IBIs (Index of Biological Integrity) can definitely be calculated with eDNA data although most IBIs need to be adjusted to take advantage of eDNA's strengths (e.g. greater diversity) and recognize its limitations (population size is hard). Contact us to see if we can generate a custom solution for you.
At this time, we are working on constructing eDNA IBIs using fish, phytoplankton, and macroinvertebrate data with NGS data from multiple states. On our end, this involves researching the pollution tolerances of indicator species and applying those tolerances to the species we've found in a sample. With what little testing we've done with fish, it seems to be effective and we intend to replicate this with phytoplankton and macroinvertebrates. We theorize that phytoplankton will be able to tell us the most about water quality, but this presents a challenge, as there is little literature out there describing phytoplankton's pollution tolerance.
If you're interested in this concept and want to learn more, please reach out and contact us.