Long-Term Changes in Nutrient Loading and Stoichiometry and Their Relationships with Changes in the Food Web and Dominant Pelagic Fish Species in the San Francisco Estuary, California

Changes in the food selectivity of zooplanktivorous fishes related to the effects of nutrient enrichment in an urban tropical estuary

Juvenile fish use estuarine ecosystems due to appropriate refuges and food supply found in these environments. The objective of this study was to investigate whether variations in the diet composition of juvenile fishes were mediated by changes in the availability of zooplankton prey in an urban estuary. Changes in fish foraging and prey selectivity were affected by nutrient enrichment. Calanoida and Cyclopoida were the most abundant items present in all zones and seasons, and for this reason, these were the items that most contributed to the fish diet. Shift in feeding strategy associated with eutrophication was registered due to a decrease in water quality. All species showed some contamination with microplastic particles and exhibited selectivity over them. The use of food resources available for fish is likely to be representative of estuarine habitat quality and may provide valuable information on the ecological status of estuaries.

Governance pathway for coastal eutrophication based on regime shifts in diatom-dinoflagellate composition of the Bohai and Baltic Seas

Regime shifts in the diatom-dinoflagellate composition have occurred in the Baltic Sea (BS) and Bohai Sea (BHS) under eutrophication and have affected the entire coastal ecosystem, damaging the regulatory, provisioning, cultural, and supporting service functions of marine ecosystems. Therefore, finding a solution to restore the balance of phytoplankton community composition and mitigate eutrophication is of utmost importance. In this study, the Driver (per capita gross domestic product)-Pressure (terrestrial inputs)-State (seawater environmental parameters)-Impact (proportions of diatoms and dinoflagellates)-Response (eutrophication governance projects) framework served as a guide for our analysis of the causal relationship among various environmental components in the coastal system. The relevant data in BS and BHS spanning from the 1950s to the 2010s were collected and used to construct a diatom-dinoflagellate composition single index, which allowed us to identify the shifts in regimes (mutation points and phases) of the diatom-dinoflagellate composition and environmental factors using sequential t-test analysis. We also identified key environmental factors that moderated the diatom-dinoflagellate composition using redundancy analysis and analyzed the partial effects of the main environmental factors on the diatom-dinoflagellate composition using a generalized additive model. Finally, the regulation of the eutrophication governance investment on diatom-dinoflagellate composition was investigated. We found that (1) BS is a "time machine," with coastal eutrophication governance and regime shift of diatom-dinoflagellate composition and environmental factors two decades earlier than that in BHS; (2) in BS, the key moderation factor of diatom proportion is SiO3-Si and those of dinoflagellates are sea surface salinity and N:P ratio; in BHS, the key moderation factors of diatom proportion are PO4-P and Si:N ratio and those of dinoflagellate are dissolved inorganic nitrogen and N:P and Si:P ratios; (3) it is projected that BHS will enter its recovery phase from eutrophication after mid-2020s. In summary, the N/P/Si stoichiometric relationships should be given greater consideration, with the exception of the "dose-response" relationship in both sea areas. Our results indicate an urgent need for an improved mechanistic understanding of how phytoplankton biodiversity changes in response to changes in nutrient load and how we should ultimately deal with the challenges that arise.

Ecosystem-level effects of re-oligotrophication and N:P imbalances in rivers and estuaries on a global scale

Trends and ecological consequences of phosphorus (P) decline and increasing nitrogen (N) to phosphorus (N:P) ratios in rivers and estuaries are reviewed and discussed. Results suggest that re-oligotrophication is a dominant trend in rivers and estuaries of high-income countries in the last two-three decades, while in low-income countries widespread eutrophication occurs. The decline in P is well documented in hundreds of rivers of United States and the European Union, but the biotic response of rivers and estuaries besides phytoplankton decline such as trends in phytoplankton composition, changes in primary production, ecosystem shifts, cascading effects, changes in ecosystem metabolism, etc., have not been sufficiently monitored and investigated, neither the effects of N:P imbalance. N:P imbalance has significant ecological effects that need to be further investigated. There is a growing number of cases in which phytoplankton biomass have been shown to decrease due to re-oligotrophication, but the potential regime shift from phytoplankton to macrophyte dominance described in shallow lakes has been documented only in a few rivers and estuaries yet. The main reasons why regime shifts are rarely described in rivers and estuaries are, from one hand the scarcity of data on macrophyte cover trends, and from the other hand physical factors such as peak flows or high turbidity that could prevent a general spread of submerged macrophytes as observed in shallow lakes. Moreover, re-oligotrophication effects on rivers may be different compared to lakes (e.g., lower dominance of macrophytes) or estuaries (e.g., limitation of primary production by N instead of P) or may be dependent on river/estuary type. We conclude that river and estuary re-oligotrophication effects are complex, diverse and still little known, and in some cases are equivalent to those described in shallow lakes, but the regime shift is more likely to occur in mid to high-order rivers and shallow estuaries.

Three Decades of Changing Nutrient Stoichiometry from Source to Sea on the Swedish West Coast

European ecosystems have been subject to extensive shifts in anthropogenic disturbance, primarily through atmospheric deposition, climate change, and land management. These changes have altered the macronutrient composition of aquatic systems, with widespread increases in organic carbon (C), and declines in nitrogen (N) and phosphorus (P). Less well known is how these disturbances have affected nutrient stoichiometry, which may be a more useful metric to evaluate the health of aquatic ecosystems than individual nutrient concentrations. The Swedish west coast has historically experienced moderate to high levels of atmospheric deposition of sulfate and N, and eutrophication. In addition, coastal waters have been darkening with damaging effects on marine flora and fauna. Here, we present three decades of macronutrient data from twenty lakes and watercourses along the Swedish west coast, extending from headwaters to river mouths, across a range of land covers, and with catchments ranging 0.037–40,000 km2. We find a high degree of consistency between these diverse sites, with widespread increasing trends in organic C, and declines in inorganic N and total P. These trends in individual macronutrients translate into large stoichiometric changes, with a doubling in C:P, and increases in C:N and N:P by 50% and 30%, showing that freshwaters are moving further away from the Redfield Ratio, and becoming even more C rich, and depleted in N and P. Although recovery from atmospheric deposition is linked to some of these changes, land cover also appears to have an effect; lakes buffer against C increases, and decreases in inorganic N have been greatest under arable land cover. Our analysis also detects coherently declining P concentrations in small forest lakes; so called (and unexplained) “oligotrophication.” Taken together, our findings show that freshwater macronutrient concentrations and stoichiometry have undergone substantial shifts during the last three decades, and these shifts can potentially explain some of the detrimental changes that adjacent coastal ecosystems are undergoing. Our findings are relevant for all European and North American waters that have experienced historically high levels of atmospheric deposition, and provide a starting point for understanding and mitigating against the trajectories of long-term change in aquatic systems.

Increases in the seaward river flux of nutrients driven by human migration and land-use changes in the tide-influenced delta

Most large megacities are located on areas adjacent to tide-influenced deltas. However, contribution of megacities to seaward nutrient fluxes in tide-influenced deltas are poorly quantified in regional and global levels. We analyzed nutrient concentrations and water current data for a large and tide-influenced delta, the Changjiang (Yangtze River) since 1980. Concentrations, species ratios and fluxes of nutrients in tide-influenced delta has been found to differ dramatically from those at upstream. Over the period 2004 to 2015, the seaward nutrient fluxes of dissolved inorganic nitrogen and dissolved silica increased by 5%-10%, but dissolved inorganic phosphorus increased by 15%-20%, in the tide-influenced delta of the Changjiang. Consequently, the DIP/DIN decreases by 11% and DIP/DSi increases by 14% at the river mouth relative to those farther upstream the tidal limit. The legacy and/or recycled contribution accounts for 10%-30% of this increased nutrient flux, hence additional sources are predominantly those involving anthropogenic land-use changes. These findings have implications not only for the Changjiang but also for other riverine systems with respect to management strategy. Nutrient dynamics in tide-influenced deltas near urban areas should receive increased research and policy attention. By not considering nutrient sources in tide-influenced deltas, knowledge of the seaward fluxes and species ratios of nutrients from land sources is incomplete and can be biased, to the point that assessments of their impacts on adjacent marine environments may be inaccurate and mitigation policies therefore ineffective.

Urea Inputs Drive Picoplankton Blooms in Sarasota Bay, Florida, U.S.A

Recent increases in global urea usage, including its incorporation in slow-release fertilizers commonly used in lawn care in Florida, have the potential to alter the form and amount of nitrogen inputs to coastal waters. This shift may, in turn, impact phytoplankton community diversity and nutrient cycling processes. An autonomous water quality monitoring and sampling platform containing meteorological and water quality instrumentation, including urea and phycocyanin sensors, was deployed between June and November of 2009 in Sarasota Bay, Florida. This shallow, lagoonal bay is characterized by extensive and growing urban and suburban development and limited tidal exchange and freshwater inputs. During the monitoring period, three high-biomass (up to 40 µg chlorophyll-a·L−1) phytoplankton blooms dominated by picocyanobacteria or picoeukaryotes were observed. Each bloom was preceded by elevated (up to 20 μM) urea concentrations. The geolocation of these three parameters suggests that “finger canals” lining the shore of Sarasota Bay were the source of urea pulses and there is a direct link between localized urea inputs and downstream picoplankton blooms. Furthermore, high frequency sampling is required to detect the response of plankton communities to pulsed events.

Spatial variability of phytoplankton in a shallow tidal freshwater system reveals complex controls on abundance and community structure

Estuaries worldwide are undergoing changes to patterns of aquatic productivity because of human activities that alter flow, impact sediment delivery and thus the light field, and contribute nutrients and contaminants like pesticides and metals. These changes can influence phytoplankton communities, which in turn can alter estuarine food webs. We used multiple approaches-including high-resolution water quality mapping, synoptic sampling, productivity and nitrogen uptake rates, Lagrangian parcel tracking, enclosure experiments and bottle incubations-over a short time period to take a "spatial snapshot" of conditions in the northern region of the San Francisco Estuary (California, USA) to examine how environmental drivers like light availability, nutrients, water residence time, and contaminants affect phytoplankton abundance and community attributes like size distribution, taxonomic structure, and nutrient uptake rates. Zones characterized by longer residence time (15-60 days) had higher chlorophyll-a concentrations (9 ± 4 µg L^-1) and were comprised primarily of small phytoplankton cells (<5 µm, 74 ± 8%), lower ammonium concentrations (1 ± 0.8 µM), higher nitrate uptake rates, and higher rates of potential carbon productivity. Conversely, zones characterized by shorter residence time (1-14 days) had higher ammonium concentration (13 ± 5 µM) and lower chlorophyll-a concentration (5 ± 1 µg L^-1) with diatoms making up a larger percent contribution. Longer residence time, however, did not result in the accumulation of large (>5 µm) cells considered important to pelagic food webs. Rather, longer residence time zones had a phytoplankton community comprised primarily of small cells, particularly picocyanobacteria that made up 38 ± 17% of the chlorophyll-a - nearly double the concentration seen in shorter residence time zones (22 ± 7% picocyanobacterial of chlorophyll-a). Our results suggest that water residence time in estuaries may have an effect as large or larger than that experimentally demonstrated for light, contaminants, or nutrients.

Toxicity of herbicides to cyanobacteria and phytoplankton species of the San Francisco Estuary and Sacramento-San Joaquin River Delta, California, USA

The herbicides glyphosate, imazamox and fluridone are herbicides, with low toxicity towards fish and invertebrates, which are applied to waterways to control invasive aquatic weeds. However, the effects of these herbicides on natural isolates of phytoplankton and cyanobacteria are unknown. Three species of microalgae found in the San Francisco Estuary (SFE)/Sacramento-San Joaquin River Delta (Delta) (Microcystis aeruginosa, Chlamydomonas debaryana, and Thalassiosira pseudonana) were exposed to the three herbicides at a range of concentrations in 96-well plates for 5-8 days. All three algal species were the most sensitive to fluridone, with IC₅₀ of 46.9, 21, and 109 µg L^-1 for M. aeruginosa, T. pseudonana and C. debaryana, respectively. Imazamox inhibited M. aeruginosa and T. pseudonana growth at 3.6 × 10⁴ µg L^-1 or higher, and inhibited C. debaryana growth at 1.0 × 10⁵ µg L^-1 or higher. Glyphosate inhibited growth in all species at ca. 7.0 × 10⁴ µg L^-1 or higher. Fluridone was the only herbicide that inhibited the microalgae at environmentally relevant concentrations in this study and susceptibility to the herbicide depended on the species. Thus, the application of fluridone may affect cyanobacteria and phytoplankton community composition in water bodies where it is applied.

Hydrodynamic Modeling Coupled with Long-term Field Data Provide Evidence for Suppression of Phytoplankton by Invasive Clams and Freshwater Exports in the San Francisco Estuary

The San Francisco Estuary (California, USA) had abundant pelagic fish in the late 1960s, but has few pelagic fish today. A primary cause for this decline in fish is thought to be a trophic cascade, triggered by declining phytoplankton. Here, we describe the changes in pelagic community structure of the San Francisco Estuary. Then, we examine whether changes in hydrodynamics due to freshwater exports, which increased exponentially beginning in 1967, in addition to the 1986 invasion by the clam Potamocorbula amurensis, explain the phytoplankton loss. Hydrodynamic variables were reconstructed back to 1956 using statistical models fit to, and cross-validated against, output from a hydrodynamic model. Then, we regressed mean summer/fall chlorophyll a-the season with the largest phytoplankton decline-against the reconstructed hydrodynamic variables and the presence/absence of P. amurensis for 1969-2014. The regression model, which explained 78% of the interannual variation in chlorophyll a, was then used to quantify the influence of P. amurensis and exports on chlorophyll a. Based on monitoring data, chlorophyll a declined 22-fold from 1969-2014, zooplankton declined 32-fold from 1972-2014, and pelagic fish declined 92-fold from 1968-2014. Averaged over 1990-2014, the chlorophyll a model ascribed an 88% decline in chlorophyll a to P. amurensis, a 74% decline to exports (at minimum), and a 97% decline to the combined influence of P. amurensis and exports (at minimum). Thus, the decline in pelagic productivity in the San Francisco Estuary has occurred largely due to the combined impacts of the P. amurensis invasion and increased freshwater exports.

Towards a New Paradigm of Urban Water Infrastructure: Identifying Goals and Strategies to Support Multi-Benefit Municipal Wastewater Treatment

Over the past decade, water professionals have begun to focus on a new paradigm for urban water systems, which entails the recovery of resources from wastewater, the integration of engineered and natural systems, and coordination among agencies managing different facets of water systems. In the San Francisco Bay Area, planning for nutrient management serves as an exemplary model of this transition. We employed a variety of methodological approaches including stakeholder analysis, multi-criteria decision-making weight elicitation, and document analysis to understand and support decision-making in this context. Based on interviews with 32 stakeholders, we delineate goals that are considered to be important for achieving the new paradigm and we highlight management strategies that can help reach these goals. We identify and analyze the social, institutional, and technical impediments to planning and implementing multi-benefit wastewater infrastructure projects and identify strategies to overcome some of these challenges. Transitioning to a new paradigm for urban water infrastructure will require stakeholders to proactively forge collaborative relationships, jointly define a shared vision and objectives, and build new rules to overcome limitations of current institutional policies.

On-road emissions of ammonia: An underappreciated source of atmospheric nitrogen deposition

We provide updated spatial distribution and inventory data for on-road NH₃ emissions for the continental United States (U.S.) On-road NH₃ emissions were determined from on-road CO₂ emissions data and empirical NH₃:CO₂ vehicle emissions ratios. Emissions of NH₃ from on-road sources in urbanized regions are typically 0.1-1.3tkm^-2yr^-1 while NH₃ emissions in agricultural regions generally range from 0.4-5.5tkm^-2yr^-1, with a few hotspots as high as 5.5-11.2tkm^-2yr^-1. Counties with higher vehicle NH₃ emissions than from agriculture include 40% of the U.S.

POPULATION

The amount of wet inorganic N deposition as NH₄⁺ from the National Atmospheric Deposition Program (NADP) network ranged from 37 to 83% with a mean of 58.7%. Only 4% of the NADP sites across the U.S. had <45% of the N deposition as NH₄⁺ based on data from 2014 to 2016, illustrating the near-universal elevated proportions of NH₄⁺ in deposition across the U.S. Case studies of on-road NH₃ emissions in relation to N deposition include four urban sites in Oregon and Washington where the average NH₄-N:NO₃-N ratio in bulk deposition was 2.3. At urban sites in the greater Los Angeles Basin, bulk deposition of NH₄-N and NO₃-N were equivalent, while NH₄-N:NO₃-N in throughfall under shrubs ranged from 0.6 to 1.7. The NH₄-N:NO₃-N ratio at 7-10 sites in the Lake Tahoe Basin averaged 1.4 and 1.6 in bulk deposition and throughfall, and deposition of NH₄-N was strongly correlated with summertime NH₃ concentrations. On-road emissions of NH₃ should not be ignored as an important source of atmospheric NH₃, as a major contributor to particulate air pollution, and as a driver of N deposition in urban and urban-affected regions.

Four decades of water quality change in the upper San Francisco Estuary

Quantitative descriptions of chemical, physical, and biological characteristics of estuaries are critical for developing an ecological understanding of drivers of change. Historical trends and relationships between key species of dissolved inorganic nitrogen (ammonium, nitrate/nitrite, total) from the Delta region of the San Francisco Estuary were modeled with an estuarine adaptation of the Weighted Regressions on Time, Discharge, and Season (WRTDS). Analysis of flow-normalized data revealed trends that were different from those in the observed time-series. Flow-normalized data exhibited changes in magnitude and even reversal of trends relative to the observed data. Modelled trends demonstrated that nutrient concentrations were on average higher in the last twenty years relative to the earlier periods of observation, although concentrations have been slowly declining since the mid-1990s and early 2000s. We further describe mechanisms of change with two case studies that evaluated 1) downstream changes in nitrogen following upgrades at a wastewater treatment plant, and 2) interactions between biological invaders, chlorophyll, macro-nutrients (nitrogen and silica), and flow in Suisun Bay. WRTDS results for ammonium trends showed a distinct signal as a result of upstream wastewater treatment plant upgrades, with specific reductions observed in the winter months during low-flow conditions. Results for Suisun Bay showed that chlorophyll a production in early years was directly stimulated by flow, whereas the relationship with flow in later years was indirect and influenced by grazing pressure. Although these trends and potential causes of change have been described in the literature, results from WRTDS provided an approach to test alternative hypotheses of spatiotemporal drivers of nutrient dynamics in the Delta.

Foraging and metabolic consequences of semi-anadromy for an endangered estuarine fish

Diadromy affords fish access to productive ecosystems, increasing growth and ultimately fitness, but it is unclear whether these advantages persist for species migrating within highly altered habitat. Here, we compared the foraging success of wild Delta Smelt—an endangered, zooplanktivorous, annual, semi-anadromous fish that is endemic to the highly altered San Francisco Estuary (SFE)—collected from freshwater (<0.55 psu) and brackish habitat (≥0.55 psu). Stomach fullness, averaged across three generations of wild Delta Smelt sampled from juvenile through adult life stages (n = 1,318), was 1.5-fold higher in brackish than in freshwater habitat. However, salinity and season interacted, with higher fullness (1.7-fold) in freshwater than in brackish habitat in summer, but far higher fullness in brackish than freshwater habitat during fall/winter and winter/spring (1.8 and 2.0-fold, respectively). To examine potential causes of this interaction we compared mesozooplankton abundance, collected concurrently with the Delta Smelt, in freshwater and brackish habitat during summer and fall/winter, and the metabolic rate of sub-adult Delta Smelt acclimated to salinities of 0.4, 2.0, and 12.0 psu in a laboratory experiment. A seasonal peak in mesozooplankton density coincided with the summer peak in Delta Smelt foraging success in freshwater, and a pronounced decline in freshwater mesozooplankton abundance in the fall coincided with declining stomach fullness, which persisted for the remainder of the year (fall, winter and spring). In brackish habitat, greater foraging ‘efficiency’ (prey items in stomachs/mesozooplankton abundance) led to more prey items per fish and generally higher stomach fullness (i.e., a higher proportion of mesozooplankton detected in concurrent trawls were eaten by fish in brackish habitat). Delta Smelt exhibited no difference in metabolic rate across the three salinities, indicating that metabolic responses to salinity are unlikely to have caused the stomach fullness results. Adult migration and freshwater spawning therefore places young fish in a position to exploit higher densities of prey in freshwater in the late spring/summer, and subsequent movement downstream provides older fish more accessible prey in brackish habitat. Thus, despite endemism to a highly-altered estuary, semi-anadromy provided substantial foraging benefits to Delta Smelt, consistent with other temperate migratory fish.

Evidence of a Shift in the Littoral Fish Community of the Sacramento-San Joaquin Delta

Many estuarine and freshwater ecosystems worldwide have undergone substantial changes due to multiple anthropogenic stressors. Over the past two decades, the Sacramento-San Joaquin Delta (Delta) in California, USA, saw a severe decline in pelagic fishes, a shift in zooplankton community composition, and a rapid expansion of invasive aquatic vegetation. To evaluate whether major changes have also occurred in the littoral fish community, we analyzed a beach seine survey dataset collected from 1995 to 2015 from 26 sites within the Delta. We examined changes in the Delta fish community at three different ecological scales (species, community, and biomass), using clustering analyses, trend tests, and change-point analyses. We found that the annual catch per effort for many introduced species and some native species have increased since 1995, while few experienced a decline. We also observed a steady pattern of change over time in annual fish community composition, driven primarily by a steady increase in non-native Centrarchid species. Lastly, we found that littoral fish biomass has essentially doubled over the 21-year study period, with Mississippi Silverside Menidia audens and fishes in the Centrarchidae family driving most of this increase. The changes in the catch per effort, fish community composition, and biomass per volume indicate that a shift has occurred in the Delta littoral fish community and that the same factors affecting the Delta's pelagic food web may have been a key driver of change.

A novel and versatile flash-freezing approach for evaluating the health of Delta Smelt

A common approach used to assess environmental impacts in aquatic environments is to measure indicators of stress (biomarkers) and condition of fish within ecosystems. Particularly in estuarine ecosystems with multiple stressors, it is often desirable to quantify a suite of biological endpoints that (1) reflect fish condition at several levels of biological organization and time scales and (2) are sensitive to a range of environmental stressors. However, established methods of preservation and processing of fish for specific endpoints are often incompatible. Here, we developed a novel flash-freezing approach for assessing the health of a small, sensitive fish, the endangered Delta Smelt (Hypomesus transpacificus) after collections from the San Francisco Estuary (SFE). We assess whether flash-freezing the entire fish ensures effective preservation of multiple tissues for subsequent biomarker analyses by comparing measurements of fresh to frozen tissue. Tissues included brain, gill, and liver for enzyme activity, kidney and spleen for pathogens, and gills, liver, and gonads for histopathology and reproduction. Although flash-freezing in liquid nitrogen altered the length, weight, and condition factor of Delta Smelt, the percent changes were small (<1.5%). Histological analyses of the cellular morphology of gills, liver, and gonads were similar between both methods. Freezing artefacts were observed in ovaries, but did not hinder the identification and interpretation of cell types and oocyte stages. Freezing did not alter bacterial isolation or the activities of ethoxyresorufin-0-deethylase (EROD) or acetylcholinesterase (AChE), but had a small, negative influence on sodium potassium adenosine triphosphatase (ATPase) activity. Thus, flash-freezing in the field is a versatile preservation method for Delta Smelt, allowing for multiple tissue collections and bioassays from an individual tiny fish exposed to a wide range of natural and anthropogenic stressors. Similar methodology may be applicable to other species for which a range of biological endpoints and histopathology data are needed.

Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta

Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic nitrification, is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.

Acclimation and toxicity of high ammonium concentrations to unicellular algae

A literature review on the effects of high ammonium concentrations on the growth of 6 classes of microalgae suggests the following rankings. Mean optimal ammonium concentrations were 7600, 2500, 1400, 340, 260, 100 μM for Chlorophyceae, Cyanophyceae, Prymnesiophyceae, Diatomophyceae, Raphidophyceae, and Dinophyceae respectively and their tolerance to high toxic ammonium levels was 39,000, 13,000, 2300, 3600, 2500, 1200 μM respectively. Field ammonium concentrations <100 μM would not likely reduce the growth rate of most microalgae. Chlorophytes were significantly more tolerant to high ammonium than diatoms, prymnesiophytes, dinoflagellates, and raphidophytes. Cyanophytes were significantly more tolerant than dinoflagellates which were the least tolerant. A smaller but more complete data set was used to estimate ammonium EC₅₀ values, and the ranking was: Chlorophyceae>Cyanophyceae, Dinophyceae, Diatomophyceae, and Raphidophyceae. Ammonia toxicity is mainly attributed to NH₃ at pHs >9 and at pHs <8, toxicity is likely associated with the ammonium ion rather than ammonia.

Nutrients in estuaries--an overview and the potential impacts of climate change

The fate and cycling of macronutrients introduced into estuaries depend upon a range of interlinked processes. Hydrodynamics and morphology in combination with freshwater inflow control the freshwater flushing time, and the timescale for biogeochemical processes to operate that include microbial activity, particle-dissolved phase interactions, and benthic exchanges. In some systems atmospheric inputs and exchanges with coastal waters can also be important. Climate change will affect nutrient inputs and behaviour through modifications to temperature, wind patterns, the hydrological cycle, and sea level rise. Resulting impacts include: 1) inundation of freshwater systems 2) changes in stratification, flushing times and phytoplankton productivity 3) increased coastal storm activity 4) changes in species and ecosystem function. A combination of continuing high inputs of nutrients through human activity and climate change is anticipated to lead to enhanced eutrophication in the future. The most obvious impacts of increasing global temperature will be in sub-arctic systems where permafrost zones will be reduced in combination with enhanced inputs from glacial systems. Improved process understanding in several key areas including cycling of organic N and P, benthic exchanges, resuspension, impact of bio-irrigation, particle interactions, submarine groundwater discharges, and rates and magnitude of bacterially-driven recycling processes, is needed. Development of high frequency in situ nutrient analysis systems will provide data to improve predictive models that need to incorporate a wider variety of key factors, although the complexity of estuarine systems makes such modelling a challenge. However, overall a more holistic approach is needed to effectively understand, predict and manage the impact of macronutrients on estuaries.

Elevated ammonium concentrations from wastewater discharge depress primary productivity in the Sacramento River and the Northern San Francisco Estuary

Primary production in the Northern San Francisco Estuary (SFE) has been declining despite heavy loading of anthropogenic nutrients. The inorganic nitrogen (N) loading comes primarily from municipal wastewater treatment plant (WTP) discharge as ammonium (NH(4)). This study investigated the consequences for river and estuarine phytoplankton of the daily discharge of 15 metric tons NH(4)-N into the Sacramento River that feeds the SFE. Consistent patterns of nutrients and phytoplankton responses were observed during two 150-km transects made in spring 2009. Phytoplankton N productivity shifted from NO(3) use upstream of the WTP to productivity based entirely upon NH(4) downstream. Phytoplankton NH(4) uptake declined downstream of the WTP as NH(4) concentrations increased, suggesting NH(4) inhibition. The reduced total N uptake downstream of the WTP was accompanied by a 60% decline in primary production. These findings indicate that increased anthropogenic NH(4) may decrease estuarine primary production and increase export of NH(4) to the coastal ocean.

Linking dissolved and particulate phosphorus export in rivers draining California's Central Valley with anthropogenic sources at the regional scale

Pollution of water resources by phosphorus (P) is a critical issue in regions with agricultural and urban development. In this study, we estimated P inputs from agricultural and urban sources in 24 catchments draining to the Central Valley in California and compared them with measured river P export to investigate hydrologic and anthropogenic factors affecting regional P retention and export. Using spatially explicit information on fertilizer use, livestock population, agricultural production, and human population, we calculated that net surface balances for anthropogenic P ranged from -12 to 648 kg P km yr in the early 2000s. Inorganic P fertilizer and manure P comprised the largest fraction of total input for all but two catchments. From 2000 to 2003, a median of 7% (range, -287 to 88%) of net annual anthropogenic P input was exported as total P (TP). Yields (kg P km yr) of dissolved inorganic P (DIP), dissolved organic P, particulate P, and TP were not significantly related to catchment-level, per area anthropogenic P input. However, there were significant relationships between mean annual P concentrations and P input from inorganic fertilizers and manure due to the concentration of agricultural land near catchment mouths and regional variation in runoff. Catchment-level P fertilizer and manure inputs explained 4 to 23% more variance in mean annual DIP and TP concentrations than percent of catchment area in agriculture. This study suggests that spatially explicit estimates of anthropogenic P input can help identify sources of multiple forms of P exported in rivers at management-relevant spatial scales.