News — CALeDNA

A day in the life of an LA River eDNA bioblitz coordinator

Check out the photos from CALeDNA lab tech, adventurous rock climber, and salamander fan Ajith Seresinghe from the last LA River bioblitz he helped run on May 26, 2023. We have a few more of these events coming up!

 
 

CALeDNA x NASA in South Africa

Collaboration with NASA uses eDNA technology to monitor biodiversity

UCSC scientists collected environmental DNA samples in South Africa as part of the BioSCape project

March 21, 2023

By Rose Miyatsu

Last September, Madeline Slimp had just completed the first year of her Ph.D. program at UC Santa Cruz when she found herself headed on a research trip to South Africa. She was joining her advisor Rachel Meyer, associate professor of ecology and evolutionary biology, as part of the first team on the ground for a large international project called BioSCape.

BioSCape is run by NASA in collaboration with the South African National Space Agency (SANSA) and the South African Environmental Observation Network (SAEON), as well as other international partners. It aims at combining cutting-edge technology like airborne imaging spectroscopy and lidar remote sensing with field observations to better understand the biodiversity of South Africa’s Greater Cape Floristic Region.

BioSCape is engaging over a dozen different teams to measure everything from soundscapes to levels of phytoplankton in the Greater Cape Region to better understand the role that biodiversity plays in South Africa’s ecosystem. Together, the groups will help NASA create a model for measuring biodiversity changes after disturbances such as wildfires, flooding, species invasion, and climate change.

Tracking biodiversity

Meyer and Slimp’s role in the BioSCape project is to collect environmental DNA (eDNA) samples along two rivers that run through the Cape. eDNA is a relatively new method for monitoring biodiversity that involves taking soil or water samples from a location of interest, then analyzing those samples in the lab to determine what kind of DNA is present. eDNA only lasts for an average of two weeks before it is degraded, so analyzing what is in the samples gives researchers a good view into what species currently inhabit a given area.

Unlike traditional methods of monitoring species’ presence in a region, which require many hours of observation over a long period of time, eDNA techniques can provide a very clear picture of the biodiversity of an area relatively inexpensively and with only a few site visits. In addition to collecting eDNA for the BioSCape project, Meyer and other scientists in the UCSC Paleogenomics Lab have a number of collaborations with national parks using eDNA to help park managers better understand the areas they are trying to conserve. Their projects have included tracing harmful algal blooms in Alaska, monitoring watersheds in Hawaii, and tracking biodiversity near the Los Angeles River.

During their trip to the Cape, Slimp and Meyer were joined by several other South African researchers and volunteers to collect samples. They traveled to a total of 34 sites, 30 along a large river called the Berg and four along the smaller Eerste River. The Berg stretches along a diverse landscape that runs from an undeveloped to an urban gradient, much like the Los Angeles River that has been the subject of many previous eDNA excursions. It runs through citrus farms and wineries, and many farmers rely on it to water their crops.

Meyer and Slimp spent more than three weeks in South Africa visiting the collection sites. Some were easily accessible, but others required climbing down 70-degree slopes and wading through rivers to collect their samples. Once their extractions are analyzed, they expect them to reveal which organisms live in and around the Berg and Eerste, and how biodiversity is organized along the river systems. The different sizes of the two rivers will also help them to determine if this organization is scale-dependent.

Adjusting to fieldwork

Because eDNA data needs to be sampled at two different times, both during and after the rainy season, Meyer and her team were the first on the ground for the BioSCape project. This was exciting but came with some challenges, particularly in learning how to communicate the mission of the project to farmers at sites where they wanted to collect data.

“The biggest challenge that I think both Rachel and I had was being outsiders to the culture and political atmosphere of South Africa,” Slimp said. “Being respectful of the culture matters a lot for international research. Listening to the stories of our collaborators has been really important.”

Slimp and Meyer said they felt lucky to have been joined by South African university students and botanists who helped them navigate both the immense biodiversity of the area as well as cultural sensitivities, particularly when asking farmers for permission to take samples on their land.

“Many of the farmers ended up being very receptive,” Slimp said. “They were interested in the project, and when we finished at a site they wanted to know what we found and what was interesting about their land.”

Meyer said that her team was committed to ethically representing South Africa’s interests in their research. For example, the team completes all the DNA extractions from their samples while they are still in South Africa so the samples will stay regulated by South Africa and not the United States.

She is planning to share some of the lessons they learned along the way with other BioSCape partners at a BioSCape conference in May. Many of the other teams have not yet had a chance to collect their samples, and Meyer is hoping that what they share will help them to be more prepared to communicate their own projects in the field. There are also many changing policies that shape how to share access to the collections and data, and how to share benefits from the project. At the conference in May, Meyer and Slimp will be running a session with South African BioSCape teams on benefit sharing and bioethics.

Processing the samples

Meyer and Slimp will embark on a second round of data collection in South Africa in October. In the meantime, there is plenty of work to do processing the extractions that they collected from their first expedition. To learn what is in them, they will match up the DNA they find in their samples with a catalog of “barcodes” of known species.

Barcoding efforts such as the California Conservation Genomics Project and the California Institute for Biodiversity partnerships, which UCSC participates in, have been making large strides in sequencing the genomes and barcodes of as many species as possible so researchers like Slimp can do this type of work. These barcodes are making eDNA an ever-more reliable method for identifying and monitoring biodiversity, even in an area that is as diverse as the South African Greater Cape.

Learning leadership

While a large overseas data collection trip certainly had its challenges, Slimp said she is very grateful for how it helped her develop as a researcher.

“It was a big growth experience,” she said. “It took a lot of strength that I didn’t know I had.”

Slimp was working with two volunteers who had just completed their master’s degrees, Jabulile Malindi from the University of the Western Cape and Ayesha Hargey from the University of Cape Town. Malindi contributed her knowledge on fynbos flora, and Hargey became an expert in eDNA collection, but both were new to eDNA and Bioscape. This placed Slimp in a position of leadership as a teacher.  

“I had to step away from being a student and think of the project,” Slimp said. “I have led things before in lab and small-scale data collection, but it was certainly a challenge to have people relying on me for direction, for information, to be a leader. I feel like I am capable of so much more now.”

“I am really excited to go back,” she added. “I just feel so inspired by everyone on the BioSCape team.”

Madeline Slimp’s research is supported in part by funding from the UC Santa Cruz Genomics Institute.

 

Announcing the UCSC CALeDNA undergraduate researchers

Last year we added a northern headquarters for CALeDNA, building a brand new lab space for storing and processing eDNA samples in the Coastal Biology Building at UC Santa Cruz. As soon as we were ready to get running, students joined the Meyer lab and started research internships during the Winter quarter, extracting and processing DNA from >300 samples in a short time. In Spring quarter, the lab work ramped down because of COVID, but we were heartened to see our student team grow in numbers and take on challenging bioinformatic analyses to do hypothesis-driven research with eDNA-based biodiversity.

I’m thrilled the be able to introduce the lab’s undergraduate researchers. Several of them graduated this quarter and are continuing research with us during the summer as alumn! Two undergraduates who are going into their senior year received CALeDNA Summer Research Internships sponsored by Dr. Beth Shapiro’s HHMI Professorship grant. We’ll be still heavily doing informatic work as we ramp up lab-based research again, and I’m confident these students will be co-authoring research papers and sharing their work on our research pages.

Undergraduates and recent graduates in the lab: Colin Fairbairn, Haylee Bregoff, Taylor Hedblad, Julian Bui, Dexter Fan, Emily Soth, Nick Dykstra, and Hailey Nava.

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Santa Monica Bioblitz last week was a smash!

Thanks for the photos and the great hang out! We collected from >30 sites at different elevations all around Malibu Creek State Park. Perfect day! Next week we’ll be going to the lagoons! Sign up for this Saturday’s (March 23) bioblitz here: https://data.ucedna.com/events/20

 

eDNA webinars

CALeDNA research results were presented today to the USGS! Check out their numerous eDNA webinars here: https://my.usgs.gov/confluence/display/cdi/eDNA+Webinars

 

Desert eDNA results are online

Nearly a year ago, eDNA surveys took place from Oak Glen to deep in the Coachella Valley, meandering through Pioneertown, Anza Borrego, the Salton Sea, and Palm Desert. Results are in! We are looking for volunteers to help us analyze the data. https://data.ucedna.com/research_projects/6

As a botanist from Palm Desert (a desert rat, as we call ourselves), I can’t help but highlight that we get some really cool plants in the eDNA results, including one of my favorites that perfumes the desert, creosote bush (Larrea). Oh, and we got both black bears and water bears (Tardigrades) in the eDNA, too.

Image from the web, no author name given. Eat your hearts out, tardigrade lovers. California is full of them (58 sites and counting).

Image from the web, no author name given. Eat your hearts out, tardigrade lovers. California is full of them (58 sites and counting).

 

CALeDNA has its largest bioblitz ever! Surprise, it's at the UC Merced Vernal Pools

Fairy shrimp were all over the place, as were people of all ages, with their phones out, gloves on, and cryotubes handy. We got lucky with the weather, too! 41 people collected samples from 6 pools including the big playa. Teenagers took off their shoes to experience the squish of vernal pool mud. Two people celebrated their birthdays at the bioblitz; one birthday crew drove all the way up from Santa Barbara to join for the day. Afterwards, we met up with professor Michael Dawson and feasted on Indian food buffet.

I’m thrilled to pass along the amazing photographs and stories of the people who attended so you can read about the experience from their vantage points. Here’s Mr. Hollister’s blog post with photos and even a video of an endemic fairy shrimp!

http://www.mrhollisterphoto.com/home/uc-merced-vernal-pool-reserve-edna-collection

The full photo collection can be viewed here:

http://www.mrhollister.com/getout/vernal%20pool%20eDNA/

Here’s a screenshot of what you would see if you clicked that link.

Thanks to everyone who came out! We’ll do another bioblitz there in late April or May. Email us at uc.caledna@gmail.com if you want to join!

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Sampling the Santa Monica Mountains affected by the Woolsey Fire

It was wrenching to see the destruction and loss of life from the fire. Communities of organisms will reassemble somehow, and an important question to ask is will they be different than before (landscape conversion)? NASA Jet Propulsion Laboratories and CALeDNA want to understand this process by combining eDNA with remote sensing data. CALeDNA has 121 sites in the Santa Monica Mountains that are in the eDNA freezer — many of these areas burned and can be used to compare biodiversity before and after the fire. Volunteers, including JPL employees, set out to collect from burned sites. Some areas were dangerous with dead branches and debris, so we wore our helmets when hard hats weren’t available. We also thank Marti Witter from the Santa Monica Mountains Resource Conservation District for helping us access these sites. Photos below courtesy of Rachel Meyer and Natasha Stavros.

 
 

CALeDNA x NHMLA Tidepool bioblitz for Snapshot Cal Coast was like opening buried treasure!

Volunteers, researchers, and curators got to hop along algae-covered rocks, and peer into the rarely exposed world of the San Pedro Point Fermin intertidal zone at dawn. It was the second-to-lowest tide of the entire year. Every few minutes you could hear a burst of "oh what! wow!" as people found and gently scooped up animals, from slimy sponges to brittle starfish to the behemoth black sea hare. Regina Wetzer and Dean Pentcheff, long time collaborators now, also collected specimens to bring back to the lab and voucher for permanent archiving as well as DNA barcoding. With these species barcoded too, we can now track them more accurately with our CALeDNA environmental DNA metabarcoding. :)

 
 

California Naturalist Partner/Instructor Training Workshop

Rachel and Maura attended the California Naturalist Partner/Instructor Training Workshop for a future collaboration and we also trained/sampled with members from the Cabrillo Marine Aquarium, Community Nature Connection, and others at the Los Angeles County Arboretum & Botanic Garden in Arcadia, CA. We look forward to strengthening our connections at the local, state, national, and international level. Thank you for such an amazing opportunity!

 

Sampling the L.A. River

We successfully collected at the L.A. River this Memorial Day Weekend and made some new friends along the way. We made the news! Addriana Weingold from CBSLA asked us of our use of the L.A. River, go to (https://cbsloc.al/2sfxQpC) to find out our answers.  

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Welcome our two new postdocs!!!

Dr. Ana Garcia Vedrenne completed her Ph.D  at UC Santa Barbara in Ecology, Evolution and Marine Biology and  Dr. Maura Palacios Mejia obtained her Ph.D at Texas A&M University in Ecology & Evolution.

Together they will contribute their expertise to develop courses for the new Environmental DNA for Science Investigation and Education Program and pursue innovative eDNA research. 

Today, they were initiated by collecting sediment samples from the Mildred E. Mathias Botanical Garden at UCLA.

Welcome to the team!

 

Younger Lagoon Natural Reserve Bioblitz

Located adjacent to the UC Santa Cruz marine campus, Younger Lagoon Natural Reserve offers protection and access to a unique undisturbed coastal wetland and restored terrace. On April 28th, UCSC undergrads, UCSC alumni, UC Davis S.E.E.D.S, and local citizen scientists worked together to collect soil across the reserve, record flora and fauna with iNaturalist, and collect washed-in trash. 

Those collecting soil split into two groups. One group tackled the terrace, focusing their sampling on the three microhabitats (grassland, wetland, shrub) the terrace supports. Being raised on the terrace, this group was able to see a group of humpback whales breaching not too far off shore in the bay! The other group got a bit muddier, sampling from the sand bar in through the mixed and freshwater zones of the lagoons edge. This group was able to explore the beauty of an undisturbed and protected beach covered in drift wood, animal bones, and shells. 

Our trash collectors filled bags of water bottles, flip flops, candy wrappers, and other detritus that continues to wash in from the ocean. And our naturalists wandered both the terrace and lagoon taking pictures of native and invasive grasses, frogs, lizards, birds, and much more! 

The amazing turnout we had for this event allowed us to collect from 23 sites, record over 300 iNatualist observations, and remove several bags of trash from the Lagoon. 

iNat link for this event: https://www.inaturalist.org/projects/younger-lagoon-reserve-bioblitz-2018

Our sampling site: https://ucnrs.org/reserves/younger-lagoon-reserve/

eDNA collection sites: http://data.ucedna.com/field_data_projects/118

 

UC Davis S.E.E.D.S will collect eDNA on Mt. Diablo

Thanks, S.E.E.D.S, for staying committed to the CALeDNA program and offering to collect on your upcoming excursion to Mt. Diablo! Hope 2018 is a great year for you with lots of new recruits. If anyone is interested in eDNA research internships this coming summer, let us know! 

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Our eDNA analysis pipeline is fast!

UCLA postdoc Dr. Emily Curd, who spearheaded the development of a new software pipeline and top quality DNA reference databases, has streamlined the pipeline to run fast. In just about two days, we've gone from 200 samples in raw fastq files to lists of species, abundance, and confidence level of the species assignment. We've processed close to 1000 samples on the pipeline, which will called Anacapa, and will soon be published and publicly available. Congratulations, Emily, Jesse, Gaurav, Bao-Chen, Zack, Rachel, and Bob!