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Biochemistry

The Entire Ocean in a Drop

Article: Stoeckle MY, Soboleva L, Charlop- Powers Z (2017) Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary. PLoS ONE 12(4): e0175186

The American eel is difficult to survey for due to a complex life history, varying habitat needs, and cryptic lifestyle. By Clinton and Charles Robertson wikipedia

Effectively managing fish populations requires accurate and timely monitoring data. Scientists and environmental managers need to know when (presence/absence data), where (location data), and how many fish (abundance data) are present in their jurisdictions during each of their (sometimes complex) life stages to manage their populations. Unfortunately, underwater environments are incredibly difficult to survey due to their size and diversity. Marine fish surveys often require expensive equipment, expert and skilled personnel, and large amounts of time to collect representative data and, as a result, usually end up compromising data quality for saved resources.

An Ocean in a Drop (or 1L jug)

Environmental DNA (or eDNA) is the genetic material contained within sloughed off cell or tissue fragments floating in the water column – like a fishy underwater dust. These DNA fragments can be used to help scientists detect fish species in a water body, without intensive in-person surveys, if they know which DNA segment belongs to which species. The International Barcode of Life reference library (iBOL and BOLD) allows scientists to do just that – it contains an extensive database of genetic profiles for thousands of the world’s plants and animals. So, if a biologist, fisheries scientist, or other surveyor can detect and amplify enough eDNA from a water sample, they can compare the DNA script to those in the database to determine which species they have in the sample, assuming that species has a genetic profile in the database. It’s just like looking up a barcode, hence the name.

Genetic analysis allows comparison of captured DNA to transcripts available on public databases. From wikimedia.org

Environmental monitoring via eDNA has been around since the mid 2000s and has been used to explore presence/absence detection of many freshwater fish. It’s been particularly successful at detecting some rare and cryptic species that are traditionally difficult to monitor. However, marine species have yet to be extensively studied with this technique because marine environments are so much larger and can be significantly more complex than freshwater.

Stoeckle and colleagues, a group from The Rockefeller University in New York, tested the success of eDNA as a detection method for marine fish species by collecting water samples from two locations in the Hudson River estuary over a period of six months. The mouth of the Hudson River is an ideal study system for testing the potential of eDNA, as it contains a diverse variety of fish species, experiences significant seasonal changes in fish abundance, has some freshwater inflow, and is heavily urbanized. There’s a lot going on in this river that could affect the successful collection and analysis of environmental DNA samples. The area has also been previously surveyed using traditional techniques, giving the researchers a baseline to compare eDNA samples to.

Here’s what they found:

  • eDNA analysis of Hudson River water samples revealed the presence of 81% of known locally common species. Species not detected were typically those known to be less abundant in the estuary environment this study took place in (in fact, in one year’s survey, only 10 out of 61 known estuary species made up 99% of individuals).
  • Detection of known rare or uncommon species was relatively low, at only 23% of known species. They did, however, detect the threatened Atlantic sturgeon and American eel.
  • Some of the species detected were commonly consumed food species from other areas, including Red snapper, European sea bass, and Atlantic salmon, presumably coming from wastewater in the river. They also found human, domestic animal, and terrestrial wildlife DNA, as is common in eDNA studies.
  • Freshwater species were rarely detected despite freshwater inflow.
  • Detection over time and different locations showed that many species moved upstream in the Spring months, matching historical survey records and known behavioural trends in these species.

The Future of Environmental Monitoring?

Study Area – The Hudson Estuary. From Stoeckle et al.

Researchers like Stoeckle are increasingly showing that eDNA is an effective technique for profiling presence/absence in marine environments. This paper also showed that eDNA is precise enough of an indicator to monitor seasonal as well as smaller-scale geographical presence/absence – two really useful applications in environmental management. eDNA offers valuable input to environmental monitoring processes and, even under current knowledge gaps, is well positioned to compliment traditional survey methods. This study looked for a large number and diverse array of species, but the researchers suggested that if surveyors seeking to use eDNA could target their investigations to specific species (ex, indicator species), locations, or seasons for optimal success, they could complete all required sample collection and analyses within one week. In their own study, collecting 76 water samples and doing genetic analysis for 85 target species cost Stoeckle et al about $10,000, not including salaries. Considering the high cost of traditional survey work (which can reach into the hundreds of thousands of dollars for similarly sized studies), the low cost of amplifying eDNA samples to detect a few target species should tempt environmental managers.

Though eDNA shows great promise, Stoeckles’ group point out that there is still work to be done. In marine, freshwater, and terrestrial environments, eDNA as a detection tool is dependent on the existence of accurate genetic profiles for every species under investigation. That means the continuation and growth of collections like BOLD, as well as other shared databases like FISHBase, MARCO, and eBIRD, are essential for the continued successful use of this tool. For marine species in particular, representation in these databases is pretty low. There are also certain limitations to the genetic technology used to amplify the eDNA found in environmental samples. Currently, DNA needs to be present in a sample in fairly significant amounts to be detected by this monitoring technique, which means species with low abundances may not be detected (as was probably the case in this study). There also aren’t many methods for estimating a species’ abundance from the amount of DNA amplified, often limiting eDNA to only a measure of presence/absence. Knowing how many fish are present in a population is important to inform management decisions about that population. The development of new and cost effective laboratory tools will therefore be invaluable to improving eDNA techniques in the next couple years. It’s an exciting time for environmental management!

R J Parker
Hi there! My name is Rebecca Parker. I’m a botanist with a side interest in science communication. Most of my research so far has focussed on population and community ecology, especially for invasive plant species and wetland systems. I’m particularly interested in population-level response to climate change, the role protected areas play in managing plant species, and carbon fluxes in wetlands. Outside of these scientific interests however, I’m also interested in how environmental outreach programs are assessed for success, how exposure to science and demography affect environmental values and behaviours, and best practices for building community capacity in stewardship. I graduated from Ryerson University’s Master of Applied Environmental Science and Management in 2014, where I studied evolution in invasion fronts, and recently moved back home to the east coast after a couple years working in environmental education and stewardship in Ontario. I currently work for the Nova Scotia Nature Trust in Dartmouth Nova Scotia.

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