Wim J. Kimmerer

The Collapse of Pelagic Fishes in the Upper San Francisco Estuary: El Colapso de los Peces Pelagicos en La Cabecera Del Estuario San Francisco

Abstract Although the pelagic fish community of the upper San Francisco Estuary historically has shown substantial variability, a recent collapse has captured the attention of resource managers, scientists, legislators, and the general public. The ecological and management consequences of the decline are most serious for delta smelt (Hypomesus transpacificus), a threatened species whose narrow range overlaps with large water diversions that supply water to over 25 million people. The decline occurred despite recent moderate hydrology, which typically results in at least modest recruitment, and investments of hundreds of millions of dollars in habitat restoration and environmental water allocations to support native fishes. In response to the pelagic fish collapse, an ambitious multi-hyphen;agency research team has been working since 2005 to evaluate the causes of the decline, which likely include a combination of factors: stock-recruitment effects, a decline in habitat quality, increased mortality rates, ...

Structure and Flow-Induced Variability of the Subtidal Salinity Field in Northern San Francisco Bay

Abstract The structure of the salinity field in northern San Francisco Bay and how it is affected by freshwater flow are discussed. Two datasets are examined: the first is 23 years of daily salinity data taken by the U.S. Bureau of Reclamation along the axis of northern San Francisco Bay; the second is a set of salinity transects taken by the U.S. Geological Survey between 1988 and 1993. Central to this paper is a measure of salinity intrusion, X2: the distance from the Golden Gate Bridge to where the bottom salinity is 2 psu. Using X2 to scale distance, the authors find that for most flow conditions, the mean salinity distribution of the estuary is nearly self-similar with a salinity gradient in the center 70% of the region between the Golden Gate and X2 that is proportional to X−12. Analysis of covariability of Q and X2 showed a characteristic timescale of adjustment of the salinity field of approximately 2 weeks. The steady-state response deduced from the X2 time series implies that X2 is proportional ...

Chronic food limitation of egg production in populations of copepods of the genusAcartia in the San Francisco estuary

Egg production of planktonic copepods, is commonly measured as a proxy for secondary production in population dynamics studies and for quantifying food limitation. Although limitation of copepod egg production by food quantity or quality is common in natural waters, it appears less common or severe in estuaries where food concentrations are often high. San Francisco Estuary, California, has unusually low concentrations of chlorophyll compared to other estuaries. We measured egg production rates of three species ofAcartia, with dominate the zooplankton biomass at salinity above 15 psu, on 36 occasions during 1999–2002. Egg production was determined by incubating up to 40 freshly collected individual copepods for 24 h in 140 ml of ambient water. Egg production was less than 10 eggs female−1 d−1 most of the year, but as high as 52 eggs female−1 d−1 during month-long spring phytoplankton blooms. Egg production was a saturating function of total chlorophyll concentration with a mean of 30 eggs female−1 d−1 above a chlorophyll concentration of 12±6 mg chl m−3. We take chlorophyll to be a proxy for total food ofAcartia, known to feed on microzooplankton as well as phytoplankton. These findings, together with long-term records of chlorophyll, concentration and earlier studies of abundance of nauplius larvae in the estuary, imply chronic food limitation ofAcartia species, with sufficient food for maximum egg production <10% of the time over the last 25 yr. These results may show the most extreme example of food limitation of copepod reproduction in any temperate estuary. They further support the idea that estuaries may provide suitable habitat forAcartia species by virtue of other factors than high food concentration.

Phytoplankton Growth Balanced by Clam and Zooplankton Grazing and Net Transport into the Low-Salinity Zone of the San Francisco Estuary

We estimated the influence of planktonic and benthic grazing on phytoplankton in the strongly tidal, river-dominated northern San Francisco Estuary using data from an intensive study of the low salinity foodweb in 2006–2008 supplemented with long-term monitoring data. A drop in chlorophyll concentration in 1987 had previously been linked to grazing by the introduced clam Potamocorbula amurensis, but numerous changes in the estuary may be linked to the continued low chlorophyll. We asked whether phytoplankton continued to be suppressed by grazing and what proportion of the grazing was by benthic bivalves. A mass balance of phytoplankton biomass included estimates of primary production and grazing by microzooplankton, mesozooplankton, and clams. Grazing persistently exceeded net phytoplankton growth especially for larger cells, and grazing by microzooplankton often exceeded that by clams. A subsidy of phytoplankton from other regions roughly balanced the excess of grazing over growth. Thus, the influence of bivalve grazing on phytoplankton biomass can be understood only in the context of limits on phytoplankton growth, total grazing, and transport.

Individual-Based Modeling of Delta Smelt Population Dynamics in the Upper San Francisco Estuary: II. Alternative Baselines and Good versus Bad Years

Abstract We used a previously described individual-based population model to further explore the population dynamics of Delta Smelt Hypomesus transpacificus in the upper San Francisco Estuary. We formulated four alternative baseline configurations of the model and used a factorial design to systematically isolate the effects of factors that determined a good versus bad year. The alternative baseline conditions were obtained by substituting different assumptions about growth, maturity, and mortality into the original baseline configuration. In the simulation experiment, we varied five factors by setting each value to its 1998 (best year) or 2001 (worst year) value: salinity, temperature, zooplankton densities, hydrodynamics, and eggs per age-1 individual at spawning. Although some of the alternative baselines resulted in lower January abundances, estimated finite population growth rates were very similar for all versions. The simulation experiment showed that juvenile growth in the winter prior to spawning...

Individual-Based Modeling of Delta Smelt Population Dynamics in the Upper San Francisco Estuary: I. Model Description and Baseline Results

Abstract Many factors have been implicated in the decline of Delta Smelt Hypomesus transpacificus in the upper San Francisco Estuary, and the importance of each factor is difficult to determine using field data alone. We describe a spatially explicit, individual-based population model of Delta Smelt configured for the upper estuary. The model followed the reproduction, growth, mortality, and movement of individuals over their entire life cycle on the same spatial grid of cells as the Delta Simulation Model (DSM2) hydrodynamics model. Daily values of water temperature, salinity, and densities of six zooplankton prey types were represented on the spatial grid. Reproduction was evaluated daily, and new individuals were introduced into the model as yolk sac larvae. Growth of feeding individuals was based on bioenergetics and zooplankton densities. Mortality sources included natural mortality, starvation, and entrainment in water diversion facilities. Movement of larvae was determined using a particle tracking...

Reevaluating the Generality of an Empirical Model for Light-Limited Primary Production in the San Francisco Estuary

Depth-integrated primary production (ΣP, in grams of carbon per square meter per day) was measured using 14C in the northern San Francisco Estuary (SFE) from March through August of 2006 and 2007. Determinations of ΣP were then used to calibrate a published light-utilization model that relates ΣP to a composite parameter of chlorophyll, solar irradiance, and photic zone depth. The resultant calibration coefficient, Ψ, varied by a factor of nearly two between 2006 and 2007 and was lower than determined in previous calibrations for the estuary. The now chronically low chlorophyll concentrations in the SFE have resulted in lower predictive power of the light-utilization model. The variation in Ψ was likely the result of interannual variation in phytoplankton assimilation number. These results suggest that using a single Ψ may yield large errors in estimated estuarine production when applied overbroad spatial and temporal scales. Given the food-limited condition of the SFE, it appears that direct measurements of primary production are necessary for accurately characterizing the base of the estuarine food web.

Human-induced biotic invasions and changes in plankton interaction networks

Summary 1. Pervasive and accelerating changes to ecosystems due to human activities remain major sources of uncertainty in predicting the structure and dynamics of ecological communities. Understanding which biotic interactions within natural multitrophic communities are weakened or augmented by invasions of non-native species in the context of other environmental pressures is needed for effective management. 2. We used multivariate autoregressive models with detailed time-series data from largely freshwater and brackish regions of the upper San Francisco Estuary to assess the topology, direction and strength of trophic interactions following major invasions and establishment of non-native zooplankton in the early 1990s. We simultaneously compared the effects of fish and clam predation, environmental temperature and salinity intrusion using time-series data from >60 monitoring locations spanning more than three decades. 3. We found changes in the networks of biotic interactions in both regions after the major zooplankton invasions. Our results imply an increased pressure on native herbivores; intensified negative interactions between herbivores and omnivores; and stronger bottom-up influence of juvenile copepods but weaker influence of phytoplankton as a resource for higher trophic levels following the invasions. We identified salinity intrusion as a primary pressure but showed relatively stronger importance of biotic interactions for understanding the dynamics of entire communities. 4. Synthesis and applications. Our findings highlight the dynamic nature of biotic interactions and provide evidence of how simultaneous invasions of exotic species may alter interaction networks in diverse natural ecosystems over large spatial and temporal scales. Efforts to restore declining fish stocks may be in vain without fully considering the trophic dynamics that limit the flow of energy to target populations. Focusing on multitrophic interactions that may be threatened by invasions rather than a limited focus on responses of individual species or diversity is likely to yield more effective management strategies.

Effects of freshwater flow and phytoplankton biomass on growth, reproduction, and spatial subsidies of the estuarine copepod Pseudodiaptomus forbesi

We examined how freshwater flow and phytoplankton biomass affected abundance and population dynamics of the introduced subtropical copepod Pseudodiaptomus forbesi in brackish and freshwater regions of the San Francisco Estuary, California, USA. This copepod is key prey for the endangered and food-limited delta smelt, Hypomesus transpacificus, in low-salinity water during summer–autumn. Long-term monitoring data showed that P. forbesi was most abundant in fresh water, where summer–autumn abundance was invariant with freshwater flow. Abundance was positively related to freshwater flow in low-salinity water. Reproductive rates in both regions during 2010–2012 were low and unresponsive to chlorophyll or freshwater flow. Development indices, calculated as ratios of laboratory-derived to field-derived stage durations, were lowest for nauplii and highest for late copepodites, but averaged below 0.5 for all stages combined. Development indices were weakly related to chlorophyll for late copepodites only, unrelated to freshwater flow, and slightly higher in low-salinity than fresh water. Thus, the principal mechanism by which flow affects the P. forbesi population is apparently transport of copepods from fresh water to low-salinity water, where copepods are available to delta smelt. This work demonstrates how freshwater flow affects estuarine foodwebs through spatial subsidies of food supply.

Miczooplankton dynamics in the low salinity zone of the San Francisco Estuary

Microzooplankton, including principally ciliates, heteroor mixotrophic dinoflagellates, rotifers, and some metazoan larvae, are the principal herbivores in many aquatic systems (GIFFORD 1988, McMANUS & EDERINGTON-CANTRELL 1992, VERITY et al. 1993, CALBET & LANDRY 2004). Because they are small and overlap in size with their phytop1ankton food, microzoop1ankton are challenging to work with experimentally. Nonethe1ess, the preponderance of evidence to date supports the idea that they comprise key trophic intermediates in the transfer of energy from primary producers to copepods and fish (STOECKER & GovoNI 1984, STOECKER & EGLOFF 1987, ÜIFFORD & DAGG 1991). The delta sme1t (Hypomesus transpacificus) is a small endemic fish that is now a principa1 species of concern for management of freshwater flow and diversions in the SacramentoSan Joaquin De1ta, and the principa1 target for restoration in the upper San Francisco Estuary (BENNETT 2005). The abundance of this federally 1isted threatened species has been 1ow since the early 1980s. Potentia1 reasons for its 1ow abundance are many, but one possibility is 1ow food supply (KIMMERER & ÜRSI 1996). We be1ieve that the feeding environment of de1ta smelt may be imp1icated in the continued 1ow abundance o f this species. Throughout their lives, delta smelt feed on zoop1ankton, principally copepods, mainly in the brackish waters ofthe western De1ta and Suisun Bay (Fig. 1). Copepod abundance is depressed in this region, and the fauna has undergone many changes in recent decades with the introductions of several Asian copepod species into the estuary (KIMMERER et al. 1994, ÜRSI & ÜHTSUKA 1999). Previous work has shown that microzoop1ankton, in particu1ar ciliates, are an important food for some copepod species in the San Francisco Estuary (KIMMERER et al. 2005, BouLEY & KIMMERER 2006). Many copepods previous1y viewed as herbivores are actually omnivores, grazing on microzoop1ankton and simultaneous1y feeding directly on phytop1ankton, especially in estuarine systems (DAM et al. 1994). Our goal is to understand the dynamics o f microzooplankton abundance and grazing impact and to evaluate the degree to which they form a key trophic 1ink between microbia1 production (bacteria1 and San Francisco Bay and Delta