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J.K. Thompson

Publications and source records attributed to J.K. Thompson.

17 recordsLinked to original sources
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↗
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↗
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↗
USGS1999

Processes governing phytoplankton blooms in estuaries. II: The role of horizontal transport

The development and distribution of phytoplankton blooms in estuaries are functions of both local conditions (i.e. the production-loss balance for a water column at a particular spatial location) and large-scale horizontal transport. In this study, the second of a 2-paper series, we use a depth-averaged hydrodynamic-biological model to identify transport-related mechanisms impacting phytoplankton biomass accumulation and distribution on a system level. We chose South San Francisco Bay as a model domain, since its combination of a deep channel surrounded by broad shoals is typical of drowned-river estuaries. Five general mechanisms involving interaction of horizontal transport with variability in local conditions are discussed. Residual (on the order of days to weeks) transport mechanisms affecting bloom development and location include residence time/export, import, and the role of deep channel regions as conduits for mass transport. Interactions occurring on tidal time scales, i.e. on the order of hours) include the phasing of lateral oscillatory tidal flow relative to temporal changes in local net phytoplankton growth rates, as well as lateral sloshing of shoal-derived biomass into deep channel regions during ebb and back into shallow regions during flood tide. Based on these results, we conclude that: (1) while local conditions control whether a bloom is possible, the combination of transport and spatial-temporal variability in local conditions determines if and where a bloom will actually occur; (2) tidal-time-scale physical-biological interactions provide important mechanisms for bloom development and evolution. As a result of both subtidal and tidal-time-scale transport processes, peak biomass may not be observed where local conditions are most favorable to phytoplankton production, and inherently unproductive areas may be regions of high biomass accumulation.

Marine Ecology Progress Series↗
USGS1998

Does the Sverdrup critical depth model explain bloom dynamics in estuaries?

In this paper we use numerical models of coupled biological-hydrodynamic processes to search for general principles of bloom regulation in estuarine waters. We address three questions: what are the dynamics of stratification in coastal systems as influenced by variable freshwater input and tidal stirring? How does phytoplankton growth respond to these dynamics? Can the classical Sverdrup Critical Depth Model (SCDM) be used to predict the timing of bloom events in shallow coastal domains such as estuaries? We present results of simulation experiments which assume that vertical transport and net phytoplankton growth rates are horizontally homogeneous. In the present approach the temporally and spatially varying turbulent diffusivities for various stratification scenarios are calculated using a hydrodynamic code that includes the Mellor-Yamada 2.5 turbulence closure model. These diffusivities are then used in a time- and depth-dependent advection-diffusion equation, incorporating sources and sinks, for the phytoplankton biomass. Our modeling results show that, whereas persistent stratification greatly increases the probability of a bloom, semidiurnal periodic stratification does not increase the likelihood of a phytoplankton bloom over that of a constantly unstratified water column. Thus, for phytoplankton blooms, the physical regime of periodic stratification is closer to complete mixing than to persistent stratification. Furthermore, the details of persistent stratification are important: surface layer depth, thickness of the pycnocline, vertical density difference, and tidal current speed all weigh heavily in producing conditions which promote the onset of phytoplankton blooms. Our model results for shallow tidal systems do not conform to the classical concepts of stratification and blooms in deep pelagic systems. First, earlier studies (Riley, 1942, for example) suggest a monotonic increase in surface layer production as the surface layer shallows. Our model results suggest, however, a nonmonotonic relationship between phytoplankton population growth and surface layer depth, which results from a balance between several 'competing' processes, including the interaction of sinking with turbulent mixing and average net growth occurring within the surface layer. Second, we show that the traditional SCDM must be refined for application to energetic shallow systems or for systems in which surface layer mixing is not strong enough to counteract the sinking loss of phytoplankton. This need for refinement arises because of the leakage of phytoplankton from the surface layer by turbulent diffusion and sinking, processes not considered in the classical SCDM. Our model shows that, even for low sinking rates and small turbulent diffusivities, a significant % of the phytoplankton biomass produced in the surface layer can be lost by these processes.

Journal of Marine Research↗
USGS1995

Benthic macrofauna data for San Francisco Bay, California, September 1986

Benthic macrofauna were collected during September 1986 to evaluate locations for long-term monitoring stations as part of the U.S. Geological Survey Regional Effects Monitoring Program in San Francisco Bay, California. Three to ten replicate samples were collected with a modified Van Veen sampler (0.05 m 2 area) at ten locations. One box core sample (0.06 m 2 area) was collected at seven to the ten locations. Six of the box core samples were split into an upper 10 cm sample and a deeper sample before analysis. Macrofauna specimens were identified to the lowest possible taxon, usually genus and species, then counted. An average of 88 percent of the benthic macrofauna specimens were identified to the species level. The fraction identified varied among stations from 54 to 98 percent. Nematodes and oligochaetes accounted for most of the unidentified specimens. Relative to the total number of species identified in five replicates at each location, an average of 90 percent of the species were collected with three replicates. In general, species with high to moderate abundances were present in all replicates, and species collected only after three or more replicates averaged less than one specimen per replicate. Results from the box cores showed that the dominant species were most abundant in the upper 10 cm, the depth of sediment that can be adequately sampled with a modified Van Veen sampler. On the basis of the number of species and their abundances at each location, seven of the ten locations were selected for sampling in the regular program, which began in March 1987.

California↗
USGS1992

Measurement of filtration rates by infaunal bivalves in a recirculating flume

A flume system and protocol for measuring the filtration rate of infaunal bivalves is described. Assemblages of multi-sized clams, at natural densities and in normal filter-feeding positions, removed phytoplankton suspended in a unidirectional flow of water. The free-stream velocity and friction velocity of the flow, and bottom roughness height were similar to those in natural estuarine waters. Continuous variations in phytoplankton (Chroomonas salinay) cell density were used to measure the filtration rate of the suspension-feeding clam Potamocorbula amurensis for periods of 2 to 28 h. Filtration rates of P. amurensis varied from 100 to 580 liters (gd)-1 over a free-stream velocity range of 9 to 25 cm s-1. Phytoplankton loss rates were usually constant throughout the experiments. Our results suggest that suspension-feeding by infaunal bivalves is sensitive to flow velocity. ?? 1992 Springer-Verlag.

Marine Biology↗
USGS1988

Food availability controls seasonal cycle of growth in Macoma balthica (L.) in San Francisco Bay, California

A 2-yr field study of growth in the bivalve Macoma balthica (L.) at four locations in San Francisco Bay, California, U.S., showed that the timing and rate of growth (increase in shell length) were related to food supply. This clam feeds on both planktonic and benthic microalgae, depending on availability. Growth was apparently food-limited during some months, during one year more than the other, and at some locations more than others. Tissue-weight changes were also related to food availability. The heaviest animals were found in that year and at those locations with the highest chl a concentrations. Tissue-weight gains usually coincided with increased shell-growth rate or with reproductive development, although some large animals showed weight gain independent of both of these factors during periods with mid-range chl a levels. Weight losses coincided with spawning or periods of low growth rate, except at one station where, during a period when most animals were reproductively ripe, food concentrations were high, and shell growth was rapid, animals lost weight. This study failed to show a relation between salinity and the timing or rate of change of either shell length or tissue weight. The mild temperatures (10-23 ??C water temperature) of the area studied resulted in no growth inhibition due to low temperature, but there was some indication that the high air temperatures found in these intertidal areas limited growth rates. ?? 1988.

Journal of Experimental Marine Biology and Ecology↗
USGS1985

Time scales of change in the San Francisco Bay benthos

Results from multi-year investigations in the San Francisco Bay estuary show that large abundance fluctuations within benthic macroinvertebrate populations reflect both (1) within-year periodicity of reproduction, recruitment, and mortality that is not necessarily coincident with seasonal changes of the environment (e.g., the annual temperature cycle), and (2) aperiodic density changes (often larger than within-year fluctuations) following random perturbations of the environment. Density peaks of the small, short-lived estuarine invertebrates that comprise the vast majority of individuals in the bay's relatively homogeneous benthic community normally occur between spring and autumn depending on the species, in large part a reflection of reproductive periodicity. However, because mild winters permit reproductive activity in some of the common species throughout much of the year, other factors are important to within-year density fluctuations in the community. Seasonally predictable changes in freshwater inflow, wind and tidal mixing, microalgal biomass, and sediment erosion/deposition patterns all contribute to observed seasonal changes in abundance. For example, the commonly observed decline in abundance during winter reflects both short-lived species that die after reproducing and the stress of winter conditions (e.g., inundation by less saline, sediment-laden water and the decline in both planktonic and benthic algal biomass - a direct source of food for the shallow-water benthos). On the other hand, data from several studies suggest that observed 'recruitment' and 'mortality' may in fact be the migration of juveniles and adults to and from study sites. For example, the common amphipod Ampelisca abdita apparently moves from shallow to deep water, or from up-estuary to down-estuary locations, coincident with periods of high river runoff in winter. Growth of individuals within the few studied species populations is also highly seasonal, and appears to be coincident with seasonal increases in the abundance of planktonic and/or benthic microalgae. Two multi-year studies have shown that, in addition to within-year periodicity, major restructuring of the benthic community can occur as a result of anomalous (usually climate-related) perturbations of the benthic habitat. For example, during wet years freshwater-intolerant species disappear from the upper part of the estuary and from shallow areas of the bay. During a two-year drought these same species colonized the extreme upper end of the estuary in large numbers. Other aperiodic perturbations include localized instances of sediment erosion or deposition and algal mat accumulations that greatly depress abundance. Additionally, there is evidence (observations that the clam Macoma balthica establishes large populations only when the amphipod A. abdita is not abundant) that species interactions can contribute greatly to interannual variations. Thus, while community composition may change little over the long term, year-to-year predictability of species abundances is low. ?? 1985 Dr W. Junk Publishers.

Hydrobiologia↗
USGS1982

Seasonal growth in the bivalve Macoma balthica near the southern limit of its range

Shell-length growth in Macoma balthica from San Francisco Bay, California, as measured on living animals in situ, is highly seasonal despite a mild Mediterranean climate: a long period of near non-growth from May to the following February is followed by a short period of rapid growth between March and May. The rapid-growth period follows the spawning period during January/February and ends as water temperature rises above about 15??C. Despite the shortness of the growth period, M. balthica grows larger at a given age in San Francisco Bay than is recorded elsewhere in the world. Application of a model, developed elsewhere from these same field measurements, shows that (1) measurable growth occurs during the summer/autumn/early winter "nongrowth" period, (2) there is an autumn recruitment, and (3) both spring and autumn recruits combine to form a single "one-year-old" size grouping. None of these features is detectable through growth-ring analysis of field samples, apparently because of indistinct climatic seasons, or through size-frequency histogram analysis because of the combined effects of slow growth and intermittent recruitment. ?? 1982 Estuarine Research Federation.

Estuaries↗