Undergraduate Summer Internship Proposal
Holly Simon, Jon Schnorr, Mariya Smit
1. Context:
A major goal of CMOP is to characterize microbial activity with respect to changes in
physical and chemical properties along coastal margins. The proposed summer intern
project will be a part of our ongoing research on analysis of gene expression in the
microbial communities of Columbia River and coastal ocean using fluorescent
microarrays and other biosensor platforms.
2. Proposed project:
Investigation of microbial nitrification along the Columbia River coastal margin using DNA
microarray data.
Microbial gene expression patterns in over 66 samples from four cruises (2007-2008)
along the Columbia River coastal margin were investigated by DNA microarray analysis.
These data provide a molecular portrait of microbial gene expression across seasons and
high gradient regions of the Columbia River, Columbia River estuary and coastal ocean.
The project developed for a CMOP undergraduate summer intern is one that involves
directed analysis of a subset of these microarray gene expression data. In particular, the
intern will analyze and compare gene expression patterns of ammonia-oxidizing archaea
and bacteria in the Columbia River, estuary, and coastal ocean. The main focus of this
research is to understand the ecology and environmental impacts of a novel group of
Archaea, the nonthermophilic Crenarchaeota. The first member of this enigmatic group
to be isolated in laboratory culture was from a marine environment and is reported to be
an aerobic chemolithoautotrophic ammonia oxidizer. This finding suggested a role for
members of this group in microbially mediated nitrification, which links the
mineralization of organic matter (formation of NH4+) to the recycling of N to the
atmosphere (denitrification of NO3-). This discovery, with reports of widespread
distribution of the gene putatively required for archaeal ammonia oxidation, suggest a
potentially enormous impact of these ubiquitous organisms on global carbon and nitrogen
biogeochemical cycles. Comparing patterns of amoA gene expression from both archaea
and bacteria will provide the intern with information leading to the development of new
hypotheses about the roles of these organisms in coastal margin nitrification. The intern
will become familiar with a suite of data analysis programs including multivariate
statistical techniques, and will additionally learn state-of-the-art microarray data
extraction and manipulation methodologies. The summer intern may also learn
techniques involved in microarray hybridization, and participate in data acquisition and
analysis. Results from this project will contribute to our overall goals in CMOP, which
are to understand biological changes with respect to chemical and physical parameters
along the Columbia River coastal margin, and to educate undergraduate students about
science and the environment using hands-on research.
3. Links with other projects:
 The intern will be co-supported by Holly Simon’s NSF CAREER grant and data
from the project will impact the Simon group’s research goals for both CMOP
and the CAREER project.

Results from this project will also impact upon a related project investigating
molecular and biogeochemical properties of nitrifiers in the Columbia River
Estuary being carried out in collaboration with Joe Needoba and Tawnya
Petersen.
4. Skills needed:
Mainly computer skills, basic laboratory skills will be developed during the project as
needed.
5. Proposed curriculum structure for the 10 weeks:
Will be developed shortly.
7. Description of the final project/report:
The final report will summarize the results of the gene expression analysis, including
figures and tables describing results. The final report may also include some analysis of
RNA isolation data in the context of environmental parameters provided by other CMOP
researchers, including sampling location, salinity, chlorophyll A content, bacterial
production, oxygen concentration, water temperature, etc. As appropriate, additional
efforts may be necessary to complete and organize a laboratory notebook.