Comprehensive Sturgeon Research Project Blog - 2020

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The USGS Comprehensive Sturgeon Research Project is a multi-year, interdisciplinary research study to determine factors leading to spawning and survival of the endangered pallid sturgeon and the closely related shovelnose sturgeon. 

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Sturgeon and Paddlefish Under the Microscope

By Killian Kelly, Marlene Dodson, Kimberly Chojnacki, and Aaron DeLonay

February 21, 2020

 

The identification of sturgeon, unhatched embryos, and drifting free embryos is essential to many research and monitoring efforts for the endangered pallid sturgeon in the Missouri and Lower Yellowstone rivers.  Identification of young pallid sturgeon collected from the river aids in determining the timing of spawning, discovering functional spawning habitat, and validating the successful survival of embryos and dispersal of free embryos.  Accurate identification is also critical to large-scale studies using releases of free embryos and larvae to assess downstream dispersal and interception processes in supportive habitats (see previous blog post “Unprecedented Pallid Sturgeon Larval Drift Experiment”).  The pallid sturgeon and the shovelnose sturgeon of the Missouri River (both, Scaphirhynchus sturgeons) and Paddlefish (Polyodon spathula) are very similar in appearance at hatching.  Free-embryo Scaphirhynchus sturgeons and paddlefishes can be differentiated by subtle external features such as, the number of barbels, eye characteristics, tail pigmentation, length of snout to the urogenital vent, and length of snout to the beginning of the dorsal finfold.  In contrast to free embryos, identification of fertilized eggs or unhatched embryos as either sturgeon or paddlefish is not possible using visual characteristics.  Eggs and developing embryos are morphologically indistinguishable between pallid sturgeon, shovelnose sturgeon, and paddlefish (all belonging to the order, Acipenseriformes).  Because the three species do all share similar developmental traits biologists can assign a developmental stage to each embryo and free-embryo specimen to provide information about how long ago spawning or hatch may have happened (see previous post, “A Change is Gonna Come”).

Comprehensive Sturgeon Research Project (CSRP) biologists at the Columbia Environmental Research Center (CERC) examine early life-stage sturgeon from many laboratory studies and field collections.  Each sample is individually examined using a research stereomicroscope then developmentally staged and cataloged to be sturgeon, paddlefish, or unknown. Unhatched embryos are determined to be viable, non-viable, or of unknown viability, and are developmentally staged if possible. Many of the specimens that are collected from the river are damaged in the process.  It takes many hours of training for biologists to identify the traits of each species and recognize milestones associated with developmental stages from damaged or partial specimens.  After microscopic assessment the specimens are sent to the Southern Illinois University Carbondale Conservation Genomics Laboratory for genetic testing to conclusively determine the species of each specimen. 

Sturgeon (Scaphirhynchus sp.) and Paddlefish (Polyodon spathula) free embryos showing diagnostic characteristics

Specimens A and B:  Sturgeon (Scaphirhynchus sp.) and Paddlefish (Polyodon spathula) free embryos showing diagnostic characteristics that allow biologists to differentiate between specimens from the two groups using research microscopes in the laboratory.

(Public domain.)

 

 

A conceptual rendering of the Ecoflume to be constructed at the U.S. Geological Survey, Columbia Environmental Research Center

A conceptual rendering of the Ecoflume to be constructed at the U.S. Geological Survey, Columbia Environmental Research Center drawn to approximate scale (A, sideview; B, overhead view).  The flume is a continuous-loop, racetrack flume 1.5 meters wide and 1.0 meters deep with transparent walls in the straight sections to observe sturgeon. (Rendering courtesy of Erik Steen, St. Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN).

(Public domain.)

Bringing the Missouri River into the Laboratory

By Aaron DeLonay, Kimberly Chojnacki, Maura Roberts, Susannah Erwin

The Comprehensive Sturgeon Research Project (CSRP) scientists from the U.S. Geological Survey, in collaboration with scientists at Saint Anthony Falls Laboratory (SAFL) at the University of Minnesota, are working to complete the design of a large, indoor Ecoflume to study the early life-stages of pallid sturgeon from egg deposition through the first year of life.  The design of the flume is guided by results of successful preliminary studies conducted at SAFL in 2018 (see previous blog post, Going with the flow) with free-embryo pallid sturgeon and by computational fluid dynamics modeling.  The proposed Ecoflume designed for CERC will be an oval, continuous-loop, racetrack flume with an overall length of approximately 11.5 meters and volume of nearly 9,500 gallons.  Water will continuously recirculate through the 1.5-meter wide by 1-meter deep channel of the Ecoflume at velocities up to 1 meter per second.  A novel, removable paddlewheel system shown to be safe for sturgeon embryos and free embryos will be used to move the water (0–0.5 meters per second) in the Ecoflume for studies with the earliest life stages.  A pump system with diffuse jets will be used to move water (0–1.0 meters per second) for studies with larvae and juveniles with greater swimming capacity.  The Ecoflume will be temperature controlled and scientists will have the ability to modify substrate and bedforms to simulate conditions like that experienced by young sturgeon in the Missouri River.  The Ecoflume will be instrumented with digital imaging systems and acoustic Doppler velocimeters to study pallid sturgeon behavior, micro-habitat selection, energetics, growth, survival, and comparative responses of shovelnose sturgeon and other native species under controlled fluvial conditions.  Studies will provide insight into monitoring activities and management actions at a scale that is not -possible in the large, turbid, Missouri River.  The Ecoflume is anticipated to be completed in spring of 2021.

Pallid sturgeon free embryos (11 days post-hatch) during preliminary design studies in the EcoFlume at Saint Anthony Falls

Pallid sturgeon free embryos (11 days post-hatch) during preliminary design studies in the EcoFlume at Saint Anthony Falls Laboratory, University of Minnesota.  A novel paddlewheel system moved water through the continuous-loop flume at 0.1 to 0.25 meters second without harming pallid sturgeon early life stages.  

(Credit: Kimberly Chojnacki, U.S. Geological Survey. Public domain.)

 

 

Biological science technician Kathryn Kelly uses a stereomicroscope to identify, measure and stage free-embryo specimens

Biological science technician Kathryn Kelly uses a stereomicroscope to identify, measure, and stage free-embryo specimens collected during the 2019 Drift Study.

(Credit: Marlene Dodson, U.S. Geological Survey. Public domain.)

Drift Study Collects 3,356 Free Embryos—What Comes Next.

By Kimberly Chojnacki, Marlene Dodson, and Killian Kelly

January 30, 2020

 

During the summer of 2019, scientists with the USGS Comprehensive Sturgeon Research Project (CSRP), along with collaborators from the U.S. Army Corps of Engineers; U.S. Fish and Wildlife Service; Montana Fish, Wildlife and Parks; and Southern Illinois University, Carbondale carried out a large-scale larval drift experiment.  The experiment began with the release of over one million day-old and five-day-old pallid sturgeon free embryos into the Upper Missouri River in Montana (see previous blog post “Unprecedented Pallid Sturgeon Larval Drift Experiment”).  For eight days, field crews sampled the river with fine-mesh ichthyoplankton nets (see previous blog post “Down to the Bottom, and Back Again…and Again”) to track the downstream movement of the free-embryo sturgeon.  The effort resulted in the collection and preservation of 3,356 potential sturgeon free embryos.

With the field collection of specimens completed, the experiment moved on to the next phase in the Larval Fish Laboratory at the USGS Columbia Environmental Research Center (CERC).  All collected specimens were shipped to CERC where CSRP biologists sorted and cataloged each individual specimen.   Once cataloged, biologists meticulously examine each specimen using research stereomicroscopes equipped with digital cameras and image analysis software.  Free embryos are preliminarily identified as either a paddlefish or sturgeon, photographed, measured, and assigned a developmental stage using a suite of externally identified morphological characteristics.  Developmental stage data allow biologists to incorporate changes in behavior and swimming ability into hydraulic models to explain changes in rates of downstream dispersal as pallid sturgeon free embryos transition into feeding larvae. To see more on developmental stages of sturgeon see previous post, “A Change is Gonna Come”.

Once each specimen has been photographed, identified, measured, and staged, they will be sent to collaborators at the Southern Illinois University Carbondale Conservation Genomics Laboratory for genetic analyses.  Genetic analyses will identify the specimens to species (shovelnose sturgeon, pallid sturgeon, or paddlefish) and determine which were pallid sturgeon free embryos stocked as part of the drift experiment.

 

 

Reach-scale maps showing depth and velocity of Lower Missouri River pallid sturgeon spawning locations.

Reach-scale maps showing depth and velocity of Lower Missouri River pallid sturgeon spawning locations.

(Public domain.)

USGS Scientists Assess Pallid Sturgeon Spawning Habitat

By Caroline Elliott and Aaron DeLonay

January 8, 2020

 

Researchers from the U.S. Geological Survey, Comprehensive Sturgeon Research Project have published the results of a unique, multi-year study of spawning habitat of the endangered pallid sturgeon in the Lower Missouri River.  The scientific journal article, “Characterization of Pallid Sturgeon (Scaphirhynchus albus) Spawning Habitat in the Lower Missouri River, “ was authored by Caroline Elliott and others and published in the Journal of Applied Ichthyology. 

 

This is the first study to present detailed quantitative measurements and maps of pallid sturgeon spawning habitat in a large, regulated, and channelized river.  For the six years between 2008–2013, biologists used acoustic telemetry to follow tagged female pallid sturgeon during their spring migrations to their spawning locations.  Hydrologists used a multibeam echosounder, and an acoustic Doppler current profiler (ADCP) georeferenced with a high-resolution real-time kinematic global positioning system (RTK GPS) to map depths and velocities at ten confirmed spawning locations.  A sidescan sonar georeferenced with sub-meter DGPS was used to map substrates.

 

Results of the study show pallid sturgeon in the Lower Missouri River select deep and fast areas in or near the navigation channel along outside revetted banks for spawning. These habitats are deeper and faster than nearby river habitats.  Spawning patches used by pallid sturgeon had a mean depth of 6.6 meters and a mean depth-averaged water-column velocity of 1.4 meters per second.  Substrates in spawning patches consisted of coarse bank revetment, gravel, sand, and bedrock.  Results indicate habitat used by pallid sturgeon for spawning may be more common and widespread in the present-day channelized Lower Missouri River relative to coarse substrates available prior to channelization.

 

Citation:  Elliott CM, DeLonay AJ, Chojnacki KA, Jacobson RB. Characterization of Pallid Sturgeon (Scaphirhynchus albus) Spawning Habitat in the Lower Missouri River. J Appl Ichthyol. 2020; 36:25–38. https://doi.org/10.1111/jai.13994

 

 

Putting the Pieces Together: 3-Dimensional Particle Tracking

By Susannah Erwin, Bruce Call, and Aaron DeLonay

January 3, 2020

 

The Comprehensive Sturgeon Research Project (CSRP) is a multi-disciplinary research framework that is designed to combine understanding of sturgeon ecology, biology and behavior with the complex physical context of a highly altered, regulated large river.  Advances in understanding of biological and physical processes reduces uncertainty of management actions designed to promote sturgeon reproduction and survival.  Numerical models - such as drift and dispersal models in use on the Upper Missouri River - are one tool scientists and managers use to evaluate the effects of varying management actions on outcomes for sturgeon.

In advance of the large-scale larval experiment in 2019, USGS geologists and hydrologists conducted statistical analyses of channel width, sinuosity and geomorphic complexity to select a representative reach of the Upper Missouri River (see previous post, “Unprecedented Pallid Sturgeon Larval Drift Experiment”).  High-resolution topographic maps of the river banks and sand bars in the reach were constructed using LiDAR (see previous post, “Mapping the River with Lasers”) and extensive hydrographic surveys using single beam hydroacoustics and an acoustic Doppler profiler (ADCP) were used to map bathymetry and water velocities (see previous post, “Fine-scale Mapping of the Complex Upper Missouri River”).  The result was a high-resolution, multidimensional hydrodynamic model that can be used to examine how water flows through the reach at a wide range of discharges.  CSRP scientists working with USGS colleagues from the USGS Modeling Support and Coordination Branch are using these complex hydraulic models to construct 3-dimensional particle tracking models.

An example of a 3-dimensional particle tracking model of a representative reach of the Upper Missouri River

An example of a 3-dimensional particle tracking model of a representative reach of the Upper Missouri River just downstream from Wolf Point, Montana.  The model shows movement of passive particles simulating “virtual” free-embryo pallid sturgeon dispersing downstream throughout the water column (red), and particles that simulate free-embryo sturgeon drifting near the bottom (blue).

(Public domain.)

Particle tracking models “seed” multidimensional flow fields with populations of virtual particles to track how the particles move through the reach in 3-dimensions.  The particles may be completely passive, or they can be given behavioral traits to simulate the movement of a pallid sturgeon free embryo as it disperses from the spawning patch downstream to supportive rearing habitats.  Particle tracking models provide crucial capabilities to managers considering managing flows, reconfiguring channels, or adjusting reservoir levels to provide for the survival of early life-stage pallid sturgeon.  As laboratory, flume and mesocosm studies increase our understanding of early life stages (see previous post, “Going with the Flow”) particle tracking models can be further refined, adding more ecological and behavioral complexity to explore complex management scenarios.

 

 

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