 March 2018: PhD day at GFZ
On PhD day at GFZ, all PhD students present their work by either oral presentation, poster presentation or a PICO presentation. ESR Stine Holm presented her project by a PICO presentation followed by a discussion of the presentation in the poster session. A description of the event is available here: https://events.gfz-potsdam.de/phd-day-2018/
Please also see page 11 of the following booklet:
12 March 2018: STEM for Britain
ESR Lucie Malard participated in Stem for Britain http://www.stemforbritain.org.uk/ in March 2018. At this event, she presented a poster entitled 'Microbial Biogeography of Arctic Terrestrial Ecosystem' in front of Royal Society judges and politicians (MPs)
27 February 2018: Project Greenland 2018
ESRs Benoit Bergk Pinto (ECL), Rose Layton (Enoveo) and Nora Els (Innsbruck) took part in an outreach activity in a secondary school in France to introduce the polar environment, their PhD research projects and global warming. They each presented (10 min) their research project in front of the students and introduced Microbiology thanks to a card minigame. They also carried out a brainstorming session with the students concerning the future of the polar environments threatened by Global Warming.
23rd February 2018: Northumbria University, Newcastle, UK.
ESR 8 Muhammad Zohaib Anwar (mBioInform) gave a presentation to undergrad and grad students from the Data Analytics and Machine Learning program at Northumbria University about the role of Big Data Analysis in Arctic Microbiology. He also introduced MicroArctic project and the application of Big Data Analysis in MicroArctic with respect to his own research question and broader network level data integration.
February 2018: Newspaper and Website Article
ESR Nora Els (Innsbruck) was interviewed for an article about her fieldwork in Greenland in the University Newspaper "wissenswert" and for a special edition of Tyrolean Daily Newspaper. To view the article: https://www.uibk.ac.at/newsroom/lernen-abseits-des-hoersaals.html.de
30th January 2018: Northumbria University, Newcastle, UK.
ESR 8 Muhammad Zohaib Anwar (mBioInform) gave a presentation on how Bioinformatics/Data Science can help solve Microbiological bottlenecks and its role in the MicroArctic project to the Microbiology group that consisted of master’s and PhD students in addition to researchers
22 January 2018:CNR-ISMAR (National Research Council - Institute of Marine Sciences) in Venice (Italy)
ESR Laura Perini (Ljubljana) gav a presentation to marine biologists and physical oceanographers about her work in MicroArctic. Below are two photos and a certificate of attendance is available here.
22January 2018- 2 February 2018 Internship student at GFZ
ESR Robin Wojcik (GFZ) was shadowed by a 14 year old student visiting the university for 2 weeks. During the student visit, he explained his research project and laboratory experiments. Robin also worked with a master's student interested in joining the Interface Geochemistry group at the university.
23 January 2018 Presentation at Liceo G. Veronese in Chioggia (Italy)
ESR Laura Perini (Ljubljana) visited this high school where she gave a talk about MicroArctic to 35 students who will receive their diploma this year. Below are two photos from the event.
13 December 2017: Austrian Public Broadcast (ORF III) science program QUANTENSPRUNG
ESR Nora Els (Innsbruck) was interviewed about about bioaerosols and their survival in extreme atmospheric conditions. For more information, please follow this link: http://tv.orf.at/orf3/stories/2883575/
4 December 2017: Northumberland College Outreach Event: Antarctica Day with Polar Scientists
ESR Lucie Malard (Northumbria) participated in this outreach event where she presented her work in the MicroArctic project. For more information about the event, please click here.
November 2017: Talk at Austrian Polar Research Institute Annual Symposium and at MILAF 2017- Biophysical atmospheric processes
ESR Nora Els and her supervisor Birgit Sattler gave a talk entitled: Airborne Inoculation Sources to Microbial Communities in Arctic and Alpine Snow Ecosystems
11 September 2017: Polar and Alpine Microbiology Conference, Nuuk, Greenland
During the conference, a 1h30 poster session was organized for the public and the local high school was invited. The students were very keen on asking questions and were very interested in the research being carried out by the MicroArctic ESRs. Here are some photos from ESRs who had posters during this outreach event.
16 August 2017: Article in Tiroler Tageszeitung Online
ESR Nora Els (Innsbruck) was interviewed about sampling and work conditions on Sonnblick Observatory in the Austrian Alps by the Tyrolean Daily Newspaper. The article in German can be found here:
July 2017: Svalbard: Discussion with Lewis Pugh, endurance swimmer and United Nations' Patron of the Oceans
Lewis Pugh and his team stopped by the UK Research Station in Ny Alesund, where ESR’s Nora Els, Melanie Hay and Diana Mogrovejo Arias were hosted during the sampling season. The ESRs talked to him about MicroArctic, their individual scientific projects as well as the importance of Arctic science and the involvement of women in our network. Several tweets were sent in reference to this interaction.
19-23 July 2017: Visindaskolinn - Science School for 11-13 year olds
ESR Ingeborg Klarenberg (Akureyri) participated in a Microscopy workshop about spoiled food attended by approximately 100 11-13 year old children in Iceland. Some information about the event organised by University of Akureyri can be found here: http://www.visindaskoli.is/is/um-visindaskolann
July 20, 2017: UNIS, Longyearbyen, Svalbard
On July 20th, ESR Lucie Malard from Northumbria University gave presentation entitled ‘Bacterial diversity in Arctic soils and impacts of climate change.’ The aim was to present the individual research work she had conducted over the summer, as part of the UNIS microbiology course. The presentation was given to fellow classmates and anyone in the university interested in attending.
13 June 2017: Presentation about Bioaerosols at Laboratoire Ampère, Lyon, France
ESR Nora Els (Innsbruck) gave a presentation about Bioaerosols and her approach to assess the potential for arctic and alpine microbial air-biogeography and bioaerosols to act as inoculation sources on snow and ice surfaces to an audience of master and PhD students from the engineering school.
May 2017: Article in “Cratschla” (journal of the Swiss National Parks) with the title: Klein aber wirksam – Alpine Mikroorganismen im Klimawandel (Small but powerful – Alpine microbes and climate change).
An experiment within ESR Johanna Donhauser's (WSL) PhD project is connected to research activities going on in Swiss parks. Therefore this particular experiment and the general importance of microbes in cold dominated habitats such as the Arctic and the Alps in the context of climate change was described in an article for the journal Cratschla reporting activities in the parkThe journal is intended to inform the public about research and processes going on in the National Park in order to direct the attention of the public towards important topics related to environmental protection. The journal is promoted at the visitor centers of the park.
30 May 2017: Participation and poster presentation at Park Research seminar in Bern (Switzerland). Title: The impact of warming on the soil microbiome assessed by soil transfer on alpine summits along an altitudinal gradient
ESR Johanna Donhauser (WSL) gave a poster presentation and personal talk with other participants at the Park Research seminar in Bern. The audience was composd of people involved in research and administration in swiss natural parcs (natural and social sciences), approximately 100 participants. An experiment within this PhD project was performed close to the Swiss National Park, this PhD project is connected to research activities going on in Swiss parcs and was therefore presented at the seminar of park research in order to promote the project among scientific participants from other fields and non-scientific participants involved in administration, polititical and public relations activities related to park research.
5 May 2017: Presentation about the MicroArctic project at Laboratoire Ampère, Lyon, France
ESR Antonio Mondini (IBB) took advantage of a visit to Ecole Centrale in Lyon to give a presentation about his project within the MicroArctic network to a group of researchers and PhD students from various fields within the engineering school.
2- 4 May, 2017 Glacier Field Course at Sonnblick Observatory
This course was held by the University of Life Sciences Vienna and Technical University Vienna. During the course, ESR Nora Els (Innsbruck) gave a talk and explanation of methods informing students about her work at the Sonnblick Observatory and her research topic and methodical approach to investigate the link of microbial presence in Snow and Air. The talk was attended by 15 students and lecturers
25 April 2017: Presentation about MicroArctic project at University of Agronomic Sciences, Romania
On April 25, ESR Antonio Mondini (IBB) gave a rpesentation about the MicroArctic project to students in the University of Agronomic Sciences in Bucharest, Romania. Students came from diverse fields of veterinary medicine, biotechnology, and molecular biology. Some photos of the event can be viewed below:
21 April 2017: "Aktionstag", Young University of University of Innsbruck.
In April 2017, the University of Innsbruck ("Young University") organized a "Aktionstag" which is an open science day for schools. More than 2000 kids came to University to explore, listen and do little experiments. Volunteering scientists made little stations including a station attended by ESR Nora Els (Uni Innsbruck) called: "Some like it hot: Life in the extremes of ice, snow and air". The kids were especially shocked by the disgusting stuff growing in air, so it had an educative effect on them what is alive in our atmosphere. Some photos from the day are available below:
13 April 2017: Science in the Arctic and the MicroArctic project
On 13th April ESR Muhammad Zohaib Anwar (mBioinform) gave a presentation about science in the Arctic and about the MicroArctic project in general at the City School International, Dubai, UAE. The presentation was to encourage students of High school and Secondary school to pursue careers in science and science in the Arctic especially. Students were very intrigued and actively participated in the event.
11-14 April, 2017: Presentation at PEI Meeting in Rovereto, Italy (Polar Educators International) Education meets Science.
Birgit Sattler (PI at Uni Innsbruck), Klemens Weisleitner, Sabrina Obwegeser and Nora Els (ESR Uni Innsbruck) gave a presentation entitled: "How to bring the paradoxon of life in ice and air into the classroom?" The audience was included experts in the field but the majority were teachers who had no specific knowledge about this field of research. The meeting (which was held in a school in Rovereto) was organised to inform teachers about science and how to find ways to use this information in schools. Also pupils of the schools could attend certain workshops.
4 April , 2017: Science on the Ice
During the MicroArctic network event held in Akureyri, Iceland from April 3-8, 2017, project coordinator, Prof. Alexandre Anesio plus all 15 ESRs took place in a large scale outreach event open to primary school students. After a brief presentation by the project coordinator, students were encouraged to interact with the ESRs to ask them questions about their experiences as researchers in the Arctic.
More information here: http://english.unak.is/en/all-events/science-on-the-ice
29 March 2017: Summerhill Infant School
ESR Gilda Varliero (Bristol) visited the Summerhll Infant School in Bristol to talk about her experience in Svalbard during the dark season. She spoke to three different classrooms of 20-30 children each. The children were aged 3-5 years old.
14-16 March 2017: British Science Week: ALGAE vs ICE SHEET
In March, more than 1500 schoolchildren from across Wales visited Aberystwyth University as part of British Science Week. The theme of the science fair was 'Change is a Constant'. This was the perfect opportunity to talk to scholars about climate change and how microbes (dark algae) can speed the rate of melt. Students and faculty including MicroArctic ESR Melanie Claire Hay created an interactive display to test how different glacial surfaces affect the melt rate. They used lightbulbs to represent the sun and big ice blocks to represent glaciers. They covered the "glaciers" in blue ice-packs to represent lakes, polystyrene chips to represent snow, black plastic pieces to represent cryoconite/algae and a control with no cover. It was a really fun interactive experiment with some wonderful questions and insights from the budding scientists. The 'dark algae' melted the ice the fastest!
13 March 2017: Project Greenland Lyon
The MicroArctic fellows recruited to Enoveo (Rose Layton) and Ecole Centrale Lyon (Benoït Bergk Pinto) as well as some of the Principal Investigators of the MicroArctic network and the project coordinator participated in an outreach event targeting high school and primary school students organised in Lyon in March 2017. A program for the event is available here. Preparatory classes to teach the fundamentals of microbiology were composed of approximately 20 children at each session concluding with the “Project Greenland” outreach day where ESRs Rose Layton (Enoveo) and Benoit Bergk Pinto (ECL) delivered talks on their research. To view photos and more details of the event, please click here.
8 March 2017: MicroArctic concepts and methods
ESR Stine Holm (GFZ) gave a presentation about her concept and methods during the Geomicobiology group meeting at GFZ. This group is made up of over 25 people working in a broad range of subjets within the field of geomicrobiology.
February 2017: Sampling in Scarisoara ice cave in Romania
Along with his lab group, ESR Antonio Mondini (IBB) went to the Scarisoara ice cave to improve his sampling techinques. This was the first research group to reach a depth of 25.13 meters. The group was interviewed for both TV and by two local newspapers. More information is available here:
December 2016-January 2017: Creation of a MicroArctic facebook account
MicroArctic fellow, Lucie Malard (Northumbria) set up and coordinates the facebook account updated by MicroArctic fellows. The goal of the facebook page is to provide inormation to the general public about MicroArctic activities. https://www.facebook.com/MicroArctic
December 2016-January 2017: Creation of a MicroArctic twitter account
MicroArctic fellow, Diana Carolina Mogrovejo Arias (Brill) set up and coordinates the twitter account updated by MicroArctic fellows. The goal of the twitter feed is to provide inormation to the general public about MicroArctic activities. https://twitter.com/MicroarcticEsrs
December 2016-January 2017: Creation of a logo for the MicroArctic Network
Following the kick-off meeting for the network held in November 2016, ESR Robin Wojcik proposed several logos for the ITN and then incorporated suggestions from the other members of the network. The official logo was presented to the group in January 2017 and will appear on any publications produced by the network.
27 January 2017: 9th Education and Career Fair of Slovenia Informativa, Gospodarsko razstavišče, Ljubljana
On January 27, ESR Laura Perini gave a presentation about the MicroArctic project at the 9th Education and Career Fair of Slovenia Informativa, which took place in Gospodarsko razstavišče, Ljubljana. It was an event intended for high school students and the general public to encourage young people to pursue careers in science. For bigger picture, please click here.
13 January 2017: Presentation to Masters' students at University of Llubljana
MicroArctic ESR, Laura Perini, gave a presentation about the MicroArctic kick-off meeting to masters' students at the University of Llubljana in the framework of their course: Microbiology of extreme environments. For bigger picture, please click here.
12 December 2016: Presentation of ITN network
On December 12th, ESR Stine Holm (GFZ) gave a presentation about the ITN kickoff meeting and a general description of the ITN network during a group meeting of the Geomicrobiology group. This group is made up of over 25 people working in a broad range of subjets within the field of geomicrobiology.
2/11/16 Access to Bristol Program
As part of a program to encourage young people to pursue a program of higher education, ESR Alexandra Holland from University of Bristol gave a presentation about how microbes grow on glaciers and the MicroArctic project to a group of local secondary school students. Photos are available here.
More information about the program here:
30/09/2016 European Researchers' Night
Hancock Museum, Newcastle, U.K.
Dr. David Pearce from Northumbria University took part in Science Uncovered at the Great North Museum: Hancock as part of European Researchers' Night. The continent-wide initiative takes scientific research and showcases it in a fun, social setting.
All Micro-Arctic Early Stage Researchers will spend time on secondment at a second host institute within the consortium. A brief review of their time spent on secondment will be posted here.
ESR Benoit Bergk Pinto (ECL)
Secondment at Aarhus University ( August-September 2019)
I had the chance to go for a secondment in the Department of Environmental Science at Aarhus university, in Denmark. During this time, I was able to present and discuss my research to get some feedback from Professor Alexandre Anesio. This was very helpful concerning the chemistry of the microcosm experiment and the writing of the article from this experiment. I also learned a lot from Zohaib Anwar, PhD student in bioinformatics, and his feedback concerning my metagenomic pipeline gave me a lot of ideas to improve it. I also had the chance to participate in a lab meeting and a breakfast organized in the lab where I met with other PhD students and had very nice and interesting discussions in addition to have the chance to participate in the social life of the lab. All these scientific and social interactions have helped me a lot to improve the interpretations from some of my results and to enhance the scientific quality of my thesis manuscript that I’m currently writing in order to defend my PhD in the next coming months!
ESR Melanie Hay (Aberystwyth)
Secondment at DEX (March-September 2019)
My second secondment was with Dynamic Extractions (DEX). I undertook the secondment in three parts. Part 1: 25 March - 28 March (1 week) After some meetings with David Rooke, Colin Bright and Luis Muir about future work and possibilities, I was shown the Dynamic Extractions High-performance counter current chromatography (HPCCC) equipment in Plas Gogerddan. I spent time with Colin Bright and PhD student, Jess Friedersdorff, learning how the column works and getting insight into how the technology can be used in non-conventional ways to separate mixtures based on almost any criteria. It was a great opportunity to see the equipment being used in real time on an actual experiment, from maintenance, quality control, checks and troubleshooting to the actual successful experiment and data collection.
Part 2: 06 May - 11 May: Tredegar to visit DEX (1 week) In the second part of my secondment I spent a week in Tredegar at the Dynamic Extractions offices where I got to see the various equipment and columns. While I was there, I gave a presentation on my research and how I thought I could apply some of DEX's equipment, workflow, and expertise in my project. I also listened to presentations from other employees on their projects and work. There is a good mix of applying their current technology on projects for clients, and also on new method development like creating and testing more environmentally friendly solvents. During the secondment I observed the separation of a specific fraction for a project they were working on and helped perform a separation on an unknown mix, which was used as an exercise to help me learn the method. After the mix separation, we determined the fractions of interest and identified the compounds for each fraction on the HPLC by comparing the spectra of standards and samples.
Part 3: 22 August- 6 September (2 weeks) The final two weeks of my secondment involved raw metabolite extractions from my soil and cryoconite samples. This is exciting data, because I have previously done shotgun metagenomics on these same samples. I have already investigated the soil and cryoconite shotgun metagenomes for biosynthetic gene clusters (BGCs) and have identified 100s of clusters that make potential antimicrobial compounds or other secondary metabolites using antiSMASH. It is going to be interesting to link the compounds identified by LCMS to the predicted compounds from my dataset. I was kindly and patiently taught to do the extractions by Sumana Bhowmick, in Luis Muir’s lab. Although I didn’t get to use the HPCCC in my project, I have become more aware of the potential of their technology to further my work. For example, interesting compounds detected from the LCMS could be tested for activity using HIDEX screening and the Dynamic Extractions HPCCC columns could be used to isolate incredibly pure fractions of the compound of interest.
ESR Diana Carolina Mogrovejo Arias (Brill)
Secondment: Aberystwyth: Feb.-March 2019
The secondment at Aberystwyth University started on February 11th, 2019 and lasted until March 22nd, 2019. The first experiments were aimed at extracting DNA from the isolates of interest using the in-house methodology as well as specific kits, in order to obtain non-fragmented, high-quality DNA. Isolates I have brought from my collection at BRILL were used for these extractions. Later on, I was taught the DNA purification methodology prior to sending the DNA for sequencing. The method involved magnetic bead purification and quantification. ESR Melanie Hay was in charge of sharing this know-how with me. During the last week, stocks of all the isolates used were prepared and left for the collection in Aberystwyth and the DNA we had prepared was sent for whole genome sequence“
ESR Melanie Claire Hay (Aberystwyth)
Secondment: ECL, Lyon 24 May – 2 July 2019
I spent just over five weeks under the supervision of Dr Catherine Larose and Prof Timothy Vogel in the Environmental Microbial Genomics Group at École Centrale de Lyon. For a change, I had a blisteringly hot summer with record-breaking heat, instead of the usual chilly Svalbard summer fieldwork of previous years. While I was in France, I worked mainly on my functional screening experiment. The aim of the experiment was to screen soil and cryoconite metagenomic DNA from Svalbard for cold-active polymerases.
Tim and Catherine helped me plan my experiment and optimise my time. As a result, it was a very productive secondment and I am very happy with all that I managed to achieve and learn in my short time there. There were two broad aims: (i) confirm the identity of my cold-sensitive mutant strains and check the complementation conditions, (ii) prepare my environmental DNA, clone into my plasmid, and transform my strains.
To confirm my strains I extracted DNA from glycerol stock replicates of each strain, and then performed PCRs using each of the primer pairs I had designed to amplify and confirm the mutation in the polymerase gene. I also did a few complementation experiments with presence/ absence of various required nutrients, antibiotics and temperatures as additional confirmation of the correct strains and growing conditions.
Once confident of my strains, I did gel-clean-ups and size selections of my soil and cryoconite DNA and then cloned the cleaned up and concentrated DNA into a plasmid. Then I prepared my strains for electroporation and performed the transformation. The cloning was successful in some of the conditions, but not all. Unfortunately, I did not manage to grow any cold-sensitive clones, but I did pick over 800 clones that grew at 37 degrees to bring back with me to Aberystwyth.
I am planning to repeat the experiments in Aberystwyth, using all that I learnt in France to optimise the experiments here. I cannot thank Tim and Catherine enough for their challenging discussions and excellent input, and Benoit for his friendship and comradery. I fell in love with France while I was there, and cannot wait to return and see more of the country.
ESR Gilda Varliero (Bristol)
Secondment: Enoveo, Lyon 01/05/2019 - 02/06/2019
The main aim of this secondment was to develop a user-friendly and comprehensive software for primer design for qPCR and PCR applications. The strength of this software is the possibility to easily tailor the primers on specific taxonomical groups. Thanks to the construction of a dynamic phylogenetic tree, it is possible to dynamically select the sequences of interest to use for the primer design. ENOVEO works on a wide range of environmental samples, having to quantify and detect the presence of genes and organisms involved in specific metabolisms. Thanks to a collaboration with Dr. Cédric Malandain I was able to get useful suggestions on oligo designing and to understand how to deliver a user-friendly software. The added value of this experience was to live, for my first time, the industry work environment! Furthermore, I also had the chance to spend few days in the Environmental Microbial Genomics Group (École Centrale de Lyon) where we had interesting discussions on some bioinformatics software available for genome reconstruction from metagenomics data.
ESR Stine Holm (GFZ)
Secondment: Warsaw University, Department of Bacterial Genetics, December 2018 - January 2019
My last secondment was carried out at Warsaw University. It was a continuation of a one month research visit, carried out mid-April to mid-May, 2017, in the group of Associated Partner Lukasz Dziewit, Department of Bacterial Genetics, Warsaw University. The main aim of the secondment was to explore the potential of plasmid DNA in permafrost environments focusing on i) plasmid abundance and diversity in permafrost affected environments ii) the ability of plasmids to carry stress response genes, important in the adaptation to the chancing conditions iii) the optimization of plasmid extraction from environmental samples. The thawing of high Arctic permafrost affected soil cause a release of nutrients and leads to higher microbial activity. These environmental conditions have been suggested to create a “hot spot” for plasmid exchange. Plasmids have the potential to rapidly transfer genetic traits within a microbial community. Generally, plasmid diversity and the plasmid-mediated plasticity of soil microorganisms are studied by metagenomic sequencing, pure isolates or transformed bacterial cultures. Our knowledge about the role of plasmids in the adaptation of microbial communities to changing environmental conditions in the Arctic is still limited. Based on our previous obtained plasmid isolations from the Siberian tundra, a manuscript draft was written within the secondment period. This secondment made a tremendous improvement in my understanding of the potential role of plasmids in permafrost environments, their replication genes, mobility elements, host range and stress genes, which potentially are important in their warming environment. This secondment therefore played an essential role in the progress of my PhD project studying microorganisms in permafrost environments.
ESR Alex Holland (Bristol)
Secondment Lyon 06/2018-07/2018
I conducted my secondment at ENOVEO and École Centrale de Lyon with Dr. Catherine Larose, Professor Timothy Vogel, Benoît Bergk Pinto (MicroArctic ESR 2) and Rose Layton (MicroArctic ESR 12). Together we designed a nutrient addition experiment for snow environments. Benoît and I created snow microcosms using snow collected from Ny-Ålesund, Svalbard to mimic the snow pack environment that exists in the Arctic. My experimental goal was to study how microorganisms found in the snow pack respond to phosphorus addition, as these environments are typically phosphorus limited. The novelty of this experiment was the use of cryoconite particles as a potential particulate phosphorus source, as opposed to the commonly studied dissolved phase. Cryoconite is a rock derived particle found in abundance in glacier and ice sheet surface environments. If microorganisms in these environments can utilize this particulate phosphorus source, then it may not be as limiting as previously thought. With Rose and Benoît’s knowledge of 16S rRNA sequencing and qPCR analysis and my biogeochemistry background we were able to address both the geochemical and microbiology perspectives of this experiment. With the help of Benoît, Rose, Dr. Larose and Professor Vogel I was able to greatly enhance my understanding of DNA sequencing and bioinformatics during my time in Lyon.
In addition to the science, my secondment provided me the opportunity to explore France and become immersed in the culture. I spent my time living with a French host family, which allowed me to practice my French, they found this quite amusing, and learn so much more about Lyon than I ever could have hoped for. It was also extremely beneficial to spend an extended period at another University and in an industry setting at ENOVEO as it helped me to learn new and different scientific techniques that will be helpful to me in my future career.
ESR Johanna Donhauser (WSL)
Secondment Lyon 15/10/2018 -15/12/2018
My second secondment took place at the École Centrale de Lyon with Dr. Catherine Larose and Prof. Timothy Vogel. Here, I worked on the data analysis of laboratory study to investigate how alpine soil microbial communities respond to warming. One important part here was a metagenome dataset for one of my soils to investigate which microbial functions are altered in response to warming. Following a long discussion with the group, I refined the aims and hypotheses of my study to target more specifically genes of interest. I learned how to annotate metagenomic reads with different databases and assigning them to functional categories and in parallel, together with Benoît (MicroArctic ESR 2), I started to develop an assembly based pipeline.
I was also able to largely improve my skills in bioinformatics working with coding languages. I am very thankful for all the input I got for my experiment, both regarding methods to use and interpretation of the results I already had. This experience helped me not only to finalize the data analysis of my experiment back in Zurich, but enabled me to generally improve both my methodological expertise as well as my skills to critically plan and interpret experiments. I also enjoyed Lyon from the personal perspective, discovering French culture and food, practicing my French and participating in social activities with the group. I am also very grateful for the support of Benoît and especially Catherine who hosted me spontaneously for a couple of days after I moved out from a problematic landlord unexpectedly and everyone who helped me to find a new housing. Thanks to them I could continue my secondment in an enjoyable way and focus on science instead of housing problems.
ESR Robin Wojcik (GFZ)
Secondments at WSL and University of Innsbruck
Over the course of my PhD, I have conducted secondments at the Swiss Federal Institute for Forest, Snow and Landscape Research (WSL) in Birmensdorf, Switzerland with Johanna Donhauser and Beat Frey as well as at the University of Innsbruck (UoI) in the department of Ecology in Austria with Nora Els and Birgit Sattler.
I conducted the 1st half of my secondment at the WSL in October 2017 for two weeks. During this time, Johanna Donhauser and I worked together on the first manuscript about the samples we collected in Svalbard. This manuscript was recently accepted for publication in the journal ‘Annals of Glaciology’. I conducted the 2nd half of my secondment at the WSL between the end of June and mid-August 2018. Johanna Donhauser and I used this time to outline the two geo- and bio-facing manuscripts based on samples collected during a 10 day field trip to Iceland in April 2017. The manuscript I am writing about this project is now in the final stage of its preparation. Besides working on manuscripts, my visits at the WSL have provided me with a great opportunity to learn about soil microbial communities and multivariate statistical analyses. Note that in addition to the visits, Johanna and I regularly converse via Skype about the common work and progress.
My secondment at the University of Innsbruck was divided into seven visits of one week. In the period between November 2017 and November 2018, I visited the UoI bi-monthly. This secondment was initiated to support a collaborative initiative with Nora Els and Birgit Sattler. My visits were the opportunity to both discuss research questions and conduct field work in the proglacial area of Vernagt glacier where we conduct a monitoring experiment.
ESR Diana Carolina Mogrovejo Arias (Brill)
Secondment in Ljubljana September 2018-November 2018
My secondment at the University of Ljubljana started on Sep. 17th, 2018 and lasted until Nov 01st, 2018. The first experiments were aimed at determining the ability of fungal and bacterial isolates to grow at temperatures that can be considered mesophilic (and thus, that could hint at potential pathogenicity for humans). Isolates I have brought from my collection at BRILL as well as bacterial and fungal isolates from the collection of LJU were used for this experiment. Later on, we determined the resistance profiles of the bacterial isolates to 8 different antibiotics using solid media with different concentrations of the compounds. During the last week, stocks of all the isolates used were prepared and left for the collection in Ljubljana.
Photos from the secondment available here.
January 17th – February 3rd, 2019:
I spent two weeks in Ljubljana carrying out activities aimed at determining the hemolytic activity of my bacterial isolates. A new protocol for extraction of secondary metabolites from actively growing bacteria was developed and optimized. The protocol was a compliment to the activities carried out during the first secondment in 2018 and constitutes an important first step for future work (summer 2019) with the collection at BRILL and at Ljubljana.
July 5th – August 9th, 2019:
During these weeks in Ljubljana, the objective was to draft a joint manuscript with ESR Laura Perini. Confirmatory experiments were performed with the isolates from the collection of both the University and Brill, based on our previous work in 2018 and early this year. At the end of the 5-week stay, a draft manuscript was ready and in review with our coauthors from both our institutions. We expect to be submitting this manuscript soon to an Special Issue of the journal Frontiers in Microbiology
ESR Johanna Donhauser (WSL)
Secondment in Aberystwyth September 2018
I conducted my first secondment with Dr. Arwyn Edwards and Melanie Hay (MicroArctic ESR 13) in Aberystwyth in Wales. We were working on a study assessing ecosystem development after glacial retreat which has been an ongoing topic in both of our groups. Melanie and Arwyn had sequenced shotgun metagenomes for me and with the help of Melanie I started to analyze this data. I learned how to quality filter, assemble and annotate the data and in addition we were able to investigate the taxonomic composition of the samples. These analyses are the first steps towards assessing which microbial functions are important at different stages of ecosystem development. This understanding becomes increasingly important as with ongoing global warming large expanses of terrain are exposed where entirely new ecosystems develop analogously to in our study site.
I am grateful that from this collaboration we were able to obtain metagenomes for our study site which importantly complements the mostly taxonomy based investigations conducted so far. I am happy to have learned the first steps in the analyses of metagenomes from Melanie and we are staying in touch integrating the knowledge and experience of both of our groups for downstream analyses and interpretation of the data. I also very much enjoyed the social life and the surroundings of Aberystwyth (I have never seen so many sheep in my life), where Melanie has been a great host showing me around. Thank you, Melanie!
ESR Lucie Malard (Northumbria University)
Secondment in Svalbard and Lyon summer 2018
My last secondment was conducted in multiple parts, in collaboration with Dr. Catherine Larose’s group in Lyon. First, I carried fieldwork in Svalbard for 5 weeks over the summer of 2018. I sampled soil and snow samples around Longyearbyen and then travelled to Hornsund, for a stay at the Polish Research Station in southern Svalbard. In the meantime, MicroArctic colleagues collected samples from Ny-Alesund. In November 2018, I worked at the Environmental Microbial Genomics Laboratory at the University of Lyon, where I extracted DNA from the Ny-Alesund samples. The extracted DNA will be analysed using 16S amplicon sequencing and metagenomics. The aim of this project is to investigate if soil colonization by snow microorganisms during snowmelt occurs. This is an essential part of my PhD project and this secondment was essential to the completion of my project. It was also a great opportunity to meet Polar microbiologists working in France and in Poland and to create new collaborations.
ESR Muhammad Zohaib Anwar (mBioInform, Aarhus University)
Secondment at the School of Biological Sciences, University of Bristol, UK: 15/11/2018 – 31/12/2018
I completed my second secondment at the School of Biological Sciences, University of Bristol with Dr. Gary Barker’s group working on Environmental Genomics and Bioinformatics. The core aim of the secondment was to optimize a computational model to understand and evaluate errors introduced by the Reverse Transcription enzyme during the process of conversion of RNA to cDNA. During my six week stay at UoB, I was able to use the data generated at Aarhus University previously as a prototype and simulate data sets to compliment the results of the model that can be used to improve the RT errors in-silico. Gary’s bioinformatics expertise and guidance helped me to run the analysis planned for the secondment. This experience at UoB was essential for the progress of my PhD with both the collaboration and learning perspective. I am very grateful to Gary for giving time on daily basis for discussions and analyses. Thanks Gilda and everyone from their group to make my stay productive and enjoyable.
ESR Stine Holm (GFZ)
Secondment summer 2018 (Fieldwork in Siberia)
My first secondment was carried out at the Samoylov Island research station, in Northeast Siberia, this summer 2018. The main aim of the secondment was to do fieldwork that investigated permafrost environments of the High Arctic Siberia. I carried out sampling for 3 main purposes
i) active layer permafrost sampling for a core microbiome study of low centered polygons
ii) Sampling for environmental plasmid isolation from thawing permafrost environments
iii) Sampling for re-isolation of a specific methanogenic archaeon (Methanosarcina soligelidi) from a permafrost environment.
Furthermore I was learning about greenhouse gas (GHG) flux measurements from active layer permafrost, supervised by Dr. Christian Knoblauch and Dr. Tim Eckhardt (Hamburg University), and Philipp Wischhöfer (Köln University). Together with associated partner. Dr. Svetlana Evgrafova (Siberian Branch of Russian Academy of Sciences, Sukachev Institute of Forest, Russia), I did gas sampling from an in situ thaw experiment. We investigated the CO2 and CH4 emission by gas chromatography from a Holocene permafrost soil incubation experiment, which had been exposed to thaw for 2 constitutive years. While at the research station I also had the opportunity to do an outreach activity about the MicroArctic project at a colloquium with joined German and Russian scientists.
This secondment made a tremendous improvement in my understanding of what permafrost environments are and how they change by warming conditions. It therefore played an essential role in the progress of my PhD project studying microorganisms in permafrost environments, and how they respond to warming conditions. I was surrounded by geologists, biologists, botanists, geophysists, hydrologists, which created an interdisciplinary environment with the shared passion for permafrost leading to good discussions. This secondment furthermore played an essential role for me in learning how to carry out permafrost soil sampling, GHG flux measurements, gas and DOC sampling by myself.
To see photos from the seondment, please click here.
ESR Laura Perini (Ljubljana)
Secondment from 30/07/2018 to 04/09/2018 (Bristol, UK)
I carried out my second secondment at the University of Bristol (UK). As last time, I ran an incubation experiment in order to clarify the type of interaction occurring between fungi and ice algae thriving on the Greenland Ice Sheet (GrIS) surface. Contrary to the previous time I had the opportunity to use fresh algal material sampled in the 2018 fieldwork season. Healthy ice algae were exposed to two fungal species –Penicillium bialowiezense-like and Articulospora sp isolated from the GrIS in 2017 – in a high concentration treatment and incubated at +4 °C. Parallel treatments were exposed to the light cycle (14/10) and to darkness. Samples for scanning electron microscopy, light microscopy, pulse amplitude-modulated (PAM) fluorometry, ergosterol quantification and secondary metabolites extraction were collected at four time points (day 0 and then every seven days). The fifth and last time point will be collected after two months from the start of the experiment. A big big thanks to Miranda Nicholes, PhD student at the University of Bristol, who helped me set up the experiment and analyse the samples.
ESR Nora Els (University of Innsbruck)
Secondment 05/03/18 - 16/04/2018 (ECL, Lyon, France)
I spent my secondment at the Laboratoire Ampere of the Ecole Centrale de Lyon in France. For more information about my work there and some photos, please click here.
ESR Muhammad Zohaib Anwar (mBioinform, Denmark)
Secondment 20/01/2018 – 04/03/2018 (Northumbria University, Newcastle).
I carried out my first secondment at Northumbria University, Newcastle with Lucie Malard and David Pearce's group. The main aim of the secondment was to collaborate for Bioinformatics analysis and data sharing. We decided to work on MicroArctic deliverable “A microbial bio-geography map of the Arctic”. I analyzed the ~200 samples collected from the Arctic over the last sampling season. We investigated the environmental factors that drive the microbial community assembly in Arctic using multiple statistical tests. We were also able to create a microbial bio-geographical map as a deliverable. We are now in process of writing a manuscript for these results.
In addition to the results, this secondment helped me to start the MicroArctic Search engine optimization process by using this data as first batch of reference. The MicroArctic Search Engine idea was proposed during the PAM conference in Greenland which was well received, and I am in the process of developing a prototype of it. This experience at Northumbria was essential for the progress of my PhD with both the collaboration and learning perspective. It gave me an opportunity to carry out methods that I had developed during the first semester of my PhD to implement on a big data. While I was in Northumbria, I also got an opportunity to do outreach activities and it gave me an idea about British culture and workplace experience which is very valuable and i am thankful to everyone at Northumbria University who helped me during my time there.
ESR Rose Layton (Enoveo, France)
Secondment: November - December 2017 (GFZ, Germany)
I carried out one of my secondments at the University of Potsdam, Germany. This took place over November and December and the main aim of the secondment was to discuss and develop environmental plasmid isolation techniques. We concluded that one of the major limitations to plasmid isolation is that plasmid DNA is thought to make up a small fraction of the total DNA in the environment. This is further exacerbated in the many pristine environments that make up the Arctic as cell densities tend to be fairly low. To circumvent this, we carried out enrichment trials of snow which had previously been used on permafrost with some success. This involved culturing snow bacteria at room temperature under the hypothesis that this would increase not only bacterial density but also plasmid concentration. We were able to visually see a rapid increase in bacterial density of the snow bacteria and could isolate DNA using the classic alkaline lysis technique. Using equipment and strategies developed for very small yields of DNA, we were able to visualise distinct DNA bands which could represent potential plasmids within snow bacteria.
This experience was essential for the progress of my PhD with both the discussion and practical element of the secondment proving critical to moving ahead with environmental plasmid isolation techniques. It gave me an opportunity to carry out methods developed in Potsdam on a new environment and sparked new methodological ideas which will help with my subsequent development on return to Lyon.
ESR Laura Perini (Ljubljana)
Secondment: 17/10/2017 to 30/11/2017 (Bristol, UK)
I spent my secondment at the University of Bristol (UK), where Alex Holland and Gilda Varliero, also from the MicroArctic project, are working on their PhD. As background, this summer I did some fieldwork on the Greenland Ice Sheet (GrIS) where I isolated several fungal species, but two of them in particular seemed to have some kind of interaction with the ice algae that are causing a darkening of the GrIS surface. A novel incubation experiment was designed to identify the type of relationship occurring between ice algae and the two fungal species Penicillium bialowiezense-like and Articulospora sp. To clarify and unravel the nature of the association we studied the three biological components of the ice environment: fungi, algae and bacteria. My work focused on the fungal component and I have been collaborating with Miranda Nicholes, PhD student at the University of Bristol, who took care of the bacterial component and Christopher Williamson, PostDoc at the University of Bristol, who took care of the algal component. After checking the algae were healthy, ice algae was exposed to the two fungal species in a high concentration treatment and incubated in a cold room with lights for four weeks. We collected samples at four time points, day 0 and then every 7 days. On those samples the following analyses were or will be performed: ergosterol quantification, secondary metabolites, scanning and electron microscopy, inorganic and organic nutrients, major ions, and algal abundance all of which will help to clarify the potential role of fungi in degradation, endophytic associations or bio-control of ice algae.
This secondment was not just about working and collecting data. It gave me an idea of how bad English weather can be, but also the opportunity to network with smart and helpful scientists. I would like to thank all the people who worked with me and helped me there; they were amazing.
ESR Antonio Mondini (IBB)
Secondment: 8/05/2017 to 30/06/2017 (WSL, Birmensdorf)
I spent almost two months for my secondment at Swiss Federal Research Institute WSL Birmensdorf (Zurich), where actually both Dr. Beat Frey and Johanna Donhauser (PhD student) are working. They are mainly focused on the influence of climate change on Arctic and Alpine soil microbes at the ecosystem level. During the secondment I improved my skills in microbiology, especially in bacterial isolation and DNA/RNA extraction from soil. I tested a new bacterial isolation method trying to recreate the bacteria’s original environment on a Petri dish and performed a heat shock experiment on soil samples in order to evaluate how the microbial community react to the increasing temperature. I learned how to extract RNA from soil samples without contamination and how to create a cDNA library. On this library, we settled up the best parameters to perform qPCR analysis avoiding contaminations and background noise. With qPCR technique, we were able to quantify the expression variation of my target genes involved in DNA/RNA synthesis after exposing the bacterial community to a thermal shock. Actually, we established a collaboration to work together on the same samples evaluating either the bacterial altered activity associated with soil formation and the different enzymatic expression of specific genes involved in DNA/RNA synthesis. During these two months, I was also able to visit Switzerland, an amazing country full of history and breathtaking landscapes. This was especially a great opportunity to create new contacts, improve my scientific network and learn how to relate with other scientists from all around the world.
Click here for photos from Antonio's secondment.
ESR Gilda Varliero (Bristol)
Secondment April-June 2017 (Akureyri)
I carried out my secondment from Bristol at University of Akureyri in Iceland in April and May 2017 under the supervision of Oddur Vilhelmsson. While in Iceland, I shared an office with Ingeborg Klarenberg, a MicroArctic PhD student. During my stay, I participated in several field sampling trips and collected many samples that will be useful for the testing of a bioinformatics pipeline to study SNPs in microbial communities. In fact, next year I will develop a tool for the annotation of SNPs in conserved domains. In particular, I will test the pipeline on this data to study the cold adaptation SNPs between communities. Samples were collected in 3 different hydrothermal areas around Akureyri and Reykjavik, and were processed while I was at the university of Akureyri. First, I performed cell cultures from the collected samples, trying to get different isolates out of them. The cultures were grown with different media and temperatures. The idea was to have representative genomes to use as references in the testing of the pipelines. Furthermore, I extracted the DNA from the samples.
This experience was essential for the progress of my PhD project. It helped me to develop my skills and have greater consciousness of the risks of sampling in dangerous environments such as a hot spring field. It also gave me a great opportunity to work in a microbiology lab, learning the cons and pros of techniques of cell isolation and giving me a better understanding also of my future bioinformatics work.
Gilda collecting samples in the field with PI Oddur Vilhelmsson (photos courtesy of Anssi Ruuska).
ESR Ingeborg Klarenberg (Akureyri)
Secondment at NHM January - April 2017
It was a huge change to go from Iceland to London and it took me some time to get used to cycling on the left, cycling in crazy traffic and the tube etiquette. Going to the Natural History Museum every day though, was like a dream coming true. I don't know how often I walked underneath the blue wale skeleton to buy a coffee. But of course I went to Anne Jungblut at the NHM for the science and spend time in the lab (with an open view for museum visitors to see scientists at work) testing primers targeting different nitrogen fixation genes for qPCR. This took longer than expected, but in the end I could do some plasmid cloning. The gene sequences were checked by sequencing and most of them belonged to Cyanobacteria. Discussing my project also helped focusing and getting the feeling that it makes sense what I am working towards. I got to meet a lot of interesting people, other PhD students working on microbiology in arctic environments and I followed a workshop on using bacterial pigments as textile dyes.
Photo below: Ingeborg in Hintze Hall
ESR Lucie Malard (Northumbria)
Secondment 01/01/2017 to 28/02/2017 (Brill)
I went on secondment to Dr Brill + Partner, Institute for microbiology in Hamburg, Germany, where Diana Mogrovejo pursues her phD. She works on pathogenicity of environmental microorganisms and investigates antibiotic resistance in arctic microorganisms. While on secondment, I further developed my skills in practical microbiology, notably in the culture of microorganisms using new media and techniques for isolation. Together, we tested methods to run antimicrobial assays on environmental organisms, aiming to determine the best parameters for growth of Arctic bacteria which can be fastidious to culture. From this work, we began determining which phyla may be interesting to test and established collaboration to work together on isolating and identifying potentially valuable microorganisms.
This secondment was a great opportunity for skill development, networking and making industry contacts. However, great experiences aren’t all about work. Living in a different country, learning German and not being able to communicate properly are all amazing experiences. During this short time, I took the opportunity to wander around Germany and discovered many cities and landscapes full of history.
ESR Alexandra Holland (Bristol)
Secondment UNIS 20/11/16-26/11/16 and 25/04/18-20/05/18
I conducted my secondment with UNIS in Svalbard in two parts, both of which centered around collaborations within the MicroArctic network. The first part of my secondment consisted of studying the glacier forefield of Longyeabyen glacier. It was a collaboration between many ESRs including Robin Wojcik, Stine Holm, Johanna Donhauser and Lucie Malard. The study aimed to investigate the change in different microbial and geochemical factors that have changed with the amount of time since the glacier’s retreat. It was a successful collaboration that resulted in a publication titled, ‘Linkages between geochemistry and microbiology in a proglacial terrain in the High-Arctic’.
The second part of my secondment took place in Ny-Ålesund, Svalbard in collaboration with Rose Layton, Benoît Bergk Pinto, Lucie Malard and Dr. Catherine Larose. This collaboration studied the seasonal snow pack environment from its initial accumulation until its eventual melt out in the spring. The aim was to investigate the microbial and geochemical distribution within the snow pack and identify changes that occurred throughout the winter and spring season. The field work was a success and I learned a great deal about correct protocols for collecting samples for microbial analyses and post sampling processing. Furthermore, we had ample interaction with Arctic scientists from around the world, which allowed us to extend our professional network and make personal connections, which will be greatly beneficial at the end of our PhD.
A number of network wide training events will be organised over the course of the MicroArctic project. A list of events is provided below and more specific information will be added for each event as the network progresses. The first network event will take place at the University Centre of Svalbard (UNIS) pictured here below.
Photo taken from: http://www.eu-atp.org/wordpress/?cat=14
20-27 November 2016
Project Kick-off meeting
Fieldwork in microbial ecology.
Schedule for the event
3-9 April 2017
Further skills in microbial ecology
Selective isolation and culturing techniques. Schedule for the event.
April 19-24, 2018
Mid term review + review of ESR projects
Innsbruck + Obergurgl
Outreach and popular scientific writing. Schedule for the event.
June 7-11, 2017
|Amplicon based microbial community analysis.|
19-24 May, 2019
Indigenous technical knowledge and scientific method
Bio prospecting, bio politics, political ecology. Schedule for the event.
8-12 September, 2017
International Polar and Alpine Microbiology Meeting
Conference plus management meeting. Programme here. Minutes from management meeting under Management tab.
19-24 May, 2019
Careers plus final network event.
CV Writing, final conference plus outreach. Schedule for the event.
State of the art training
Training activities which may be of interest to certain ESRs but not necessarily to the entire group will be posted here:
PHREEQC-i Short Course on Geochemical Modelling: July 17-21, 2017
For more information about this short course offered at GFZ, Potsdam, please view the attached flyer.
Conferences which may be of interest to ESRs will be posted here:
Polar and Alpine Microbiology 2019: Hamilton, New Zealand (4-8 February, 2019)
For more information: https://www.confer.nz/pam2019/programme/
EGU 2018: Vienna, Austria (8 - 13 April 2018)
For more information: https://egu2018.eu/home.html
Polar 2018: Davos, Switzerland (15-26 June 2018)
For more information about this conference: http://www.polar2018.org
International Glaciological Society Symposium on Cryosphere and Biosphere: Kyoto, Japan (14–19 March 2018)
For more information about this conference: https://www.igsoc.org/symposia/2018/kyoto/
Polar and Alpine Microbiology 2017: Nuuk, Greenland (8-12 September 2017)
For more information about this conference: http://pam2017.org
Goldschmidt Conference 2017: Paris, France (13-18 August 2017)
For more information about this conference: https://goldschmidt.info/2017/
Clare Desplats is the project manager for the MIcroArctic network.
Clare has worked as a project manager in various Marie Curie Action's projects and other international projects for over 10 years and will work closely with all consortium members, ESRs and the European Commission for the successful management of the MicroArctic network.
For any questions related to the MicroArctic nework, please contact Clare at: