HFF adds high-tech invertebrate sampling to water-quality network

Photo of invertebrate sampling in the Henry's Fork near Ashton Reservoir.
Photo of Brett Marshall using a net to collect invertebrates.
Photo of Brett and David in the river near St. Anthony.
Photo of Robert and Rob scraping invertebrates off of a rock.

Last week, aquatic invertebrate experts David Richards and Brett Marshall met us on the river to kick off an exciting new project that will allow HFF to monitor numbers and types of aquatic insects and other invertebrates using DNA “bar-coding”. Former HFF Board Chair Robert Dotson joined us for part of the day.

For over 30 years, aquatic invertebrates have served as standardized, biological indicators of the health and productivity of streams and rivers. Invertebrates are excellent indicators of habitat and water quality because each species has different habitat requirements and different tolerances to physical and chemical sources of degradation. For example, large-bodied mayflies and stoneflies such as the green drake and giant salmonfly, require large spaces among cobbles on the stream bottom for cover. Thus, high abundance of these types of insects indicates good-quality habitat. However, if these spaces have been filled with fine sediment, these types of insects will be reduced in abundance or absent altogether, indicating habitat degradation. Similarly, high abundance of species that are especially tolerant of warm water temperatures, fine sediment, or specific chemical contaminants can indicate degradation of water and habitat quality. Aquatic ecologists have developed what we call “invertebrate metrics,” which are numerical scores derived from the quantity and types of invertebrates present in a particular sample. These invertebrate metrics can be added to the chemical and physical parameters we are measuring through our water-quality monitoring network to give a complete picture of the health and productivity of our streams and their ability to support wild trout.

Over the years, HFF has sampled aquatic invertebrates in the Henry’s Fork and its tributaries as part of several different research and monitoring efforts. In the 1990s, we sampled invertebrates from every major stream reach and tributary as part of our watershed-wide habitat assessment. In the early 2000s, invertebrates were sampled every year at a few selected monitoring sites. Through these efforts, we established baseline knowledge of invertebrate assemblages throughout the watershed. However, the high cost of processing invertebrate samples has hindered our ability to use invertebrates as indicators of water and habitat quality over long periods of time and across numerous sites—until now.

In the past, the only way to process invertebrate samples was to pick through them by hand—one individual at a time. A typical sample from the Henry’s Fork might contain several hundred to over a thousand individual invertebrates. Counting them accurately and identifying each individual to genus or species requires specialized equipment and training and a large amount of time. Laboratories specializing in invertebrate processing charge several hundred dollars per sample. Compare this to the $8 to $20 cost of analyzing a water sample for typical parameters such as sediment or phosphorus. Thus, when David and Brett first told us that new technology could reduce the cost of processing invertebrate samples from several hundred dollars each down to nearly the same cost as a water-chemistry sample, we invited them to help bring this technology to HFF.

The new technology uses DNA to identify the invertebrates present in the sample. The DNA acts like a “bar code” that can be used to identify individual species. Over the years, scientists have been accumulating large databases of these bar codes, and they exist now for thousands of different species. The idea is that if the bar codes of all of the species present in a given stream or watershed appear in the database, then invertebrates from that watershed can be identified through DNA analysis, which is an automated process that does not require a person to sort through the sample under a dissecting scope. The sample is simply ground up into a slurry and analyzed by a machine. The only catch is that when this technology is applied to a new stream, samples must be analyzed both the old-fashioned way and with the DNA technology to match up the bar codes with the actual invertebrates in the stream.

We took the first steps toward this matching process last week. We collected three samples of invertebrates at each of five locations on the river: Flatrock, Last Chance, Osborne Bridge, Ashton, and St. Anthony. We selected these locations because, based on previous work, these five locations combined contain nearly all of the invertebrate species present in the whole watershed. Brett’s laboratory in Bozeman is currently sorting these samples the old-fashioned way and will provide us with a complete species list in a few months. After his lab completes the manual analysis, David will send the same samples to a DNA laboratory at the University of Utah to obtain the DNA analysis. By the end of 2015, they will have matched the individual invertebrates with the DNA bar codes so that in the future, we can use the DNA method in lieu of the expensive hand-sorting method to calculate invertebrate metrics.

Our plan is to the repeat the same sampling we did last week during 2016, 2017, and 2018 and use the DNA method to track changes in invertebrate abundance, species composition, and metrics over the next three years at these five sites. Of course, once the DNA database for our watershed has been developed, we can use the DNA-based technology to analyze any and all invertebrate samples we collect, regardless of when, where or why we collect them. The greatly decreased cost of processing samples with the DNA technology will allow us to use invertebrate metrics as part of our routine water-quality monitoring throughout the watershed and as a component of site-specific assessments. This technology can even be applied to studies of trout diet, insect emergence timing, and response of invertebrate assemblages to climate change.

As we obtain results from this effort, we will circulate results widely, so that anglers will have a good idea of what insects the trout are likely to be eating in different reaches of the river. After all, what would be the Henry’s Fork fishing experience without the insects?