Geology topics

Rachel C. Johnson

Publications and source records attributed to Rachel C. Johnson.

10 recordsLinked to original sources

USGS2026

Fatty acid profiles recorded in ocean prey and California salmonine eggs reveal maternal ocean diets linked to thiamine deficiency

Following the principle ‘you are what you eat’, fatty acid signatures (FASs) of adult fish tissues, when compared with those of potential prey, can link diet to nutritional status. In 2020, thiamine (vitamin B 1 ) deficiency was diagnosed for the first time in multiple anadromous salmon populations in California. However, direct information linking ocean diet to thiamine status in marine-feeding salmonines is typically unavailable. This research aimed to link diet composition and egg total thiamine concentration of anadromous Chinook salmon, coho salmon and steelhead using FAS analysis. From 2020 to 2022, unfertilized eggs from these California salmonine species were collected alongside key forage species from the Pacific Ocean. FASs in eggs and prey were quantified using gas chromatography/mass spectrometry and total thiamine concentrations were quantified using high-performance liquid chromatography. Eggs rich in oleic acid (18:1n-9) reflected a diet dominated by Pacific herring and exhibited higher total thiamine concentrations. Conversely, eggs rich in eicosapentaenoic acid (20:5n-3) indicated a diet dominated by northern anchovy or euphausiid krill and were more likely to have low total thiamine concentrations. Polyunsaturated fatty acid proportions and the egg unsaturation index were strongly negatively correlated with egg total thiamine concentration, emphasizing the importance of lipid quality over quantity as a driver of egg thiamine concentration. This study highlights the utility of FASs for tracking the impacts of a changing ocean prey base on diet and underscores how dietary shifts can directly impact egg thiamine status in anadromous salmonines.

California↗

USGS2025

Widespread thiamine deficiency in California salmon linked to an anchovy-dominated marine prey base

Thiamine (vitamin B 1 ) deficiency in marine systems is a globally significant threat to marine life. In 2020, newly hatched Chinook salmon ( Oncorhynchus tshawytscha ) fry in California’s Central Valley (CCV) hatcheries swam in corkscrew patterns and died at unusually high rates due to a lack of this essential vitamin. We subsequently investigated the impacts and causes of thiamine deficiency in California’s anadromous salmonids. Our laboratory studies defined the relationship between thiamine concentrations in Chinook salmon eggs and early life-stage survival in offspring; we used these data to develop a model that estimated 26 to 48% thiamine-dependent fry mortality across consecutive years (2020–2021) for winter-run Chinook salmon. We established an egg surveillance effort that found widespread thiamine deficiency in CCV Chinook salmon in 2020 and 2021, and emerging thiamine deficiency in Klamath River and Trinity River coho salmon ( Oncorhynchus kisutch ) in 2021. We determined that thiamine injections into adults raised egg thiamine concentrations above levels found to impact early life-stage survival and swimming behavior. Ocean surveys, prey nutrition, salmon gut contents, and stable isotope data link thiamine deficiency to an ocean diet dominated by a booming population of northern anchovy ( Engraulis mordax ). This forage fish had low thiamine, high lipid, and high thiaminase activity levels consistent with both a thiaminase and oxidative stress hypothesis for causing thiamine deficiency in California salmon. Our research suggests California’s already stressed anadromous salmonids will continue to be impacted by thiamine deficiency as long as their ocean forage base and diet are dominated by northern anchovy.

Proceedings of the National Academy of Sciences↗

USGS2022

Ocean connectivity drives trophic support for consumers in an intermittently closed coastal lagoon

Estuarine food webs are complex, as marine, freshwater, and terrestrial inputs combine and contribute variable amounts of organic material. Seasonal fluctuations in precipitation amplify the dynamism inherent to estuarine food webs, particularly in lagoonal estuaries, which can be seasonally closed and disconnected from the ocean in low-runoff periods (bar-built lagoons). Despite their abundance along coastlines in Mediterranean climates, the organic matter sources fueling bar-built lagoon food webs are poorly understood, particularly with respect to seasonal hydrologic variability, episodic marine connections, and internal nutrient cycling. In this study, we evaluate the food web of a bar-built lagoon with respect to seasonal differences in lagoon water quality, the sources of organic matter which support consumers, and the trophic ecology of resident fishes. Observed water quality conditions reflected biogeochemical processes associated with salinity-driven stratification and high lagoon residence times and were associated with strong seasonal differences in the contribution of different organic matter sources to lagoon consumers. A variety of organic matter sources supported consumers; marine inputs were important to lagoon food webs in spring when the lagoon was open, while summer food webs were largely driven by phytoplankton which was likely fueled by internal nutrient cycling. Fish diets were largely comprised of crustaceans and fish eggs, with clearly defined trophic niches in spring but high overlap in summer. This study demonstrates that the seasonal changes in bar-built lagoon food webs are largely dependent on ocean connectivity and internal cycling within the lagoon, rather than watershed processes as is typical for many estuaries.

California↗

USGS2022

Eye lenses reveal ontogenetic trophic and habitat shifts in an imperiled fish, Clear Lake hitch (Lavinia exilicauda chi)

Stable isotopes recorded in fish eye lenses are an emerging tool to track dietary shifts coincident with use of diverse habitats over the lifetime of individuals. Eye lenses are metabolically inert, sequentially deposited, archival tissues that can open avenues to chronicle contaminant exposures, diet histories, trophic dynamics and migratory histories of individual fishes. In this study, we demonstrated that trophic histories reconstructed using eye lenses can resolve key uncertainties regarding diet and trophic habitat shifts. Clear Lake hitch ( Lavinia exilicauda chi ), a threatened cyprinid, inhabits a single lake (Clear Lake, Lake County, California) and utilizes tributary streams for reproduction. Bayesian mixing models applied to δ 13 C and δ 15 N recorded in eye lenses uncovered ontogenetic diet shifts that corresponded with shifts in occupation of habitats providing spawning (tributary streams), rearing (littoral lake), and growth (pelagic lake) functions. The reconstruction of size-structured trophic and habitat information can provide vital information needed to manage and conserve imperiled species such as the Clear Lake hitch.

California↗

USGS2020

Disease in Central Valley salmon: Status and lessons from other systems

Chinook Salmon ( Oncorhynchus tshawytscha ) are increasingly vulnerable to anthropogenic activities and climate change, especially at their most southern species range in California’s Central Valley. There is considerable interest in understanding stressors that contribute to population decline and in identifying management actions that reduce the impacts of those stressors. Along the west coast of North America, disease has been linked to declining numbers of salmonids and identified as a key stressor resulting in mortality. In the Central Valley, targeted studies have revealed extremely high prevalence of infectious agents and disease. However, there has been insufficient monitoring to understand the effect that disease may have on salmon populations. In order to inform future research, monitoring, and management efforts, a two-day workshop on salmon disease was held at UC Davis on March 14-15, 2018. This paper summarizes the science presented at this workshop, including the current state of knowledge of salmonid disease in the Central Valley and current and emerging tools to better understand its impacts on salmon. We highlight case studies from other systems where successful monitoring programs have been implemented. First, in the Klamath River where the integration of several data collection and modeling approaches led to the development of successful management actions, and second in British Columbia where investment in researching novel technologies led to breakthroughs in the understanding of salmon disease dynamics. Finally, we identify key information and knowledge gaps necessary to guide research and management of disease in Central Valley salmon populations.

California↗

USGS2020

Lifetime chronicles of selenium exposure linked to deformities in an imperiled migratory fish

Aquatic ecosystems worldwide face growing threats from elevated levels of contaminants from human activities. Toxic levels of selenium (Se) shown to cause deformities in birds, fish, and mammals can transfer from parents to progeny during embryonic development or accumulate through Se-enriched diets. For migratory species that move across landscapes, tracking exposure to elevated Se is vital to mitigating vulnerabilities. Yet, traditional toxicological investigations resolve only recent Se exposure. Here, we use a novel combination of X-ray fluorescence microscopy and depositional chronology in a biomineral to reveal for the first time provenance, life stage, and duration of toxic Se exposure over the lifetime of an organism. Spinal deformities observed in wild Sacramento Splittail ( Pogonichthys macrolepidotus ), an imperiled migratory minnow, were attributed to elevated Se acquired through maternal transfer and juvenile feeding on contaminated prey. This novel approach paves the way for diagnosing sources, pathways, and potential for a cumulative exposure of Se relevant for conservation.

California↗

USGS2020

Resolving selenium exposure risk: Spatial, temporal, and tissue-specific variability of an endemic fish in a large, dynamic estuary

Estuaries provide critical habitat for a vast array of fish and wildlife but are also a nexus for core economic activities that mobilize and concentrate contaminants that can threaten aquatic species. Selenium (Se), an essential element and potent reproductive toxin, is enriched in parts of the San Francisco Estuary (SFE) to levels known to cause toxicity, yet the risk of Se to species that inhabit the SFE is not well understood. We quantified Se concentrations in muscle, liver and ovary of the demersal cyprinid Sacramento Splittail from six regions in the SFE at three time points to evaluate Se exposure risk. Selenium levels exceeded proposed EPA criteria in ovary and thresholds of concern for liver in 15% and 20%, respectively, of fish collected in the fall of 2010, preceding the discovery of juvenile Splittail displaying a high incidence (>40%) of spinal deformities characteristic of Se toxicity, and again in 2011. No exceedances were detected in muscle tissue. Selenium concentrations varied significantly among regions for muscle (F 5,113 = 20.49, p < 0.0001), liver (F 5,113 = 28.4, p < 0.0001) and ovary (F 5,112 = 19.3, p < 0.0001) but did not vary between the wet and dry years, nor were they influenced by foraging trophic level or prey selection. Foraging location along the salinity gradient, defined by δ 34 S values, explained regional Se exposures in Splittail. Relationships between tissues varied among regions for muscle and liver and muscle and ovary, but a single global relationship could be defined for ovary and liver Se concentrations. Our results suggest that the proposed EPA Se criteria for muscle tissue in Splittail may be under-protective as it would not have predicted exceedances in liver or ovary tissue and that the relationship between muscle tissue and ovary and liver may be Se concentration and seasonal dependent.

California↗

USGS2019

Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all Pacific salmon and steelhead (Oncorhynchus spp.) listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units, and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories.

California↗

USGS2019

Strontium isotopes reveal ephemeral streams used for spawning and rearing by an imperiled potamodromous cyprinid--Clear Lake hitch Lavinia exilicauda chi

Identification of habitats responsible for the successful production and recruitment of rare migratory species is a challenge in conservation biology. Here, a tool was developed to assess life stage linkages for the threatened potamodromous cyprinid Clear Lake hitch Lavinia exilicauda chi . Clear Lake hitch undertake migrations from Clear Lake (Lake County, CA, USA) into ephemeral tributary streams for spawning. An aqueous isoscape of strontium isotopic ratios ( 87 Sr/ 86 Sr) was constructed for Clear Lake and its watershed to trace natal origins and migration histories of adult recruits. Aqueous 87 Sr/ 86 Sr differentiated Clear Lake from 8 of 10 key tributaries and clustered into 5 strontium isotope groups (SIGs) with 100% classification success. Otolith 87 Sr/ 86 Sr showed all five groups contributed variably to the population. The age at which juveniles migrated from natal streams to Clear Lake ranged from 11 to 152 days (mean ± s.d., 43 ± 34 days) and was positively associated with the permanency of natal habitat. This information can be used by resource managers to develop conservation actions for Clear Lake hitch. This study demonstrates the utility of strontium isotopes in otoliths as a tool to identify important freshwater habitats occupied over the lifespan of an individual that would otherwise be challenging or impossible to trace with other methods.

California↗

USGS2017

Science advancements key to increasing management value of life stage monitoring networks for endangered Sacramento River winter-run Chinook salmon in California

A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life stages that span broad geographic regions. Quantitative metrics (e.g., abundance, movement, survival, life history diversity, and condition) at multiple life stages are needed to inform how management actions (e.g., hatcheries, harvest, hydrology, and habitat restoration) influence salmon population dynamics. The existing monitoring network for endangered Sacramento River winterrun Chinook Salmon (SRWRC, Oncorhynchus tshawytscha) in California’s Central Valley was compared to conceptual models developed for each life stage and geographic region of the life cycle to identify relevant SRWRC metrics. We concluded that the current monitoring network was insufficient to diagnose when (life stage) and where (geographic domain) chronic or episodic reductions in SRWRC cohorts occur, precluding within- and among-year comparisons. The strongest quantitative data exist in the Upper Sacramento River, where abundance estimates are generated for adult spawners and emigrating juveniles. However, once SRWRC leave the upper river, our knowledge of their identity, abundance, and condition diminishes, despite the juvenile monitoring enterprise. We identified six system-wide recommended actions to strengthen the value of data generated from the existing monitoring network to assess resource management actions: (1) incorporate genetic run identification; (2) develop juvenile abundance estimates; (3) collect data for life history diversity metrics at multiple life stages; (4) expand and enhance real-time fish survival and movement monitoring; (5) collect fish condition data; and (6) provide timely public access to monitoring data in open data formats. To illustrate how updated technologies can enhance the existing monitoring to provide quantitative data on SRWRC, we provide examples of how each recommendation can address specific management issues.

California↗