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Award Detail

Doing Business As Name:Institute for Systems Biology
  • Monica V Orellana
  • (206) 543-4043
  • Nitin Baliga
Award Date:06/19/2013
Estimated Total Award Amount: $ 1,800,000
Funds Obligated to Date: $ 1,800,000
  • FY 2013=$1,800,000
Start Date:07/01/2013
End Date:06/30/2018
Transaction Type:Grant
Awarding Agency Code:4900
Funding Agency Code:4900
CFDA Number:47.074
Primary Program Source:040100 NSF RESEARCH & RELATED ACTIVIT
Award Title or Description:Ocean Acidification: A Systems Biology Approach to Characterize Diatom Response to Ocean Acidification and Climate Change
Federal Award ID Number:1316206
DUNS ID:135646524
Program:Cellular Dynamics and Function
Program Officer:
  • Charles Cunningham
  • (703) 292-2283

Awardee Location

Street:401 Terry Avenue North
Awardee Cong. District:07

Primary Place of Performance

Organization Name:Institute for Systems Biology
Street:401 Terry Avenue North
Cong. District:07

Abstract at Time of Award

Diatoms account for approximately 40 percent of primary production in the world's oceans and are the most productive marine phytoplankton group. They form the basis of food webs in coastal and ocean upwelling areas that support important fisheries and have a major role in global carbon and silicon cycles. The goal of this project is to understand the impact of ocean acidification, in combination with other stressors, on the marine diatom Thalassiosira pseudonana. This project will generate a predictive model of expression of all genes of this diatom that can be used to forecast the diatom's response to projected environmental scenarios to an acidifying ocean. A combination of laboratory and field studies will be used; diatoms will be grown under carbon dioxide concentrations that reflect today's values as well as future predicted conditions and light levels and nutrients concentrations will also be varied. Physiological and gene expression responses will be measured and integrated using computational and modeling methods to gain an unbiased, systems-level understanding of the response of diatoms to ocean acidification. This combined approach will enable the forecasting and prediction of the diatom's response to environmental change and the elucidation and genomic interpretation of biochemically relevant processes in natural environment. Broader impacts: Results and the predictive model from this study can be coupled with environmental models to forecast the role and behavior of diatoms in the changing seas. In addition to the multidisciplinary training of a post-doctoral fellow and a graduate student this project will engage 3 high school teachers and their students. The investigators will continue to develop educational tools to increase the understanding of global carbon cycles by K-12 students, a generation that will be increasingly affected by the environmental changes that include ocean acidification.

Publications Produced as a Result of this Research

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Hennon, G. M. M.,,Ashworth, J., Groussman, R. D., Berthiaume, C., Morales, R.L., Baliga, N.S., Orellana, M. V., Armbrust, E. V. "Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression" Nature Climate Change,, 2015, p.http://ww. doi:10.1038/NCLIMATE2683 

Ludwig, C. M., M. V. Orellana, M. DeVault, Z. Simon, and N. S. Baliga. "Engaging students in solving a systems-level, global problem." The Science Teacher, v.82, 2015, p.41.

Hennon, G.M.M., P. Quay, R. Morales, L. Swanson and E.V. Armbrust "Acclimatation conditions modify physiological response of the diatom Thalassiosira pseudonana to elevated CO2 concentrations in a nitrate limited chemostat" J. Phycol., v.50, 2014, p.243-253.

Ashworth, J., S. Turkarslan, M. Harris, M.V. Orellana, and N. S. Baliga. "Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum" Marine Genomics, v.26, 2016, p.21. doi: 

Valenzuela J.J., A. López García de Lomana, A. Lee, E.V. Armbrust, M.V. Orellana and N.S. Baliga. "Ocean acidification conditions increase resilience of marine diatoms." Nature communication, v.9, 2018, p.2328.

Project Outcomes Report


This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Intellectual Merit: Diatoms are unicellular photosynthetic eukaryotic algae that account for about 40% of total marine primary production. They form the base of many food webs in coastal and upwelling areas, that support important fisheries and livelihoods. Diatoms are central to the biogeochemical cycling of important nutrients such as carbon, nitrogen and silicon and have influenced the world’s climate by changing the flux of carbon into the oceans. Using the model species Thalassiosira pseudonana, we demonstrated in a detailed physiological and gene survey that approximately 40 percent of the transcriptome varied significantly and recurrently, reflecting large, reproducible cell-states and cell- transitions between four principal states: I) light, II) dark, III) exponential growth and nutrient replete, IV) stationary phase and nutrient depleted. Repeated shifts in the gene expresision levels of hundreds of genes encoding sensory, signaling, and regulatory functions accompanied the four cell-state transitions, provided a map of the highly coordinated regulatory program under varying conditions. These results explain, in  detail, how the diatom operates under varying environmental conditions. Furthermore, we have shown that T. pseudonana rapidly responds to increasing CO2 by a shift in regulation and metabolism re-arrangement. Additionally, we also recently demonstrated that diatoms are more sensitive to collapse when at low carbon and facing multiple perturbations and suggest that ocean acidification will stabilize diatom populations with a potential to see an increase in their distribution. In addition, we have integrated all existing publicly available data for the diatom models T. pseudonana and Phaeodactylum tricornutum online, and is explorable through the Diatom Portal. This detailed knowledge of the dynamic molecular process is invaluable for new hypothesis generation and the interpretation of genetic, and environmental data. The diatom portal is popular with the research community, and actively visited from more than 80 countries. 

Broader Impacts: We successfully integrated interdisciplinary research and education efforts. We developed an inquiry-based high school education module to teach the process of systems biology in the context of climate change, carbon cycling and ocean acidification using T. pseudonana as a model system. We have improved science education and making STEM more accessible to all students and teachers.  Through our  program, the students develop their own hypotheses and experiments related to the overall topic, perform experiments, and analyze data. Students are exposed to the idea that large, systems-level problems need to be studied from several angles, and groups of students focus on different approaches. At the end, the students synthesize results from all approaches. Our website is widely accessed  ( and an average of 25,000 students complete these lessons each month.  In addition, this curriculum has been incorporated into the California State High School Three-course model framework.  This framework and the curriculum within are used by approximately 1.8 million public high school students each year.


Last Modified: 11/16/2018
Modified by: Monica Orellana

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