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  • 1
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    Online Resource
    Convening Expert Taxonomists to Build Image Libraries for Training Automated Classifiers
    Wiley ; 2023
    In:  Limnology and Oceanography Bulletin Vol. 32, No. 3 ( 2023-08), p. 89-97
    Details
    In: Limnology and Oceanography Bulletin, Wiley, Vol. 32, No. 3 ( 2023-08), p. 89-97
    Abstract: Digital imaging technologies are increasingly used to study life in the ocean. To deal with the large volume of image data collected over space and time, scientists employ various machine learning and deep learning algorithms to perform automated image classification. Training of classifiers requires a large number of expertly curated sets of images, a time‐consuming process that requires taxonomic knowledge and understanding of the local ecosystem. The creation of these labeled training sets is the critical bottleneck for building skillful automated classifiers. Here, we discuss how we overcame this barrier by leveraging taxonomic knowledge from a group of specialists in a workshop setting and suggest best practices for effectively organizing image annotation efforts. In our experience, this 2 day workshop proved very insightful and facilitated classification of over 4 years of plankton images obtained at Scripps Pier (La Jolla, CA), focusing on diatoms and dinoflagellates. We highlight the importance of facilitating a dialog between taxonomists and engineers to better integrate ecological goals with computational constraints, and encourage continuous involvement of taxonomic experts for successful implementation of automated classifiers.
    Type of Medium: Online Resource
    ISSN: 1539-607X , 1539-6088
    URL: Issue
    URL: Article
    DOI: 10.1002/lob.v32.3
    DOI: 10.1002/lob.10584
    Language: English
    Publisher: Wiley
    Publication Date: 2023
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  • 2
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    Larval cross‐shore transport estimated from internal waves with a background flow: The effects of larval vertical position and depth regulation
    Wiley ; 2021
    In:  Limnology and Oceanography Vol. 66, No. 3 ( 2021-03), p. 678-693
    Details
    In: Limnology and Oceanography, Wiley, Vol. 66, No. 3 ( 2021-03), p. 678-693
    Abstract: Cross‐shore velocities in the coastal ocean typically vary with depth. The direction and magnitude of transport experienced by meroplanktonic larvae will therefore be influenced by their vertical position. To quantify how swimming behavior and vertical position in internal waves influence larval cross‐shore transport in the shallow (~ 20 m), stratified coastal waters off Southern California, we deployed swarms of novel, subsurface larval mimics, the Mini‐Autonomous Underwater Explorers (M‐AUEs). The M‐AUEs were programmed to maintain a specified depth, and were deployed near a mooring. Transport of the M‐AUEs was predominantly onshore, with average velocities up to 14 cm s −1 . To put the M‐AUE deployments into a broader context, we simulated  〉  500 individual high‐frequency internal waves observed at the mooring over a 14‐d deployment; in each internal wave, we released both depth‐keeping and passive virtual larvae every meter in the vertical. After the waves' passage, depth‐keeping virtual larvae were usually found closer to shore than passive larvae released at the same depth. Near the top of the water column (3–5‐m depth), ~ 20% of internal waves enhanced onshore transport of depth‐keeping virtual larvae by ≥ 50 m, whereas only 1% of waves gave similar enhancements to passive larvae. Our observations and simulations showed that depth‐keeping behavior in high‐frequency internal waves resulted in enhanced onshore transport at the top of the water column, and reduced offshore dispersal at the bottom, compared to being passive. Thus, even weak depth‐keeping may allow larvae to reach nearshore adult habitats more reliably than drifting passively.
    Type of Medium: Online Resource
    ISSN: 0024-3590 , 1939-5590
    URL: Issue
    URL: Article
    DOI: 10.1002/lno.v66.3
    DOI: 10.1002/lno.11632
    Language: English
    Publisher: Wiley
    Publication Date: 2021
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    SSG: 14
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  • 3
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    A novel cross‐shore transport mechanism revealed by subsurface, robotic larval mimics: Internal wave deformation of the background velocity field
    Wiley ; 2020
    In:  Limnology and Oceanography Vol. 65, No. 7 ( 2020-07), p. 1456-1470
    Details
    In: Limnology and Oceanography, Wiley, Vol. 65, No. 7 ( 2020-07), p. 1456-1470
    Abstract: Coastal physical processes are essential for the cross‐shore transport of meroplanktonic larvae to their benthic adult habitats. To investigate these processes, we released a swarm of novel, trackable, subsurface vehicles, the Mini‐Autonomous Underwater Explorers (M‐AUEs), which we programmed to mimic larval depth‐keeping behavior. The M‐AUE swarm measured a sudden net onshore transport of 30–70 m over 15–20 min, which we investigated in detail. Here, we describe a novel transport mechanism of depth‐keeping plankton revealed by these observations. In situ measurements and models showed that, as a weakly nonlinear internal wave propagated through the swarm, it deformed surface‐intensified, along‐isopycnal background velocities downward, accelerating depth‐keeping organisms onshore. These higher velocities increased both the depth‐keepers' residence time in the wave and total cross‐shore displacement, leading to wave‐induced transports twice those of fully Lagrangian organisms and four times those associated with the unperturbed background currents. Our analyses also show that integrating velocity time series from virtual larvae or mimics moving with the flow yields both larger and more accurate transport estimates than integrating velocity time series obtained at a point (Eulerian). The increased cross‐shore transport of organisms capable of vertical swimming in this wave/background‐current system is mathematically analogous to the increase in onshore transport associated with horizontal swimming in highly nonlinear internal waves. However, the mechanism described here requires much weaker swimming speeds (mm s −1 vs. cm s −1 ) to achieve significant onshore transports, and meroplanktonic larvae only need to orient themselves vertically, not horizontally.
    Type of Medium: Online Resource
    ISSN: 0024-3590 , 1939-5590
    URL: Issue
    URL: Article
    DOI: 10.1002/lno.v65.7
    DOI: 10.1002/lno.11400
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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  • 4
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    Data_Sheet_1.pdf
    Frontiers Media SA ; 2020
    In:  Frontiers in Marine Science Vol. 7 ( 2020-7-28)
    Details
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 7 ( 2020-7-28)
    Type of Medium: Online Resource
    ISSN: 2296-7745
    URL: Article
    URL: Article
    DOI: 10.3389/fmars.2020.00602
    DOI: 10.3389/fmars.2020.00602.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
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  • 5
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    Environmental drivers of population variability in colony‐forming marine diatoms
    Wiley ; 2020
    In:  Limnology and Oceanography Vol. 65, No. 10 ( 2020-10), p. 2515-2528
    Details
    In: Limnology and Oceanography, Wiley, Vol. 65, No. 10 ( 2020-10), p. 2515-2528
    Abstract: Many aquatic microbes form colonies, yet little is known about their abundance and fitness relative to single‐celled taxa. The formation of diatom chains, in particular, has implications for diatom growth, survival, and carbon transfer. Here, we utilize an autonomous underwater microscope, combined with traditional microscopy, to develop a novel, multiyear record of the abundance of single‐cell and colony‐forming diatoms at Scripps Pier, a coastal location in the Southern California Bight. The total abundance of diatoms was lower during the warmer and more stratified conditions from 2015 to early 2016, but increased in cooler and less stratified conditions in mid‐2016 to late 2017. Diatom blooms were dominated by chain‐forming taxa, whereas solitary diatoms prevailed during low‐biomass conditions. The abundance of dinoflagellates, some of which are important diatom predators, is highest when colonies (chains) are most abundant. These observations of the diatom assemblage are consistent with a trade‐off between resource acquisition and predator defenses. Solitary diatom cells dominated during conditions with weak nutrient supply because they have a greater diffusive catchment area per cell in comparison to cells living in colonies. In contrast, during bloom conditions when nutrient supply is high and predators are abundant, forming a colony may reduce predation losses to quickly growing microzooplankton predators, and afford chains a higher fitness despite the costs of sharing resources with neighboring cells. These results highlight the contrasting ecology of single‐cell and chain‐forming diatoms, and the need to differentiate them in monitoring campaigns and ecological models.
    Type of Medium: Online Resource
    ISSN: 0024-3590 , 1939-5590
    URL: Issue
    URL: Article
    DOI: 10.1002/lno.v65.10
    DOI: 10.1002/lno.11468
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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    detail.hit.zdb_id: 412737-7
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  • 6
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    The Scripps Plankton Camera system: A framework and platform for in situ microscopy
    Wiley ; 2020
    In:  Limnology and Oceanography: Methods Vol. 18, No. 11 ( 2020-11), p. 681-695
    Details
    In: Limnology and Oceanography: Methods, Wiley, Vol. 18, No. 11 ( 2020-11), p. 681-695
    Abstract: The large data sets provided by in situ optical microscopes are allowing us to answer longstanding questions about the dynamics of planktonic ecosystems. To deal with the influx of information, while facilitating ecological insights, the design of these instruments increasingly must consider the data: storage standards, human annotation, and automated classification. In that context, we detail the design of the Scripps Plankton Camera (SPC) system, an in situ microscopic imaging system. Broadly speaking, the SPC consists of three units: (1) an underwater, free‐space, dark‐field imaging microscope; (2) a server‐based management system for data storage and analysis; and (3) a web‐based user interface for real‐time data browsing and annotation. Combined, these components facilitate observations and insights into the diverse planktonic ecosystem. Here, we detail the basic design of the SPC and briefly present several preliminary, machine‐learning‐enabled studies illustrating its utility and efficacy.
    Type of Medium: Online Resource
    ISSN: 1541-5856 , 1541-5856
    URL: Issue
    URL: Article
    DOI: 10.1002/lom3.v18.11
    DOI: 10.1002/lom3.10394
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2161715-6
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  • 7
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    Phytoplankton Responses to Mesoscale and Submesoscale Processes in a Tropical Meander
    American Geophysical Union (AGU) ; 2024
    In:  Journal of Geophysical Research: Oceans Vol. 129, No. 6 ( 2024-06)
    Details
    In: Journal of Geophysical Research: Oceans, American Geophysical Union (AGU), Vol. 129, No. 6 ( 2024-06)
    Abstract: We present the first physical‐biological measurements of a Brazil Current cyclonic meander drawing high chlorophyll shelf waters offshore Eddy pumping raised nutricline to the euphotic zone driving subsurface phytoplankton enhancement at eddy center and invisible to satellites Distinct hydrodynamic regimes modulated the phytoplankton response in the center, rim, surface, and subsurface of the eddy
    Type of Medium: Online Resource
    ISSN: 2169-9275 , 2169-9291
    URL: Article
    DOI: 10.1029/2023JC020685
    Language: English
    Publisher: American Geophysical Union (AGU)
    Publication Date: 2024
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    detail.hit.zdb_id: 161667-5
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    SSG: 16,13
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  • 8
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    Dinoflagellate vertical migration fuels an intense red tide
    Proceedings of the National Academy of Sciences ; 2023
    In:  Proceedings of the National Academy of Sciences Vol. 120, No. 36 ( 2023-09-05)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 120, No. 36 ( 2023-09-05)
    Abstract: Harmful algal blooms (HABs) are increasing globally, causing economic, human health, and ecosystem harm. In spite of the frequent occurrence of HABs, the mechanisms responsible for their exceptionally high biomass remain imperfectly understood. A 50-y-old hypothesis posits that some dense blooms derive from dinoflagellate motility: organisms swim upward during the day to photosynthesize and downward at night to access deep nutrients. This allows dinoflagellates to outgrow their nonmotile competitors. We tested this hypothesis with in situ data from an autonomous, ocean-wave-powered vertical profiling system. We showed that the dinoflagellate Lingulodinium polyedra ’s vertical migration led to depletion of deep nitrate during a 2020 red tide HAB event. Downward migration began at dusk, with the maximum migration depth determined by local nitrate concentrations. Losses of nitrate at depth were balanced by proportional increases in phytoplankton chlorophyll concentrations and suspended particle load, conclusively linking vertical migration to the access and assimilation of deep nitrate in the ocean environment. Vertical migration during the red tide created anomalous biogeochemical conditions compared to 70 y of climatological data, demonstrating the capacity of these events to temporarily reshape the coastal ocean’s ecosystem and biogeochemistry. Advances in the understanding of the physiological, behavioral, and metabolic dynamics of HAB-forming organisms from cutting-edge observational techniques will improve our ability to forecast HABs and mitigate their consequences in the future.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2304590120
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2023
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  • 9
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    Environmental and ecological drivers of harmful algal blooms revealed by automated underwater microscopy
    Wiley ; 2023
    In:  Limnology and Oceanography Vol. 68, No. 3 ( 2023-03), p. 598-615
    Details
    In: Limnology and Oceanography, Wiley, Vol. 68, No. 3 ( 2023-03), p. 598-615
    Abstract: In recent years, harmful algal blooms (HABs) have increased in their severity and extent in many parts of the world and pose serious threats to local aquaculture, fisheries, and public health. In many cases, the mechanisms triggering and regulating HAB events remain poorly understood. Using underwater microscopy and Residual Neural Network (ResNet‐18) to taxonomically classify imaged organisms, we developed a daily abundance record of four potentially harmful algae ( Akashiwo sanguinea , Chattonella spp., Dinophysis spp., and Lingulodinium polyedra ) and major grazer groups (ciliates, copepod nauplii, and copepods) from August 2017 to November 2020 at Scripps Institution of Oceanography pier, a coastal location in the Southern California Bight. Random Forest algorithms were used to identify the optimal combination of environmental and ecological variables that produced the most accurate abundance predictions for each taxon. We developed models with high prediction accuracy for A. sanguinea (), Chattonella spp. (), and L. polyedra (), whereas models for Dinophysis spp. showed lower prediction accuracy (). Offshore nutricline depth and indices describing climate variability, including El Niño Southern Oscillation, Pacific Decadal Oscillation, and North Pacific Gyre Oscillation, that influence regional‐scale ocean circulation patterns and environmental conditions, were key predictor variables for these HAB taxa. These metrics of regional‐scale processes were generally better predictors of HAB taxa abundances at this coastal location than the in situ environmental measurements. Ciliate abundance was an important predictor of Chattonella and Dinophysis spp., but not of A. sanguinea and L. polyedra . Our findings indicate that combining regional and local environmental factors with microzooplankton populations dynamics can improve real‐time HAB abundance forecasts.
    Type of Medium: Online Resource
    ISSN: 0024-3590 , 1939-5590
    URL: Issue
    URL: Article
    DOI: 10.1002/lno.v68.3
    DOI: 10.1002/lno.12297
    Language: English
    Publisher: Wiley
    Publication Date: 2023
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    detail.hit.zdb_id: 412737-7
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  • 10
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    Deformation of ambient chemical gradients by sinking spheres
    Cambridge University Press (CUP) ; 2020
    In:  Journal of Fluid Mechanics Vol. 892 ( 2020-06-10)
    Details
    In: Journal of Fluid Mechanics, Cambridge University Press (CUP), Vol. 892 ( 2020-06-10)
    Abstract: A sphere sinking through a chemical gradient drags fluid with it, deforming the gradient. The sphere leaves a trail of gradient enhancement that persists longer than the velocity disturbance in the Reynolds $10^{-2}\leqslant Re\leqslant 10^{2}$ , Froude $10^{-1}\leqslant Fr\leqslant 10^{3}$ and Péclet $10^{2}〈Pe\leqslant 10^{6}$ regime considered here. We quantify the enhancement of the gradient and the diffusive flux in the trail of disturbed chemical left by the passing sphere using a combination of numerical simulations and scaling analyses. When $Fr$ is large and buoyancy forces are negligible, dragged isosurfaces of chemical form a boundary layer of thickness $\unicode[STIX]{x1D6FF}_{\unicode[STIX]{x1D70C}}$ around the sphere with diameter $l$ . We derive the scaling $\unicode[STIX]{x1D6FF}_{\unicode[STIX]{x1D70C}}/l\sim \mathit{Pe}^{-1/3}$ from the balance of advection and diffusion in the chemical boundary layer. The sphere displaces a single isosurface of chemical a maximum distance $\mathit{L}_{Def}$ that increases as $\mathit{L}_{Def}/l\sim l/\unicode[STIX]{x1D6FF}_{\unicode[STIX]{x1D70C}}\sim \mathit{Pe}^{1/3}$ . Increased flux through the chemical boundary layer moving with the sphere is described by a Sherwood number, $Sh\sim l/\unicode[STIX]{x1D6FF}_{\unicode[STIX]{x1D70C}}\sim \mathit{Pe}^{1/3}$ . The gradient enhancement trail extends much farther than $\mathit{L}_{Def}$ as displaced isosurfaces slowly return to their original positions through diffusion. In the reference frame of a chemical isosurface moving past the sphere, a new quantity describing the Lagrangian flux is found to scale as $\mathit{M}\sim (\mathit{L}_{Def}/l)^{2}\sim \mathit{Pe}^{2/3}$ . The greater $\mathit{Pe}$ dependence of $\mathit{M}$ versus $Sh$ demonstrates the importance of the deformation trail for determining the total flux of chemical in the system. For $\mathit{Fr}\geqslant 10$ , buoyancy forces are weak compared to the motion of the sphere and the preceding results are retained. Below $\mathit{Fr}=10$ , an additional Froude dependence is found and $l/\unicode[STIX]{x1D6FF}_{\unicode[STIX]{x1D70C}}\sim Sh\sim Re^{1/6}Fr^{-1/6}Pe^{1/3}$ . Buoyancy forces suppress gradient deformation downstream, resulting in $\mathit{L}_{Def}/l\sim Re^{-1/3}Fr^{1/3}Pe^{1/3}$ and $\mathit{M}\sim Re^{-1/3}Fr^{1/3}Pe^{2/3}$ . The productivity of marine plankton – and therefore global carbon and oxygen cycles – depends on the availability of microscale gradients of chemicals. Because most plankton exist in the fluids regime under consideration, this work describes a new mechanism by which sinking particles and plankton can stir weak ambient chemical gradients a distance $\mathit{L}_{Def}$ and increase chemical flux in the trail by a factor of  $\mathit{M}$ .
    Type of Medium: Online Resource
    ISSN: 0022-1120 , 1469-7645
    URL: Article
    DOI: 10.1017/jfm.2020.191
    Language: English
    Publisher: Cambridge University Press (CUP)
    Publication Date: 2020
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