Proof of life using molecular tools
Scientists at Cawthron Institute have explored the role of RNA in identifying living organisms when using metabarcoding for marine biosecurity applications.
Their results have been published in the international journal PLOS ONE as a research article authored by Dr Xavier Pochon, Anastasija Zaiko, Lauren Fletcher, Olivier Laroche, and Susie Wood, ‘Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications.’
Cawthron marine phylogeneticist Dr Xavier Pochon said, “By looking at DNA and RNA molecules together, it's possible to not only know the organisms present in an environment, but also by comparing the signals from two molecules we are now able to decipher which are dead and which are alive. This knowledge has the potential to greatly benefit marine biosecurity.”
Molecular tools are an emerging technology on the science scene. Scientists can use these tools to rapidly detect DNA and RNA in an environment. This means, with the help of an ever-growing database, they quickly know the organisms present.
It’s cutting-edge science.
The findings from this latest study suggest it’s also possible to use molecular tools to ‘take the pulse’ of detected organisms. This is because environmental samples with DNA-only traces may represent dead organisms, whereas detection of DNA/RNA combined or RNA-only traces are more likely to reveal the presence of living organisms.
Dr Pochon explained the use for this information in cases where a different biosecurity response may be required depending on whether an organism is alive or dead.
“For some marine biosecurity applications analysis, eDNA-only data maybe sufficient, however there are an increasing number of instances where distinguishing the living portion of a community is essential.
“For example, it’s important to understand the viability of marine organisms in the ballast waters of large vessels, because these can become invasive pests when released,” said Dr Pochon.
There are a couple of difficulties. Working with RNA is tricky as it degrades quickly and processing is relatively expensive. But, the potential for technology in this space is growing as it gets cheaper and better.
The research published in PLOS ONE was funded through NIWA’s Coasts and Oceans Research Programme 6 (Marine Biosecurity), which involves several other R&D initiatives for molecular-based surveillance and detection. Cawthron is also in the process of developing novel methods for en-route ballast water monitoring and tests for compliance with IMO regulations.
The authors of the article published recommend further research to improve understanding of the persistence of RNA in the environment, and the underlying reasons for the presence of RNA-only organisms in environmental samples.