Thursday, August 30, 2012

I spy with my little eye

New successful eDNA experiments

Environmental DNA (eDNA) allows us to detect the presence of organisms without direct observation. Plants and animals shed cellular material in their surrounding environment, and this material can be collected and analyzed. Traces of DNA extracted from environmental samples can be used to determine if a target species has been in the vicinity of a sampling site. 

Generally there are two different approaches that utilize eDNA. The first is to design specific probes (e.g. TaqMan probes for real-time PRC assays) which are used to detect DNA of particular species in environmental samples. This method has great potential for invasive and endangered species detection and has been used e.g. to detect bullfrogs in French wetlands or Asian carp in the Great Lakes

The second approach uses Next-Generation Sequencing technology to gather sequence information from assemblages of specimens. This method has been called "environmental sequencing", environmental barcoding", or even "meta-barcoding". Name it as you please the idea remains the same: An environmental sample is filtered, homogenized, and all DNA is extracted from it. The DNA is amplified with a marker of your choice, e.g. the COI Barcode region, or more species- or group-specific markers or a combination of them. Subsequent massive parallel pyrosequencing will result in thousands of sequences that represent a genetic fingerprint of the ecosystem sampled. This snapshot is limited in its ability to identify all sequences in a given sample but the chance of comparing genetic diversity of different standardized samples at a single locus will help to understand and show community differences. This could include differences between regions, changes over time, or responses to environmental changes. Eventually changes could be monitored by looking at the full picture instead of relying on single representatives such as indicator species.  The challenge lies in the standardization of such datasets that would allow the observation of real differences and similarities in patterns.

Thomsen et al. 2012
Yesterday two papers of researchers from Denmark have been published in PLoS ONE describing the detection of macro-organisms through eDNA from marine water samples. One group was looking for fish and the other for mammals. This is the first time eDNA detection was successfully done with marine samples while it was already applied to terrestrial sediment samples, ancient cave sediments, ice cores, and freshwater samplesThe first group was able to identify 15 different fish species, including both species important for fisheries, as well as species rarely or never recorded by conventional monitoring programs. Interestingly they also detected 4 bird species in their sample among those the Red-throated loon (Gavia stellata) that passes through the sampling region only occasionally during migration. The authors were also able to prove that their eDNA method is as good as or mostly better than methods traditionally used for monitoring fish such as trawl and pots.

The second study tested the potential use of eDNA for genetic monitoring by using specific primers to detect the presence of  the harbor porpoise, Phocoena phocoena, both in a controlled environment and in natural locations. Results for the natural sites were compared to the current method of choice - detection of echolocation clicks by static acoustic monitoring devices. The genetic results were not as consistent as acoustic monitoring but the authors are confident that they will be able to change this by optimization of their protocol and the use of larger sample volumes.

Bottom line is that half a litre of seawater can contain traces of local fish and whale faunas and combat traditional fishing methods - not bad.

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