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  • Bacterial community profiling at sewage treatment plant outfalls


Northwest Fisheries Science Center (NWFSC) Environmental and Fisheries Sciences


Penn Cove microbial profiling
Bacterial community profiling at sewage treatment plant outfalls
Penn Cove (in the Whidbey Basin) is designated as a category 5, 303d impaired water body due to low dissolved oxygen. In addition to runoff from adjacent developed and agricultural lands, treated effluent from two sewage treatment plants (STPs) and freshwater from the nearby Skagit River flow into Penn Cove. This project investigates the structure and function of microbial communities in the context of inorganic nutrients and physical parameters to assess any detectable influence of STPs.

Work is conducted by NOAA personnel with assistance from undergraduate research interns. Data collected across four different seasons include bacterial/archeal abundance (biomass), heterotrophic production (productivity), bacterial diversity, chlorophyll A, inorganic nutrient concentrations, dissolved oxygen concentration, and seawater temperature.

Anticipated products are presentations at scientific meetings related to marine dissolved oxygen and to local management authorities (e.g., county government) as well as publication in the referred literature. The project is a seed project to develop further capacity to assess additional low dissolved oxygen sites.

Research Themes

Habitats to support sustainable fisheries and recovered populations
Healthy oceans, coastal waters, and riverine habitats provide the foundation for aquatic resources used by a diversity of species and society. Protecting marine, estuarine and freshwater ecosystems that support these species relies on science to link habitat condition/processes and the biological effects of restoration actions. The NWFSC provides the habitat science behind many management actions taken by NOAA Fisheries and other natural resource agencies to protect and recover aquatic ecosystems and living marine resources. The NWFSC also maintains a longstanding focus on toxic chemical contaminants, as a foundation for regional and national research on pollution threats to fisheries and protected resources.

Research Foci

Characterize the interaction of human use and habitat distribution, quantity and quality
The ability to define the state of an ecosystem requires insight into the natural processes within habitats, and how anthropogenic interactions with these processes can alter ecosystems and marine organisms. A wide diversity of human activities -- land use and water withdrawals, industrialization and dredging, fishing practices and climate change (e.g., ocean acidification) -- directly and indirectly impact critical freshwater, estuarine, and marine habitats. To best manage west coast marine, estuarine and freshwater habitats in a sustainable fashion, it is necessary to map the spatial and temporal footprint of human impacts and review their potential biological impact on each species of interest. Measurement parameters will be developed to determine the full range of human impacts using spatial data and improved habitat classification.


Puget Sound
Puget Sound
bacterial communities
microbial ecology measure
chlorophyll A
microbial ecology measure
heterotrophic production
microbial ecology measure
low dissolved oxygen
water quality indicators
marine microbes
all microbes
microbial abundance
microbial ecology measure
water quality indicators


Final report to Internal Grants Program
Final report on project to funding source
Looking closer to home: microbial ecology studies in Puget Sound
Oceans & Human Health seminar series
Microbial assessments of a marine bay with chronic low dissolved oxygen
manuscript describing study
Profiling microbial features in a Whidbey Basin bay with low dissolved oxygen
Salish Sea Ecosystem Conference, Vancouver BC
Profiling microbial features in a marine bay with chronic low dissolved oxygen
Keystone Symposia: Microbial Communities as Drivers of Ecosystem Diversity; Breckenridge, CO


Kingdom Archaea
Kingdom Bacteria
Phylum Bacillariophyta


Linda Rhodes
Principal Investigator