UC Davis Nematologist Chris Pagan, now PhD, to Present Exit Seminar on Metabarcoding

Nematologist Christopher Pagan, who received his doctorate in the fall of 2024 from UC Davis, will deliver his exit seminar on "Soil Nematode Community Analysis: Insights from 28S Metabarcoding" at a seminar hosted by the UC Davis Department of Entomology and Nematology at 4:10 p.m., Monday, Feb. 3 in 122 Briggs Hall.

His seminar also will be on Zoom (https://ucdavis.zoom.us/j/95882849672).

Pagan, who studied with major professor UC Davis distinguished professor Steve Nadler, former chair of the department, earlier presented a talk on "Nematode Community Structure in the Rhizopsheres of Southern California Creosote (Larrea trientata)," at the 2024 meeting of the Society of Nematologists, held in Park City, Utah. 

In his abstract, Pagan wrote: "Creosote bush (Larrea tridentata) is widely distributed across the arid regions of the southwestern United States. These resilient shrubs restructure and enrich the soil beneath them, creating islands of fertility that support relatively dense and diverse nematode communities. We employed a metabarcoding approach to survey nematode diversity and abundance in the rhizospheres of creosote bushes across 11 desert habitats in Southern California. Nematodes were extracted from 64 soil samples using Baermann funnels, and pooled nematodes from each sample were PCR-amplified with 5' 28S barcoding primers. The amplified products were sequenced on the PacBio Sequel II platform."

"However," he adds, "we still face challenges such as sequencing artifacts, underdeveloped reference databases, and unreliable abundance estimates. This talk will cover some insights gleaned from the study of nematode diversity in Southern California desert soils using a 28S D1-D2 metabarcoding approach and multiple sequencing technologies."

Pagan describes nematodes as "among the most abundant and diverse organisms on Earth, occurring nearly everywhere life can exist. With over a million estimated species, their diversity remains underexplored, largely due to the challenges of accurate identification. Traditional taxonomy requires specialized expertise and is prohibitively time-consuming for large environmental samples. High-throughput sequencing (HTS) technologies have transformed biodiversity studies by increasing throughput and sensitivity, and DNA metabarcoding offers a faster and more scalable approach through the sequencing of bulk samples."

Pagan received his bachelor of science degree in biochemistry and molecular biology in 2003 from UC Davis. His fiancée, Stacy Hishinuma, a regional entomologist with the U.S. Forest Service Pacific Southwest Region, received her doctorate from UC Davis, studying with the late Steve Seybold (1959-2019). 

Nematologist Amanda Hodson, assistant professor, UC Davis Department of Entomology and Nematology, coordinates the weekly seminars, held every Monday at 4:10 p.m. in 122 Briggs Hall. She may be reached at akhodson@ucdavis.edu for any Zoom issues.

The seminar recordings are archived at https://entnem.ucdavis.edu/seminars.