Geology topics

Brian Mahardja

Publications and source records attributed to Brian Mahardja.

10 recordsLinked to original sources

USGS2026

The effects of scientific uncertainty and values trade-offs on flow management decisions for an endangered fish

Consumptive use of freshwater is of concern in many estuarine ecosystems, and various frameworks have been used to prescribe environmental flows to benefit native species. However, few of these frameworks explicitly examine the potential trade-offs between socioeconomic and conservation-oriented values. This is exemplified in California, USA, where freshwater management has been an area of focus and controversy. Operations of numerous reservoirs and water diversion facilities distributed throughout the state, while critical for economic and public health benefits, have contributed to the decline of many native species. The endangered delta smelt ( Hypomesus transpacificus ) is endemic to the Sacramento-San Joaquin Delta, the heart of California's complex water conveyance system. To aid recovery of delta smelt, fall-timed freshwater pulse flows were implemented, which require water to be either released from reservoirs, or made unavailable to export for consumptive uses. Previous research has indicated that the effectiveness of the current pulse flow action could be improved by reconsidering the timing and magnitude; however, uncertainties in the predicted fish response to flow pulses may hinder decision-making about flow management. Using a water resource planning model, different iterations of an individual-based life cycle model, and decision analysis tools, we assessed the importance of sources of uncertainty to hypothetical flow management decisions, including uncertainty surrounding the predicted responses in delta smelt population growth rates, and variability of decision-maker's values. We found both the choice of which (if any) flow action to take for delta smelt, and the expected value of further research, depended on how decision-makers weight the delta smelt and water supply objectives. There was expected value of information (VOI) only if a decision-maker weighted the delta smelt objective ≥0.59, and within this range, research to improve estimates of changes in delta smelt prey items related to flow actions could be prioritized over other sources of uncertainty to improve outcomes of decision-making. Our study demonstrates how uncertainty, even if large, may not be equally relevant to different decision-makers (e.g., with different agency missions), and how VOI analysis can be used to guide management in an overallocated water system such as California.

California↗

USGS2025

Rapid structured decision making for Hypomesus transpacificus (delta smelt) summer–fall freshwater outflow management

Managers of the Central Valley Project (CVP) and State Water Projects (SWP) in California are confronted with difficult tradeoffs between water uses and associated values affected by water management decisions. These decisions involve altering the timing and magnitude of water releases from dams and reservoirs, which can affect habitats for economically important and Federally and State-listed endangered fish species, water deliveries for agriculture or municipalities, and water quality. In this report, we describe the results of a rapid structured decision-making process used to assist management agencies in evaluating tradeoffs while gathering input from cooperating agencies, rightsholders, or interested parties (hereafter participants) through facilitated workshops in spring 2025. Consideration of alternative water management actions was initiated by the continued decline of Hypomesus transpacificus (delta smelt) populations and the issuance of a new biological opinion for the CVP and SWP long-term operations on the effects on delta smelt and other Endangered Species Act-listed species in November 2024. An Executive Order was also issued in January 2025, directing the Bureau of Reclamation to maximize water deliveries. Participants, led by the U.S. Geological Survey and cooperating agencies, identified 8 fundamental values (hereafter objectives) and 11 alternative water management scenarios (or “alternative management actions” based on the PrOACT model). Using multicriteria decision analysis, we evaluated performance (or “consequences” based on a consequence table analysis) and analyzed tradeoffs of alternative water management actions to the fundamental objectives. We ranked the alternative water management actions based on four participants’ objective weights and composite utility scores calculated using a linear value function. The three highest ranking alternative water management actions had the poorest performance for delta smelt but performed best for CVP and SWP water exports and objectives related to coldwater pool operations for salmonids. An optimum strategy that could prevent the extinction of delta smelt was not determined for this study. However, insights gained from our rapid decision analysis suggested nonflow scenarios could benefit the delta smelt population, including in drier years, and could be considered to avoid curtailment of water exports.

Open-File Report↗

USGS2022

Relative bias in catch among long-term fish monitoring surveys within the San Francisco Estuary

Fish monitoring gears rarely capture all available fish, an inherent bias in monitoring programs referred to as catchability. Catchability is a source of bias that can be affected by numerous aspects of gear deployment (e.g., deployment speed, mesh size, and avoidance behavior). Thus, care must be taken when multiple surveys—especially those using different sampling methods—are combined to answer spatio-temporal questions about population and community dynamics. We assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary: the Bay Study Otter Trawl (BSOT), the Bay Study Midwater Trawl (BSMT), the Fall Midwater Trawl (FMWT), and the Suisun Marsh Otter Trawl (SMOT). We used generalized additive models with a spatio-temporal smoother and survey as a fixed effect to predict gear-specific estimates of catch for 45 different fish species within large and small size classes. We used estimates of the fixed effect coefficients for each survey (e.g., BSOT) relative to the reference gear (FMWT) to develop relative measures of catchability among taxa, surveys, and fish-size classes, termed the catch-ratio. We found higher relative catchability of 27%, 22%, and 57% of fish species in large size classes from the FMWT than in the BSMT, BSOT, or SMOT, respectively. In the small size class, relative catchability was higher in the FMWT than the BSMT, BSOT, or SMOT for 50%, 18%, and 25% of fish species, respectively. As expected, relative catchability of demersal species was higher in the otter trawls (BSOT, SMOT) while relative catchability of pelagic species was higher in the midwater trawls (FMWT, BSMT). Our results demonstrate that catchability is a source of bias among monitoring efforts within the San Francisco Estuary, and assuming equal catchability among surveys, species, and size classes could result in significant bias when describing spatio-temporal patterns in catch if ignored.

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USGS2022

Warming in the upper San Francisco Estuary: Patterns of water temperature change from five decades of data

Temperature is a key controlling variable from subcellular to ecosystem scales. Thus, climatic warming is expected to have broad impacts, especially in economically and ecologically valuable systems such as estuaries. The heavily managed upper San Francisco Estuary supplies water to millions of people and is home to fish species of high conservation, commercial, and recreational interest. Despite a long monitoring record (> 50 yr), we do not yet know how water temperatures have already changed or how trends vary spatially or seasonally. We fit generalized additive models on an integrated database of discrete water temperature observations to estimate long-term trends with spatio-seasonal variability. We found that water temperatures have increased 0.017°C yr −1 on average over the past 50 yr. Rates of temperature change have varied over time, but warming was predominant. Temperature increases were most widespread in the late-fall to winter (November to February) and mid-spring (April to June), coinciding with the winter development of juvenile Chinook salmon and spring spawning window of the endangered delta smelt. Warming was fastest in the northern regions, a key fish migration corridor with important tidal wetland habitat. However, no long-term temperature trends were detected in October and were only observed in some regions in May, July, and August. These results can help identify optimal areas for restoration or refugia to buffer the effects of a warming climate, and the methods can be leveraged to understand the spatiotemporal variability in climate warming patterns in other aquatic systems.

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USGS2021

Resistance and resilience of pelagic and littoral fishes to drought in the San Francisco Estuary

Many estuarine ecosystems and the fish communities that inhabit them have undergone substantial changes in the past several decades, largely due to multiple interacting stressors that are often of anthropogenic origin. Few are more impactful than droughts, which are predicted to increase in both frequency and severity with climate change. In this study, we examined over five decades of fish monitoring data from the San Francisco Estuary, California, USA, to evaluate the resistance and resilience of fish communities to disturbance from prolonged drought events. High resistance was defined by the lack of decline in species occurrence from a wet to a subsequent drought period, while high resilience was defined by the increase in species occurrence from a drought to a subsequent wet period. We found some unifying themes connecting the multiple drought events over the 50‐yr period. Pelagic fishes consistently declined during droughts (low resistance), but exhibit a considerable amount of resiliency and often rebound in the subsequent wet years. However, full recovery does not occur in all wet years following droughts, leading to permanently lower baseline numbers for some pelagic fishes over time. In contrast, littoral fishes seem to be more resistant to drought and may even increase in occurrence during dry years. Based on the consistent detrimental effects of drought on pelagic fishes within the San Francisco Estuary and the inability of these fish populations to recover in some years, we conclude that freshwater flow remains a crucial but not sufficient management tool for the conservation of estuarine biodiversity.

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USGS2021

Recruitment dynamics of non-native largemouth bass within the Sacramento-San Joaquin delta

Largemouth bass (LMB; Micropterus salmoides ) recruitment is limited by a critical developmental period during early life stages, but this mechanism may be less important within non-native habitats. We conducted boat electrofishing surveys in four tidal lakes of California’s Sacramento–San Joaquin Delta (SSJD) from 2010 to 2011 to describe introduced LMB recruitment dynamics. We evaluated growth, proximate composition, and health indices of young-of-the-year (YOY) LMB among tidal lakes and developed an integrated count model to determine how factors known to affect LMB recruitment shape SSJD population structure. Our results show a mismatch among growth, nutrition, and YOY abundance, where the tidal lake with the most abundant and fastest-growing LMB had the poorest nutritional status. The warm winter water temperatures and lack of a hatching-cohort growth advantage suggests overwinter starvation plays a less important role in SSJD LMB recruitment than in many native LMB habitats. Collectively, our results suggest that habitat characteristics (submerged aquatic vegetation) and not overwinter mortality shapes SSJD LMB population structure, a mechanism consistent with contemporary hypotheses about the altered fish community structure of the SSJD.

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USGS2021

Interagency Ecological Program long-term monitoring element review: Pilot approach and methods development (2020)

This report describes the first-year, pilot-phase of what is intended to be a larger, multiple-year review of all IEP core long-term monitoring elements (LTMEs). Here we hope to provide evidence that the review team arrangement and communication schedule was effective at developing a framework to objectively evaluate a suite of LTMEs. We focused on developing methods for an effective review, documenting the process of methods development, and compiling recommendations for applications of these methods to future reviews. We also gathered recommendations to improve data collection, catchability-adjustment, and record keeping processes which will be useful for all LTMEs regardless of when they are to be reviewed. Although we did not complete a comprehensive review of the long-term monitoring elements due to our short timeline, we believe this report represents a substantial effort towards that review and will serve as an invaluable guide for subsequent IEP LTME reviews.

Report↗

USGS2021

Synthesis of data and studies relating to Delta Smelt biology in the San Francisco Estuary, emphasizing water year 2017

In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious management issue. It is especially contentious with regards to the Delta Smelt (Hypomesus transpacificus), a species endemic to the SFE that has been listed as threatened under the Federal Endangered Species Act and endangered by the State of California. Early studies of Delta Smelt distribution within the SFE suggested that Delta Smelt habitat is determined largely by freshwater flow; however, the exact mechanisms and processes producing such benefits remained unclear. In the summer of 2017, the Flow Alteration Management, Analysis, and Synthesis Team (FLOAT-MAST) was established to analyze, synthesize, and summarize the data collected from the various flow-related monitoring and special studies occurring in 2017(see Table Intro 4). This report will focus on the 2017 summer-fall status of Delta Smelt and its habitat following a record wet year. There has been a long-term decline in the abundance of Delta Smelt associated with a decline in other pelagic fishes. Investigators concluded that the decline has likely been caused by the interactive effects of several causes, including changes in both physical and biotic habitats, many of which are tied to amount and timing of freshwater flow. For this report, we formulated a number of basic predictions about the likely effects of high flows in 2017 on Delta Smelt and their habitat (Table 3). We use a qualitative weight of evidence approach to evaluate whether these predictions were supported by available data. Data sources included a variety of long-term monitoring surveys conducted by Interagency Ecological Program (IEP) agencies, as well as model outputs. Delta Smelt population, health, and life history metrics rarely responded as predicted. Water temperature appears to have a stronger effect on Delta Smelt growth rate and some metrics of life history diversity than outflow or X2 position. Other life history diversity attributes varied but did not appear to be driven by outflow or temperature. Health status was difficult to interpret. Low prevalence of lesions and improved nutritional condition during the drought was contradicted by declining overall population levels. Because of the sparse catches of Delta Smelt in the post-POD years, we consider the data insufficient to reach firm conclusions about the predictions concerning range and distribution of Delta Smelt, especially in the fall. The prediction of high survival was not supported. The 2017 Delta Smelt year class began with poor recruitment in spring of 2017 and below average survival for spring to summer and summer to fall. Thus, low production and low survival led to low abundance of all life stages. During the fall to winter period survival improved, yet the resulting adults were low in number. Foraging success of the fish captured, as measured by stomach fullness, was high for juveniles and adults in 2017 relative to recent years associated with the higher densities of common zooplankton prey that occurred in 2017.

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USGS2020

Inter-population differences in salinity tolerance of adult wild Sacramento splittail: osmoregulatory and metabolic responses to salinity

The Sacramento splittail ( Pogonichthys macrolepidotus ) is composed of two genetically distinct populations endemic to the San Francisco Estuary (SFE). The allopatric upstream spawning habitat of the Central Valley (CV) population connects with the sympatric rearing grounds via relatively low salinity waters, whereas the San Pablo (SP) population must pass through the relatively high-salinity Upper SFE to reach its allopatric downstream spawning habitat. We hypothesize that if migration through SFE salinities to SP spawning grounds is more challenging for adult CV than SP splittail, then salinity tolerance, osmoregulatory capacity, and metabolic responses to salinity will differ between populations. Osmoregulatory disturbances, assessed by measuring plasma osmolality and ions, muscle moisture and Na + -K + -ATPase activity after 168 to 336 h at 11‰ salinity, showed evidence for a more robust osmoregulatory capacity in adult SP relative to CV splittail. While both resting and maximum metabolic rates were elevated in SP splittail in response to increased salinity, CV splittail metabolic rates were unaffected by salinity. Further, the calculated difference between resting and maximum metabolic values, aerobic scope, did not differ significantly between populations. Therefore, improved osmoregulation came at a metabolic cost for SP splittail but was not associated with negative impacts on scope for aerobic metabolism. These results suggest that SP splittail may be physiologically adjusted to allow for migration through higher-salinity waters. The trends in interpopulation variation in osmoregulatory and metabolic responses to salinity exposures support our hypothesis of greater salinity-related challenges to adult CV than SP splittail migration and are consistent with our previous findings for juvenile splittail populations, further supporting our recommendation of population-specific management.

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USGS2016

Inter-population differences in salinity tolerance and osmoregulation of juvenile wild and hatchery-born Sacramento splittail

The Sacramento splittail ( Pogonichthys macrolepidotus ) is a minnow endemic to the highly modified San Francisco Estuary of California, USA and its associated rivers and tributaries. This species is composed of two genetically distinct populations, which, according to field observations and otolith strontium signatures, show largely allopatric distribution patterns as recently hatched juveniles. Juvenile Central Valley splittail are found primarily in the nearly fresh waters of the Sacramento and San Joaquin rivers and their tributaries, whereas San Pablo juveniles are found in the typically higher-salinity waters (i.e. up to 10‰) of the Napa and Petaluma Rivers. As the large salinity differences between young-of-year habitats may indicate population-specific differences in salinity tolerance, we hypothesized that juvenile San Pablo and Central Valley splittail populations differ in their response to salinity. In hatchery-born and wild-caught juvenile San Pablo splittail, we found upper salinity tolerances, where mortalities occurred within 336 h of exposure to 16‰ or higher, which was higher than the upper salinity tolerance of 14‰ for wild-caught juvenile Central Valley splittail. This, in conjunction with slower recovery of plasma osmolality, but not ion levels, muscle moisture or gill Na + ,K + -ATPase activity, in Central Valley relative to San Pablo splittail during osmoregulatory disturbance provides some support for our hypothesis of inter-population variation in salinity tolerance and osmoregulation. The modestly improved salinity tolerance of San Pablo splittail is consistent with its use of higher-salinity habitats. Although confirmation of the putative adaptive difference through further studies is recommended, this may highlight the need for population-specific management considerations.

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