Direct sampling of microorganism DNA from the environment is a powerful way of determining the biological diversity in an ecosystem. Metagenomics, the study of the genetic material of all of the organisms recovered directly from environmental samples, means sets of genomes can be reconstructed from complex DNA mixtures representing the different microbial species in that environment.
This Environmental DNA (eDNA) data being used to research the genomes of simple viruses will help us to understand their function in aquatic health, and the interaction between viruses and the host bacteria they infect.
Our work
Postdoctoral fellow Dr Michael Hoggard set out to better understand what viruses are found in the Waiwera River north of Auckland, their interactions with bacteria, and how this affects the ecosystem dynamics, particularly their role in nutrient cycling.
Michael’s analysis recovered more than 30,000 viral sequences from the estuary dataset alone, including 352 complete or near-complete viral genomes spanning five viral families. The research is so ground-breaking that most viral genomes recovered were not able to be assigned to a known organism family due to their novelty. Such novel results highlight the power of genomics to uncover hidden biological diversity.
Analysis indicates the viruses modify or enhance a range of the host’s functions, including photosynthesis, biosynthesis, DNA repair and evasion of host defences.
These findings suggest that viruses can significantly manipulate microbial communities and biogeochemistry in the terrestrial subsurface. This new understanding at both the microbial and virus level enables a more comprehensive overview of the Waiwera Estuary composition and function.
Additional analysis will further explore evidence of direct interactions between viruses and bacteria, including bacterial defence mechanisms, the potential effect of viral infection on overall microbial community structure and functioning, and viral manipulation of host metabolism.
What this means
The study provides new insight into virus and host diversity across a salinity gradient from freshwater to marine, as well as biological responses to changes in this highly dynamic environment.
“We can’t manage waterways without this core knowledge – genomics has given us the tools to understand basic biology at a fundamental level and build from there. This is becoming the foundation for understanding and maintaining water quality,” Michael said.
“It’s an on-going story but we’re continuing to fill in gaps, gaining a good understanding of the roles and interactions among bacteria, microorganisms and viruses and their nutrient needs in sediment as well as water.”
Very importantly, the research is also providing a model of genomics-based tools that can be applied to understand microbial interactions in other waterways and coastal environments, for use by other researchers. This is a fundamental step in long-term planning for managing our waterways; it has massive potential for improving Aotearoa’s environment.
Read more about Environmental Microbiomes here