PicoBlog

In November, we celebrated our 6th anniversary, so we’re reflecting back on how Bob Wayne and other UC faculty raised the funds from the University of California to get this crazy citizen science eDNA thing going when we had no model to follow. Here’s a photo from one of our early workshops where we planned CALeDNA and other conservation genomics activities.

And now, 6 years later, we’re thrilled to be able to show our program to state legislators! Here’s Senator Laird visiting our UCSC headquarters in Fall 2022.

We are grateful that our National Park Service partnership is growing! We continued research on biodiversity, anadromous fish, and invasive species in Hawaii, Alaska, and added a project in California at Pt Reyes. We also began a harmful algal bloom study with the Hoonah Tribe and Glacier Bay National Park in Alaska. Postdoc Dr. Van Wishingrad and undergraduate lab tech D. Rasch carried the heavy load of the lab and analytical work, with dozens on NPS staff volunteering time to collect samples.

This year, UC Merced expanded its eDNA work, focusing on Central California’s agriculture and riparian environments. UC Merced team Jacob Nesslage, Dr. Erin Hestir, and UCSC postdoc Dr. Jen Quick-Cleveland are integrating eDNA with remote sensing. Erin’s lab is also looking at invasive species and water management in the valley, and started a project with UCSC graduate student Madeline Slimp to look at how invasive water primrose affects the total biotic community. Another UC Merced team, led by Dr. Jason Sexton and former postdoc Dr. Dannise Ruiz-Ramos, published their vernal pools eDNA study in the journal Environmental DNA.

Here’s Erin and team mucking through the water primrose, followed by remote sensing scientists (Jacob Nesslage and Bailey Morrison) learning how to do metabarcoding. Yep, we train almost everyone and anyone.

Many of us attended the 2nd National Marine eDNA meeting, which Rachel helped organize. As a follow up to the meeting, we are looking for your great manuscripts (see call HERE) to submit to Environmental DNA for a special issue. We also had a World Biodiversity Forum workshop on eDNA and remote sensing for spatial ecology, and a big presence at other national conferences this summer.

At the Marine eDNA meeting, we announced our new big web tool under development, the eDNA Explorer, which will launch in early 2023. You can sign up to be one of the first users here! www.eDNAexplorer.org. This tool is being developed by Dr. Ariel Levi Simons, Max Yasuda (née Ogden), Hector Baez, Dr. Lenore Pipes, and Drs. Rachel Meyer, Beth Shapiro, and Rasmus Nielsen, and the design and web build out is by Sliced Bread Design and Sumo Creations. We are so stoked for this to launch soon! If you’re a computer nerd, check out Lenore’s pre-print of Tronko, the eDNA taxonomic assignment tool we’ll be supporting through the Explorer.

We are grateful that the California Institute for Biodiversity (CIB) was keen to launch a unique kind of reciprocal collaboration, whereby CALeDNA researchers at the UCSC Paleogenomics Laboratory metabarcode and shotgun sequence DNA from small amounts of ethanol drawn off of invertebrate specimen collections in museums to provide leads for where there are species that need DNA barcoding. CIB then sequences the species, allowing CALeDNA to improve our invertebrate bioinventories by looking for those sequences in our existing data. Lab tech Ajith Seresinghe is moving this project along now, after completing a DNA barcoding project focused on Sierra Streams with the Sierra Streams Institute. CAMINO fellow Malia Mosser was also a crucial, awesome biologist working on this project.

Here’s Ajith transferring samples and ethanol in the most entertaining way possible because he refuses to ever sit in a chair.

In 2022, we wrote a manuscript of the massive LA River eDNA project ‘Protecting Our River’ that Bob Wayne’s lab led (funded by Metabolic Studio), and are finalizing it to send to co-authors. We also started monitoring 5 LA River sites on a bimonthly basis. Hundreds of community scientists have joined the fun this year! We thank the Los Angeles County Board of Supervisors for grant funds that are partially supporting the sentinel site eDNA sequencing. Our next bioblitz date is Jan 28. Check out our events page to sign up.

Look at these smiling volunteers not minding the 90+ degree heat!

Congratulations to Drs. Kim Ballare, Chloé Orland, Maura Palacios Mejia and Ana Garcia-Vedrenne on getting their eDNA education module on wolves accepted for publication on CourseSource! We’ll be sharing it soon. This paper wraps up an HHMI Professors grant to PIs Wayne and Shapiro that supported a lot of student activities for 5 golden years. Hundreds of students went through the three tiers of the program, and many are now professional biologists, nature stewards, and activists.

This summer we inaugurated the ASPIRE fellows program, supported by a generous gift from Claudia and Alec Webster. ASPIRE is an undergraduate Fellowship program that supports UCSC students to engage with state-of-the-art biodiversity science during the summer. It’s leadership team includes Beth Shapiro, Jen Quick-Cleveland, Rachel Meyer and Wendy Bussiere, and the field teams were led by UCSC graduate students Cali Gallardo and Milagros Rivera (who also worked on the LA River). Part of the UCSC Genomics Institute and CALeDNA, ASPIRE students receive training in field sampling and lab-based research, design experiments, and gain valuable understanding of the scientific process and, most importantly, come to identify as scientists. The data collected by ASPIRE fellows will be used by scientists to track changes in biodiversity over time across large and diverse landscapes using eDNA. ASPIRE traveled throughout California collecting soil and water samples. Sites included University of California Reserves, Wildlands Conservancy Lands, State Parks, and private properties, with an aim to better understand how ecosystems recover from fire at a microbial level. The ASPIRE team successfully collected 1,000 samples, which have been archived and sorted for processing. Over the next several months we will generate data from a select subset of samples to detect changes in biodiversity that correspond to wildfire timing and intensity.

Check out DNA 101 by the ASPIRE fellows on Youtube HERE:

Dr. Jen Quick-Cleveland is a senior postdoc who brings biochemical expertise to CALeDNA and a lot of heart for her local environment. She’s studying ASPIRE samples from Swanton Ranch, which burned recently, but she also leads a lot of fieldwork in the Santa Cruz area! She ran a series of bioblitzes on Pinto Lake, a lake that is often unsafe for swimming or fishing due to annual harmful algal blooms. We hope eDNA data can help managers restore these important places. Join Jen’s events next year if you’re in the Santa Cruz area — they are REALLY fun and educational! I regret I can’t find the pics of the kayaks sinking or capsizing…

What have some of our former postdocs done? Dr. Maura Palacios Mejia is now faculty at Mt SAC and has been working on several eDNA projects. One focuses on microbe-plant dynamics in restoration of grasslands and chaparral at the Wildlife Sanctuary. The team consists of six Mt SAC undergraduate researchers and the two co-directors. She has also partnered with Dr. Joes Heras to sample Bolsa Chica estuary to explore the diversity of species across seasons. Lastly, she is working with Prospering Backyards team to monitor for change in microbial communities with remediation using zeolites and reduction in lead contamination in the East L.A. community. And Dr. Ana Garcia-Vedrenne joined UC Irvine as an assistant professor of Teaching in Ecology and Evolutionary Biology continuing eDNA research as well!

And did you know CALeDNA went abroad? Dr. Ren Larison at UCLA, Chloé and Rachel went to Rwanda to run an eDNA workshop with the University of Rwanda and Akagera National Park. We collected surface soil samples and also collected from lake sediment cores to try to go back in time and survey the wildlife. It was THE BEST time. Thanks National Geographic!

We’re proud of the fieldwork, lab work, computational analysis, manuscripts and publications from this distributed team that are moving the needle forward on eDNA applications for biodiversity management in California and around the world. From Kim Ballare’s Oasis manuscript and Zack Gold and team’s Port of Long Beach fish survey published in PeerJ, to a consortium of scientists thinking about eDNA estuary monitoring, we’re broadening the applications of metabarcoding to support a biodiversity-enabled economy with innovation happening at the grassroots level. Thanks for continuing to work with us. Please get in touch with us any time at uc.caledna@gmail.com. See you in the Newt Year!

-Rachel Meyer, CALeDNA director, UCSC

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