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CMOP Team Employs Game-changing Technology in the Columbia River Estuary

When traditional methods used in aquatic science, such as sporadic shore-based or ship-based sampling, repeatedly failed to provide necessary spatial and temporal context, and proved ineffective in consistently capturing changing water masses or the true range of variability in microbial communities, the scientists at CMOP shifted to an innovative sampling strategy for microbiological studies in the Columbia River estuary. With the integration of an autonomous robotic sampler, the ESP (Environmental Sample Processor), developed at the Monterey Bay Aquarium Research Institute, and SATURN (Science and Technology University Research Network), CMOP’s observation and prediction system, the process of collecting data became substantially more precise and beneficial.

With it’s impressive ability to sample automatically, the ESP can be initiated at either pre-determined times, or adaptively when one or more in situ sensor-monitored parameters such as salinity, turbidity, dissolved oxygen meet user-defined values. The sensor information is communicated through a centralized computer, triggering the ESP to collect a sample. “ESP-SATURN integrates observations, model predictions and robotic sampling, representing a major innovation for ESP deployment and microbiological sampling strategies. By relying on both contemporary observations and simulations based on historical collections of physical and biogeochemical data, CMOP's novel approach captures ecologically-important transient events by enabling the collection of precisely timed samples,” said team leader Dr. Holly Simon.

The complexity of the Columbia River estuary makes it an ideal test bed for technology designed to capture and dissect microbial community responses associated with a rapidly changing environment. Indeed, this estuary is a highly dynamic environment, characterized by a mixing of riverine and oceanic water masses, strong currents, short water residence times, and high but variable suspended particulate matter concentrations. Adding to these characteristics are reoccurring, but transient, estuarine events that are ecologically important microbiological hotspots. These events include the (1) Estuarine Turbidity Maxima, which are sedimentary features (sediment suspension) generated during tidal reversals; (2) intrusion of oxygen-depleted ocean waters during coastal upwelling periods; and (3) late summer blooms of the mixotrophic ciliate Mesodinium major. The use of ESP-SATURN, through collection of targeted water samples - together with contextual environmental data, facilitates effective characterization of the microbiological response to these events.

CMOP’s scientists have carried out numerous ESP deployments in the Columbia River estuary at two interdisciplinary monitoring stations, SATURN-03 and SATURN-04 with deployment goals including the assessment of the responses from microbial populations to nutrient and energy fluxes in this active environment. Specifically, sampling missions were designed to study the dynamics of (1) ammonia-oxidizing archaea, key microbes in the nitrogen cycle; (2) cryptophytes, the endosymbiotic algal prey of the estuarine bloom-forming M. major. (Related link: CMOP’s award-winning film: These studies, which were based on quantitative analysis of specific DNA genes as biomarkers, have demonstrated that the invasion of oxygen-depleted oceanic water influences the composition of Estuarine Turbidity Maxima microbial assemblages. Preliminary results also suggest that cryptophyte prey abundance might not be a limiting factor for M. major blooms in the main estuary channels. The ongoing acquisition of size-fractionated samples (>3µm and 0.2-3µm) for environmental ‘omics’ analyses will further our understanding of the impact of these events on microbial activities related to ecosystem function. Through a Community Sequencing Program grant awarded to CMOP by the Department of Energy’s Joint Genome Institute (JGI), high-throughput Illumina sequencing and analysis of DNA metagenomes and RNA metatranscriptomes for more than 250 estuarine samples will soon take place.

As CMOP scientists continue their research on the impact of phytoplankton-bacterial interactions on estuarine carbon-cycle fluxes, they are also planning "cluster" deployments to combine the sampling capabilities of the ESP and other technologically innovative instrumentation, such as the University of Washington's SeaFlow and CMOP's FlowCAM during field campaigns.  Both of these latter instruments are designed to measure in near real-time the abundance and composition of small and large phytoplankton communities, respectively. Data collected on phytoplankton will be used to trigger ESP sampling of estuarine water, for example when high numbers of M. major cells are detected. Combined measurements from the three instruments are expected to provide unprecedented detail about phytoplankton-bacterial interactions in the estuary.

Columbia River estuary showing the location of CMOP’s interdisciplinary monitoring stations, including SATURN-03 and SATURN-04 where the Environmental Sample Processor (ESP) has been deployed.