Wet lab

The wet lab focuses on larval fish, mysid, zooplankton, and copepod sampling and identification. Samples collected in the field throughout the year are brought to the wet lab, sorted through, and later processed for organism identification. Here we also conduct fish dissections, and extract various useful tissues such as gonads, fin clips, and intestines. This research aids in finding San Francisco Bay tributaries that may be good spawning areas for Longfin smelt.


Images and body measurements are taken of all specimens before dissection. Here we have a longfin smelt being prepared for otolith and gonad extraction.

Internal view of a longfin smelt. This is a mature female, whose abdomen is full of eggs. These eggs will be extracted, and subsequently counted to gather valuable information on longfin fecundity.


Eggs extracted from a mature longfin smelt. Currently, egg counts are being conducted within our wet lab to help us learn more about longfin fecundity, which provides crucial information that can be used to better manage the remaining populations.

Otolith lab 

Sample preparation
Our lab performs otolith extraction, polishing, and imaging later used for age and growth analysis. After this process, specific otoliths are chosen to be mounted on slides and analyzed for their elemental and isotopic composition in collaboration with the Center for Plasma Mass Spectrometry, University of California, Davis. This data is combined to provide valuable insights into the life histories of fishes.


Image of whole, paired longfin smelt otoliths. These samples will be sanded and analyzed for information on longfin age and growth.

Age and Growth analysis
We process fish scales, fin rays, and otoliths to generate age and growth data. State of the art laser scanning confocal microscopes are used to provide high-resolution images of otoliths, producing precise daily age estimates for larval and juvenile fishes, and precise yearly age estimates for adult fishes. Image Pro digital image analysis software is used to measure age increments for growth rate and pattern analysis. This data is combined to provide valuable insights into the age and growth patterns of fishes.

An adult long fin otolith that has been sanded transversally. Sections such as this allow us to gain valuable information about the age and life history of these fish.

Analytical facilities

We collaborate directly with the UC Davis Interdisciplinary Center for Inductively-Coupled Plasma Mass Spectrometry. We specialize in laser ablation ICP-MS for quantifying trace and minor element chemistry in fish otoliths, fin rays, and scales. The center uses a New Wave Nd: Yag 213nm laser system coupled to a 7500a Agilent quadrupole ICP-MS, providing concentrations in the parts per million to parts per billion range. The New Wave laser system can provide a variety of laser configurations with a circular laser spot shape and diameters ranging from 5 to 120 microns. Typical parameters for fish otoliths are in the 20-40 diameter providing ~weekly resolution.

We are also directly involved in the development and application of laser ablation multi-collector ICP-MS to quantify isotopes of strontium in the parts-per-billion range. The use of strontium isotope ratios has distinct advantages over trace element chemistry for determining natal origins and migration histories of freshwater fishes in that chemical signatures in waters are not physiologically regulated by the fish and often directly match otolith chemistry, simplifying matching fish to natal habitats.


Field Work

The OGFL is pursuing several projects that involve collecting data and samples from the field. We conduct monthly otter trawls surveys in the Alviso Salt Pond Restoration Area to maintain a long-term database focused on the aquatic assemblage.

Sampling occurs in the south bay of the San Francisco Estuary. We utilize otter trawls to help capture and observe species of interest. We capture and record a large variety of species including various elasmobranchs, gobies, clupeids, and flatfish such as the starry flounder pictured above.


Recently, the OGFL has taken on a project analyzing the mercury concentration in the tissues of commonly caught fish in the salt ponds and sloughs of south bay. This study combines otter trawls with beach seine surveys, in order to get a better idea of the biodiversity present in the targeted areas.

Beach seines are useful tools for sampling smaller fish species in a restricted area. They posses a float line on top, and a lead line on the bottom to ensure the net covers the entirety of the water column. This enables us to catch a variety of pelagic and demersal species including gobies, flatfish, clupeids, and benthic invertebrates.


For the last five years, Longfin Smelt, a Californian native threatened species, has been showing up during their spawning season in our monthly trawls. This spurred its own research questions that has evolved into a broodstock collection program wherein Longfin Smelt are brought to an aquaculture facility to develop spawning technics necessary for a future (captive) broodstock population.

Otter trawling allows us to sample a variety of organisms throughout the water column. Here the net is being prepared for deployment, and subsequently being spooled back onto the winch after the allotted trawl time has passed.


After the net has been pulled in, the catch is sorted and all caught species are recorded. Additional information, such as length and sex, are recorded for species of particular interest such as longfin smelt.