Environmental DNA Provides Lessons On Life

Using eDNA, we can figure out where shy animals like this platypus live without disturbing them (Image credit: Amber Noseda, Great Ocean Photography, CC BY 2.0)

As an undergraduate student, more than twenty years ago, discussions of species often referenced ‘lumpers’ and ‘splitters’. Some biologists were more likely to ‘lump’ all variation within a single species while others attributed variation to distinct subspecies, and ‘split’ organisms as such. Back then, we talked about biomes such as forests and grasslands but the term ‘microbiome’ barely existed. Now, even the concept of an organism is questioned as some scientists argue that the individual cannot be separated from the microbiome it hosts. Thanks to advances in molecular biology, every organism is now an ecosystem.

A microbiome includes all the microbes (and their DNA) from a particular environment. A plant leaf has a microbiome, as does soil. It may not be welcome news to learn that drinking water has a microbiome. The human gut microbiome is a popular topic these days but we have microbiomes associated with many other parts of our bodies, including our skin.  We walk around in a microbial cloud and leave a trail of DNA in our midst, consisting of our human DNA and that of the microbes that call us home.

Environmental DNA, or eDNA for short, is DNA collected from the environment which might be water, soil, sediment, or air. Water or air samples are often pumped through a filter to concentrate diffuse DNA. These eDNA samples will contain the DNA trail left by animals (skin, fur, faeces, scales) and the DNA of the associated microbiome. DNA collected from the environment can be used to track the occurrence of organisms, in some cases from thousands of years ago.

Back in the lab, all of this DNA, from whatever source, gets separated or ‘extracted’ from the other stuff in the sample through a series of chemical processes. In my PhD research, I found this step extremely nerve wracking as months of fieldwork became minute samples, each containing a single drop of fluid. How the universe of DNA in this single drop gets dissected, duplicated, and decoded depends on what you are looking for.

DNA contains four compounds: adenine, thymine, guanine, and cytosine, which are encoded by A,T,G, and C. Can you imagine trying to send a note using only four letters? What DNA lacks in letters, however, it makes up for in length. Each letter is paired up with its mirror image on the other DNA strand to form a ‘base pair (bp)’. The human genome contains three billion bp, while lungfish genomes hold hundreds of billions of base pairs. 

If we imagine the base pairs of the human genome arranged in a book, there would be one million pages. When comparing different organisms, many of the pages of each book will be identical and many won’t contain enough detail to distinguish different species, so molecular research identifies the best pages for describing groups of organisms. Page 57 might describe different frogs but is totally useless for telling a story about snails. The technology that decodes DNA handles about 400 bp so ultimately, we need to know which paragraph on which page we are looking for.

A DNA barcode is like a paragraph in a (very) large book. (Image credit: Emma Hess, CC BY 2.0)

The selected genetic material (the paragraph in our example) needs to be duplicated to create a measurable sample. The PCR process, which stands for polymerase chain reaction, duplicates, or amplifies the selected section. PCR has become a familiar term because it is a critical step in most Covid-19 testing. It’s shortages in PCR equipment and supplies which have delayed testing. In Covid testing, a fluorescent ‘label’ is included that binds only to the unique Covid-19 sequence so the sample glows if the viral genetic material is present. 

A similar process is used in eDNA research when there is a single species of interest. An example is the detection of platypus in waterways around Sydney and Melbourne. Managers and volunteers collect water samples from a broad network of sites. Then, scientists extract, amplify, and detect platypus DNA to understand where they live and shape strategies to support healthy populations. eDNA is incredibly helpful in the detection of shy or cryptic species, and it’s also used as a sampling technique in rivers that are too dangerous for a researcher to take more traditional samples. You wouldn’t want to go electrofishing when a river is full of hippos or crocodiles, but a quick dip of a bucket might work.

As amazing as it is that we can detect imperilled or invasive species by sampling their environment, I am even more excited about how DNA metabarcoding is revealing new life in new places. In this case, the genetic ‘sequence’ that forms a paragraph in our example is referred to as a ‘barcode’ and ‘metabarcoding’ considers the barcodes of multiple organisms. Metabarcoding is exploding our understanding of microbiomes because traditionally, microbiology required lab culturing and only a small fraction of microbes have been successfully cultured.

In my DNA metabarcoding research on stream biofilm, I looked at three different paragraphs, one each for algae, fungi, and bacteria. DNA sequencing revealed about 5000 different organisms across the three broad groups. Sometimes a barcode matches an existing, documented species but in many cases, the fine-scale taxonomy is missing because the organism may not have been sequenced previously or may be new to science. In either case, barcodes can be mapped onto a very cool, interactive tree of life that I couldn’t have imagined early in my career. Some microbial branches of the tree have fine tips of individual species while others are thick with samples awaiting further classification.

As I’ve watched the news coverage of the smoke from fires in the western United States spreading around the world, I keep thinking about Leda Kobziar’s research on the smoke microbiome. She and her team have found living bacterial and fungal communities in wildfire smoke and documented differences in these communities associated with different land management practices. 

Has smoke from the massive fires in Australia and California this year shifted microbial communities elsewhere in the world? If so, are these changes ecologically significant? We may never know but certainly, DNA technology is demonstrating epic levels of biological connectivity and complexity. In one sense, DNA is revealing a Russian doll of life within life, although ‘fractal biology’ might be a better descriptor for the infinite pattern of relationships. 

Smoke from Australian bushfires in January, 2020 spreading across the Pacific. (Image credit: Andrej Flis)

Although today we can’t place a drop of water in a machine and catalogue all the life it contains, we might be able to tomorrow. I saw a suggestion from a molecular biologist that our phones may someday be capable of sequencing DNA. This somehow feels creepier to me than a drinking water microbiome but perhaps that’s just my age. 

Krista Bonfantine is a PhD student at Deakin University studying the effectiveness of environmental flows using DNA metabarcoding and citizen science. Her background includes water and fire management and her passion is connecting science and society for a better, wetter world. Learn more on her website or follow her on Twitter.

* I would like to thank Vasco Elbrecht (@VascoElbrecht) for the DNA sequencing book analogy.

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