In the bug lab, we work on sorting, identifying, and analyzing data collected on benthic macroinvertebrates (BMI) from creeks, streams, and rivers throughout the northern and central Sierra Nevada range. BMI are indicators that allow us to understand the health of the water ecosystem, like a canary in a coal mine. For example, certain BMI will be absent in a creek that has high nutrient input, whilst others will thrive in this environment. Stoneflies have a very low tolerance for pollutants, so if the creek supports a thriving stonefly population, water quality must have been good for some time. By studying which BMI are present and absent, we can build up a long term picture of the health of our waterways. We have volunteers and interns that help our staff and we do fee for service work too. Want more information? Email us at bugs@sierrastreamsinstitute.org!
What is a benthic macroinvertebrate?
A BMI is an animal without a backbone – invertebrate – that we can see with our naked eye – macro – who completes at least some of their life cycle on or in the substrate of an aquatic habitat – benthic. In the case of our collections, we are interested in the BMI that live on and in the creek bed.
How do we collect BMI?
Each summer and fall, we do a number of creek surveys to collect the BMI. We survey 100 meters and use a net to collect BMI every 10 meters, giving us 11 collections. We pick out any large debris that we caught in the net before transferring the BMI into a solution of eugenol to anesthetize them. Then we transfer them into an ethanol solution to euthanize and preserve them.
We also collect other relevant data to assess the health of the creek. These include: algae, chlorophyll, organic matter, physical habitat, eDNA, and water quality measurements.
Timeline of a benthic macroinvertebrate sample
Once the BMI have been collected, the sample is stored in ethanol until it can be sorted and identified. Then we pick out the bugs from the plant and algae matter and sort them into vials depending on their taxonomic order. The BMI are then identified to their highest taxonomic classification using the SSI Bug Book and other BMI guides and keys. (Taxonomic classification notes similarities and evolutionary relationships between organisms and categorizes them accordingly.) The data is stored and analyzed in house and is available on request.
Our long-standing volunteers deliberate over the taxonomic identification of a BMI
What are we currently up to?
Since 2001, Sierra Streams Institute has monitored the length of Deer Creek and its tributaries. In 2016, we expanded to encompass the Bear River and its tributaries. We survey every June and October, taking samples from numerous sites across these two waterways and identify BMI collected to the highest possible taxon. This provides a fantastic and comprehensive data set, both spatially and temporally, so we can understand long term impacts on the waterways.
In 2025, SSI received a grant from the Delta Research Awards to study headwater streams that will eventually drain into the Delta. This grant allowed SSI to expand into watersheds beyond Deer Creek and the Bear River. Crews are collecting BMI samples from 9 major watersheds, from the Pitt River to the Stanislaus River, in the summers of 2025 and 2026. The BMI Lab will be identifying the BMI collected and analyzing the community compositions to give us an indication of creek health in those systems.
The State of California has a huge project where they want a DNA barcode of every organism in the state. A DNA barcode is a piece of DNA that is unique for each species. We are working with the State of California to provide DNA barcode sequences for BMI in the northern Sierra Nevada Watersheds. Freshwater invertebrates are often overlooked when gathering species information in ecosystems and so we are providing invaluable data for understanding California’s rich biodiversity.
The BMI Lab also helps to study the impacts of restoration projects. We have in-house restoration efforts that require BMI monitoring, like our riverbank restoration project at the BEALE Airforce Base, and external projects, such as the restoration of an acid mine. By establishing a baseline and then monitoring the changes in the BMI community as these projects develop, we can see what impact these restoration efforts are having on the aquatic ecosystem.
Our high school intern searches for BMI amongst the algae and organic matter.
Research
Who lives where? – Riffle vs Pool Habitat
We are studying the differences in benthic macroinvertebrate (BMI) communities between two key habitats in streams: riffles and pools. Riffles are areas of faster shallower moving water and pools are areas of slower deeper water. Sediment tends to move through riffle habitats and collect in pool habitats. With drought, riffle habitats are being reduced, because when flows are low, there is not enough water to maintain riffles. We want to understand how BMI communities are changing along the streams with these changes in weather patterns.
What are the BMI up to in Deer Creek? – Trends in BMI in Deer Creek
For over two decades we have been monitoring the Deer Creek watershed. A watershed is an area of land that drains into a river or other water system. We have data on water quality and benthic macroinvertebrate (BMI) across the length of the creek. We have been analyzing our data to try and find trends in the data, both across time and across space.
One trend is that the diversity of species is higher in the upper watershed when compared with the lower watershed.
Another trend is that the species in the lower watershed are more generalist species, meaning that they can tolerate a broader range of environmental conditions, whereas the species in the upper watershed tend to be more specialized.
To die or not to die? – Humane BMI Collection
This year, the SSI monitoring team challenged ourselves to survey and collection BMI in a more humane way. Traditionally in this industry, surveyors collect BMI from the streams by submerging them in a 70% alcohol solution. Whilst this does effectively kill and preserve them for further ID work, recent scientific literature has challenged this method. Invertebrates are widely accepted to feel pain and some researchers are pushing for the use of anesthesia when collecting / handling invertebrates. Also, our staff and volunteers didn’t enjoy submerging the BMI into ethanol and watching the invertebrates pain response, and so we sought alternatives to using just an ethanol solution.
In April and May 2025, we conducted preliminary field studies with common aquatic anesthetic solutions, and the SSI monitoring team found that a solution of eugenol was effective as an anesthetic for BMI. Eugenol is an oil naturally derived from clove oil. We rolled out the use of eugenol in our BMI collections prior to submersion in ethanol in our summer 2025 creek surveys and it had major success. We will we using an anesthetic agent in our BMI collection from now on!
Another way to study BMI more humanely is to not have to kill them all at! The monitoring team are working with the SSI restoration team to implement live field picks for their restoration monitoring programs rather than a collection in alcohol. This involves sorting the BMI alive and in the field before returning them to the stream. Since the restoration team are using a lower taxonomic resolution for their study, a live field pick achieves the resolution requires whilst eliminating the need to euthanize BMI to bring back to the lab.
Do we have to collect BMI? – Metabarcoding and eDNA
All life is programmed by DNA. DNA lives in cells and codes for proteins that make up life. DNA is unique to each organism, whether on an individual level (unless you’re an identical twin!) or a species level. Organisms shed cells into the environment, which carry their unique DNA. When DNA is free in the environment, we call this ‘eDNA’ or environmental DNA. This allows us to survey for organisms without needing to find them, since we can collect their eDNA instead.
We are comparing how the collected eDNA compares to the species we find from our bi-annual collections. We are asking the question: does eDNA give us an accurate idea of what BMI are living in a stream?
We collect eDNA from the stream when we also collect BMI samples. We identify the BMI communities in our in house lab, and the eDNA samples get analyzed elsewhere in labs specialized in DNA sequencing. When we get the eDNA results back, we can compare what we identified and what the eDNA results show us.
It is early days, but so far we have found that, whilst eDNA compliments our collections and helps with ID, it does not capture the full diversity of what we find in our streams. We need to continue to study this more to understand just how useful eDNA could be for future stream survey work.
Fee for service
We work with external organizations and restoration projects to identify the BMI in their target streams and rivers. We will also train individuals and organizations on BMI identification. For more information on services and fees, please reach out to us at bugs@sierrastreamsinstitute.org.
We also sell our SSI Bug Book if you require a family level guide to the BMI found in California and western North America.
Want to get involved?
Every first Wednesday of the month (October – May) we are open to new volunteers. Interns also help out in the BMI Lab during the fall, spring, and summer semester. Volunteers and interns can also help on June and October creek surveys. Reach out to bugs@sierrastreamsinstitute.org to inquire about volunteer and internship opportunities.
Watch a video here about this intern’s job and experience in the BMI lab, and learn about the scientific discovery they made whilst working in our bug lab!
You can find our calendar schedule on the SSI Calendar.
Our long-standing volunteer is identifying BMI down to their highest taxonomic classification
