Cassie Ettinger, Ph.D.

A place for all the projects that don't merit their own page (yet). Currently these include (1) metagenomic data from hot springs in Kamchatka, Russia, (2) metagenomic data from aquariums, and (3) genomics of plant-associated bacteria.

(1) Metagenomic data from two thermal pools in Kamchatka, Russia

This project was a collaboration with Dr. Laetitia Wilkins. Together we assembled draft metagenome-assembled genomes (MAGs) from two hot springs located in the Kamchatka peninsula in Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We recovered 36 total MAGs including members that were taxonomically assigned to groups previously underrepresented in available genome data, including candidate phyla with relatively little genomic representation. This included several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. The breadth of undiscovered microbial diversity on this planet is extreme, particularly when it comes to uncultured archaea whose abundance has likely been underestimated because of primer bias for years. By incorporating metagenomic efforts into the wealth of pre-existing knowledge about these extreme ecosystems, we can begin to putatively characterize the ecological roles of microorganisms in these hydrothermal systems.

Phylogenetic placement of MAGs into the tree of life.

Related publications:

• Ettinger CL*, Wilkins LGE*, Jospin G & Eisen JA. 2019. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia. Scientific Reports. DOI: 10.1038/s41598-019-39576-6 *co-first authors

Previously, members of the Eisen lab sampled aquaria as part of an undergraduate research project that investigated microbial community assembly in the fall of 2012. As part of that work, metagenomes were generated from various aquaria. Later, using these metagenomes we were able to recover 11 MAGs reconstructed from freshwater and saltwater aquaria, including representatives of Polynucleobacter, Anaerolinea, Roseobacter, Flavobacteriia, Octadecabacter, Mycobacterium, and Candidate Phyla Radiation (CPR) members.

Related publications:

• Ettinger CL, Bryan J*, Tokajian S, Jospin G, Coil D & Eisen JA. 2021. Reconstruction of metagenome-assembled genomes from aquaria. Microbial Resource Announcements. DOI: 10.1128/MRA.00557-21 *undergraduate author

I have been involved in several projects focused on the genomics of plant-associated bacteria. These projects involved genomic assembly and annotation of bacterial isolates, which were then used as resources for papers focused on molecular assessment of these bacteria.

Related publications:

• Shehata HR, Ettinger CL, Eisen JA, & Raizada MN. 2016. Genes Required for the Anti-fungal Activity of a Bacterial Endophyte Isolated from a Corn Landrace Grown Continuously by Subsistence Farmers Since 1000 BC. Frontiers in Microbiology. DOI: 10.3389/fmicb.2016.01548
• Mousa WK, Shearer, C, Limay-Rios, V, Ettinger CL, Eisen JA & Raizada MN. 2016. Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum. Nature Microbiology. DOI: 10.1038/nmicrobiol.2016.167
• Ettinger CL, Mousa WM, Raizada MN, Eisen JA. 2015. Draft genome sequence of Enterobacter sp. strain UCD-UG_FMILLET (phylum Proteobacteria). Genome Announcements. DOI: 10.1128/genomeA.01461-14
• Ettinger CL, Shehata HR, Johnston-Monje D, Raizada MN, Eisen JA. 2015. Draft genome sequence of Burkholderia gladioli strain UCD-UG_CHAPALOTE (phylum Proteobacteria). Genome Announcements. DOI: 10.1128/genomeA.01462-14