2023-07-07 11:18:19
A CSIC team has 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 the samples very quickly and thus improve the sampling design.
This novel experimental approach, the success of which was demonstrated during the last Spanish Antarctic campaign through the study of communities of microorganisms of terrestrial ecosystems in the Livingston and Deception Islandshas been developed by the National Center for Biotechnology (CNB) and the National Museum of Natural Sciences (MNCN), both of the CSIC, within the framework of the Rock-Eaters project (State Research Agency, Ministry of Science and Innovation).
The CNB investigator Javier Tameswhich has 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 has deployed a portable lab 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 have managed to speed up and automate the entire process of identifying microorganisms from their DNA sequences”.
In Antarctica there are unexplored regions where microorganisms live, many of them still unknown
“Never before has it been possible to generate such comprehensive information on the composition and function of a microbial community in such a short time. This opens the door to numerous applications where speed in analysis is essential”, adds Tamames.
In Antarctica there are unexplored regions where microorganisms inhabit, 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 that are later analyzed in laboratories using massive genomic sequencing techniques and bioinformatic analysis. The members of the Rock-Eaters project have gone a step further, bringing to the field the necessary technology to carry out the experimental and bioinformatic analysis as the samples were taken.
The device allows experimental and bioinformatic analysis to be performed as samples are taken
“This methodology has allowed us to process the sequencing data during field work and thus design the samples and experiments in a dynamic and more accurate way, making decisions quickly, without having to wait for our return to Spain to finish the process. ”, comments the MNCN researcher Assumption of the Rivers.
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 obtaining 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.
Fuente: SINC
Rights: Creative Commons.
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