CSUSM BLUE Laboratory
Research
Founded in 2019, the BLUE Lab (Biomes of Littoral and Urban Ecosystems) studies how urbanization influences coastal ecosystems, focusing on the impacts of urban runoff and other human-derived inputs on microbial communities using integrated genomics and ecological approaches.
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The lab is located within California State University San Marcos, a primarily undergraduate institution. Therefore, field work, sample isolation and processing, next-generation sequencing, and bioinformatics pipelines are all performed by outstanding CSUSM undergraduate students.
Ongoing Projects
Impacts of urbanization on Mission Bay, CA
We are examining how pollution shapes coastal microbial ecosystems and how endogenous microbes may help restore environmental health. One focus characterizes how water-column microbial communities vary across locations and seasons, linking shifts in taxonomic and functional profiles to urban runoff and other point-source stressors to better understand ecosystem impacts across the bay. Complementary efforts focuses on PFAS contamination in Mission Bay wetlands, using metagenomic and cultivation-based approaches to identify sediment microbes and metabolic pathways capable of degrading PFAS and related compounds. Together, these efforts integrate microbial ecology, pollution monitoring, and bioremediation to generate actionable insights for conservation and restoration in Mission Bay.
Microbiomes and gene exchange on plastic pollution
Our lab studies how plastic pollution reshapes microbiomes in coastal ecosystems. Using whole metagenome sequencing, we compare microbes living on marine plastic debris to those in surrounding waters and substrates, and investigate the plastic mobilome that may carry antibiotic resistance and virulence genes. By examining how plastics create novel niches for gene exchange and microbial evolution, our work explores the ecological and public health implications of plastic pollution in California’s nearshore environments
Effects of rainstorm runoff on coastal microbial communities and antibiotic resistomes
Rainstorm runoff results in the flushing of urban and agricultural buildup into our coastal ecosystems, resulting in the known "72-hour rule" where fecal indicator bacterial counts are high in coastal waters for three days following rainstorms. In addition to bacteria, antibiotic waste and antibiotic resistance genes are also part of these runoffs. Through a combination of chromatin capture assays and next-generation sequencing approaches, the Becket lab seeks to quantify the changes to coastal microbiome and resistome profiles year-round and surrounding rainstorms.
Effects of antibiotic exposure and climate change conditions on horizontal gene transfer in coastal microbiomes
Microbial antibiotic resistance (AR) is easily spread between microbial community members, as genes that encode antibiotic resistance can be transferred between microbes through horizontal gene transfer (HGT). Exposure to antibiotics has been shown to induce the exchange of genetic material through HGT. Coastal environments are particularly at risk, as anthropogenic inputs such as sewage, aquaculture/agricultural contaminants, and climate change conditions can influence the spread of antibiotic resistance genes. Thus, we seek to explore the mobility of the AR genes in coastal microbial populations in response to common antibiotics seen in agricultural and urban waste through a combination of enrichment assays and genomic approaches.
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NIH R15 project summary towards these goals: https://reporter.nih.gov/project-details/10203465
Colorful Food Microbes!
Thanks to a beef soup lovingly made by Dr. Becket's mom being left to spoil in the back of the fridge, the lab has embarked on what makes spoiled foods turn the colors they do (and what microbes make it happen)! People from around the world send swabs of their colorful spoiled food to the lab for characterization - from blue to purple to pink!
