A CSIC team developed a system that combines new technologies to obtain and analyze metagenomic sequencing data on site. It is a field laboratory that allows researchers to extract information from samples very quickly and thus improve sample design.
This new experimental approach, whose success was demonstrated during the last Spanish Antarctic Campaign through the study of communities of microorganisms from terrestrial ecosystems in the Livingston and Deception Islandswas developed by the National Biotechnology Center (CNB) and the National Museum of Natural Sciences (MNCN), both from the CSIC, within the framework of the Rock-Eaters project (National Research Agency, Ministry of Science and Innovation).
The CNB Investigator Javier Tamameswho implemented the system, explains that “the combination of technologies allows us to extract microbial DNA, purify it and also sequence it with a small commercial sequencer, directly at the sampling site”.
Process automation
The team deployed a portable laboratory capable of operating autonomously in the field. “For this, it has been essential to have a tool for bioinformatics analysis software developed by us, the SqueezeMeta software, with which we managed to streamline and automate the entire process of identifying microorganisms from their DNA sequences”.
“Never before has it been possible to generate such comprehensive information about the composition and function of a microbial community in such a short time. This opens the door to numerous applications where analysis speed is essential,” adds Tamames.
In Antarctica there are unexplored regions where microorganisms live, many of them still unknown, such as those that colonize the rocks that are exposed after the retreat of ice in glaciers or volcanic lava.
To identify them, samples are usually collected and later analyzed in laboratories using massive genomic sequencing techniques and bioinformatics analyses. Members of the Rock-Eaters project went a step further, bringing the technology needed to perform the experimental and bioinformatics analyzes as samples were collected into the field.
“This methodology allowed us to process the sequencing data during field work and thus design the samples and experiments dynamically and more precisely, making decisions quickly, without having to wait for our return to Spain to finalize the process.”, comments the MNCN researcher Asunción dos Rios.
With this work system, adds the researcher, “you know if you are on the right path from the beginning and based on that you can select the sampling areas and guarantee that you are getting the data you need for the investigation”.
Microorganisms and ecosystem
The results obtained are of great interest to understand the role of microorganisms in Antarctic terrestrial ecosystems. “By identifying the microorganisms present in Antarctic rocks, we can better assess their contribution to the functioning of the ecosystem”, he concludes. Fernando Garridoalso from the MNCN.