Bhattacharya Lab - Fatima Foflonker

image of Fatima Foflonker I am a graduate student from the Microbial Biology graduate program working in the Bhattacharya lab to investigate the evolutionary history, physiological, and genomic, and functional genomic characteristics of the biofuel candidate green alga Picochlorum SENEW3 (SE3).

image of Fatima Foflonker

Picochlorum cultures are challenged with different abiotic stresses in a shaking incubator

This organism was isolated in 2011 from a shallow brackish-water lagoon in San Diego, California. This environment is subject to extreme stresses including high light, high temperature, and broadly fluctuating salinity. We asked the question, what insights can exploring biodiversity in the environment provide into selecting good biofuel feedstock candidate algae?


To answer this question I looked for clues in the genome and the transcriptome under salinity stress, and found that it has one of the smallest genomes for a free-living eukaryote and a simple genome structure that enhance its reaction time to environmental changes and may make it amenable to genetic engineering.


Fatima Foflonker studying Picochlorum

Counting cells using a microscope to capture images and ImageJ software to count cells for growth rate analysis

Physiological characterizations show that it is highly robust under a broad range of abiotic stresses and efficient at photosynthesis, which indicates that Picochlorum SE3 may be suitable for large-scale open pond biofuel feedstock cultivation. We also found that novel gene of bacterial origin acquired through horizontal gene transfer contribute to Picochlorum SE3 stress tolerance abilities. We will be further investigating the role of horizontal gene transfer and the evolutionary history of stress tolerance in Picochlorum SE3 by doing a genome comparison of several other Picochlorum species. By examining Picochlorum SE3, we gain insight into how the environment has designed a highly efficient and robust species.

I became interested in this project because I have been interested in functional genomics as a tool to understand molecular mechanisms in response to abiotic stresses, before I even knew what that meant. I remember doing a science fair project in high school about the effect of light and temperature on growth rates of a harmful algal bloom related species, and thinking "wouldn't it be cool if I could understand exactly what is going on in the cell under these stresses". Finally being able to get insight into what algae are doing and why is very exciting, and I hope to continue similar work in the future.


image of Fatima Foflonker

Picochlorum cell grown on plates


image of Fatima Foflonker

Cultures are tested for bacterial contamination in a laminar flow hood

Foflonker F, Price DC, Qiu H, Palenik B, Wang S, Bhattacharya D. 2014. Genome of the halotolerant green alga Picochlorum SENEW3 reveals strategies for thriving under fluctuating environmental conditions. Environ Microbiol. 2015 Feb;17(2):412-26. Epub 2014 Jul 24 doi | pubmed