DNA buried in sediments helps scientists imagine ecosystems of the past | Science News-thread


Industrialization changed the Bagnoli Bay in Italy. Analysis of the DNA that was trapped in the sediment offers a record of what was lost and a clue on how to recover it.
Photonapoli / Alamy Stock Photo

This article is from Hakai Magazine, an online publication on science and society in coastal ecosystems. Read more stories like this at hakaimagazine.com.

Today, Bagnoli Bay in Italy is badly degraded and largely devoid of marine life. But it was not always like this. By studying environmental DNA trapped in sediments, known as DNA silk, the researchers turned back the clock 200 years to get a step-by-step view of the decay of the ecosystem. Beyond showing how much the ecosystem has declined, the scientists say this technique could be a valuable part of restoration efforts in Bagnoli Bay and other degraded areas.

In 1827, the Bay of Bagnoli was a picturesque vision of the Mediterranean coast: it was covered with meadows of neptune grass and home to a wide variety of worms, sea squirts, sponges and tiny planktonic organisms, says Lorena Romero, a marine ecologist at Italy’s Anton Dohrn Zoological Station who has worked on environmental DNA analysis.

The scientists’ research revealed that from around 1851 until the early 20th century, the construction of a steel mill and asbestos plant, along with modifications to the bay, such as the construction of a causeway between an island and the mainland, caused the sea ​​grass and much more of the marine life that depended on it to disappear. This included species whose DNA scientists found buried in the sediment but are not found in any databases, suggesting they are not known to science.

It’s a classic example of habitat degradation, Romero says, where specialists die off, leaving only those species that can survive under stressful conditions.

The research effort included local scientists who had seen firsthand the most recent phases of Bagnoli Bay’s decline. Marco Cavaliere, a marine ecologist at the University of Urbino who lives nearby, says the quest to better understand what the bay looked like before the Industrial Revolution stemmed from efforts to restore it. Although Bagnoli Bay is now much cleaner than when it was more polluted, ecological recovery has been limited, he says.

A particularly difficult aspect of conservation efforts is knowing what any ecosystem was like before modern anthropogenic impacts.

Nicole Foster, a marine biologist at the Smithsonian Institution who was not involved in the study, sees sedaDNA as a way to address a problem known as shifting baseline syndrome. Looking at coastal environments, what we see has often been shaped by ongoing and historical human actions, she says.

“When we go to restore an area, we often don’t know exactly what we are restoring,” he continues. That makes it much more difficult to set realistic restoration goals. “Having these long-term data sets allows us to see what the system was like before human-induced changes,” he says.

SedaDNA offers more than a before and after snapshot. Because sediment is often deposited in layers over time, it allows researchers to track how species abundances changed over decades. In the Bagnoli Bay investigation, for example, core sampling revealed the different phases of decline throughout the late 19th and early 20th centuries.

Also adding Eric Capo, an aquatic microbial ecologist at Umeå University in Sweden who was also not involved in the research, it offers a way to reconstruct that historical baseline even for times and places where no proper study of the ecosystem had ever been done. “So this is a very powerful tool,” says Capo, who has used the technique to study lake ecosystems.

As promising as sedaDNA can be, it has limitations. For example, DNA naturally breaks down over time, Capo says. For that and other reasons, Lucy Coals, a graduate student at Australia’s Deakin University and Project Seagrass who was not involved in the study, says sedaDNA is not a panacea. But it can be part of a toolbox to better understand how ecosystems have changed over time.

This article is from Hakai Magazine, an online publication on science and society in coastal ecosystems. Read more stories like this at hakaimagazine.com.

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