A Summer Placement with AstrobiologyOU

My interest for the area of astrobiology stems from the study of microbiology as an undergraduate student in biological sciences. Our microbiology courses are co-lectured by different UCL faculties, and the lectures delivered by Joanne Satini based on her research of arsenic metabolism has drawn my interest into the field of extremophilic microbiology. She introduced not only resistance to arsenic contamination, but also the intriguing ability of incorporating arsenate into genetic material as analogue of phosphate, as well as arsenite oxidisers from hypersaline environments. The potential for arsenic to play a role in biochemistry has led to speculations about its role in the origin of life on Earth, as well as the possibility of arsenic-based life on other planets. My first learning of “arsenic-based life” and its association with the origin of life had led me to a large amount of curious questions about microbial metabolisms and stress responses under extreme environments.

I have always had interest in continuing my study in extremophilic microbiology due to my undergraduate background in microbiology, genetics, and computation. However, my previous experiences from my institution, internships, or summer projects are mainly focused on pathogenic bacteria related to clinical application. Therefore, in the fall term of my second-year study, I started to think about the possibility of participating in a summer project that is related to the genomic study of environmental microbes, or ideally extremophiles. I fortunately had the chance to reach for Dr Michael Macey from Astrobiology OU and discuss a summer studentship opportunity. We proposed a plan to investigate the methanogenic metabolism in hypersaline environments, based on the sequencing data and previous work from a current PhD researcher in the group, Velislava Ilieva.

The project is based on Veli and Michael’s past work using samples collected from Western Sahara salt plains and Central Spain hypersaline lagoons that are considered as potential Mars analogues. In the past two years, Veli has been working on the microbial diversity and the metabolisms of sulfate reducing bacteria (SRBs) in those samples. My work in the short term was focused on the potential competitors of SRB involved in C1 metabolisms, which are methanogenic archaea. I used cultivation-dependent and -independent method to identify potential methane production, community profiling, and genes associated with methanogenesis. The first week of the placement was mainly self-study of methanogen literature review and bioinformatics. I managed to make myself familiar with the methanogenic pathways, methane cycling, and geological settings associated with the Martian Noachian-Hesperian period.

With the help and supervision of Veli, I established enrichments of methanogens according to the four methanogenic pathways. In the meantime, I also did cultivation-independent analysis on the metagenome data from the Western Sahara samples, allowing 4-6 weeks’ time for the microbes to grow, with the restricted time for microbial cultivation representing the main limitation of this project. Fortunately, I was able to identify the growth of viable cells through live/dead microscopy. Another problem we encountered is that Veli and I are not specialised in gas chromatography. But with the help from Sophie Alexander, we have successfully performed the analysis of gas production in the headspace and identified methane production in our enrichments under specific conditions. Along with the tree construction, taxonomic identification, and the identification of potential genes associated with methanogenic pathways, our results suggest the potential for methanogenesis in these sulphate-rich hypersaline environments.

Surprisingly, the metagenomic analysis process of this summer studentship also helped my final year research project within my institution. My final year project involves Mycobaterium genomic study regarding the molecular sequence features (e.g., mutations, motifs, genes) associated to pathogenicity. The summer project in AstrobiologyOU has familiarised me with bioinformatics pipeline including genome QC, annotation, and community profiling which are essential for the early stage analysis of my final year project. The project also inspired and confirmed my area of interest for the graduate study. For the current stage, I am making application for graduate programs, and if I ever had chance to receive the offer from the Open University, I really hope I will have the opportunity to continue on the unresolved questions during my summer project due to time constraints, including Central Spain metagenome analysis and long-term cultivation.

Written by Yifan Zhu