2nd semester


Month 1: (October 2023) – Extensive research in the field of bioinformatics, related to the outcome of the crash course attended at the end of September 2023, particularly in the direction of HPC (High Performance Computing) metagenomic tools implementation and compatibility. 

Month 2: (November 2023) – Obtained access to the University of Innsbruck’s HPC resources. Started testing different bioinformatic tools and pipelines, in light of the newly gained computational resources, to optimize processing speed and especially output quality. As anticipated in the previous report, preliminary data on cryoconite communities time series is available for processing and analyses. Started a biostatistics course ecology-oriented to gain deeper methodological knowledge to be implemented in the future paper. Collected air samples from the Stubai Glacier to test extraction efficiency. 

Month 3: (December 2023) – Preliminary data briefly presented during midterm check. First extractions on test samples reveal very low DNA contents. Continuous research on bioinformatics and biostatistics. 

Month 4: (January 2024) – More DNA extractions, various protocol modifications to maximize DNA retrieval. Continuous research on bioinformatics and biostatistics. Different assembly and binning testing. 

Month 5: (February 2024) – High school outreach activity in Novara, Italy. Second ICEBIO meeting in Grenoble, France. Continuous research on bioinformatics and biostatistics. 

Month 6: (March 2024) – Reshaping of research question #1 hypotheses in light of new inputs during the Grenoble meeting and consistently low DNA in air samples.


DC11 Julien Cergneux OCTOBER 23 - MARCH 24 

Month 7: During this 7th month (October 2023), I increased my database by sampling 4 glaciers and glacier-fed streams (GFSs) in the Swiss Alps. Several 1m ice cores (6 per glacier) were taken from each glacier. For GFSs, the same sampling protocol as in the Pamir was followed. A total of 24 ice cores were collected, as well as 16 sites in the GFS. 

Month 8: During this 8th month (November 2023), the samples collected in October had to be processed. I slowly melted the ice cores at low temperature to avoid changes in their bacterial composition. The melted ice was then filtered and sampled in the same way as GFS water. During this month I also I had my first opportunity to present my work during the weekly lab meeting. 

Month 9: (December 2023) I took part in a whole week of very interesting bioinformatics courses. Since I am taking courses as part of my thesis, the end of the year also marks the end of the semester, with work due in consequence. On the 22nd of December I went to a high school class to raise student’s awareness of glaciers and the life they support, and to explain the involvement of the Icebio network. The rest of the time was dedicated to a preliminary analysis of the data collected during the autumn. 

Month 10: (January 2023) The early part of 2024 has been largely devoted to putting in place a research plan for the continuation of my thesis, with a view to sitting my candidacy exam in the spring. This 10th month was therefore dedicated to literature review, hypothesis development, and writing the research plan. 

Month 11: (February 2023) The continuation and conclusion of the bioinformatics course I attended in December lasted one week. The rest of the time was dedicated to developing the research plan. At the end of the month, I went to Grenoble for the Icebio meeting! 

Month 12: During this 12th month (March 2023), we decided that the candidacy exam would finally take place in May. I took the opportunity to improve my research plan, and to work on analyses of diversity in GFSs around the world, using a database previously compiled by our group.