Joseph A. Needoba

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.

Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=−0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.

Applications of Fluorescence Spectroscopy for Predicting Percent Wastewater in an Urban Stream

Dissolved organic carbon (DOC) is a significant organic carbon reservoir in many ecosystems, and its characteristics and sources determine many aspects of ecosystem health and water quality. Fluorescence spectroscopy methods can quantify and characterize the subset of the DOC pool that can absorb and re-emit electromagnetic energy as fluorescence and thus provide a rapid technique for environmental monitoring of DOC in lakes and rivers. Using high resolution fluorescence techniques, we characterized DOC in the Tualatin River watershed near Portland, Oregon, and identified fluorescence parameters associated with effluent from two wastewater treatment plants and samples from sites within and outside the urban region. Using a variety of statistical approaches, we developed and validated a multivariate linear regression model to predict the amount of wastewater in the river as a function of the relative abundance of specific fluorescence excitation/emission pairs. The model was tested with independent data and predicts the percentage of wastewater in a sample within 80% confidence. Model results can be used to develop in situ instrumentation, inform monitoring programs, and develop additional water quality indicators for aquatic systems.

Coastal upwelling supplies oxygen-depleted water to the columbia river estuary

Low dissolved oxygen (DO) is a common feature of many estuarine and shallow-water environments, and is often attributed to anthropogenic nutrient enrichment from terrestrial-fluvial pathways. However, recent events in the U.S. Pacific Northwest have highlighted that wind-forced upwelling can cause naturally occurring low DO water to move onto the continental shelf, leading to mortalities of benthic fish and invertebrates. Coastal estuaries in the Pacific Northwest are strongly linked to ocean forcings, and here we report observations on the spatial and temporal patterns of oxygen concentration in the Columbia River estuary. Hydrographic measurements were made from transect (spatial survey) or anchor station (temporal survey) deployments over a variety of wind stresses and tidal states during the upwelling seasons of 2006 through 2008. During this period, biologically stressful levels of dissolved oxygen were observed to enter the Columbia River estuary from oceanic sources, with minimum values close to the hypoxic threshold of 2.0 mg L−1. Riverine water was consistently normoxic. Upwelling wind stress controlled the timing and magnitude of low DO events, while tidal-modulated estuarine circulation patterns influenced the spatial extent and duration of exposure to low DO water. Strong upwelling during neap tides produced the largest impact on the estuary. The observed oxygen concentrations likely had deleterious behavioral and physiological consequences for migrating juvenile salmon and benthic crabs. Based on a wind-forced supply mechanism, low DO events are probably common to the Columbia River and other regional estuaries and if conditions on the shelf deteriorate further, as observations and models predict, Pacific Northwest estuarine habitats could experience a decrease in environmental quality.

Red Waters of Myrionecta rubra are Biogeochemical Hotspots for the Columbia River Estuary with Impacts on Primary/Secondary Productions and Nutrient Cycles

The localized impact of blooms of the mixotrophic ciliate Myrionecta rubra in the Columbia River estuary during 2007–2010 was evaluated with biogeochemical, light microscopy, physiological, and molecular data. M. rubra affected surrounding estuarine nutrient cycles, as indicated by high and low concentrations of organic nutrients and inorganic nitrogen, respectively, associated with red waters. M. rubra blooms also altered the energy transfer pattern in patches of the estuarine water that contain the ciliate by creating areas characterized by high primary production and elevated levels of fresh autochthonous particulate organic matter, therefore shifting the trophic status in emergent red water areas of the estuary from net heterotrophy towards autotrophy. The pelagic estuarine bacterial community structure was unaffected by M. rubra abundance, but red waters of the ciliate do offer a possible link between autotrophic and heterotrophic processes since they were associated with elevated dissolved organic matter and showed a tendency for enhanced microbial secondary production. Taken together, these findings suggest that M. rubra red waters are biogeochemical hotspots of the Columbia River estuary.

Nutrient Loading and Transformations in the Columbia River Estuary Determined by High-Resolution In Situ Sensors

The Columbia River estuary is characterized by relatively large tidal currents and water residence times of a few days or less. These and other environmental conditions tend to suppress water column productivity and favor the export of riverborne nutrients to the coastal ocean. However, hotspots of biological activity may allow for significant nutrient transformation and removal within the estuary, but these processes have previously been difficult to quantify due to the challenges of obtaining measurements at appropriate frequency and duration. In this study, nutrient biogeochemical dynamics within the salt-influenced region of the estuary were quantified using high-resolution in situ observations of nutrients and physical water properties. During 2010, three autonomous nutrient sensors (Satlantic SUNA, SubChem Systems Inc. APNA, WET Labs Cycle-PO4) that together measured nitrate + nitrite, orthophosphate, ammonium, silicic acid, and nitrite were deployed on fixed observatory platforms. Hourly measurements captured tidal fluctuations and permitted an analysis of river and ocean end-member mixing. The results suggested that during summer, the lower estuary released high concentrations of ammonium and phosphate despite low concentrations in the river and coastal ocean. This was likely a result of organic matter accumulation and remineralization in the estuarine turbidity maximum and the lateral bays adjacent to the main channel.

Infrastructure for collaborative science and societal applications in the Columbia River estuary

To meet societal needs, modern estuarine science needs to be interdisciplinary and collaborative, combine discovery with hypotheses testing, and be responsive to issues facing both regional and global stakeholders. Such an approach is best conducted with the benefit of data-rich environments, where information from sensors and models is openly accessible within convenient timeframes. Here, we introduce the operational infrastructure of one such data-rich environment, a collaboratory created to support (a) interdisciplinary research in the Columbia River estuary by the multi-institutional team of investigators of the Science and Technology Center for Coastal Margin Observation & Prediction and (b) the integration of scientific knowledge into regional decision making. Core components of the operational infrastructure are an observation network, a modeling system and a cyber-infrastructure, each of which is described. The observation network is anchored on an extensive array of long-term stations, many of them interdisciplinary, and is complemented by on-demand deployment of temporary stations and mobile platforms, often in coordinated field campaigns. The modeling system is based on finiteelement unstructured-grid codes and includes operational and process-oriented simulations of circulation, sediments and ecosystem processes. The flow of information is managed through a dedicated cyber-infrastructure, conversant with regional and national observing systems.

Fortnightly Tidal Modulations Affect Net Community Production in a Mesotidal Estuary

Optical in situ chemical sensors enable sampling intervals and durations that rival acoustic techniques used for measuring currents. Coupling these high-frequency biogeochemical and physical measurements in estuaries to address ecosystem-scale questions, however, is still comparatively novel. This study investigated how tides affect ecosystem metabolism in a mesotidal estuary in central California (Elkhorn Slough). Dissolved oxygen measurements were used to estimate the terms in a control volume budget for a tidal creek/marsh complex at tidal timescales over several weeks. Respiration rates were 1.6 to 7.3 g O2 m−2 day−1; net community production approached 20 g O2 m−2 day−1. We found that aquatic NCP integrated throughout the creek complex varied significantly over the spring-neap cycle. The intertidal contribution to aquatic metabolism was net heterotrophic during spring tides and generally in balance during neap tides because spring-tide marsh inundation was limited to nighttime, and therefore the marsh could not contribute any primary production to the water column. At the estuary scale, the fortnightly export of oxygen from the main channel to the intertidal was largely balanced by an advective flux up-estuary.

Hydrologic control of dissolved organic matter concentration and quality in a semiarid artificially drained agricultural catchment

Agricultural practices have altered watershed-scale dissolved organic matter (DOM) dynamics, including in-stream concentration, biodegradability, and total catchment export. However, mechanisms responsible for these changes are not clear, and field-scale processes are rarely directly linked to the magnitude and quality of DOM that is transported to surface water. In a small (12 ha) agricultural catchment in eastern Washington State, we tested the hypothesis that hydrologic connectivity in a catchment is the dominant control over the concentration and quality of DOM exported to surface water via artificial subsurface drainage. Concentrations of dissolved organic carbon (DOC) and humic-like components of DOM decreased while the Fluorescence Index and Freshness Index increased with depth through the soil profile. In drain discharge, these characteristics were significantly correlated with drain flow across seasons and years, with drain DOM resembling deep sources during low-flow and shallow sources during high flow, suggesting that DOM from shallow sources bypasses removal processes when hydrologic connectivity in the catchment is greatest. Assuming changes in streamflow projected for the Palouse River (which contains the study catchment) under the A1B climate scenario (rapid growth, dependence on fossil fuel, and renewable energy sources) apply to the study catchment, we project greater interannual variability in annual DOC export in the future, with significant increases in the driest years. This study highlights the variability in DOM inputs from agricultural soil to surface water on daily to interannual time scales, pointing to the need for a more nuanced understanding of agricultural impacts on DOM dynamics in surface water.

Development of an economical, autonomous pHstat system for culturing phytoplankton under steady state or dynamic conditions

Laboratory investigations of physiological processes in phytoplankton require precise control of experimental conditions. Chemostats customized to control and maintain stable pH levels (pHstats) are ideally suited for investigations of the effects of pH on phytoplankton physiology, for example in context of ocean acidification. Here we designed and constructed a simple, flexible pHstat system and demonstrated its operational capabilities under laboratory culture conditions. In particular, the system is useful for simulating natural cyclic pH variability within aquatic ecosystems, such as diel fluctuations that result from metabolic activity or tidal mixing in estuaries. The pHstat system operates in two modes: (1) static/set point pH, which maintains pH at a constant level, or (2) dynamic pH, which generates regular, sinusoidal pH fluctuations by systematically varying pH according to user-defined parameters. The pHstat is self-regulating through the use of interchangeable electronically controlled reagent or gas-mediated pH-modification manifolds, both of which feature flow regulation by solenoid valves. Although effective pH control was achieved using both liquid reagent additions and gas-mediated methods, the liquid manifold exhibited tighter control (±0.03pH units) of the desired pH than the gas manifold (±0.10pH units). The precise control provided by this pHstat system, as well as its operational flexibility will facilitate studies that examine responses by marine microbiota to fluctuations in pH in aquatic ecosystems.

Dynamics of Teleaulax-like cryptophytes during the decline of a red water bloom in the Columbia River Estuary

The mixotrophic ciliate, Mesodinium rubrum, is a globally distributed ciliate that relies on the acquisition and use of chloroplasts derived from its cryptophyte prey. The ecology and physiology of the cryptophytes is not well known, nor is it clear how their growth influences M. rubrum blooms. A 4-week survey was conducted in the Columbia River estuary in 2013 during the decline of the annual M. rubrum bloom to better understand how environmental factors influence the dynamics of the cryptophyte prey, Teleaulax amphioxeia. Abundances and division rates of freeliving Teleaulax-like cryptophytes were continuously monitored using flow cytometry. Cryptophyte division rates, estimated in situ for the first time using a size-structured division rate model, ranged from 0.2 to 1.5 d, with the highest rates observed in accordance with high abundances. These division rates were positively correlated with concentrations of dissolved inorganic nitrogen and phosphorus, suggesting nutrient availability limited the growth of Teleaulax-like cryptophytes at that time. Assuming a minimum ingestion rate of ~1 cryptophyte ciliate day, the growth of M. rubrum may have been limited by the low abundance of Teleaulax-like cryptophytes during the M. rubrum bloom decline. Our results highlight the importance of prey availability for understanding the dynamics of red water blooms.