Geology topics

J. E. Cloern

Publications and source records attributed to J. E. Cloern.

At least 19 recordsLinked to original sources

USGS2012

Drivers of change in estuarine-coastal ecosystems: Discoveries from four decades of study in San Francisco Bay

Poised at the interface of rivers, ocean, atmosphere and dense human settlement, estuaries are driven by a large array of natural and anthropogenic forces. San Francisco Bay exemplifies the fast-paced change occurring in many of the world's estuaries, bays and inland seas in response to these diverse forces. We use observations from this particularly well-studied estuary to illustrate responses to six drivers that are common agents of change where land and sea meet: water consumption and diversion; human modification of sediment supply; introduction of non-native species; sewage input; environmental policy; and climate shifts. In San Francisco Bay, responses to these drivers include, respectively, shifts in the timing and extent of freshwater inflow and salinity intrusion; decreasing turbidity; restructuring of plankton communities; nutrient enrichment; elimination of hypoxia and reduced metal contamination of biota; and food web changes that decrease resistance of the estuary to nutrient pollution. Detection of these changes and discovery of their causes through environmental monitoring have been essential for establishing and measuring outcomes of environmental policies that aim to maintain high water quality and sustain services provided by estuarine-coastal ecosystems. The wide range of variability time scales and the multiplicity of interacting drivers place heavy demands on estuarine monitoring programs. But the San Francisco Bay case study illustrates why the imperative for monitoring has never been greater.

California↗

USGS2008

Complex seasonal patterns of primary producers at the land-sea interface

Seasonal fluctuations of plant biomass and photosynthesis are key features of the Earth system because they drive variability of atmospheric CO 2 , water and nutrient cycling, and food supply to consumers. There is no inventory of phytoplankton seasonal cycles in nearshore coastal ecosystems where forcings from ocean, land and atmosphere intersect. We compiled time series of phytoplankton biomass (chlorophyll a ) from 114 estuaries, lagoons, inland seas, bays and shallow coastal waters around the world, and searched for seasonal patterns as common timing and amplitude of monthly variability. The data revealed a broad continuum of seasonal patterns, with large variability across and within ecosystems. This contrasts with annual cycles of terrestrial and oceanic primary producers for which seasonal fluctuations are recurrent and synchronous over large geographic regions. This finding bears on two fundamental ecological questions: (1) how do estuarine and coastal consumers adapt to an irregular and unpredictable food supply, and (2) how can we extract signals of climate change from phytoplankton observations in coastal ecosystems where local‐scale processes can mask responses to changing climate?

Ecology Letters↗

USGS2006

Ecological values of shallow-water habitats: Implications for the restoration of disturbed ecosystems

A presumed value of shallow-habitat enhanced pelagic productivity derives from the principle that in nutrient-rich aquatic systems phytoplankton growth rate is controlled by light availability, which varies inversely with habitat depth. We measured a set of biological indicators across the gradient of habitat depth within the Sacramento–San Joaquin River Delta (California) to test the hypothesis that plankton biomass, production, and pelagic energy flow also vary systematically with habitat depth. Results showed that phytoplankton biomass and production were only weakly related to phytoplankton growth rates whereas other processes (transport, consumption) were important controls. Distribution of the invasive clam Corbicula fluminea was patchy, and heavily colonized habitats all supported low phytoplankton biomass and production and functioned as food sinks. Surplus primary production in shallow, uncolonized habitats provided potential subsidies to neighboring recipient habitats. Zooplankton in deeper habitats, where grazing exceeded phytoplankton production, were likely supported by significant fluxes of phytoplankton biomass from connected donor habitats. Our results provide three important lessons for ecosystem science: (a) in the absence of process measurements, derived indices provide valuable information to improve our mechanistic understanding of ecosystem function and to benefit adaptive management strategies; (b) the benefits of some ecosystem functions are displaced by water movements, so the value of individual habitat types can only be revealed through a regional perspective that includes connectedness among habitats; and (c) invasive species can act as overriding controls of habitat function, adding to the uncertainty of management outcomes.

Ecosystems↗

USGS2006

What is causing the phytoplankton increase in San Francisco Bay?

The largest living component of San Francisco Bay is the phytoplankton, a suspension of microscopic cells that convert sunlight energy into new living biomass through the same process of photosynthesis used by land plants. This primary production is the ultimate source of food for clams, zooplankton, crabs, sardines, halibut, sturgeon, diving ducks, pelicans, and harbor seals. From measurements made in 1980, we estimated that phytoplankton primary production in San Francisco Bay was about 200,000 tons of organic carbon per year (Jassby et al. 1993). This is equivalent to producing the biomass of 5500 adult humpback whales, or the calories to feed 1.8 million people. These numbers may seem large, but primary production in San Francisco Bay is low compared to many other nutrient-enriched estuaries.

California↗

USGS2005

Climate anomalies generate an exceptional dinoflagellate bloom in San Francisco Bay

We describe a large dinoflagellate bloom, unprecedented in nearly three decades of observation, that developed in San Francisco Bay (SFB) during September 2004. SFB is highly enriched in nutrients but has low summer‐autumn algal biomass because wind stress and tidally induced bottom stress produce a well mixed and light‐limited pelagic habitat. The bloom coincided with calm winds and record high air temperatures that stratified the water column and suppressed mixing long enough for motile dinoflagellates to grow and accumulate in surface waters. This event‐scale climate pattern, produced by an upper‐atmosphere high‐pressure anomaly off the U.S. west coast, followed a summer of weak coastal upwelling and high dinoflagellate biomass in coastal waters that apparently seeded the SFB bloom. This event suggests that some red tides are responses to changes in local physical dynamics that are driven by large‐scale atmospheric processes and operate over both the event scale of biomass growth and the antecedent seasonal scale that shapes the bloom community.

California↗

USGS2005

Detritus fuels ecosystem metabolism but not metazoan food webs in San Francisco estuary's freshwater delta

Detritus from terrestrial ecosystems is the major source of organic matter in many streams, rivers, and estuaries, yet the role of detritus in supporting pelagic food webs is debated. We examined the importance of detritus to secondary productivity in the Sacramento and San Joaquin River Delta (California, United States), a large complex of tidal freshwater habitats. The Delta ecosystem has low primary productivity but large detrital inputs, so we hypothesized that de tritus is the primary energy source fueling production in pelagic food webs. We assessed the sources, quantity, composition, and bioavailability of organic matter among a diversity of habitats (e.g., marsh sloughs, floodplains, tidal lakes, and deep river channels) over two years to test this hypothesis. Our results support the emerging principle that detritus dominates riverine and estuarine organic matter supply and supports the majority of ecosystem metabolism. Yet in contrast to prevailing ideas, we found that detritus was weakly coupled to the Delta's pelagic food web. Results from independent approaches showed that phytoplankton production was the dominant source of organic matter for the Delta's pelagic food web, even though primary production accounts for a small fraction of the Delta's organic matter supply. If these results are general, they suggest that the value of organic matter to higher trophic levels, including species targeted by programs of ecosystem restoration, is a function of phytoplankton production.

Estuaries↗

USGS2005

Phytoplankton community ecology: Principles applied in San Francisco Bay

In his seminal 1961 paper 'The paradox of the plankton' Am Nat 95:137-147, G. E. Hutchinson asked why many species of phytoplankton can coexist while competing for a small number of limiting resources in an unstructured habitat. Hutchinson anticipated the resolution of his paradox, recognizing that communities are organized by processes beyond resource competition including species interactions, habitat variability and dispersal. Since 1961 we have made fundamental discoveries that have revolutionized our conceptual understanding of pelagic ecology, including (1) habitat heterogeneity at all scales relevant to plankton population dynamics, (2) community shifts in response to global climate cycles, (3) fast and selective predation as a powerful top-down force to shape phytoplankton communities, (4) turbulent mixing as a physical process that selects species on the basis of their size and form, (5) mixotrophy that allows some algal species to tap organic nutrient pools and function at multiple trophic levels, (6) taxon-specific life cycles including alternating vegetative and resting stages, and (7) the pelagic as an open system where communities are continually reshaped by species immigration. Here we synthesize these discoveries to show how they validate and amplify Hutchinson's hypothesis that phytoplankton communities are assembled by many processes. Our synthesis is built around observations of phytoplankton species composition from a decade of study in San Francisco Bay, used as a case study to illustrate the contemporary principles of phytoplankton community ecology. We apply these principles to address 2 central questions: (1) What processes assemble phytoplankton communities? (2) How does phytoplankton community composition influence ecosystem functions such as production in pelagic and benthic food webs?

California↗

USGS2003

Metal uptake by phytoplankton during a bloom in South San Francisco Bay: Implications for metal cycling in estuaries

The 1994 spring phytoplankton bloom in South San Francisco Bay caused substantial reductions in concentrations of dissolved Cd, Ni, and Zn, but not Cu. We estimate that the equivalent of ~60% of the total annual input of Cd, Ni, and Zn from local waste‐water treatment plants is cycled through the phytoplankton in South Bay. The results suggest that processes that affect phytoplankton bloom frequency or intensity in estuaries (e.g. nutrient enrichment) may also affect metal trapping. The bloom was characterized by hydrographic surveys conducted at weekly intervals for 9 weeks. Metal samples were collected from the water column on three occasions, timed to bracket the period when the bloom was predicted. Factors that might confound observations of biological influences, such as freshwater inputs, were relatively constant during the study. Before the bloom, concentrations of dissolved Cd were 0.81 ± 0.02 nmol kg −1 , Zn concentrations were 19.8 ± 1.5 nmol kg −1 , Ni were 42 ± 1.4 nmol kg −1 , and Cu were 37 ± 1.4 nmol kg −1 . These values are elevated relative to riverine and coastal end‐members, reflecting inputs from wastewater and(or) sediments. At the height of the bloom, dissolved Zn, Cd, and Ni were reduced to 19, 50, and 75% of their prebloom concentrations, respectively. Dissolved Cu concentrations increased 20%. The mass of Cd taken up by phytoplankton was similar to the mass of Cd removed from solution if particle settling was considered, and Cd concentrations estimated in phytoplankton were higher than concentrations in suspended particulate material (SPM). Particulate concentrations of Zn and Ni during the bloom appeared to be dominated by the influence of changes in resuspension of Zn and Ni‐rich sediments.

California↗

USGS2003

Lessons from monitoring water quality in San Francisco Bay

San Francisco Bay is the defining landscape feature of the place we call ‘The Bay Area,’ but most of us only experience the Bay as we view it from an airplane window or drive across one of its bridges. These views from afar suggest that the Bay is static and sterile, but this impression is deceptive. If you are one of the many thousands of students who have experienced the Bay through a school excursion with the Marine Science Institute or other educational programs, you observed its rich plankton soup under a microscope, sorted clams and worms and crustaceans from mud samples, and identified the gobies, sole, halibut, bat rays, sharks, sardines, and smelt caught with trawls. San Francisco Bay is much more than a landscape feature. It is a dynamic ecosystem, continually changing and teeming with life. The Bay once supported the most valuable fisheries on the west coast of the United States, but commercial fishing for shellfish, shrimp, sturgeon, shad, salmon, and striped bass ended many decades ago because of habitat loss, pollution, invasive species and over harvest. Bay Area residents feel a sense of responsibility to protect San Francisco Bay and keep it healthy. Some even dream about the recovery of fish stocks so they can sustain commercial fishing once again inside the Bay. How is our Bay doing? Is it highly polluted or pretty clean? How does its health compare with other estuaries in the United States? Are things getting better or worse? Does costly wastewater treatment have benefits? What are the biggest threats to the Bay and how can we reduce or eliminate those threats? How will the Bay change in the future? These questions can only be answered with investments in study and monitoring, and they are the driving force behind the Regional Monitoring Program (RMP). We describe here some selected results from water quality surveillance conducted by the U.S. Geological Survey (USGS) as one component of the RMP. We present results as lessons about how the Bay works as a complex dynamic system, and we show how these lessons are relevant to the broad RMP objectives supporting Bay protection and management.

California↗

USGS2002

Bioavailability of organic matter in a highly disturbed Estuary: The role of detrital and algal resources

The importance of algal and detrital food supplies to the planktonic food web of a highly disturbed, estuarine ecosystem was evaluated in response to declining zooplankton and fish populations. We assessed organic matter bioavailability among a diversity of habitats and hydrologic inputs over 2 years in San Francisco Estuary's Sacramento-San Joaquin River Delta. Results show that bioavailable dissolved organic carbon from external riverine sources supports a large component of ecosystem metabolism. However, bioavailable particulate organic carbon derived primarily from internal phytoplankton production is the dominant food supply to the planktonic food web. The relative importance of phytoplankton as a food source is surprising because phytoplankton production is a small component of the ecosystem's organic-matter mass balance. Our results indicate that management plans aimed at modifying the supply of organic matter to riverine, estuarine, and coastal food webs need to incorporate the potentially wide nutritional range represented by different organic matter sources.

Proceedings of the National Academy of Sciences of↗

USGS2002

Stable carbon and nitrogen isotope composition of aquatic and terrestrial plants of the San Francisco Bay estuarine system

We report measurements of seasonal variability in the C‐N stable isotope ratios of plants collected across the habitat mosaic of San Francisco Bay, its marshes, and its tributary river system. Analyses of 868 plant samples were binned into 10 groups (e.g., terrestrial riparian, freshwater phytoplankton, salt marsh) to determine whether C‐N isotopes can be used as biomarkers for tracing the origins of organic matter in this river‐marsh‐estuary complex. Variability of δ 13 C and δ 15 N was high (~5–10‰) within each plant group, and we identified three modes of variability: (1) between species and their microhabitats, (2) over annual cycles of plant growth and senescence, and (3) between living and decomposing biomass. These modes of within‐group variability obscure any source specific isotopic signatures, confounding the application of C‐N isotopes for identifying the origins of organic matter. A second confounding factor was large dissimilarity between the δ 13 C‐δ 15 N of primary producers and the organic matter pools in the seston and sediments. Both confounding factors impede the application of C‐N isotopes to reveal the food supply to primary consumers in ecosystems supporting diverse autotrophs and where the isotopic composition of organic matter has been transformed and become distinct from that of its parent plant sources. Our results support the advice of others: variability of C‐N stable isotopes within all organic‐matter pools is high and must be considered in applications of these isotopes to trace trophic linkages from primary producers to primary consumers. Isotope‐based approaches are perhaps most powerful when used to complement other tools, such as molecular biomarkers, bioassays, direct measures of production, and compilations of organic‐matter budgets.

California↗

USGS2002

Effects of tidal shallowing and deepening on phytoplankton production dynamics: A modeling study

Processes influencing estuarine phytoplankton growth occur over a range of time scales, but many conceptual and numerical models of estuarine phytoplankton production dynamics neglect mechanisms occurring on the shorter (e.g., intratidal) time scales. We used a numerical model to explore the influence of short time-scale variability in phytoplankton sources and sinks on long-term growth in an idealized water column that shallows and deepens with the semidiurnal tide. Model results show that tidal fluctuations in water surface elevation can determine whether long-term phytoplankton growth is positive or negative. Hourly-scale interactions influencing weekly-scale to monthly-scale phytoplankton dynamics include intensification of the depth-averaged benthic grazing effect by water column shallowing and enhancement of water column photosynthesis when solar noon coincides with low tide. Photosynthesis and benthic consumption may modulate over biweekly time scales due to spring-neap fluctuations in tidal range and the 15-d cycle of solar noon-low tide phasing. If tidal range is a large fraction of mean water depth, then tidal shallowing and deepening may significantly influence net phytoplankton growth. In such a case, models or estimates of long-term phytoplankton production dynamics that neglect water surface fluctuations may overestimate or underestimate net growth and could even predict the wrong sign associated with net growth rate.

Estuaries↗

USGS2002

Functional variability of habitats within the Sacramento-San Joaquin Delta: Restoration implications

We have now entered an era of large-scale attempts to restore ecological functions and biological communities in impaired ecosystems. Our knowledge base of complex ecosystems and interrelated functions is limited, so the outcomes of specific restoration actions are highly uncertain. One approach for exploring that uncertainty and anticipating the range of possible restoration outcomes is comparative study of existing habitats similar to future habitats slated for construction. Here we compare two examples of one habitat type targeted for restoration in the Sacramento-San Joaquin River Delta. We compare one critical ecological function provided by these shallow tidal habitats - production and distribution of phytoplankton biomass as the food supply to pelagic consumers. We measured spatial and short-term temporal variability of phytoplankton biomass and growth rate and quantified the hydrodynamic and biological processes governing that variability. Results show that the production and distribution of phytoplankton biomass can be highly variable within and between nearby habitats of the same type, due to variations in phytoplankton sources, sinks, and transport. Therefore, superficially similar, geographically proximate habitats can function very differently, and that functional variability introduces large uncertainties into the restoration process. Comparative study of existing habitats is one way ecosystem science can elucidate and potentially minimize restoration uncertainties, by identifying processes shaping habitat functionality, including those that can be controlled in the restoration design.

California↗

USGS2000

Spatial and temporal variability of picocyanobacteria Synechococcus sp. in San Francisco Bay

We collected samples monthly, from April to August 1998, to measure the abundance of autotrophic picoplankton in San Francisco Bay. Samples taken along a 160-km transect showed that picocyanobacteria (Synechococcus sp.) was a persistent component of the San Francisco Bay phytoplankton in all the estuarine habitats, from freshwater to seawater and during all months of the spring-summer transition. Abundance ranged from 4.6 X 106 to 5.2 X 108 cells L-1, with peak abundance during the spring bloom (April and May) and during July with a persistent spatial pattern of smallest abundance near the coastal ocean and highest abundance in the landward domains of the estuary. The picocyanobacterial component (as estimated percentage of chlorophyll a concentration) was, on average, 15% of total phytoplankton biomass during the summer-autumn nonbloom periods and only 2% of chlorophyll biomass during the spring bloom. This result is consistent with the emerging concept of a gradient of increasing importance of picocyanobacteria along the gradient of decreasing nutrient concentrations from estuaries to the open ocean.

Limnology and Oceanography↗

USGS2000

Dynamics of nutrient cycling and related benthic nutrient and oxygen fluxes during a spring phytoplankton bloom in South San Francisco Bay (USA)

Benthic oxygen uptake and nutrient releases of N, P and Si were measured weekly at 2 sites in South San Francisco Bay around the 1996 spring bloom. Exchanges across the sediment-water interface were estimated from whole core incubations performed in the laboratory at in situ temperature and in dark. Fluxes changed significantly on a weekly time scale. Over a period of 15 wk the fluxes of dissolved inorganic N, P and Si ranged from -40 to +200, 0 to 13 and from 30 to 400 µmol m -2 h -1 respectively. Sediment oxygen demand increased from 10 before to 64 mg O 2 m -2 h -1 just after the bloom period. During the bloom, nutrient fluxes represented about 20, 16 and 9% of the Si, P and N requirements for primary production. Before and after the bloom period, Si fluxes contributed up to 30 and >100% of this requirement and P and N fluxes up to 15 and 50% respectively. Simple empirical models explain most of the spatial-temporal variability of benthic fluxes of Si, P and NH 4 (but not NO 3 ) from 3 predictor variables: sediment porosity, nutrient concentration in bottom waters and chlorophyll content of surficial sediments. These models show that algal blooms influence benthic-pelagic nutrient exchange through 2 processes: (1) depletion of nutrients from the water column (which enhances gradient-driven transports across the sediment-water interface) and (2) sedimentation of labile phytodetritus (which promotes remineralization in or on the surficial sediments). Rates and patterns of nutrient cycling were very different at the shallow and deep study sites, illustrating the challenge of extrapolating measurements of coupled algae-nutrient dynamics to whole ecosystems.

Marine Ecology Progress Series↗

USGS2000

Patterns of water-quality variability in San Francisco Bay during the first six years of the regional monitoring program, 1993-1998

Monitoring Results presents data from the Status and Trends portion of the 1998 San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP). A list of reports on Pilot and Special Studies, as well as other RMP related activities can be found at the end of this document. These reports provide perspective and insight on important contaminant issues identified by the RMP, and they describe results from projects that took advantage of RMP field operations. For a summary of the conditions of the Estuary see The Pulse . A print copy may also be ordered by contacting the San Francisco Estuary Institute (SFEI). In 1998, the San Francisco Regional Water Quality Control Board (Regional Board) and seventy-three federal, state, and local agencies and companies participated in the RMP as funders and service providers (Table 1.1). Participants also assist in directing the Program through input or participation on the Steering and Technical Review Committees. The RMP’s overall goal is to provide data and interpretation that helps to address certain information needs of the Regional Board. In general, these efforts fall under five major objectives which provide a framework for efforts to respond to more specific management questions. 1. Describe patterns and trends in contaminant concentration and distribution. 2. Describe general sources and loadings of contamination to the Estuary. 3. Measure contaminant effects on selected parts of the Estuary ecosystem. 4. Compare monitoring information to relevant water quality objectives and other guidelines. 5. Synthesize and distribute information from a range of sources to present a more complete picture of the sources, distribution, fates, and effects of contaminants in the Estuary ecosystem.

California↗

USGS1999

The relative importance of light and nutrient limitation of phytoplankton growth: A simple index of coastal ecosystem sensitivity to nutrient enrichment

Anthropogenic nutrient enrichment of the coastal zone is now a well-established fact. However, there is still uncertainty about the mechanisms through which nutrient enrichment can disrupt biological communities and ecosystem processes in the coastal zone. For example, while some estuaries exhibit classic symptoms of acute eutrophication, including enhanced production of algal biomass, other nutrient-rich estuaries maintain low algal biomass and primary production. This implies that large differences exist among coastal ecosystems in the rates and patterns of nutrient assimilation and cycling. Part of this variability comes from differences among ecosystems in the other resource that can limit algal growth and production - the light energy required for photosynthesis. Complete understanding of the eutrophication process requires consideration of the interacting effects of light and nutrients, including the role of light availability as a regulator of the expression of eutrophication. A simple index of the relative strength of light and nutrient limitation of algal growth can be derived from models that describe growth rate as a function of these resources. This index can then be used as one diagnostic to classify the sensitivity of coastal ecosystems to the harmful effects of eutrophication. Here I illustrate the application of this diagnostic with light and nutrient measurements made in three California estuaries and two Dutch estuaries.

Aquatic Ecology↗

USGS1999

Processes governing phytoplankton blooms in estuaries. I: The local production-loss balance

The formation and spatial distribution of phytoplankton blooms in estuaries are controlled by (1) local mechanisms, which determine the production-loss balance for a water column at a particular spatial location (i.e. control if a bloom is possible), and (2) transport-related mechanisms, which govern biomass distribution (i.e. control if and where a bloom actually occurs). In this study, the first of a 2-paper series, we use a depth-averaged numerical model as a theoretical tool to describe how interacting local conditions (water column height, light availability, benthic grazing) influence the local balance between phytoplankton sources and sinks. We also explore trends in the spatial variability of the production-loss balance across the topographic gradients between deep channels and lateral shoals which are characteristic of shallow estuaries. For example, under conditions of high turbidity and slow benthic grazing the highest rates of phytoplankton population growth are found in the shallowest regions. On the other hand, with low turbidity and rapid benthic grazing the highest growth rates occur in the deeper areas. We also explore the effects of semidiurnal tidal variation in water column height, as well as spring-neap variability. Local population growth in the shallowest regions is very sensitive to tidal-scale shallowing and deepening of the water column, especially in the presence of benthic grazing. A spring-neap signal in population growth rate is also prominent in the shallow areas. Population growth in deeper regions is less sensitive to temporal variations in tidal elevation. These results show that both shallow and deep regions of estuaries can act as sources or sinks for phytoplankton biomass, depending on the local conditions of mean water column height, tidal amplitude, light-limited growth rate, and consumption by grazers.

Marine Ecology Progress Series↗