Jason Kindopp - Academia.edu (original) (raw)
Papers by Jason Kindopp
Thiamine Deficiency Complex (TDC) is a major emerging threat to global populations of culturally ... more Thiamine Deficiency Complex (TDC) is a major emerging threat to global populations of culturally and economically important populations of salmonids. Salmonid eggs and embryos can assimilate exogenous thiamine, and evidence suggests that microbial communities in benthic environments can produce substantial amounts of thiamine. We therefore hypothesize that microbially produced thiamine in both riverine surface water and hyporheic zones could serve to rescue early life stages of salmonids suffering from TDC. The distributions of thiamine and its metabolically related compounds (dTRCs) have never been determined in freshwater systems. Similarly, the microbial cycling of these compounds has never been investigated. Here we determine that all dTRCs are present in femto-picomolar concentrations across diverse salmon spawning habitats in California’s Sacramento River system. We observed that thiamine concentrations in the Sacramento River are orders of magnitude lower than marine environm...
Applied and Environmental Microbiology, Dec 11, 2023
California fish and wildlife journal, Jul 10, 2023
Real-time PCR, also called quantitative PCR or qPCR, can provide a simple and elegant method for ... more Real-time PCR, also called quantitative PCR or qPCR, can provide a simple and elegant method for determining the amount of a target sequence that is present in a sample. Its very simplicity can sometimes lead researchers to overlook some of the critical factors that make it work. This review will highlight the factors that must be considered when setting up and evaluating a real-time PCR reaction.
San Francisco Estuary and Watershed Science, Jun 24, 2022
Effective species management depends on accurate estimates of population size. There are, however... more Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon ("spring run"), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento-San Joaquin Delta ("Delta") from the Sacramento Valley. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers, and scientists to review some of the key aspects of spring-run biology, examine the management and conservation importance of a JPE, identify knowledge gaps, introduce new tools, and discuss alternative approaches to forecasting the number of spring run emigrating from the Sacramento River drainage and into the Delta. This paper summarizes the spring-run biology, monitoring, and emergent methods for assessment considered at the workshop, as well as the guiding concepts identified by workshop participants necessary to develop a JPE for springrun Chinook Salmon.
California Fish and Wildlife Journal
We performed a five-year (2015–2020) survey of juvenile natural Chinook Salmon (Oncorhynchus tsha... more We performed a five-year (2015–2020) survey of juvenile natural Chinook Salmon (Oncorhynchus tshawytscha), adult salmon carcasses, and river water from the lower Feather River to determine infection prevalence, distribution, and spore quantity of the myxozoan parasite Ceratonova shasta. Average prevalence of infection in juvenile salmon collected from the high flow channel ranged from 45–58% depending on assay method. Initial infection of fry and detection of actinospore stage in river water began in late January or early February. Overt disease occurred in March and was lethal. Infection of the gill was detected weeks ahead of intestinal infection. Water-borne spore measurement and fish infection demonstrate an infectious zone beginning at the outlet of the Thermalito Afterbay. This zone is expanding downriver past the confluence of the Yuba River. Adult carcasses produce billions of myxospores annually that move downriver over the winter. C. shasta infection is one of several fact...
San Francisco Estuary and Watershed Science
Effective species management depends on accurate estimates of population size. There are, however... more Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers, and s...
Canadian Journal of Fisheries and Aquatic Sciences
Fall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento–San Joaquin River system f... more Fall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento–San Joaquin River system form the backbone of California’s salmon fishery and are heavily subsidized through hatchery production. Identifying temporal trends in the relative contribution of hatchery- versus wild-spawned salmon is vital for assessing the status and resiliency of wild salmon populations. Here, we reconstructed the proportion of hatchery fish on natural spawning grounds in the Feather River, a major tributary to the Sacramento River, using strontium isotope (87Sr/86Sr) ratios of otoliths collected during carcass surveys from 2002 to 2010. Our results show that prior to the 2007–2008 salmon stock collapse, 55%–67% of in-river spawners were of hatchery origin; however, hatchery contributions increased drastically (89%) in 2010 following the collapse. Data from a recent hatchery marking program corroborate our results, showing that hatchery fish continued to dominate (∼90%) in 2011–2012. Though the reb...
ABSTRACT In the Feather River below Lake Oroville, California, the relative importance of water t... more ABSTRACT In the Feather River below Lake Oroville, California, the relative importance of water temperature and flow regimes on fish populations was assessed by comparing two distinct river segments, the low flow channel (LFC) and high flow channel (HFC). Rotary screw traps and beach seining surveys were used to assess distribution, abundance, and emigration patterns of fishes between 1997 and 2001. Both sampling methods revealed similar patterns in species composition. Chinook salmon Oncorhynchus tshawytscha dominated seining (46%) and rotary screw trap (99%) catch by number. More than 80% of Chinook salmon captured were less than 50 mm, demonstrating that most Feather River Chinook salmon emigrate before smolting. In multiple linear regression models, Chinook salmon spawn timing (P < 0.001) and water temperature (P = 0.036) were statistically significant predictors of weekly Chinook salmon catch in the LFC, while Secchi depth was statistically significant (P = 0.007) for the HFC catch. Most steelhead Oncorhynchus mykiss were captured in the LFC, particularly in 2001, which accounted for 82% of all steelhead collected. The total relative abundance of alien fishes was low, 7.2% and 0.1% from beach seining and rotary screw trap sampling, respectively. Alien fishes were more abundant in the HFC. Native fish species were found throughout the study area. Canonical correspondence analysis suggested that river kilometer, water temperature, and year were highly significant (P = 0.001), while season (P = 0.01) and flow (P = 0.01) were significant to observed fish assemblages within LFC. Water temperature, river kilometer, year, and season were highly significant (P = 0.001) to observed fish assemblages within the HFC. Our results demonstrate that native fishes can be successful in a regulated river environment, despite an unnatural flow regime. These findings provide valuable information in assessing the impacts of dam operations and in implementing river restoration actions by flow and water temperature manipulation.
In the Feather River below Lake Oroville, California, the relative importance of water temperatur... more In the Feather River below Lake Oroville, California, the relative importance of water temperature and flow regimes on fish populations was assessed by comparing two distinct river segments, the low flow channel (LFC) and high flow channel (HFC). Rotary screw traps and beach seining surveys were used to assess distribution, abundance, and emigration patterns of fishes between 1997 and 2001. Both sampling methods revealed similar patterns in species composition. Chinook salmon Oncorhynchus tshawytscha dominated seining (46%) and rotary screw trap (99%) catch by number. More than 80% of Chinook salmon captured were less than 50 mm, demonstrating that most Feather River Chinook salmon emigrate before smolting. In multiple linear regression models, Chinook salmon spawn timing (P < 0.001) and water temperature (P = 0.036) were statistically significant predictors of weekly Chinook salmon catch in the LFC, while Secchi depth was statistically significant (P = 0.007) for the HFC catch. ...
Thiamine Deficiency Complex (TDC) is a major emerging threat to global populations of culturally ... more Thiamine Deficiency Complex (TDC) is a major emerging threat to global populations of culturally and economically important populations of salmonids. Salmonid eggs and embryos can assimilate exogenous thiamine, and evidence suggests that microbial communities in benthic environments can produce substantial amounts of thiamine. We therefore hypothesize that microbially produced thiamine in both riverine surface water and hyporheic zones could serve to rescue early life stages of salmonids suffering from TDC. The distributions of thiamine and its metabolically related compounds (dTRCs) have never been determined in freshwater systems. Similarly, the microbial cycling of these compounds has never been investigated. Here we determine that all dTRCs are present in femto-picomolar concentrations across diverse salmon spawning habitats in California’s Sacramento River system. We observed that thiamine concentrations in the Sacramento River are orders of magnitude lower than marine environm...
Applied and Environmental Microbiology, Dec 11, 2023
California fish and wildlife journal, Jul 10, 2023
Real-time PCR, also called quantitative PCR or qPCR, can provide a simple and elegant method for ... more Real-time PCR, also called quantitative PCR or qPCR, can provide a simple and elegant method for determining the amount of a target sequence that is present in a sample. Its very simplicity can sometimes lead researchers to overlook some of the critical factors that make it work. This review will highlight the factors that must be considered when setting up and evaluating a real-time PCR reaction.
San Francisco Estuary and Watershed Science, Jun 24, 2022
Effective species management depends on accurate estimates of population size. There are, however... more Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon ("spring run"), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento-San Joaquin Delta ("Delta") from the Sacramento Valley. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers, and scientists to review some of the key aspects of spring-run biology, examine the management and conservation importance of a JPE, identify knowledge gaps, introduce new tools, and discuss alternative approaches to forecasting the number of spring run emigrating from the Sacramento River drainage and into the Delta. This paper summarizes the spring-run biology, monitoring, and emergent methods for assessment considered at the workshop, as well as the guiding concepts identified by workshop participants necessary to develop a JPE for springrun Chinook Salmon.
California Fish and Wildlife Journal
We performed a five-year (2015–2020) survey of juvenile natural Chinook Salmon (Oncorhynchus tsha... more We performed a five-year (2015–2020) survey of juvenile natural Chinook Salmon (Oncorhynchus tshawytscha), adult salmon carcasses, and river water from the lower Feather River to determine infection prevalence, distribution, and spore quantity of the myxozoan parasite Ceratonova shasta. Average prevalence of infection in juvenile salmon collected from the high flow channel ranged from 45–58% depending on assay method. Initial infection of fry and detection of actinospore stage in river water began in late January or early February. Overt disease occurred in March and was lethal. Infection of the gill was detected weeks ahead of intestinal infection. Water-borne spore measurement and fish infection demonstrate an infectious zone beginning at the outlet of the Thermalito Afterbay. This zone is expanding downriver past the confluence of the Yuba River. Adult carcasses produce billions of myxospores annually that move downriver over the winter. C. shasta infection is one of several fact...
San Francisco Estuary and Watershed Science
Effective species management depends on accurate estimates of population size. There are, however... more Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers, and s...
Canadian Journal of Fisheries and Aquatic Sciences
Fall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento–San Joaquin River system f... more Fall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento–San Joaquin River system form the backbone of California’s salmon fishery and are heavily subsidized through hatchery production. Identifying temporal trends in the relative contribution of hatchery- versus wild-spawned salmon is vital for assessing the status and resiliency of wild salmon populations. Here, we reconstructed the proportion of hatchery fish on natural spawning grounds in the Feather River, a major tributary to the Sacramento River, using strontium isotope (87Sr/86Sr) ratios of otoliths collected during carcass surveys from 2002 to 2010. Our results show that prior to the 2007–2008 salmon stock collapse, 55%–67% of in-river spawners were of hatchery origin; however, hatchery contributions increased drastically (89%) in 2010 following the collapse. Data from a recent hatchery marking program corroborate our results, showing that hatchery fish continued to dominate (∼90%) in 2011–2012. Though the reb...
ABSTRACT In the Feather River below Lake Oroville, California, the relative importance of water t... more ABSTRACT In the Feather River below Lake Oroville, California, the relative importance of water temperature and flow regimes on fish populations was assessed by comparing two distinct river segments, the low flow channel (LFC) and high flow channel (HFC). Rotary screw traps and beach seining surveys were used to assess distribution, abundance, and emigration patterns of fishes between 1997 and 2001. Both sampling methods revealed similar patterns in species composition. Chinook salmon Oncorhynchus tshawytscha dominated seining (46%) and rotary screw trap (99%) catch by number. More than 80% of Chinook salmon captured were less than 50 mm, demonstrating that most Feather River Chinook salmon emigrate before smolting. In multiple linear regression models, Chinook salmon spawn timing (P < 0.001) and water temperature (P = 0.036) were statistically significant predictors of weekly Chinook salmon catch in the LFC, while Secchi depth was statistically significant (P = 0.007) for the HFC catch. Most steelhead Oncorhynchus mykiss were captured in the LFC, particularly in 2001, which accounted for 82% of all steelhead collected. The total relative abundance of alien fishes was low, 7.2% and 0.1% from beach seining and rotary screw trap sampling, respectively. Alien fishes were more abundant in the HFC. Native fish species were found throughout the study area. Canonical correspondence analysis suggested that river kilometer, water temperature, and year were highly significant (P = 0.001), while season (P = 0.01) and flow (P = 0.01) were significant to observed fish assemblages within LFC. Water temperature, river kilometer, year, and season were highly significant (P = 0.001) to observed fish assemblages within the HFC. Our results demonstrate that native fishes can be successful in a regulated river environment, despite an unnatural flow regime. These findings provide valuable information in assessing the impacts of dam operations and in implementing river restoration actions by flow and water temperature manipulation.
In the Feather River below Lake Oroville, California, the relative importance of water temperatur... more In the Feather River below Lake Oroville, California, the relative importance of water temperature and flow regimes on fish populations was assessed by comparing two distinct river segments, the low flow channel (LFC) and high flow channel (HFC). Rotary screw traps and beach seining surveys were used to assess distribution, abundance, and emigration patterns of fishes between 1997 and 2001. Both sampling methods revealed similar patterns in species composition. Chinook salmon Oncorhynchus tshawytscha dominated seining (46%) and rotary screw trap (99%) catch by number. More than 80% of Chinook salmon captured were less than 50 mm, demonstrating that most Feather River Chinook salmon emigrate before smolting. In multiple linear regression models, Chinook salmon spawn timing (P < 0.001) and water temperature (P = 0.036) were statistically significant predictors of weekly Chinook salmon catch in the LFC, while Secchi depth was statistically significant (P = 0.007) for the HFC catch. ...