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Using next-generation RNA sequencing and bioinformatics to understand the effect of ocean acidification on marine ecosystems

February 2017 - A new study examining how ocean acidification may negatively affect some juvenile rockfish, a key marine prey base to the California ecosystem, was published by researchers from Moss Landing Marine Labs of SJSU, CSUMB and UC Santa Cruz. The research, which suggests potential negative effects to the structure and function of marine ecosystems that support coastal fisheries and communities, was conducted in collaboration with researchers at the National Oceanic and Atmospheric Administration’s Southwest Fisheries Science Center and the Monterey Bay Aquarium Research Institute.

Rockfish

This study is the first to examine a comprehensive suite of physiological, behavioral and genomic responses to ocean acidification in temperate fishes. Published in PLOS ONE, this paper is the first of several that will come out of this collaborative team funded by the National Science Foundation and California SeaGrant.

The implications of the new publication are that the fish communities inhabiting rocky reefs and kelp beds may change in the future, in favor of species more tolerant of changing ocean chemistry. Rockfish are the most diverse group of fishes living on the U.S. West Coast, comprising more than 65 species that support important recreational and commercial fisheries. Changes in the prey base due to climate change are likely to affect marine food webs, with potentially negative effects on coastal fisheries and communities.

Dr. Cheryl Logan, who holds a doctorate in biology, led the genomics portion of the study along with student researchers April Makukhov, Lauren Tobosa and Kirsten Boyer.

“It’s exciting to involve undergraduates in cutting-edge research,” said Logan, “our students are learning how to use next-generation ribonucleic acid (RNA) sequencing and bioinformatics to address a global problem: how ocean acidification will affect marine ecosystems.”

All three students are graduates of CSUMB who worked in Logan’s lab during their undergraduate studies. Makukhov is currently a Ph.D. student at the University of Vermont, Tobosa is a scientific aide at the Calif. Department of Fish and Wildlife and Boyer is now a master’s student in CSUMB’s Applied Marine and Watershed Science program. All three student co-authors were members of Logan’s Marine Experimental Physiology capstone course where they developed the advanced physiology and genomics skills used to contribute to the new study.

“The research project format of Dr. Logan’s capstone course was one of the most valuable experiences I had at CSUMB and most related to what I chose to do after I graduated,” said Emily King, who is now a Ph.D. student at University of California Berkeley and conducting genomics research of her own.

This semester, students will continue investigating the combined effects of ocean acidification and hypoxia on rockfish physiology and genomics and will be presenting their findings at the capstone festival this May.

Story contains contributions by the Monterey Bay Aquarium Research Institute.

Story taken from CSUMB News.

School of Natural Sciences

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