Bioassessments measure both the physical condition of a water body, and the integrity of the associated biological communities. Adding such physical and biological metrics to standard chemical and toxicological assessments provides a more comprehensive evaluation of the condition of a given body of water. Resident organisms can be better indicators of overall environmental health than measurements of individual stressors (such as toxic chemicals or other pollutants) or more general ecosystem attributes.
This form of assessment provides information on the condition of a site based on the taxonomic composition and a priori knowledge about tolerances of some taxa to pollution or other stressors. However, this can be a roadblock as the use of coarse taxonomic resolution can obscure patterns in bioassessment metrics and hinder detection of biological impacts. Thus, fine-scale taxonomic resolution is desirable to maximize the diagnostic capability of assessment tools.
I am sure by now every regular reader knows where this is going. It is well-known that obtaining such detailed taxonomic data is challenging because identifications typically are done by using morphological characteristics. There are a lot of issues with that especially for standardized and repeated assessments. Limited taxonomic resources, cryptic species, small size, damaged specimens, and polymorphism just to name a few of those.
A group of US researchers now compared the ability of several commonly used bioassessment metrics calculated with data derived from morphology and from DNA Barcoding to detect differences in stream condition of 6 paired sites in southern California with relatively subtle impacts to habitat. Their paper has now been officially published in Freshwater Science which was previously titled Journal of the North American Benthological Society.
The results of this study are very interesting as the authors focused more on the level of sensitivity a DNA barcoding approach provides and not so much on the question if it would work in general. They found increased metric sensitivity associated with barcoding was most pronounced at high-quality (i.e., relatively unimpacted) sites, which often have higher species richness and are inhabited by undescribed, cryptic, or regionally rare species. For example, 43% of the additional taxa identified through barcoding consisted of 1 or 2 individuals and occurred at only 1 stream. The presence or absence of rare species may be diagnostic of specific environmental changes, so the increased information provided by barcoding at taxon-rich sites allows finer-scale resolution of sources of stress and increases our ability to detect subtle changes in environmental quality.
The conclusions are fairly positive:
The DNA barcoding approach can improve existing BMI [benthic macroinvertebrate]-based bioassessment programs by enabling development of new or improved metrics based on taxonomic groups that currently are under-described and underused. Additional benefits include applications for quality control, taxonomic standardization, and improvement of taxonomic keys (Pilgrim et al. 2011, Sweeney et al. 2011). Barcoding probably will be used with increasing frequency to augment or support existing methods and to provide cost-effective improvement of taxonomic capacity.
Potential challenges and solutions to meet them are also discussed:
However, full integration of barcode data in routine bioassessment will be challenging. First, a robust barcode reference library must be developed and vouchered. Standard handling and quality-control procedures must be developed to reduce risk of loss of samples because of contamination or DNA degradation (as happened for 1 of the sites in our study). Improved primers are needed for certain taxonomic groups to minimize bias caused by differential amplification. More research is needed on the effect of short-sequence reads on conclusions about taxonomic resolution.
Overall this paper is a very good read. It is clear, concise, and provides an objective assessment of a new approach to freshwater bioassessments.