Expert Exchange: Training on metagenomic analysis to study the potential role of microbes in the precipitation of carbonates associated with Andean stromatolites

Europlanet 2024 RI’s Expert Exchange Programme aims to support the planetary community to share expertise and best practice, and to prepare new facilities and services. The programme provides funding for short visits (up to one week).

Estela Mlewski of the IMBIV-CONICET-UNC in Argentia visited Karen Olsson-Francis at the Open University, UK, from 25 November – 06 December 2023.

The purpose of expert exchange was to analyse the microbial diversity and microbial communities function of unexplored microbialites and lithifying microbial mats from a Mars analogs lake in the Puna Plateau (Catamarca, Argentina). Also, to explore and assess the metabolism involved in the calcium carbonate precipitation process (through a metagenomic-focused approach), particularly metabolisms related to photosynthesis, enitrification, ureolysis and the sulfur cycle. This project was done to allow us to characterise and correlate microbial metabolisms with specific mineral precipitation processes, gaining insight into the different taxa potentially involved in carbonate precipitation. During my stay, I took advantage of the low biomass capabilities developed in the Astrobiology OU and the bioinformatic facilities with Prof. Karen Olsson-Francis and her team.

During my first day I received training in Lab induction and risk assessment for molecular, microbiology and the low biomass laboratory. I extracted DNA using manual extraction methods using the low biomass facility. After DNA was measured with excellent values in concentration. Also during my first day I started with my computer-based techniques learning to analyse the diversity of microorganisms from the lithified and non-lithified microbial mats and microbialites from Laguna Negra to attempt to identify and correlate diversity with main metabolisms related to carbonate precipitation. So, on Day One, I received training on introduction to online databases, K base introduction and loading of my data.

The rest of the week I learned on setting the data for trimmomatic and assembly. To use different assemblers such as MEGAHIT and metaSPAdes, and quality. Afterwards, I continued my training on binning and metagenome-assembled genomes (MAGs). Later I continued my Bin analysis using dastool and after GTDB and DRAM. Finally I used Kaiju for taxonomy of metagenomic data and RAST and BlastKOALA for automatic annotation. In the middle of my visit I gave a talk in a lab meeting showing our research on microbial and mineral interaction using different techniques as microdissector and confocal microscopy. This talk gave me the opportunity to share my work with other people from the Astrobiology department and new ideas and collaborations arise. Thus, reinforcing the exchange of experience between the astrobiological communities from different continents. In summary, the opportunity of learning how to analyse my data led me to the progression of my new line of research and formation of PhD students in Argentina.

Expert Exchange Objectives covered by this visit: Transnational Access Training.

Find out more about the Europlanet Expert Exchange Programme.