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James E. Cloern

Publications and source records attributed to James E. Cloern.

At least 55 records · Page 3Linked to original sources
USGS2007

Effects of flow diversions on water and habitat quality: Examples from California's highly manipulated Sacramento–San Joaquin Delta

We use selected monitoring data to illustrate how localized water diversions from seasonal barriers, gate operations, and export pumps alter water quality across the Sacramento-San Joaquin Delta (California). Dynamics of water-quality variability are complex because the Delta is a mixing zone of water from the Sacramento and San Joaquin Rivers, agricultural return water, and the San Francisco Estuary. Each source has distinct water-quality characteristics, and the contribution of each source varies in response to natural hydrologic variability and water diversions. We use simulations with a tidal hydrodynamic model to reveal how three diversion events, as case studies, influence water quality through their alteration of Delta-wide water circulation patterns and flushing time. Reduction of export pumping decreases the proportion of Sacramento- to San Joaquin-derived fresh water in the central Delta, leading to rapid increases in salinity. Delta Cross Channel gate operations control salinity in the western Delta and alter the freshwater source distribution in the central Delta. Removal of the head of Old River barrier, in autumn, increases the flushing time of the Stockton Ship Channel from days to weeks, contributing to a depletion of dissolved oxygen. Each shift in water quality has implications either for habitat quality or municipal drinking water, illustrating the importance of a systems view to anticipate the suite of changes induced by flow manipulations, and to minimize the conflicts inherent in allocations of scarce resources to meet multiple objectives.

California↗
USGS2007

Remote sensing of tidal chlorophyll-a variations in estuaries

Simultaneous acquisition of surface chlorophyll-a concentrations for 39 samples from boats and Daedalus 1260 Multispectral Scanner data from a U-2 aircraft was conducted in the northern reaches of San Francisco Bay on 28 August 1980. These data were used to develop regression models for predicting surface chlorophyll-a concentrations over the study area for ebb-tide (8.40 a.m. P.D.T. (Pacific Daylight Time)) and flood-tide (3.10 p.m. P.D.T.) conditions. After selection of a single ‘best fitting’ model for both morning and afternoon data sets, the chlorophyll-a concentration was predicted for ebb and flood tide for the entire study area at approximately 40m × 40m resolution. The predicted spatial display of chlorophyll-a revealed a localized area of high phytoplankton biomass that has been inferred from field surveys and appears to be a common summer phenomenon. Knowledge of the distribution of phytoplankton and the location of this zone of high biomass is valuable in establishing management policies for this ecologically important estuary. Furthermore, the techniques used here may provide an alternative cost-effective method for assessing water-quality conditions and they may prove useful for studying spatial variations (patchiness) and seasonal variations in phytoplankton biomass in other estuaries and coastal waters.

California↗
USGS2007

Habitat connectivity and ecosystem productivity: implications from a simple model.

The import of resources (food, nutrients) sustains biological production and food webs in resource-limited habitats. Resource export from donor habitats subsidizes production in recipient habitats, but the ecosystem-scale consequences of resource translocation are generally unknown. Here, I use a nutrient-phytoplankton-zooplankton model to show how dispersive connectivity between a shallow autotrophic habitat and a deep heterotrophic pelagic habitat can amplify overall system production in metazoan food webs. This result derives from the finite capacity of suspension feeders to capture and assimilate food particles: excess primary production in closed autotrophic habitats cannot be assimilated by consumers; however, if excess phytoplankton production is exported to food-limited heterotrophic habitats, it can be assimilated by zooplankton to support additional secondary production. Transport of regenerated nutrients from heterotrophic to autotrophic habitats sustains higher system primary production. These simulation results imply that the ecosystem-scale efficiency of nutrient transformation into metazoan biomass can be constrained by the rate of resource exchange across habitats and that it is optimized when the transport rate matches the growth rate of primary producers. Slower transport (i.e., reduced connectivity) leads to nutrient limitation of primary production in autotrophic habitats and food limitation of secondary production in heterotrophic habitats. Habitat fragmentation can therefore impose energetic constraints on the carrying capacity of aquatic ecosystems. The outcomes of ecosystem restoration through habitat creation will be determined by both functions provided by newly created aquatic habitats and the rates of hydraulic connectivity between them.

American Naturalist↗
USGS2003

Big Soda Lake (Nevada). 1. Pelagic bacterial heterotrophy and biomass

Bacterial activities and abundance were measured seasonally in the water column of meromictic Big Soda Lake which is divided into three chemically distinct zones: aerobic mixolimnion, anaerobic mixolimnion, and anaerobic monimolimnion. Bacterial abundance ranged between 5 and 52 x 10 6 cells ml &minus;1 , with highest biomass at the interfaces between these zones: 2&ndash;4 mg C liter &minus;1 in the photosynthetic bacterial layer (oxycline) and 0.8&ndash;2.0 mg C liter &minus;1 in the chemocline. Bacterial cell size and morphology also varied with depth: small coccoid cells were dominant in the aerobic mixolimnion, whereas the monimolimnion had a more diverse population that included cocci, rods, and large filaments. Heterotrophic activity was measured by [methyl- 3 H]thymidine incorporation and [ 14 C]glutamate uptake. Highest uptake rates were at or just below the photosynthetic bacterial layer and were attributable to small (<1 &micro; m) heterotrophs rather than the larger photosynthetic bacteria. These high rates of heterotrophic uptake were apparently linked with fermentation; rates of other mineralization processes (e.g. sulfate reduction, methanogenesis, denitrification) in the anoxic mixolimnion were insignificant. Heterotrophic activity in the highly reduced monimolimnion was generally much lower than elsewhere in the water column. Therefore, although the monimolimnion contained most of the bacterial abundance and biomass (&sim;60%), most of the cells there were inactive.

Nevada↗
USGS2003

Big Soda Lake (Nevada). 4. Vertical fluxes of particulate matter: Seasonality and variations across the chemocline

Vertical fluxes of particulate organic matter were measured with sediment traps above and below the chemocline of Big Soda Lake to define the seasonality of sinking losses from the mixolimnion and determine the effectiveness of the chemocline (pycnocline) as a barrier to the sinking of biogenic particles. Seasonality of sedimentation rates reflected seasonal changes in the community of autotrophs. During summer-autumn, when production is dominated by autotrophic bacteria, vertical fluxes were small: 100 mg C m −2 d −1 and ≅0.5 mg Chl a m −2 d −1 . Following the winter diatom bloom, vertical fluxes increased markedly: ≅570 mg C m −2 d −1 and 23 mg Chl a m −2 d −1 . The bulk of the seston (> 80%) and particulate carbon (≅ 65%) sinking to the chemocline passed through it, showing that this very sharp density discontinuity does not effectively retard the sinking of particulate matter. However sinking losses of particulate carbon were generally small (≅10%) relative to previous measures of primary productivity, indicating that the mixolimnion is a zone of efficient carbon cycling. Exceptions occurred following the winter bloom when sinking losses were a larger fraction (≅40%) of productivity.

Nevada↗
USGS2003

Molecular and isotopic tracers used to examine sources of organic matter and its incorporation into the food webs of San Francisco Bay

Multiple indicators (Chl a , C : N ratios, [ &delta; 13 C]POC, and two classes of lipid biomarker compounds- sterols and phospholipid ester-linked fatty acids) were used to evaluate spatial and temporal variations in the origin of particulate organic matter (POM) in the San Francisco Bay (SFB) estuary. Comparisons were made between the northern and southern subestuaries of SFB, as well as along the salinity gradient of northern SFB. Two sample types were collected-seston, which was used to characterize the bulk POM, and tissues of the suspension-feeding bivalve Potamocorbula amurensis -in order to evaluate the assimilable portion of the POM. Samples were collected around biological and physical events (phytoplankton blooms and freshwater inflow) thought to be the primary mechanisms controlling temporal variability in organic matter sources. Seston samples indicate that phytoplankton sources of POM are important throughout the entire SFB system, with additional inputs of organic matter from bacterial and terrestrial vascular plant sources delivered to the northern region. Analysis of biomarker compounds in P. amurensis tissues indicates that phytoplankton supply a large fraction of the assimilable carbon to clams throughout SFB, although isotopic analysis of clam tissues suggests that the origin of this reactive carbon varies spatially and that freshwater algae are an important source of reactive organic matter to clams living in northern SFB.

California↗
USGS2003

An empirical model of the phytoplankton chlorophyll : carbon ratio-the conversion factor between productivity and growth rate

We present an empirical model that describes the ratio of phytoplankton chlorophyll a to carbon, Chl: C, as a function of temperature, daily irradiance, and nutrient-limited growth rate. Our model is based on 219 published measurements of algal cultures exposed to light-limited or nutrient-limited growth conditions. We illustrate an approach for using this estimator of Chl: C to calculate phytoplankton population growth rate from measured primary productivity. This adaptive Chl: C model gives rise to interactive light-nutrient effects in which growth efficiency increases with nutrient availability under low-light conditions. One implication of this interaction is the enhancement of phytoplankton growth efficiency, in addition to enhancement of biomass yield, as a response to eutrophication.

Limnology and Oceanography↗
USGS2003

Phytoplankton fuels Delta food web

Populations of certain fishes and invertebrates in the Sacramento-San Joaquin Delta have declined in abundance in recent decades and there is evidence that food supply is partly responsible. While many sources of organic matter in the Delta could be supporting fish populations indirectly through the food web (including aquatic vegetation and decaying organic matter from agricultural drainage), a careful accounting shows that phytoplankton is the dominant food source. Phytoplankton, communities of microscopic free-floating algae, are the most important food source on a Delta-wide scale when both food quantity and quality are taken into account. These microscopic algae have declined since the late 1960s. Fertilizer and pesticide runoff do not appear to be playing a direct role in long-term phytoplankton changes; rather, species invasions, increasing water transparency and fluctuations in water transport are responsible. Although the potential toxicity of herbicides and pesticides to plank- ton in the Delta is well documented, the ecological significance remains speculative. Nutrient inputs from agricultural runoff at current levels, in combination with increasing transparency, could result in harmful algal blooms.

California↗
USGS2002

A comment on the use of flushing time, residence time, and age as transport time scales

Applications of transport time scales are pervasive in biological, hydrologic, and geochemical studies yet these times scales are not consistently defined and applied with rigor in the literature. We compare three transport time scales (flushing time, age, and residence time) commonly used to measure the retention of water or scalar quantities transported with water. We identify the underlying assumptions associated with each time scale, describe procedures for computing these time scales in idealized cases, and identify pitfalls when real-world systems deviate from these idealizations. We then apply the time scale definitions to a shallow 378 ha tidal lake to illustrate how deviations between real water bodies and the idealized examples can result from: (1) non-steady flow; (2) spatial variability in bathymetry, circulation, and transport time scales; and (3) tides that introduce complexities not accounted for in the idealized cases. These examples illustrate that no single transport time scale is valid for all time periods, locations, and constituents, and no one time scale describes all transport processes. We encourage aquatic scientists to rigorously define the transport time scale when it is applied, identify the underlying assumptions in the application of that concept, and ask if those assumptions are valid in the application of that approach for computing transport time scales in real systems.

Limnology and Oceanography↗
USGS2002

Annual primary production: Patterns and mechanisms of change in a nutrient-rich tidal ecosystem

Although nutrient supply often underlies long-term changes in aquatic primary production, other regulatory processes can be important. The Sacramento-San Joaquin River Delta, a complex of tidal waterways forming the landward portion of the San Francisco Estuary, has ample nutrient supplies, enabling us to examine alternate regulatory mechanisms over a 21-yr period. Delta-wide primary productivity was reconstructed from historical water quality data for 1975&ndash;1995. Annual primary production averaged 70 g C m &minus;2 , but it varied by over a factor of five among years. At least four processes contributed to this variability: (1) invasion of the clam Potamocorbula amurensis led to a persistent decrease in phytoplankton biomass (chlorophyll a) after 1986; (2) a long-term decline in total suspended solids&mdash;probably at least partly because of upstream dam construction&mdash;increased water transparency and phytoplankton growth rate; (3) river inflow, reflecting climate variability, affected biomass through fluctuations in flushing and growth rates through fluctuations in total suspended solids; and (4) an additional pathway manifesting as a long-term decline in winter phytoplankton biomass has been identified, but its genesis is uncertain. Overall, the Delta lost 43% in annual primary production during the period. Given the evidence for food limitation of primary consumers, these findings provide a partial explanation for widespread Delta species declines over the past few decades. Turbid nutrient-rich systems such as the Delta may be inherently more variable than other tidal systems because certain compensatory processes are absent. Comparisons among systems, however, can be tenuous because conclusions about the magnitude and mechanisms of variability are dependent on length of data record.

California↗
USGS2002

Microphytobenthos potential productivity estimated in three tidal embayments of the San Francisco Bay system

In this paper we describe a three-step procedure to infer the spatial heterogeneity in microphytobenthos primary productivity at the scale of tidal estuaries and embayments. The first step involves local measurement of the carbon assimilation rate of benthic microalgae to determine the parameters of the photosynthesis-irradiance (P-E) curves (using non-linear optimization methods). In the next step, a resampling technique is used to rebuild pseudo-sampling distributions of the local productivity estimates; these provide error estimates for determining the significance level of differences between sites. The third step combines the previous results with deterministic models of tidal elevation and solar irradiance to compute mean and variance of the daily areal primary productivity over an entire intertidal mudflat area within each embayment. This scheme was applied on three different intertidal mudflat regions of the San Francisco Bay estuary during autumn 1998. Microphytobenthos productivity exhibits strong (ca. 3-fold) significant differences among the major sub-basins of San Francisco Bay. This spatial heterogeneity is attributed to two main causes: significant differences in the photosynthetic competence (P-E parameters) of the microphytobenthos in the different sub-basins, and spatial differences in the phase shifts between the tidal and solar cycles controlling the exposure of intertidal areas to sunlight. The procedure is general and can be used in other estuaries to assess the magnitude and patterns of spatial variability of microphytobenthos productivity at the level of the ecosystems.

California↗
USGS2001

Our evolving conceptual model of the coastal eutrophication problem

A primary focus of coastal science during the past 3 decades has been the question: How does anthropogenic nutrient enrichment cause change in the structure or function of nearshore coastal ecosystems? This theme of environmental science is recent, so our conceptual model of the coastal eutrophication problem continues to change rapidly. In this review, I suggest that the early (Phase I) conceptual model was strongly influenced by limnologists, who began intense study of lake eutrophication by the 1960s. The Phase I model emphasized changing nutrient input as a signal, and responses to that signal as increased phytoplankton biomass and primary production, decomposition of phytoplankton-derived organic matter, and enhanced depletion of oxygen from bottom waters. Coastal research in recent decades has identified key differences in the responses of lakes and coastal-estuarine ecosystems to nutrient enrichment. The contemporary (Phase II) conceptual model reflects those differences and includes explicit recognition of (1) system-specific attributes that act as a filter to modulate the responses to enrichment (leading to large differences among estuarine-coastal systems in their sensitivity to nutrient enrichment); and (2) a complex suite of direct and indirect responses including linked changes in: water transparency, distribution of vascular plants and biomass of macroalgae, sediment biogeochemistry and nutrient cycling, nutrient ratios and their regulation of phytoplankton community composition, frequency of toxic/harmful algal blooms, habitat quality for metazoans, reproduction/growth/survival of pelagic and benthic invertebrates, and subtle changes such as shifts in the seasonality of ecosystem functions. Each aspect of the Phase II model is illustrated here with examples from coastal ecosystems around the world. In the last section of this review I present one vision of the next (Phase III) stage in the evolution of our conceptual model, organized around 5 questions that will guide coastal science in the early 21st century: (1) How do system-specific attributes constrain or amplify the responses of coastal ecosystems to nutrient enrichment? (2) How does nutrient enrichment interact with other stressors (toxic contaminants, fishing harvest, aquaculture, nonindigenous species, habitat loss, climate change, hydrologic manipulations) to change coastal ecosystems? (3) How are responses to multiple stressors linked? (4) How does human-induced change in the coastal zone impact the Earth system as habitat for humanity and other species? (5) How can a deeper scientific understanding of the coastal eutrophication problem be applied to develop tools for building strategies at ecosystem restoration or rehabilitation?

Marine Ecology Progress Series↗
USGS2000

Nutrient pollution of coastal rivers, bays, and seas

Over the past 40 years, antipollution laws have greatly reduced discharges of toxic substances into our coastal waters. This effort, however, has focused largely on point-source pollution of industrial and municipal effluent. No comparable effort has been made to restrict the input of nitrogen (N) from municipal effluent, nor to control the flows of N and phosphorus (P) that enter waterways from dispersed or nonpoint sources such as agricultural and urban runoff or as airborne pollutants. As a result, inputs of nonpoint pollutants, particularly N, have increased dramatically. Nonpoint pollution from N and P now represents the largest pollution problem facing the vital coastal waters of the United States. Nutrient pollution is the common thread that links an array of problems along the nation’s coastline, including eutrophication, harmful algal blooms, ”dead zones,” fish kills, some shellfish poisonings, loss of seagrass and kelp beds, some coral reef destruction, and even some marine mammal and seabird deaths. More than 60 percent of our coastal rivers and bays in every coastal state of the continental United States are moderately to severely degraded by nutrient pollution. This degradation is particularly severe in the mid Atlantic states, in the southeast, and in the Gulf of Mexico. A recent report from the National Research Council entitled “Clean Coastal Waters: Understanding and Reduc- ing the Effects of Nutrient Pollution” concludes that: Nutrient over-enrichment of coastal ecosystems generally triggers ecological changes that decrease the biologi- cal diversity of bays and estuaries. While moderate N enrichment of some coastal waters may increase fish production, over-enrichment generally degrades the marine food web that supports commercially valuable fish. The marked increase in nutrient pollution of coastal waters has been accompanied by an increase in harmful algal blooms, and in at least some cases, pollution has triggered these blooms. High nutrient levels and the changes they cause in water quality and the makeup of the algal community are detrimental to the health of coral reefs and the diversity of animal life supported by seagrass and kelp communi- ties. Research during the past decade confirms that N is the chief culprit in eutrophication and other impacts of nutrient over-enrichment in temperate coastal waters, while P is most problematic in eutrophication of freshwa- ter lakes. Human conversion of atmospheric N into biologically useable forms, principally synthetic inorganic fertilizers, now matches the natural rate of biological N fixation from all the land surfaces of the earth. Both agriculture and the burning of fossil fuels contribute significantly to nonpoint flows of N to coastal waters, either as direct runoff or airborne pollutants. N from animal wastes that leaks directly to surface waters or is volatilized to the atmosphere as ammonia may be the largest single source of N that moves from agricultural operations into coastal waters. The National Research Council report recommended that, as a minimum goal, the nation should work to reverse nutrient should be taken to assure that the 40 percent of coastal areas now ranked as healthy do not develop symptoms of nutrient pollution in 10 percent of its degraded coastal systems by 2010 and 25 percent of them by 2020. Also, action should be taken to assure that the 40 percent of coastal areas now ranked as healthy do not develop symptoms of nutrient pollution. Meeting these goals will require an array of strategies and approaches tailored to specific regions and coastal ecosystems. There is an urgent need for development and testing of techniques that can reliably pinpoint the sources of N pollutants to an estuary. For some coastal systems, N removal during treatment of human sewage may be sufficient to reverse nutrient pollution. For most coastal systems, however, the solutions will be more complex and may involve controls on N compounds emitted during fossil fuel combustion as well as incentives to reduce over-fertilization of agricul- tural fields and nutrient pollution from animal wastes in livestock feedlot operations.

Alabama, California, Connecticut, Delaware, Florid↗
USGS2000

Primary food resources in the Sacramento-San Joaquin Delta

The Sacramento-San Joaquin River Delta, a complex mosaic of tidal freshwater habitats, is now a focus of ecosystem rehabilitation because of changes in critical functions associated with its geographic location at the landestuary interface. One of these functions is the production, transport, and transformation of organic matter that constitutes the “primary food supply,” that is, the food supply to the base of the food web. Interest in the primary food supply is motivated by evidence for sub-optimal food quantity or quality at trophic levels that support fish recruitment, including primary consumers such as clams, mysids, cladocerans, rotifers, and native copepods. We used the historical data set to examine the magnitudes of the most important organic matter sources for the Delta, the factors underlying their interannual and longer-term variability, and the implications of ecosystem rehabilitation actions for these sources. Here, we present a summary of the first phase of the analysis, including the quantitative importance of different organic matter sources and some of the hydrological controls on their year-to-year variability. The full report of this first phaseincluding data sources, the methods of calculation, and references, is in press elsewhere (Jassby and Cloern forthcoming). The historical data analysis is part of a larger project in which measurements of stable isotopes and biogeochemical markers, and experiments on organic matter biodegradation and zooplankton growth rates, are being used collectively to define the primary food resources and their quality.

California↗
USGS1997

Studies of the San Francisco Bay, California, estuarine ecosystem regional monitoring program results, 1996

As part of a regional monitoring program, water samples were collected in the San Francisco Bay estuary during 21 cruises from January through December 1996. Conductivity, temperature, light attenuation, turbidity, oxygen, and in-vivo chlorophyll fluorescence were measured longitudinally and vertically in the main channel of the estuary from south of the Dumbarton Bridge in the southern part of the Bay to Rio Vista on the Sacramento River. Discrete water samples were analyzed for chlorophyll a, phaeopigments, suspended participate matter, and dissolved oxygen. Water density was calculated from salinity, temperature, and pressure (depth), and is included in the data summaries.

California↗
USGS1996

Phytoplankton bloom dynamics in coastal ecosystems: A review with some general lessons from sustained investigation of San Francisco Bay, California

Phytoplankton blooms are prominent features of biological variability in shallow coastal ecosystems such as estuaries, lagoons, bays, and tidal rivers. Long-term observation and research in San Francisco Bay illustrates some patterns of phytoplankton spatial and temporal variability and the underlying mechanisms of this variability. Blooms are events of rapid production and accumulation of phytoplankton biomass that are usually responses to changing physical forcings originating in the coastal ocean (e.g., tides), the atmosphere (wind), or on the land surface (precipitation and river runoff). These physical forcings have different timescales of variability, so algal blooms can be short-term episodic events, recurrent seasonal phenomena, or rare events associated with exceptional climatic or hydrologic conditions. The biogeochemical role of phytoplankton primary production is to transform and incorporate reactive inorganic elements into organic forms, and these transformations are rapid and lead to measurable geochemical change during blooms. Examples include the depletion of inorganic nutrients (N, P, Si), supersaturation of oxygen and removal of carbon dioxide, shifts in the isotopic composition of reactive elements (C, N), production of climatically active trace gases (methyl bromide, dimethylsulfide), changes in the chemical form and toxicity of trace metals (As, Cd, Ni, Zn), changes in the biochemical composition and reactivity of the suspended particulate matter, and synthesis of organic matter required for the reproduction and growth of heterotrophs, including bacteria, zooplankton, and benthic consumer animals. Some classes of phytoplankton play special roles in the cycling of elements or synthesis of specific organic molecules, but we have only rudimentary understanding of the forces that select for and promote blooms of these species. Mounting evidence suggests that the natural cycles of bloom variability are being altered on a global scale by human activities including the input of toxic contaminants and nutrients, manipulation of river flows, and translocation of species. This hypothesis will be a key component of our effort to understand global change at the land-sea interface. Pursuit of this hypothesis will require creative approaches for distinguishing natural and anthropogenic sources of phytoplankton population variability, as well as recognition that the modes of human disturbance of coastal bloom cycles operate interactively and cannot be studied as isolated processes.

California↗