Skip to main content Skip to navigation

Departments & Programs


Julian Damashek

Title:Graduate Student, Department of Environmental Earth System Science
Primary Affiliation:Department of Environmental Earth System Science
Office Location:Green Earth Sci. 233
Research Lab:Francis Lab

Biographical Information

Born in Baltimore. Raised in Carroll County, Maryland. Schooled in western Massachusetts.

Cut my scientific teeth sequencing genes from Lycium (with the Miller Lab at Amherst College), and making 16S clone libraries from shale gas wells (with the Martini Lab at Amherst College, in collaboration with Matt Kirk). Started a PhD in EESS with the Francis Lab in summer 2010. I have also taken, TA'ed, and highly recommend the Hopkins Microbiology Course.


I am interested in the ecology of aquatic ecosystems.

Primary interests include, but are hardly limited to: biogeochemistry/nutrient cycling, the nitrogen and carbon cycles, interactions between organisms and inorganic nutrients, land/river/estuary/coastal sea connections, and the microbial ecology of estuaries. 

Broad questions that guide my thinking include, but are hardly limited to: How do microscopic organisms affect macroscopic changes on ecosystem processes? What are the drivers of biogeochemistry in estuaries and coastal seas, and how accurately can field measurements of nutrient cycling get scaled up into predictive models? How do nutrient concentrations affect primary productivity, and visa versa? How does nutrient cycling in the benthos affect the water column, and visa versa? How will estuarine microbial populations and nutrient cycles change as the climate changes? Why do coastal ecosystems differ in their responses to eutrophication, and can we develop models to predict these responses?

My research is focused on nitrogen (N) cycling within San Francisco Bay. All of my work revolves around the general idea of understanding how anthropogenic alteration of the N cycle (which has been massive, due to industrial fertilizer production and wastewater treatment discharge) affects estuaries, the critical interface between the land and the sea. Despite chronic nutrient enrichment due to urban runoff (7 million people around its shores), wastewater discharge (42 treatment plants directly discharging into the bay), and agricultural runoff (from a 140,000 sq-km watershed that includes the entire Central Valley), quite little is known about what happens to N once it enters the waters of the bay. Current projects use methods from biogeochemistry and microbiology, allowing questions to be approached from both macro and micro scales.

Research projects include:

  • A monthly time series characterizing microbial ammonia-oxidizing microbial populations in the sediment and water column of San Francisco Bay (collaboration with USGS Water Quality of San Francisco Bay)
  • Investigation of the contribution of pelagic nitrification to N cycling in San Francisco Bay, and how pelagic ammonia oxidizing microbial populations change in response to environmental drivers, using samples collected for our monthly time series and a one-time spatially resolved sampling expedition (collaboration with the Casciotti LabUSGS Water Quality of San Francisco Bay, and the San Francisco Estuary Institute)
  • Determination of the relationships between benthic nitrification potential, ammonia oxidizer gene abundance/expression, and environmental variables in San Francisco Bay (collaboration with the San Francisco Estuary Institute)
  • Investigation of fluctuations of the N cycle and ammonia oxidizing microbes in the South San Francisco Bay water column surrounding the spring phytoplankton bloom (collaboration with USGS Water Quality of San Francisco Bay)
  • General microbial ecology (based on high throughput sequencing of the 16S gene) of San Francisco Bay water and sediments (collaboration with the Earth Microbiome Project)
  • Studying the interactions between ammonium concentration, ammonia-oxidizing communities, nitrification rates, and phytoplankton communities in San Francisco Bay (collaboration with the Arrigo Lab and the Casciotti Lab)

I also love teaching, especially when it involves undergraduates, whether in a classroom, laboratory, or on a boat. One day I hope to blog about the science that gets me excited. No blog yet, but I do love to tweet.

Stellar undergraduates I have mentored at Stanford include:

  • Kofi Christie (Summer 2013: SURGE 2013 Scholar and a Morehouse College student). Kofi measured nitrification rates in two urban creeks draining into the Baylands Nature Preserve (Palo Alto, CA) and compared these rates to a host of physical and chemical parameters in the waters. He is now a wizard at measuring ammonium concentrations and nitrate isotopes.
  • Kade Pettie (Summer 2013: Schupf Scholar and Amherst College student). Kade extracted nucleic acids from filters collected in the Chukchi Sea (by the Arrigo Lab) and analyzed the ammonia-oxidizing communities. He pipettes like a pro and gained much experience troubleshooting qPCR runs.
  • Yari Greaney (Fall 2012-Spring 2013: Stanford University student). Yari worked in the Francis Lab for a year and extracted DNA from dozens of sediment samples from San Francisco Bay. She then mastered PCRing ammonia oxidizer functional genes from these samples before jetting off to Australia to study abroad.


I am a graduate student consultant through Stanford's Center for Teaching and Learning, and encourage any TAs to contact me or browse the CTL's website for more information about teaching at Stanford.

News & Media