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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 Benoît 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

The work that I have done during these first five months has been essential to structure my research for the coming months. In particular, I have deepened my knowledge on metagenomics and metatranscriptomics analysis and I have learnt a set of coding languages and programs that will constitute my main tools for conducting my research during the upcoming years. Two months ago I began to develop a web tool for the design of primers that will be soon available to the public.During these months I have extracted the DNA from samples of a Welsh water basin where the presence of geosmin and MIB has been detected. Part of the further analysis on these samples will be carried on with the primers that will be designed by my primers design tool.In these months I have also been planning the secondment that I will conduct at the University of Akureyri during the months of April and May.

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

Second Progress Reports

ESR 1 Alexandra Holland: University of Bristol

Great progress was made during my second reporting period. I produced enough data from the 2016 Greenland samples to be able to present a poster at two major conferences around the world. My results showed Concentrations of inorganic nutrients ranged 0.5-3ppb for PO43-, 13-22ppb for NH4+, and 0-9.5ppb for NO31 across the five representative habitats. In contrast, nutrients were found in higher concentrations in their respective dissolved organic phases with TP reaching 1.5-7ppb and TN reaching 8.5-250ppb. Concentrations of dissolved organic phosphorus (DOP) were found to be 9 times higher than inorganic fractions, while 97% of nitrogen was found in the dissolved organic phase (DON). DOC concentrations ranged from 80ppb to as high as 7ppm. The high relative concentrations of DON, DOP, and DOC, provide strong evidence for efficient nutrient cycling by microbial communities on the ice surface. Relatively low concentrations of DON, DOP and DOC in supraglacial stream water suggest that microbial habitats facilitate retention of such nutrients within the ice surface, permitting their continual reuse and recycling. Additionally, I completed a six-week long field season in Greenland where I collected the samples necessary to complete the second chapter of my thesis. Analysis on those samples will begin soon.

This is a photo taken of me during field work in Greenland this past June. This photo shows me digging a snow pit that I would later use for one of my experiments. This experiment was part of my research into documenting the elution of nutrients from the snow pack into the supraglacial environments. By studying the transition season from snow to slush to bare ice, we hope to document the initial algal bloom and research what inputs and factors affect the success of the bloom.

ESR2 Benoît Bergk Pinto: Ecole Centrale Lyon

Based on metatranscriptomic and metagenomic analysis of Arctic microbial communities living in frozen drysnowpacks, microorganisms appear to not only be interacting with their chemical environment, but also with each other.

Indeed, the study of antibiotic resistant genes has highlighted a positive correlation between the level ofcarbon in the environment and the level of transcription of such genes. This trend could be a first clue thatbacterial competition can become more intense when the snow becomes less oligotrophic.

Predicted response in ARGD (Antibiotic Resistance Gene Determinants) diversity (grey dots) and bacterial (positive) interaction network average connectivity (orange dots) to changes in carbon content in Arctic snow environments. In the networks, red dots represent OTUs, red lines represent (positive) interactions.

ESR 3 Lucie Malard: Northumbria University

These past few months, I planned and conducted fieldwork in the Arctic, notably Iceland, Svalbard and Norway and planned sample collection with collaborators in Alaska, Canada and Russia. I also further developed my skills, notably in bioinformatics with a large focus on sequencing analyses. I also started learning GIS and will pursue my learning in more depth over the next few months. The rest of my time was dedicated to literature review and manuscript writing for publications.

ESR 4 Nora Els: University of Innsbruck

During the last six months, I took a range of air samples from alpine and several arctic environments. The planning, organisation, preparation and fieldwork took a major part of my time. I also tried to further refine the lab analysis to get consistent results and discussed obtained values with atmospheric scientists. I had the chance to contribute on a paper on Airborne Bacteria above Svalbard and submitted an abstract for a conference. I further supervised two Bachelor students, who helped me greatly with lab- and fieldwork.

Further, I identified potential cooperations within the project and am currently working on further defining and preparing collaborative work. In the coming months, I will spend a lot of time on sample processing and data analysis to get a first idea about spatial and temporal variation of bioaerosols.

The picture shows an impression from fieldwork in NyAlesund (Svalbard, 79°N) on Vestre Broggerbreen Glacier. Due to the high wind speed and strong wind gusts we had to stabilize the tripod with the air sampler with the heaviest we had in the field: the backpack of the supervisor and one of our guns for polar bear protection. In the picture it seems as if the sampling setup is situated on bare ice, but in reality it was very wet granular melting slush, so during the time waiting for the sampler to finish we got cold wet feet. However, fieldwork is amazing !

ESR 5 Stine Holm: GFZ

In this reporting period as an ESR in the MicroArctic ITN network, two main projects were started up. The first project was aimed at describing the circum-Arctic abundance of methanogenic archaea. The second project is about the effect of permafrost thaw on circum-Arctic methanogenic communities. An abstract was submitted to the Polar and Alpine Microbiology conference (PAM), 2017, about this project. A month long visit in the laboratory of Dr. Lukasz Dziewit was conducted at the University of Warsaw, Poland. The aim of the visit was to study the abundance of plasmids in permafrost environments, their potential to carry stress related genes and genes involved in methane cycling. A report was carried out about this visit and the outcome. An experimental design for a methanogenic archaeal enrichment culture experiment is in process, with the aim of isolating plasmids from the methanogenic archaeal community.

I attended the 2nd ITN meeting in Akureyri, Iceland, which involved workshops about geochemistry, microscopy, geology, ArcGIS, experimental design, glaciology and much more, all having the fantastic topic of research in the Arctic in common.

A week long course in bioinformatics was carried out at mbioinform in Copenhagen. The course covered the workflow from preparing amplicon libraries for sequencing, sequencing methods, the analysis of the sequences and the statistically evaluation.

Furthermore a cross ESR project about  weathering effects, geochemical cycling and microbial succession at a glacial fore field cronosequence in Svalbard is in progress, with the aim of submission in late October. This project will furthermore be presented by a poster presentation at the Goldschmidt conference, Paris, France, 2017, and at the Polar and Alpine Microbiology conference, Nuuk, Greenland, 2017.

The figure presents the experimental design behind the currently ongoing study of 1) the methanogenic abundance in circum-Arctic and 2) The response of the methanogenic archaea community to thawing permafrost due to global warming.

ESR 6 Robin Wojcik: GFZ

After the second MicroArctic network meeting that was held in Akureyri, Johanna Donhauser MicroArctic ESR, my supervisor Liane G. Benning and I sampled 16 sites along a chronosequence in the forefield of the Fláajökull glacier, Iceland. Analyzing complementary interdisciplinary data sets has allowed us to develop a generic framework for how co-succession of microbial and chemical changes linked to weathering lead to time-dependent soil development gradient along the chronosequence. The soil samples will be analyzed using X-Ray fluorescence and X-Ray diffraction to determine their chemical and mineralogical composition. The relative variation of chemical and mineralogical composition between soil samples will be used to characterize weathering along the chronosequence.

Changes in weathering and nutrient content along the chronosequence will be related to quantify the role of autochthonous weathering processes in nutrient cycling. The link between weathering and nutrients will be investigated in different geomorphological settings. Additionally, we will relate carbon and nutrient availability with microbial community structures activity and evaluate the effects on abiotic and biotic parameters on weathering rates in Arctic soils.

ESR 7 Johanna Donhauser: WSL

In this project, the impact of global warming on the Arctic and Alpine soil microbiome is assessed in field and laboratory based approaches. In 2016 a soil transfer experiment along an altitudinal gradient serving as a proxy for climate change was established on three summits in the Swiss Alps. In July 2017 an analogous experiment was set up in the Scandes (Northern Sweden) enabling comparison of Arctic and Alpine habitats as two distinct cold dominated habitats which are especially vulnerable to climate change. Microbial diversity will be assessed by amplicon sequencing of fungal and bacterial phylogenetic marker genes and related to functional properties.

In a complementary laboratory experiment, North and South exposed soils from a 700 m altitudinal gradient presumably exhibiting a distinct temperature adaptation depending on their origin were subjected to different temperature regimes for one month. DNA was extracted and the bacterial 16S rRNA gene was PCR amplified in order to perform Illumina amplicon sequencing. At the DNA level, we will be able to track temperature adaptation by selective turnover leading to enrichment of species adapted to a certain temperature. In addition, RNA was isolated and the bacterial 16S rRNA gene will be analysed by amplicon sequencing allowing for detection of changes in activity of certain species in response to temperature. Moreover, temperature adaptation was assessed at the functional level using 3H-leucine incorporation as a measure of bacterial growth in a temperature dependent manner. Surprisingly, all soils exhibited growth maxima between 25 and 30 °C at the beginning of the experiment, even though they had been stored at 4 °C for several months. During the experiment soils reacted only to treatment temperatures above the optimal growth temperature shifting the growth optimum to the respective treatment temperature.

In common work with four other MicroArctic ESRs, we sampled a glacier forefield chronoseuqence in Longyearbyen, Svalbard in November 2016. Bacterial and fungal ribosomal marker genes were analysed by Illumina sequencing in order to assess shifts in microbial diversity along the chronosequence. Both bacterial and fungal community structures were shown to shift gradually from more recently deglaciated soils to older soils where especially the youngest soil exhibits a very distinct community structure compared to the two older soils. These results will be interpreted in the context of biogeochemical gradients along the forefield that were assessed by the other ESRs.

In my PhD project, I investigate the effect of global warming on the Arctic and the Alpine soil microbiome. To this end, I use a combination of field and laboratory based approaches. In the field, temperature differences along an altitudinal gradient and between aspects are used as a proxy for climate change. To assess how soil microbes react to temperature changes soil was transplanted along such a gradient in the Swiss Alps and in the Scandes (Northern Sweden), respectively. Complementary to the field experiment, soils were incubated in the lab under controlled conditions at different temperatures. Bacterial temperature adaptation is assessed at the DNA, RNA and functional level using 3H-leucine incorporation.

ESR 8 Muhammad Zohaib Anwar: mBioinform

During the second reporting period, I attended training courses at EMBL, Heidelberg about analysing transcriptomics data and its integration with proteomics data and at Aalborg University, Esbjerg on Multivariate data analysis. These courses helped to look at multivariate data generated by the samples collected in Svalbard. I also simulated synthetic mock communities and trained quality data consistent to real time data from Svalbard to test and optimize the total RNA pipeline.

Moreover, I collaborated with University of Southern California to work on analysing microbial communities using the optimized 16S pipeline from the last reporting period. This reporting period was very exciting as we conducted a week long Microbial Bioinformatics training course where I participated and presented 3 tutorials along with my fellow colleagues at mBioInform.

ESR 9 Laura Perini: University of Ljubljana

During these six months I continued with the analysis of samples collected by Dr. Alexandre Anesio on the Greenland Ice Sheet in 2016. We isolated potentially new species from the following genera: Penicillium, Articulospora and Psychrophila. We are currently working on their characterization and description. During the summer months I focused primarily on fieldwork. I spent two weeks sampling on the Greenland Ice Sheet with ESR Alexandra Holland (it was amazing!) where I collected “black” ice, clear ice, supragalcial water, cryoconite and fresh snow samples. Later, I stayed for ten days in Ny-Ålesund, Svalbard, with my co-mentor Cene Gostinčar, collecting samples of subglacial ice, sea water, glacial water, lake water, sea ice and tap water. Currently I am working on isolation, DNA extraction and identification of isolates obtained from previously described samplings.

ESR 10 Antonio Mondini: Institute of Biology Bucharest

During the second reporting period, I have made significant progress on the laboratory analyses of my samples collected from Svaldbard (ice cores) in 2016 and Iceland (subglacial soil). I am interested in the functional response of the ice and soil microcosms to temperature variations by RNA quantification of specific genes related to DNA synthesis, after exposure to heat shock steps in order to understand how they could be affected by climate changes in a melting-glacier model experiment. I am continuing to analyze my data to compare the soil and ice RT-PCR results of the 16S rRNA and pyrB genes, respectively, and the stability of the microbial community from these two types of habitat at temperature extreme variations. The next step will be to continue purifying the recombinant enzymes ATC, DHO, CPS and CK from the psychrophilic Glaciibacter superstes DSM 21135 strain expressed in E. coli, and measure their enzymatic activity and stability. During these six months, I spent 60 days at WSL Institute in Zurich, where I had the opportunity to meet new researchers, to see a different laboratory environment and learn new molecular microbiology techniques.

Preliminary data after heat shock and RNA extraction from arctic soil. Here is clear that there is an increasing production of RNA after heat shock compared with microbial community not exposed to heat shock.

New bacterial isolation method trying to recreate the bacteria’s original environment on a Petri dish.

ESR 11 Ingeborg Klarenberg: University of Akureyri

During the second part of the first year working at the University of Akureyri, I continued trying to perform theacetylene reduction assay to detect nitrogen fixation rates, I tested primers for several nif genes on cyanobacterial andenvironmental dna, I got some first bacterial 16S sequences isolated from mosses and lichens. Furthermore I collected about 300 lichen and moss samples from an open top chamber experiment in northern Iceland and sampled along a chronosequence on a nunatak in Vatnajökull, Iceland.

In April 2017, a network training event took place in Akureyri: further skills in microbial ecology. In June 2017, I followed a course on amplicon sequencing and metagenomics together with other microbiologists from MicroArctic, in Copenhagen.

ESR 12 Rose Layton: Enoveo

During this reporting period I have focussed on two key areas (1) analysing existing sequencing data to assist in answering my research questions and (2) generating sequencing data using unconventional laboratory methodologies. In the first instance, I have used my self-curated database of plasmid-specific marker genes to mine both Arctic metagenomes and metagenomes from environments previously suggested as horizontal gene transfer (HGT) hotspots. Surprisingly, the relative abundance of these plasmid-specific marker genes in snow metagenomes is strikingly higher relative to any of the metagenomes interrogated. Moreover, glacial, frost flower and sea ice metagenomes demonstrated large relative abundances of these sequences when compared to the other metagenomes in the complement. This supports my hypotheses that plasmids play a role in the robustness of microbes to unstable and dynamic environments, a feature often characterised by Arctic ecosystems. I am also working toward assembling plasmid contigs/scaffolds from metagenomic data to identify any accessory functions carried adjacent to plasmid-specific genes. With regards to generating my own sequence data, the laboratory methodologies are still under development. It is hoped that through buoyant density centrifugation, environmental plasmids can be isolated from other environmental DNA, ultimately producing an uncontaminated plasmid metagenome. During ultracentrifugation, the plasmid and chromosomal DNA are separated into bands in the tube which is then fractioned into small volumes. These volumes show variation in DNA concentration suggesting plasmid DNA and chromosomal DNA have been successfully separated. The preliminary results for this method show promise but require further refinement and other methodologies are being considered.

ESR 13 Melanie Claire Hay: University of Aberystwyth

The aim of my project is to screen metagenomes from a range of Arctic environments for (1) industrially useful enzymes and (2) antimicrobial compounds.

Collected a range of environmental samples:
In late June – early July I collected samples in Ny-Ålesund, Svalbard, with my supervisors Andy and Arwyn, and fellow ESRs, Nora and Diana. I collected snow, slush, surface meltwater, proglacial water, seawater, soil and air. In the next 6 months, I hope to extract DNA and sequence the metagenomes from all of the samples and begin constructing my clone libraries.

Industrially useful enzymes
I have been using a number of bioinformatics tools to conduct preliminary analyses looking for industrially relevant cold-active enzymes from seven previously sequenced metagenomes from Svalbard. I will be presenting a poster of the results at the Polar and Alpine Microbiology Conference in Greenland (PAM).

Antimicrobial compounds
I zoomed in from the Literature Review I conducted in the first semester, and focussed more specifically on a mini-review article on antimicrobial secondary metabolites from polar microorganisms. I worked on this review with a fellow PhD student, Aliyah Debbonaire.

Training
We had excellent training events in Akureyri, Iceland and Copenhagen, Denmark. The Iceland trip included excellent lectures directly relevant to my project, on cold-active enzymes and their evolution, as well as biotechnological applications of extremophiles. The fieldtrips were spectacular, and prepared me for some aspects of field sampling I experienced in Svalbard. The mBioInform course in Copenhagen was a revelation, with a balance of inspiring, informative and entertaining lectures; with a lot of hands-on training in the methods we were taught.

Overview
It has been six months of travel, adventure, learning, deepening friendships with fellow MicroArctic ESRs and exciting progress on various aspects of my project.

ESR 14 Gilda Varliero: University of Bristol

I have acquired bioinformatics skills both by myself and by attending bioinformatics courses at the University of Birmingham and at mBioInform in Copenaghen.
I have worked on the pipeline for metagenomics analysis; testing it on metagenomics data of microbial communities of the forefield of the Midtre Lovénbreen glacier.
I have done a secondment at the University of Akureyri. During it, I had the opportunity to take samples from several mild and hot springs in Iceland.
Then, I have extracted the environmental DNA and isolated bacterial cells from the samples. This data will be used to test a pipeline for metagenomics and SNPs analysis that I will be developing during the next months.

ESR 15 Diana Carolina Mogrovejo Arias: Brill

A considerable number of bacterial isolates have been obtained and purified from the samples of Svalbard and Iceland. Those isolates have been morphologically characterized and their potential for haemolysis and antimicrobial resistance is being tested.

In addition, a summer sampling season was carried out successfully in Ny Alesund, Norway during June/July, during which many samples were collected for the activities planned ahead.

Semester 2

Available September 2017

Semester 3

Third Progress Reports

ESR 1 Alexandra Holland: University of Bristol

To begin this reporting period, I attended and presented a poster at the 2017 Polar Alpine Microbiology conference in Nuuk, Green land. This was an incredible experience as I was able to present sorne of my results from my 2016 Greenland field work and interact with some of the leaders in cryosphere research . After the conference I spent most ofthe remaining reporting period in the laboratory. I finished the analyses on my 2016 Greenland samples and began work on the samples collected in 2017. It has been busy and exciting in the !ab as new instruments were installed, which will allow for much more accurate measurements of my samples. Finally, I have begun writing my first paper, which will encompass the work I conducted on the 2016 Greenland samples and work to fill the current  literature gap on biogeochemistry of supraglacial environments.

This photo was taken of me presenting at the Polar Alpine Microbiology Conference, September 2017, in Nuuk, Greenland. In this photo I am particpating in an outreach event, where students from local schools attended an open poster presentation. During this event I was able to discuss with them about my current research on the Greenland Ice Sheet and their individual interests in science, as well as their hopes to pursue a career in science.

ESR2 Benoît Bergk Pinto: Ecole Centrale Lyon

Using network analysis to describe microbial interactions in the snow and coupling these to metagenomic/metatranscriptomic analyses highlights the impact of organic acids on microbial communities. Based on our results, we hypothesize that when organic acids increase in the snow, the competition between microorganisms is enhanced, while cooperation is favoured at low organic acid concentrations.

Predicted response in ARGD (Antibiotic Resistance Gene Determinants) diversity (grey dots) and bacterial (positive) interaction network average connectivity (orange dots) to changes in carbon content in Arctic snow environments. In the networks, red dots represent OTUs, red lines represent (positive) interactions.

ESR 3 Lucie Malard: Northumbria University

These past few months, I finished fieldwork in Norway and received samples from Alaska, Canada, Greenland and Russia. I attended the Polar and Alpine Microbiology conference in Greenland where I participated in a poster flash talk session. I conducted DNA extractions, sequenced all the samples and conducted preliminary analyses. I also spent time writing manuscripts and various parts of my thesis. The next steps will be to fully analyse all the sequenced data in order to gain a high-resolution picture of microbial diversity in Arctic terrestrial ecosystems. I will also conduct pilot microcosms for the second part of my thesis and conduct more fieldwork in Svalbard. A lot of the time will be spent improving my bioinformatics skills, being out on the field, in the lab or writing.

ESR 4 Nora Els: University of Innsbruck

After extensive field work in the summer, I had time to go to a range of meetings and process samples and my first dataset. Thus I could gain major insights which of my methods and approaches make sense, and what can be used for further samplings. I could refine clean air sampling methods and reached a minimum of contamination. Further I learned a range of new approaches in molecular biology and bioinformatics that will help me greatly for further analysis.

 

ESR 5 Stine Holm: GFZ

In this third reporting period as an ESR in the MicroArctic ITN network two main projects were in focus. Firstly, a study on methane producing archaea in Siberian permafrost and their response to thaw. The size of the methanogenic community was found to be very big considering the frozen state of the permafrost for thousands of years and thaw was found to stimulate methanogenesis in permafrost environments where an initial active community was present. The response of methanogenic communities to thaw was furthermore found to depend on the conditions, under which the community was deposited, with warmer and wetter conditions enhancing the activity of the specific community. I submitted an abstract for a presentation at the Polar18 conference on this topic entitled"Methane producing archaea in Siberian permafrost and their response to thaw".

Secondly, progress on the project about the ecological role of plasmids in Siberian permafrost was made. Great challenges were faced with isolating plasmid directly from the environment, and trials of cell washing and isolation from enrichments was applied. Three months of work on plasmid isolation gave the following output: 1) The basis for an ecological paper of plasmids isolated from Siberian permafrost soils and a broad knowledge about plasmids and their potential to carry stress related genes was achieved. 2) The basis for a methological paper on the limits behind plasmid isolation. 3) Establishment of the plasmid isolation and screening at the German Research Centre for Geosciences (GFZ).

I attended the Polar and Alpine Microbiology Conference (PAM) in Greenland giving a flash poster presentation entitled" The effect of permafrost thaw on circum Arctic methanogenic communities". Furthermore a 2h public poster presentation was given at the PAM conference, which gave the opportunity to talk about the research posters with local high school students, which lead to good discussions.

The joint ESR project on "Geochemical and microbial co-succession in a High-Arctic proglacial area" was submitted to FEMS Microbiology Ecology thematic issue on Polar and Alpine Microbiology. The archaeal community of the proglacial area of Svalbard showed a shift from Euryarchaeota towards a dominance of Thaumarchaeota with increasing distance from the glacier. This is in line with previous observed studies where Euryarchaeota has been found to colonize the bare soil and Thaumarchaeota to colonize later successional stages.

A project overview for a master's student was formed with the overall topic of methanogenic archaea in a warming Arctic, specifically focusing on plasmid DNA from the methanogenic communities in Siberian permafrost soils. The master's project will be conducted at the GFZ and this will add teaching experience and cooperation skills. An outreach activity was carried out at my former high school, Lemvig High School, Denmark. The presentation was entitled; 'What happens when the permafrost of our world thaws?' It addressed the following topics 1) The way to becoming a MicroArctic ESR 2)The MicroArctic network, (responsibilities, courses, fieldwork, opportunities 3) Climate change -with particular focus on thawing permafrost 4) Field work in the Arctic.

The figure presents the two studies in focus during the third reporting month. To the left the plasmid isolation method from active layer soil from Siberia, from enrichments (i) and from pure cultures (ii). To the right the study of methane producing archaea in Siberian permafrost, and their response to thaw.

ESR 6 Robin Wojcik: GFZ

My major achievement for the reported period has been to submit the first paper of my PhD (Geochemical and microbial co-succession in a High-Arctic proglacial area) to FEMS Microbiology Ecology in collaboration with four MicroArctic ESRs (ESR1, ESR3, ESR5 and ESR7). In addition, I designed and initiated an aeolian deposition monitoring experiment on Vernagt glacier, Austria, to examine the role of dust deposition on carbon and nutrient cycling in recently deglaciated environments. This is a new collaboration (and secondment) that I initiated with ERS x from Innsbruck. I also had the opportunity to partake in a unique field sampling campaign in the Southern Alps of New Zealand to learn more about ecological successions along landslide and proglacial chronosequences together with an interdisciplinary research team of the GFZ. Although the collected samples will not be part of my PhD workload, this experience gave me a unique insight into other research fields and was provided me with a great interdisciplinary training opportunity.

This picture shows the passive aerosol sampler designed to collect the aeolian dust on the forefield of Vernagt glacier, Austria that I deployed during my first visit in November 2017. This project primarily aims to provide a quantitative estimate of the relative importance of autochthonous (weathering) compare to allochthonous (aeolian and subglacial) nutrient pathways in fertilizing a recently deglaciated Alpine terrain. Copyright Robin Wojcik.

ESR 7 Johanna Donhauser: WSL

In August, I sampled a soil transfer experiment in the Swiss Alps that had been set up the previous year in order to assess the impact of warming on the soil microbiome. In September, I attended the Conference on Polar and Alpine microbiology where I had the great opportunity to give an oral presentation on the colonization of glacier forefieldsfollowing glacial retreat. Otherwise I spent the last few months mostly writing. Together with Robin Wojcik (ESR6), I completed a manuscript on microbial and geochemical succession in an High-arctic glacier forefield. The sampling had taken place in a joint effort of five MicroArctic ESRs during the kick-off meeting in Svalbard in November 2016.Thanks to the contribution of the PhD students and their supervisors we created an interesting interdisciplinary dataset. Writing up the manuscript was an exciting experience for all ESRs involved. In addition, I finished a manuscript synthesizing current knowledge on alpine microbial ecology that was submitted in December.

 

ESR 8 Muhammad Zohaib Anwar: mBioinform

During this reporting period I made considerable progress in my first PhD question "Development of a unified non-PCR biased approach for Arctic studies". Comparison of different approaches coupled with Precision v/s Recall at different thresholds to add another layer of testing. Preliminary results were presented in multiple International conferences and Symposiums to get feedback and improve subsequently. I am preparing these scripts as standalone to be available on the GitHub Repository. Additionally, I have collaborated with ESR 3 on her project linked to MicroArctic deliverable D2.1 "A microbial biogeography map of the Arctic" during my secondment. Currently we are analysing the samples collected throughout Arctic sites. In addition to analysing data for our hypothesis I will also use these samples as a prototype for the MicroArctic Search Engine (a module that we added for MicroArctic data optimization and dissemination). Moreover, I also attended advanced Bioinformatics training at the European Bioinformatics lnstitute which was very relevant and helpful for my research question.

ESR 9 Laura Perini: University of Ljubljana

During the past six months I had the chance to participate in my first international congress PAM - Polar and Alpine Microbiology in Nuuk (Greenland), where I presented the poster “Tropical diversity of Arctic penicillia”. I worked with fungal species isolated from the Greenland Ice Sheet (GrIS) in June 2017 and from the glacial environments around Ny-Ålesund (Svalbard, Norway) in July 2017. I was able to investigate the fungal biodiversity of different ice environments. I also identified several potentially new fungal species that will be described in the future. In October and November 2017 I did my first secondment in Bristol, UK, where I ran an incubation experiment with two fungal species isolated from the GrIS in 2016 and non-cultivable ice algae covering the GrIS surface. More details regarding the secondment and the experiment can be found on the secondments page of the MicroArctic website.

ESR 10 Antonio Mondini: Institute of Biology Bucharest

During these months, I have been working on bacteria obtained from cold environments. I have made significant progress investigating the thermal response of total and active ice-contained microbiome from a Svalbard glacier ice core and a psychrophilic model bacterium (Glaciibacter superstes). Changes in the total and active microbiome composition after heat shock treatment are currently under investigation by Shotgun metagenomic and metatranscriptomic analyses. Quantitation by qPCR of the aspartate transcarbamoylase (ATC) expression, a key enzyme of pyrimidine nucleotides biosynthesis in the psychrophilic bacterium and ice microbial community, submitted to heat shock cycles is currently under way in order to propose an enzymatic biomarker for ice microbiome response to temperature variations when changing habitats due to glaciers melting.

ESR 11 Ingeborg Klarenberg: University of Akureyri

After a fieldwork period this summer, this autumn I mainly focused on processing the collected moss and lichen samples. This involved a lot of laboratory work. RNA and DNA were extracted from 215 samples and cDNA was synthesised from the extracted RNA.

At the Polar and Alpine Microbiology conference in Nuuk, Greenland, I got the chance to present a poster with preliminary results on lichen and moss associated bacterial communities collected in autumn 2016 and spring 2017. I also attended the Icelandic Biology Conference and chaired a session on botany. In January 2018, I started a secondment with Anne Jungblut at the Natural History Museum in London.

ESR 12 Rose Layton: Enoveo

DProgress has been made in a number of projects over the past 6 months. As a continuation of the last reporting period, the initial bioinformatic survey of metagenomic data as well as the exploitation of fully sequenced plasmids was completed to address questions regarding plasmid relative abundance and functional carriage in Arctic settings. This culminated in an oral presentation at the Polar and Alpine Microbiology conference and will comprise part of a review paper, currently under preparation. Secondly, sampling of artificial sea ice, grown at the University of East Anglia, in the Roland Von Glasow sea ice chamber was completed. We have processed the samples which have been submitted for sequencing and will be used to explore the mechanisms influencing colonisation of sea ice, brine and frost flowers including the potential role of mobile genetic elements in these processes. Finally, a strategy for the isolation of environmental plasmids from pristine environments is still under development. A secondment at Potsdam university in the latter months of 2017 highlighted the limitations of the techniques currently published. This knowledge has been used in developing a number of strategies I am currently testing.

ESR 13 Melanie Claire Hay: University of Aberystwyth

In September 2017, I attended the Polar and Alpine Microbiology Conference (PAM) in Nuuk, Greenland, and presented a poster on “Mining the Arctic microbial metagenome for industrially useful cold-active enzymes”. Since returning from Greenland, I have extracted DNA from the samples I collected in Ny-Ålesund, Svalbard in July 2017. There was a range of sample types: air, snow, slush, meltwater, proglacial water, seawater and soil, and I spent a significant amount of last year optimising extraction protocols- particularly for the extraction of DNA from clay-rich soil. In addition, I attended a demanding, but brilliant, course at Aberystwyth University on Bioinformatics. The course, aimed at Biologists, covered statistics in R and introduced high performance computing. I have since used what I have learnt to start developing a workflow for analysing shotgun metagenome data for biosynthetic gene cluster discovery. I plan to use this workflow to analyse the shotgun metagenomes from my Svalbard samples, and will continue to improve the workflow based on my experiences mining these datasets. In the following six months I anticipate receiving back 16S amplicon data from all of my samples, shotgun metagenomes, some Nanopore data and chemistry data. I intend to mine this data for interesting biosynthetic gene clusters, and interesting enzymes, and the results of these analyses will be used to design my sampling strategy for fieldwork this year, and my functional screening approach.

ESR 14 Gilda Varliero: University of Bristol

During the last six months, I have been mainly working on the pipeline for the analysis of whole metagenomics data. Thanks to the implementation of the pipeline in a web interface, the user will be able to easily annotate microbial DNA sequences to a database of known proteins and to retrieve gene and taxon abundance information of the studied microbial communities. In particular, I have been working on the sorting of the gene nomenclature, and I have been also implementing a tool for the single nucleotide polymorphism (SNP) detection. Providing a tool for the SNP calling in microbial communities could help to resolve whether they adopt DNA/protein adaptations in different environments in order to overcome different stresses (i.e. temperature) that they have to deal with in severe habitats, such as the Arctic. This will also allow us to mine for amino acid substitutions associated with cold adaptation; these could be of commercial interest. I have also tested the pipeline on a microbial chronosequence sampled from the Midtre Lovénbreen forefield (Svalbard). So far, the results that I have obtained from this analysis are encouraging as they show trends in the taxonomic and gene composition that fit well with geochemical and environmental data collected in the Midtre Lovénbreen forefield and that have been previously observed in other similar studies (Rime et al., 2015; Bajerski and Wagner, 2013; Zumsteg et al., 2011; Frey et al., 2010; Knelman et al., 2012; Bradley et al., 2016). Furthermore, I have extracted the DNA from the englacial samples that I had collected at the Storglaciären (Sweden) last July and from ice samples from a Canadian Moulin. I have amplified the 16S rRNA and 18S rRNA genes in order to study the taxonomic composition of the communities that thrive in these englacial systems.

ESR 15 Diana Carolina Mogrovejo Arias: Brill

Good quality DNA has been obtained from the isolates of the Svalbard and Iceland samples. The possible duplicates have been discarded and a comprehensive description of each isolate, as well as their phenotype (with special interest in their haemolytic potential and antimicrobial resistance profile) is available.

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