Community Patterns and Environmental Associations for Pelagic Fishes in a Highly Modified Estuary

Abstract

Understanding how natural and human‐induced processes interact to influence ecosystem responses is essential for their effective management and conservation. Long‐term environmental degradation of the upper San Francisco Estuary, California, has resulted in numerous species declines. In this study, we used pelagic fish monitoring and hydrodynamic data during winter–spring 2002–2014 to evaluate how natural and human‐induced environmental changes in the upper San Francisco Estuary may have influenced the distribution, abundance, and community structure of the pelagic fishes. Delta outflow and turbidity tended to decline and salinity tended to increase since the early 2000s. Twelve of the 27 pelagic fish species sampled were introduced, most of which were freshwater‐dominant species in highly altered upstream areas. Overall mean relative abundance was similar between native and introduced fishes across all study areas. The upstream distribution of the eight most abundant pelagic fishes was generally associated with their salinity habitat components. Among these species, the Delta Smelt Hypomesus transpacificus and the introduced Threadfin Shad Dorosoma petenense had the highest rates of population decline over the period 2002–2014 and the largest relative increase in salinity predicted in their habitats due to hydrological alteration. Community structure was significantly related to abiotic factors (water temperature, salinity, and turbidity) and spatiotemporal variation (longitude and month), which accounted for 30–33% of the variation. Low to intermediate outflows due to droughts and water diversions since the early 2000s likely interacted synergistically with multiple factors, decreasing the abundance of several pelagic species. Management actions linking ecologic, hydrologic, and geomorphic processes with multiple stressors could help to reverse the long‐term decline of Delta Smelt and other threatened and endangered fishes in the San Francisco Estuary.

Modeling the Influence of Outflow and Community Structure on an Endangered Fish Population in the Upper San Francisco Estuary

“…The complexity of estuarine ecosystems is influenced by the broad range and extent of anthropogenic effects in these transitional waters [1,2], including morphological and hydrological alteration [3,4], entrainment of plankton and nekton to water pumps [5,6], contaminants [3,7], introduced species [8,9], and climate change [10,11]. Changes in freshwater flow, natural or otherwise, can perturb the estuarine salinity gradient [12,13], and influence the abundance and distribution of estuarine organisms through a variety of flow-mediated processes (e.g., [9,14,15]). Moreover, estuarine food webs can be sensitive to small variations in the freshwater input [16,17].…”

“…The identification of specific ecological mechanisms linking species responses to freshwater flow in estuaries remains challenging due to the highly complex nature of such ecosystems [17,23]. In particular, there is a pressing need for analytical tools to evaluate ecological hypotheses in such ecosystems, and to inform adaptive management of freshwater flows to conserve fish species at risk of extinction (e.g., [9,24]). Because species interactions are notoriously difficult to quantify [25], qualitative analysis of the community matrix is particularly suited to model ecological interactions since essential community properties can be determined by ecosystem topology and sign structure of the interactions, rather than by the values of variables and parameters themselves [26][27][28].…”

“…The upper San Francisco Estuary (hereafter upper SF Estuary; California; Figure 1) is an imperiled ecosystem and the central hub of California's water supply infrastructure [38]. Outflow is the most ecologically important source of freshwater to the SF Estuary and represents the net flow at Chipps Island in the Suisun Region (river km 74; Figure 1) after subtracting water diversions and depletions in the upper SF Estuary and its watershed [6,9]. An ecologically meaningful metric of outflow forcing on the upstream distribution of the salinity field in the SF Estuary is X2, which is defined as the distance (km) from the mouth of the estuary (Golden Gate Bridge), to upstream locations where the near-bottom tidally averaged salinity is 2 psu [39].…”

“…Although several of the predicted abiotic and biotic responses in that study could not be confirmed from available field data, the abundance of delta smelt in 2011 and early 2012 was one the highest reported since the early 2000s. Yet, delta smelt became very rare during the 2012-2016 drought and failed to increase its abundance during the wet year 2017, indicating the need to evaluate new management options (e.g., [7,9,46]).…”

Did a Shifting Ecological Baseline Mask the Predatory Effect of Striped Bass on Delta Smelt?

“…Comparison of the numbers of Striped Bass (SB) and Delta Smelt (DS) collected from 18 fish community studies of the San Francisco Estuary. The exception isCastillo et al (2018) who reported fish densities (number × 10 4 m 3 ). Studies in which Delta Smelt catches outnumbered Striped Bass catches are shaded.…”