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Progress reports semester 1 semester 2 semester 3 semester 4 semester 5

Progress reports

MicroArctic fellows will provide semi-annual progress reports detailing their research to date. As the reports become available, they will be posted here.  See the side nav bar for reports by semester.

 

 

 

 

 

 

 

 

 

Semester 1

First Progress Reports

ESR 1 Alexandra Holland: University of Bristol

During the first reporting period l have made significant progress on the Jaboratory analyses of my samples collected from the Greenland Ice Sheet in 2016. 1 have learned how to operate multiple instruments l have never used before, and understand the different methods required for each analysis. My laboratory analyses have included a complete nutrient profile and TOC levels in over 150 samplescollected during the 2016 Green land field season . l have also begun to collaborate my results with other members of the project who are investigating the microbiology of the samples. Additionally, 1 am involved in a collaborative project with other ESRs that investigates the geochemical and microbial succession in the Longyearbyen glacial forefield, with samples collected during the MicroArctic kick-off meeting in Svalbard.

The figure below shows that under the term glaciology there are many different subtopics to special ize in. I specialize in Biogeochemistry, which means that l analyse many different factors that make up the surface chemistry of a glacier or ice sheet. By studying this we can better understand how the microorganisms are able to survive in such an extreme environment and why certain species survive better than others.

ESR2 Benoït Bergk Pinto: Ecole Centrale Lyon

I am looking for possible syntrophic relationships between bacteria that are involved in different geochemical cycles. The initial step is to sample the bacterial community and use both ‘omic methods (metagenomics, metatranscriptomics) and 16S rRNA gene OTUs to describe the genes and microorganisms present. Then I will apply bioinformatics tools to find co-occurrences between genes involved in pathways related to different geochemical cycles ( in the figure: Nitrogen = blue, Sulfur = yellow/orange and carbon = red). This step will identify organisms that are potentially in syntrophic relationships. These candidates might need to be isolated by enrichment experiments and further studies.

ESR 3 Lucie Malard: Northumbria University

These few months have been essential in the development of the project. First, DNA extractions were practiced and the sequencing protocol, refined. Soil samples were collected from Svalbard in November 2016 and used for microorganism culture, DNA extraction and sequencing. This has also been the time to plan future field work in various locations and prepare the first secondment in Germany, where I currently am. This time is to refine microbiology techniques and protocols, culture microorganism from various types of samples from Svalbard and run antimicrobial/virucidal assays on these cultures.

ESR 4 Nora Els: University of Innsbruck

I started with a comprising literature research about aerobiology. After the first field work in Longyearbyen I worked on establishing and improving field and lab methods and inquired their variability. Currently I consider on which metadata to use, and how to obtain it and try to improve field sampling methods for cold and dry conditions.

ESR 5 Stine Holm: GFZ

In the first month as an ESR in the Microarctic ITN network I started by planning a sampling of a glacial forefield at Svalbard. This implied considerations on how to cope with the challenges of sampling in the dark winter period of Svalbard, the transportation of the samples, and hypothesis behind the sampling. In addition considerations on which analysis to carry out and how to work together as a group of ESR microbiologists and biochemists to create an interesting scientific story behind the sampling. From a microbiological perspective the sampling was a study of how the microbial community changes along with soil formation. The sampling was carried out in connection with the first network meeting at Svalbard, November 2016. I was processing the samples by extracting total nucleic acid, quantification of DNA and running PCR targeting the overall 16srRNA, archaeal community and also specific the methanogenic community of the samples. The samples are being amplicon sequenced according to 16srRNA miseq illumina sequencing. I have been developing my main concepts and the methods behind by carrying out a literature search. The concepts were planned based on main topics, the sampling material to analyse, and which methods to use. Next step will be to finalize lab work and sequencing analysis of Svalbard samples and present the work at the next ITN meeting primo April 2017. Secondly to start up a project in corporation with Dr. Dziewit from Warsaw University to study the abundance of plasmids in permafrost environments, their potential to carry cold adaptation genes and genes involved in methane cycling. In addition to start up a project focusing on methanogenic Archaea in permafrost, their abundance and their response to thawing in terms of methane production.

ESR 6 Robin Wojcik: GFZ

The first six months of my project were mostly dedicated to literature studies and definition of my research objectives. I will investigate the links between weathering and subsequent properties of nutrients in different landforms and ecological units of forefields in Arctic settings. This way I will hope to derive an integrated and interdisciplinary overview of the dominant parameters driving the variability of weathering and assess what determines their heterogeneity in the landscape. First set of samples collected in a forefield chronosequence on the Longyearbreen glacier, Svalbard are being analysed. I am planning the next field sampling campaign to Iceland in April, where I will collect samples in diverse proglacial areas. I am working on producing data for abstracts for summer conferences.

Chronosequences enable us to study the time-dependent soil biogeochemical succession sequences in receding glacier forefields. Recently deglaciated areas gradually develop into soils as they are affected by weathering, ecological colonization and soil forming processes. Besides time, geomorphological processes and vegetation cover variability are dominant factors controlling the heterogeneity of soil development through weathering. The geomorphological setting of forefield is the result of the overlap of various glacial, glacio-fluvial, periglacial, slope and eolian landforms. Each of the diverse forefield landform units are characterized by specific and consistent properties such as topography, composition and physical properties of surface material, ecological communities and hydrological conditions. Weathering is responsible for the cycling and possible build-up of labile autochthonous nutrient pools in the early stages of soil development. In conjunction with any time-dependent changes, landform units can be used as a spatial support to investigate the heterogeneity of settings that link weathering to nutrient cycling in glacial forefield.

ESR 7 Johanna Donhauser: WSL

In my PhD project, I assess the influence of climate change on Arctic and Alpine soil microbes at the ecosystem level. To this end, I use both field and laboratory based approaches investigating various Arctic and Alpine environments such as high alpine soils, permafrost and glacier forefields which will all be strongly affected by climate change. As a field based experiment, in 2016, a soil transfer experiment was established along an elevational gradient on mountain summits and between the north and the south side of the summit in order to mimic climate change by transferring soils along these natural climatic gradients. The same experiment will be established in the Arctic in 2017. Moreover, at a different site, an experiment to study permafrost thaw under field conditions was established. Microbial diversity and function in these experiments will be analysed at the genetic level with a focus on N-cycling genes using a suit of molecular tools amplicon sequencing, qPCR and metagenomics.

ESR 8 Muhammad Zohaib Anwar: mBioinform

The first reporting period was mainly about understanding the research questions and meeting fellow ESRs and PIs in MicroArctic meetings. Additionally, my individual major task was to standardize the pipeline for Amplicon based microbial community analysis by comparing different environments such as Qiime, Qiime 2 and Vsearch/usearch including different algorithms at each level of pipeline. This task was completed in the first reporting period.

ESR 9 Laura Perini: University of Ljubljana

During these months I have been working on fungi and bacteria obtained from two different samplings from cold environments (Greenland and Svalbard). From the Greenland samples we isolated different fungal species. According to the sequences analyses we found 4 new species. Interestingly, one species was dominant in all samples. This dominant Penicillium sp. appears to be a new species from Greenland, which could be involved in the degradation of the algal biomass causing the black colouring of the ice. From the Svalbard sampling we obtained several Penicillium- and Cladosporium-like isolates, but also some other fungal genera. We are waiting for the results of the selected phylogenetic markers sequencing.

ESR 10 Antonio Mondini: Institute of Biology Bucharest

During these months, I have been working on bacteria obtained from cold environments (Alaskan and Siberian ice wedge). The study covered: strain cultivation on M92 liquid and solid media (Glaciibacter superstes) and on liquid and solid media (Psychrobacter arcticus), glycerol stocks preservation of both strains, genomic DNA extraction of both strains, PCR amplification of 5 genes encoding for aspartate transcarbamoylase, carbamoyl phosphate synthetase (CLN and SYN subunits), dihydroorotase, carbamate kinase from Glaciibacter superstes, bacterial expression and partial purification of aspartate transcarbamoylase gene from G. superstes. Bacterial colonies were isolated from samples collected from Svalbard lake ice (6 colonies) and marine sediments (10 colonies) using R2B/R2A and MB media, respectively, at 4 and 15°C.

ESR 11 Ingeborg Klarenberg: University of Akureyri

During the first months, a research plan was written and research questions were formulated. In October, lichen and moss samples were collected in the Icelandic highlands. DNA was extracted from all of them and from some of them RNA was extracted During the last two months of the first half year work on bacterial isolates from lichens was started.

ESR 12 Rose Layton: Enoveo

A preliminary review of the literature has revealed a significant deficit of research regarding horizontal gene transfer (HGT) in the Arctic. Given HGT is evidenced as a major driver of evolution in microbial communities, it has the potential to provide a fundamental role in the adaption of Arctic communities to the dramatic changes seen as a result of climate change. Plasmids are considered major vehicles of HGT. Therefore, my main research progress has been in the development of a method suitable for isolating the environmental plasmid community for metagenomic sequencing. I am also curating a database of plasmid specific genes, as no such database currently exists in order to analyse metagenomic datasets for plasmid marker genes.

ESR 13 Melanie Claire Hay: University of Aberystwyth

In my first six months, I have spent time finding my feet in a new country (UK) and town (Aberystwyth), researching a new field (microbiology), travelling to exotic locations (Svalbard) and getting to know my new supervisors, colleagues, ESRs and friends. I have received training in a number of lab techniques at Aberystwyth University and in field safety in Svalbard. I have also been mentoring third-year dissertation students and making the lab feel like home. The most significant work in this period has been the completion of a Literature Review, which I used as a tool to outline the scope of my project. I feel well situated to dive into the meat of my project in the next 6 months.

ESR 14 Gilda Varliero: University of Bristol

These few months have been essential in the development of the project. First, DNA extractions were practiced and the sequencing protocol, refined. Soil samples were collected from Svalbard in November 2016 and used for microorganism culture, DNA extraction and sequencing. This has also been the time to plan future field work in various locations and prepare the first secondment in Germany, where I currently am. This time is to refine microbiology techniques and protocols, culture microorganism from various types of samples from Svalbard and run antimicrobial/virucidal assays on these cultures. This is a photo of me in front of the computer cluster in the School of Biological Sciences at the University of Bristol. Being a bioinformatician often involves dealing with huge amounts of data, requiring more processing power, memory and storage than can be achieved on a desktop computer.

ESR 15 Diana Carolina Mogrovejo Arias: Brill

The first samples of snow, ice and water were collected in Svalbard, Norway. Several culture media were assayed to promote the growth of the bacteria present in the sample and the optimum media concentration was determined. A few isolates have been obtained from the samples already (at different incubation temperatures)

Semester 2

Available September 2017

Semester 3

Available March 2018

Semester 4

Available September 2018

Semester 5

Available March 2019

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