An ecosystem in a teaspoon

Dr Anjani Ganase discusses the use of DNA studies and technology to understand and manage our environment.

When William Blake wrote in the late 18th century, “To see a world in a grain of sand and heaven in a wildflower; hold infinity in the palm of your hand and eternity in an hour,” did he envisage that within two centuries later, scientists could explore an entire ecosystem from minute traces of matter? This is how we are learning more about the earth’s history. Will we be able to use this information to help us create a better future?

The study of ecology allows scientists to explore and immerse themselves in observing the relationships between an organism and its physical and chemical surroundings. Everything an organism does in its environment is evident in the DNA tracks left behind. DNA, or deoxyribonucleic acid, is the genetic instruction carried in the cells of all living organisms.

DNA is everywhere: in sloughed off dead cells, any drop of saliva or remnant of what was once alive.

Today, the use of hostless DNA found in the environment (environmental DNA or eDNA for short) has become useful for dramatically extending our observations to the unseen, unheard and unobserved life in the environment. Environmental DNA refers to any DNA collected in samples such as soil, sediment or water, that contains material shed by living organisms. From the samples, we can detect the presence of known species and ascertain the species diversity of multiple creatures – animals, plants, fungi, even pathogens – in a given location. Collection over time can give an indication of the degree of interaction or sharing of the same habitat and how the habitat may have changed.

How does it work?

Environmental samples, whether from soil or sediment or water samples collected from the river or the ocean, can be examined for DNA. All DNA present in the sample is extracted and then DNA of interest is amplified using a PCR (polymerase chain reaction – yes, the same used for detecting covid19). A DNA barcode is used to select a specific section of the DNA which is matched with a known reference library of species DNA.

Recreating ancient ecosystems

This was the tool used to recreate ancient ecosystems. Scientists would extract eDNA from soil samples taken from sediment cores. Within the sediment cores, scientists can observe the presence of pollen and seeds to identify the trees and plants that may have existed thousands of years ago. Now with the use of eDNA (that has not decomposed) they can identify all forms of life that have left traces.

Many studies have identified the presence of extinct mammals, birds, plants even fungi and insects. In this way, a more comprehensive picture of ancient ecosystems has emerged. For example, the eDNA method showed that there was significant overlap in time between the woolly mammoth and humans in North America and it was likely that the woolly mammoths may have survived as recently as 5,000 years ago, much later than previously thought based on fossil records. This opens many questions on the interaction between humans and woolly mammoths and how might we have been responsible for their extinction.

Apart from humans and mammoths, the same study also identified the co-existence of over 60 other animals, mostly megaherbivores – bison, horses, mammoths, sheep, reindeer – along with some predators such as the grey wolf, and rodents and birds. The plant habitat was recreated with identification of 60 plant species and families, including grasses, woody plants, pines, representing their grazing habitat. Through eDNA we have been able to track the changes in the presence of the animals and plants 30,000 – 3,000 years before present.

Similar studies were applied to ice cores of glaciers to assess the plant biodiversity and the changes over time in north Italy. The application of eDNA filled in many gaps in samples already investigated for pollen and the chemical composition of the ice.

Today’s environments

More recently the methods have been applied to living ecosystems that are more difficult to access, such as underwater environments, lakes, estuaries, coral reefs, and bays. In the marine environment, eDNA does not last long, as the salt water rapidly degrades eDNA within hours. This method therefore most accurately identifies life currently present in the area.

In New York, scientists have used the methods to track the presence of whales and dolphins in the area. They were able to identify several different species of whales and dolphins as well as the bait fish they feed on, as they pass through the New York bight. This was also applied to coral reefs in Hawaii where scientists were able to correlate the presence, abundance, and diversity of living corals accurately with the use of eDNA methods. Broader applications include the comparison with more degraded reef systems and there is the potential for DNA-based biomonitoring on coral reefs. It may not replace the joy of marine biologists to dive and explore reefs, but it would extend the observational scope to larger areas, deeper reefs, remote locations and hard to access areas. For marine researchers or managers, time saved from underwater observations and basic assessments means more time to work on deeper research and monitoring activities.

Applications to management

eDNA is also used to detect the presence of invasive species, even pathogens, that can go unseen in habitats. For example, it has been used to monitor the American bullfrog, as well as invasive fish species such as the Asian carp and the bluegill sunfish in the US. Environmental monitoring agencies in the US will regularly look for eDNA of invasive species in their rivers in order to detect the presence of non-native fish, weeds, snails, mussels and even parasites of the commercially important salmon family. Early detection has advanced their management efforts to remove invasive species, such as the zebra and quagga mussels that rapidly settle and reproduce on hard surfaces, blocking pipes and fouling infrastructure and even outcompete the native mussels.

Since Watson and Crick first described DNA (1953), scientists have not looked back. At the UWI, St Augustine, the DNA of Trinidad’s cocoa has been studied; and human genetics research is flourishing. How might eDNA applications be used to describe the conditions for conservation and restoration of Trinidad’s natural biodiversity, or Tobago’s coral reefs? These are enterprises that would certainly give us a view of our place on these islands, and help us build resilience to climate change.