Feature image: The tree of life with numerous species dangling from its branches. The ripple pattern on the seafloor indicates a high current regime on the edge of the Gulf Stream. A basket star, numerous flytrap anemones, two brisingid sea stars, holothurians high in the branches, brittle stars, and numerous other creatures are evident. (Caption and photo credit: Bioluminescence 2009 Expedition, NOAA/OER)

Like an obscure alien underworld, the deep sea beholds unique habitats and wonderfully weird creatures, from walking fish to spiky cucumbers and Casper the Octopod! Covering 65 percent of the planet’s surface, the deep sea is the world’s largest ecosystem, yet one of the least explored. However, a recent study by Ramón Gallego and colleagues, published in Communications Biology found that sea sponges can hold a genetic catalogue of deep, salty secrets. 

With an average depth of more than 3,500 metres (11,000 feet), the deep sea is a costly ecological frontier. Immense pressures, near-freezing temperatures and pitch-black darkness make studying life in the deep sea one of biodiversity’s greatest tests. Conventional methods to collect basic data near the ocean surface are prohibitively expensive and technically challenging in deeper waters. 

Despite these difficulties, it is crucial to know which species live on the seafloor and where. Without this knowledge, rare and fragile habitats—including cold-water coral and sponge gardens—are threatened by overexploitation, bottom trawling, oil site prospecting, and deep-sea mining of rare metals.

In recent years, a relatively low-budget approach to collecting genetic data from seawater has revolutionised biodiversity monitoring and management in remote areas such as the deep sea. Every living thing sheds DNA into the air, soil, or water surrounding it. This genetic material, known as ‘environmental DNA’ or ‘eDNA’, can be used to determine the presence of different species. A mere 500 ml sample of seawater can contain thousands of shed animal cells, from which DNA can be extracted to identify which species recently passed through. 

However, such samples are often inundated by single-celled microbes and capture relatively little information on corals, fish, and other large marine animals. Studies have also revealed that this method is restricted to capturing DNA within a relatively short temporal window—since eDNA degrades over time, this is the period during which it remains detectable and usable. 

Researchers from the National Museum of Madrid recently revealed a new ‘high resolution’ method for sampling eDNA by harnessing the natural filtering power of sea sponges. Their approach yields an unprecedented treasure trove of genetic data. Sea sponges are stationary creatures that continually filter large volumes of water, naturally accumulating and consuming microscopic particles such as cells shed by other animals. 

Compared to seawater samples, sea sponges can harbour genetic material from far larger areas. This is likely because of their enormous filtering capacity, with a 1-kg sponge pumping up to 24,000 litres of water per day. A study from 2022 also found that certain sponges capture eDNA across a longer time period than seawater samples, making them an incredibly valuable inventory of eDNA. 

Gallego and colleagues sampled 1 cm-sized pieces of tissue from 97 deep-sea sponges across four species from the Arctic and North Atlantic. The remarkable accuracy of eDNA obtained from sponges allowed the researchers to identify over 400 animal species, including several ‘indicator species’ like corals, that are used to help identify vulnerable marine ecosystems (VMEs). 

VMEs are ecosystems designated as ‘highly threatened’ by human pressures and protected through UN policy against destructive fishing practices. However, mapping the presence of VME indicator species in the deep sea currently faces significant financial, technical, and logistical hurdles. Recent advancements in ‘sponge DNA’ biomonitoring provide a transformative, cost-effective tool to inform deep-sea management and protection. 

Unexpectedly, non-native species such as the North American horseshoe crab were also documented by the study. The team suggests that ‘sponge DNA’ can reliably detect species undergoing a shift in their distribution due to rapid climate change. For instance, the authors found evidence of a phenomenon called ‘atlantification’, whereby typically Atlantic-dwelling species are gradually colonising warming Arctic waters.

Looking ahead, the team aims to identify which species of sponge capture and store the most eDNA. They hope this will enable even more detailed data collection and further improve cost efficiency for deep-sea biodiversity monitoring.

Further Reading

Cai, W., L. R. Harper, E. F. Neave, P. Shum, J. Craggs, M. B. Arias, A. Riesgo et al. 2022. Environmental DNA persistence and fish detection in captive sponges. Molecular Ecology Resources 22(8): 2956–66. https://doi.org/10.1111/1755-0998.13677.  

Collins, R. A., O. S. Wangensteen, E. J. O’Gorman, S. Mariani, D. W. Sims and M. J. Genner. 2018. Persistence of environmental DNA in marine systems. Communications Biology 1: 185. https://doi.org/10.1038/s42003-018-0192-6. 

Gallego, R., M. B. Arias, A. Corral-Lou, C. Díez-Vives, E. F. Neave, C. Wang, P. Cárdenas, et al. 2024. North Atlantic deep-sea benthic biodiversity unveiled through sponge natural sampler DNA. Communications Biology 7: 1015. https://doi.org/10.1038/s42003-024-06695-4.