DNA barcoding: how can bioassessments better scan freshwaters for life?

Sampling for macroinvertebrates. Credit: Gary Peeples / USFWS
http://www.fws.gov/asheville/

Bioassessment programs monitor the different plants and animals in ecological communities as a means of understanding the health of an ecosystem and how it might respond to changing environmental conditions over time.  A journal article “Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods?” published in PLOS ONE by researchers in California and Canada examines whether DNA ‘barcoding’ technology – where a species is identified by DNA in tissue samples – is more effective, affordable and quicker than traditional visual, morphological techniques.  As also shown in last week’s post about the potential of drone sensing of freshwaters, ecologists around the world are currently assessing the promise of new technology for monitoring, understanding and protecting freshwater ecosystems.

The article, published in April by Eric Stein and colleagues, found that bioassessments using DNA barcoding technology currently cost between 1.7 and 3.4 times as much as traditional, morphological (i.e. visual assessments of a species’ structure and form) methods.  However, DNA barcoding approaches can process samples much quicker and at a higher resolution than traditional morphological techniques, potentially helping rapid, adaptive management of environmental issues.  After identifying a large global market for bioassessment technologies – particularly in governmental monitoring schemes in the USA and Europe – Stein and colleagues suggest that further research and development of DNA barcoding technologies is necessary and warranted, in order to bring costs down and encourage widespread adoption.

Aquatic bioassessments generally focus on particular ‘indicator’ species – often fish and insects – whose presence (or otherwise) gives an indication of the health of the wider ecosystem.  Bioassessments are often repeated over time using groups (or ‘assemblages’) of indicator species which are particularly sensitive to changes in water quality – e.g. invertebrates – to study how an ecosystem responds to stressors such as pollution or overfishing.  In the USA, bioassessments are used to assess how far different States comply with environmental legislation such as the Clean Water Act.

Stein and colleagues assessed whether bioassessments can be carried out more cheaply and efficiently by using DNA barcoding technology. Currently, bioassessments using morphological techniques require a significant amount of time and resources to allow trained taxonomists to study different ecosystems.  As a result, the quality and level of taxonomic resolution (i.e. the detail in which different organisms are studied and categorised) may vary across different regions, depending on the experience and training of available taxonomists. Another drawback of current bioassessment practice is that it may take six months or more for field data to be translated into the biological indices required for environmental management and policy making – a lag which may prevent quick responses to environmental problems.

Typical freshwater sampling kit for invertebrates: can new technologies help make this process more efficient? Image: Tatiana Gettelman | Flickr CC

DNA barcoding identifies animal species by analysing a short strip of their DNA (see, for more information, the Barcode of Life website, this Wikipedia article and this journal article by Hebert et al (2003).  Unknown specimens collected in fieldwork can be referenced to a DNA database such as Barcode of Life Data Systems or GenBank.  As is often the case with new technologies, it has been suggested that DNA barcoding has the potential to make bioassessment programs more efficient and affordable, by reducing the amount time spent by taxonomists in identifying specimens, and providing quicker results.

Stein and colleagues first compared the time and cost of traditional bioassessment methods with those of DNA barcoding: from initial sampling through to an identification endpoint which could be used for assessing the health of the sampled ecosystem.  Twelve field sites were sampled for macroinvertebrates (which are common freshwater indicator species) along the San Gabriel watershed in California, ranging from mountain streams to urban flood control channels.  Traditional bioassessment methods were carried out in a labroratory on one sample, whilst the a second set were shipped in two batches to the Canadian Center for DNA Barcoding (CCDB) for DNA barcoding.  DNA analyses were carried out both with current Sanger approach for single species, and the ‘next generation’ IonTorrent approach for bulk samples of organisms.

This first strand to the research found that despite the promise of new technologies streamlining monitoring work, bioassessments using DNA barcoding technology currently cost between 1.7 and 3.4 times as much as traditional, morphological methods.  However, DNA barcoding approaches can process much quicker than morphological approaches – the paper suggests that DNA approaches can analyse samples 3-4 times faster than traditional techniques.  Similarly, DNA barcoding has the potential to analyse samples at a much higher resolution and taxonomic accuracy than traditional morphological techniques – see Stein’s paper in Freshwater Science for more on this – potentially aiding rapid, adaptive management of environmental issues identified by bioassessment.

The second strand to this research was an analysis on the market and demand for bioassessment technologies.  In the USA alone, the research found that more than 13 million samples from 19,500 sites are analysed in bioassessments annually, most notably through country-wide federal monitoring programs.  Similarly, bioassessments are regularly used by monitoring programs for the Water Framework Directive in Europe and the Assessment of River Health in Australia.

The authors suggest that as DNA barcoding technology continues to advance, the costs involved will drop.  They suggest that bulk sampling technology like IonTorrent – where individual organisms don’t have to be picked and sorted from large samples, and instead DNA can be extracted in bulk to produce a list of all species present – has the potential to significantly reduce time and money requirements in the future, given appropriate investment.  They conclude that the potential market demand for new, more efficient and streamlined DNA barcoding technologies is large enough – particularly in the USA and Europe – to justify continued research and development with the intention that costs will be reduced enough to encourage widespread adoption.