In a big step towards better monitoring the biodiversity of ocean ecosystems, new research recently published in the journal Environmental DNA details how scientists at the Monterey Bay Aquarium Research Institute (MBARI) use unmanned underwater robots to sample environmental DNA (eDNA).
eDNA allows researchers to identify the presence of aquatic species from the tiny bits of genetic material they release. This DNA cluster provides insights into variations in biodiversity in sensitive regions, the presence of uncommon or endangered species, and the increase in invasive species – all important for understanding, promoting and preserving a healthy ocean. .
For the research, scientists integrated two unique autonomous systems created by MBARI: the Environmental Sample Processor (ESP) and the Long Range Autonomous Underwater Vehicle (LRAUV).
The LRAUV is a skilled robot that can travel to remote areas of the ocean for an extended period of time. The ESP is a robotic “laboratory in a box” that sifts seawater and stores eDNA for future research. By providing an ESP with LRAUV technology, scientists can increase the scale of marine monitoring in space and time.
In contrast, conventional ocean eDNA sampling requires weeks on an expensive research vessel limited to a localized region. Innovative technologies like this are transforming attempts at marine conservation.
We know eDNA is an incredibly powerful tool for studying ocean communities, but we’ve been limited by what we can accomplish using manned research vessels. Today, autonomous technology helps us make better use of our time and resources to study new parts of the ocean.
Kobun Truelove, lead study author and biological oceanographer, MBARI
Ocean biodiversity is a measure of the large number of species and individuals in the seas. This variety of interconnected organisms – from the smallest plankton to the largest whales – create the air we breathe, support food webs and control our climate. Autonomous tools such as ESP and LRAUV allow MBARI scientists to maintain a constant presence in the ocean and track variations in delicate ecosystems in a way that was not feasible in the past.
Organisms move as conditions change in our oceans and Great Lakes, affecting the people and economies that depend on these species. We need cheaper and more agile approaches to monitoring biodiversity at scale. This study provides the synergistic development of eDNA and unmanned technologies that we need, in direct response to the priorities set out in NOAA’s Omics Strategic Plan.
Kelly Goodwin, study co-author and collaborator, National Oceanic and Atmospheric Administration
For this study, MBARI worked with scientists from the National Oceanic and Atmospheric Administration (NOAA) Atlantic Oceanographic and Meteorological Laboratory and the University of Washington to conclude three expeditions to the Monterey Bay National Marine Sanctuary. . The team synchronized sample collection between MBARI’s three research vessels, a fleet of MBARI LRAUVs, and the NOAA fishing vessel Reuben Lasker.
A ship-based team dropped bottles at a particular depth to collect and preserve water samples. In the meantime, an ESP-equipped LRAUV autonomously sampled and preserved eDNA at analogous depths and locations. The eDNA samples were sent to the lab for detailed sequencing.
Interconnected organisms share typical sections of DNA, called genetic markers. For this research, the team examined eDNA samples via a method called metabarcoding. This technique searches for short DNA extracts and offers a distribution of the groups observed in the sample.
This method is particularly useful for interpreting eDNA data in a measure of biodiversity. The scientists looked at four different types of genetic markers, each signifying a slightly different level of the food web. Together, the results produced a more complete picture of community composition. Samples collected from research vessels and unmanned vehicles showed similar forms of biodiversity.
Truelove observed that the results of the study represent an exciting advance for monitoring ocean ecosystems.
“This work is about scaling up eDNA research. Instead of looking at an individual species, we can begin to characterize the biological community structure in the ocean more broadly,” he stated.
Good data is the foundation of sustainable ocean management. Regular monitoring of environmental DNA tells us who is there and what is changing over time. When it comes to understanding the impacts of climate change, one of the greatest threats to the health of the oceans, this information is essential.
Francisco Chavez, lead scientist and co-author of the study, MBARI
LRAUVs can travel continuously for weeks as well as hundreds of kilometers. They can facilitate more frequent sampling in regions of interest than conventional research vessels, which visit isolated sites only occasionally.
Autonomous robots will allow scientists to explore hitherto unexplored areas of the deep sea. Closing these data holes is important for establishing the health of the oceans worldwide. Shipboard exploration will continue to play an important role in oceanographic studies, but the integration of a new autonomous platform into the toolbox will increase the capacity for research, monitoring and resource management.
Ultimately, MBARI scientists plan to position a fleet of LRAUVs equipped with ESP technology.
The study received support from the David and Lucile Packard Foundation, NOAA/OAR/NOPP, NOAA/OAR/’Omics, and NASA projects #80NSSC20M0001 and 80NSSX21M003.
Environmental DNA: how to see the genetic clues left in a drop of water
Environmental DNA (eDNA) helps researchers identify marine animals by the DNA fingerprint they leave behind. Video Credit: © 2022 MBARI
Truelove, NK, et al. (2022) Expanding Temporal and Spatial Scales of Environmental DNA Research with Autonomous Sampling. Environmental DNA. doi.org/10.1002/edn3.299.