Gene-picking robots are hidden in the silent sea

Unlike footprints in mud, they are more difficult to detect traces left by animals in the ocean. This is good for creatures that do not want to follow, but it is not recommended for researchers who want to study where certain organisms are and how they move through a changing water world.

However, hard does not mean impossible. In fact, measuring the distribution of DNA or eDNA in the environment — what’s more at a glance — has allowed scientists to identify what animals they have visited in a particular area without hearing it through a camera or hydrophone. A team of ocean scientists from the Monterey Bay Aquarium Research Institute and the National Oceanic and Atmospheric Administration have shown that they can effectively use a fleet of specialized robots to gather this type of evidence in a new study published in the journal last week. DNA in the environment.

This stand-alone eDNA collection technique may be useful for scientists studying the impact of climate change on the behavior of ocean animals and for caring for endangered and invasive species.

MBARI / Monterey Bay Aquarium

All living things shed traces of genetic material through mucus, debris, and dead skin cells. Some organic matter falls like sea snow down the water column. There may be a set of freely floating material in a sample of collected seawater, and these bits are what is called environmental DNA (or eDNA). Different species have specific genetic codes, and when these samples are sequenced, these sections of the gene can be used as barcodes to detect the presence of certain groups of animals — a process also known as eDNA metabarkoding. Fish scales can also provide valuable genetic information about what has passed through this area.

[Related: Scientists are tracking down deep sea creatures with free-floating DNA]

The robot programmed to follow these EDNAs is a long-range autonomous underwater vehicle equipped with an “Environmental Sample Processor” and is a kind of “in a can in a laboratory,” according to a press release. MBARI. As the robot itself travels endless miles across the ocean, it can suck and sift through the seawater it traverses to obtain genetic waste left by animals, viruses, and microorganisms. Within the platform, the chemicals break down the organic waste suspended in the sample to release proteins and DNA strands. The ESP platform has a carousel of cartridges in a single deployment that can collect, process and conserve 60 samples of seawater.

“We can extract DNA and use techniques similar to forensic techniques to take DNA sequences and access them into a database,” says Kobun Truelove, MBARI’s chief research technician and paper author. “But instead of being a forensic database of suspects, it’s a biological database of animals living in the marine environment, and we’re trying to link DNA sequences to that.”

For the investigation, robots, three MBARI research vessels and NOAA Fishing Vessels Reuben Lasker, conducted three expeditions in 2017 and 2018 from the northern California coast to the Monterey Bay National Marine Sanctuary, where similar sample collection sites, water. depths, and times about half a mile. The aim was to compare the results of the samples received by the robots with the samples received by ship.

Without the robot, human crews and scientists would have to constantly throw a bottle into the side waters of a ship. The bottle would be lowered to a pre-set depth and opened and immediately closed to take the water and return it to the container. The use of robots with the ESP platform could provide a way to scale this method of automatic eDNA collection and processing for marine biodiversity conservation, and to expand its coverage to distant oceanic areas that have historically been little studied or costly to navigate.

[Related: These free-floating robots can monitor the health of our oceans]

Once the samples are collected by boat or robot, they are processed in the laboratory using a “broader diversity style of PCR,” says Truelov, a technology that copies genes and compares them to genes from known species. The team used a type of PCR to study a variety of bacterial species, and they were able to study invertebrates, seaweed, and vertebrates (from anchovies to blue whales) as they climbed the food chain with PCR. Sampling of many species and families instead of looking for specific organisms now creates a more complete picture of the appearance of an ecosystem. Measuring marine biodiversity (the community of organisms present and the number of each species) can help scientists determine how different species respond to changes in ecosystems and how this may affect the food web.

In the overall picture, both robotic and boat-based methods observed the same large-scale patterns for the types of organisms detected, except for a few variations in the number of animals in the selected family of fish and invertebrates. One of the reasons for this change could be that the marine environment is different even for a couple of meters. Another reason may be how each technique takes water. The bottle on the side of the boat can hold 5 to 10 liters in the blink of an eye, while the vehicle takes an hour to get into a liter. “Water can be a little different in that time frame,” Truelov says.

In addition to saving the cost of crew and ship operations, the robot is able to do things that ships cannot do. For example, these robots can drift with a stream while sampling water. “One of the next studies we’re investigating is the signal from the surrounding DNA that a robot would drift from a strong current in Monterey Bay to see if there were any patterns of species we receive within that current. Out of the current,” says Truelov. doing so: effectively drifting and constantly testing in such a stream “.

At the moment, the robot has yet to report it to the lab after completing 60 samples for gene analysis, but the team is working to automate the entire molecular lab and miniaturize access to one of these autonomous vehicles, Truelove says. . “What we’re working on now is to be able to have everything in the vehicle over the next two years, from sampling to DNA sequencing and data analysis.”

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