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Limnology and Oceanography: Methods

Wiley

All preprints, ranked by how well they match Limnology and Oceanography: Methods's content profile, based on 11 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

1
Using dilution grazing assays to measure size fractionated phytoplankton mortality rates across the freshwater-to-marine continuum

Barnard, M. A.; Paerl, H. W.

2022-02-24 ecology 10.1101/2022.02.23.481667 medRxiv
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There is a need for a unified grazing method that can be used across the freshwater-to-marine continuum. To accomplish this, this research utilized dilution grazing assays across the freshwater-to-marine continuum and across the oligotrophic-to-hypereutrophic gradient by measuring size fractions of dilution-based mortality. This was investigated by using 0.7 {micro}m and 0.2 {micro}m prefiltered water and major ion solutions (MIS) as diluent media for use in the Landry-Hassett grazing bioassays run in lake, river, estuarine (riverine and lagoonal), and oceanic shelf systems. Because MIS does not include vitamins that would be in prefiltered natural water, vitamin effects on grazing rate determination were also investigated for the MIS bioassays. Results show that the dilution grazing method can be broadly applied across the freshwater-to-marine continuum and across trophic gradients.

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The Plankton Imager (Pi-10): An imaging instrument for automated and continuous zooplankton data collection

Scott, J.; Pitois, S.; Culverhouse, P.; Blackwell, R.; Close, H.; Tilbury, J.

2025-01-28 ecology 10.1101/2025.01.27.635045 medRxiv
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The Pi-10 is the latest iteration of the Plankton Imager: a high-speed colour line-scan camera that images particles in a flow-through system. The Pi-10 is a cost-effective, easy to install and low maintenance automated instrument that can be used on any platform with access to water and power supply. We tested the Pi-10 on the research vessel Cefas Endeavour, connected to a continuous water supply pumping water at 34 L min-1. The instrument collected images of particles, within the size range of 180 {micro}m - 3.5 cm, automatically and continuously, alongside other vessel operations, in all weathers over a period of 18 days. The Pi-10 successfully captured and saved up 5000 images per minute, translating into a 46 GB of digital storage per day. When particle density exceeded 147 per litre, the instrument stopped saving all images, while still recording the number of particles that passed through the system. This is akin to subsampling, with more sub-sampling required in areas or times of high particle density (e.g at the time of spring plankton bloom or in turbid waters). The Pi-10 collects high volumes of data in a continuous manner, thus providing unprecedented fine spatial data. The high frequency nature of the instrument opens the door to new areas of research. These include, in particular, the observation of fine scale processes, the move towards real-time sampling, and the increased capability to build a digital twin of the oceans. As technologies continue evolving the Pi-10 performance will increase, being able to collect and save more and more images.

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Detritus identification in FlowCAM using a simple binary classifier

Garcia-Oliva, O.

2024-11-19 ecology 10.1101/2024.11.18.624123 medRxiv
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Phytoplankton and detritus particles may be co-captured in Flow-CAM systems, leading to misrepresentation of phytoplankton abundance. In this study, I use logistic regression as a binary classifier to identify detritus particles in FlowCAM data from the Southern North Sea. Standard particle features from the manufacturers software were used as inputs, with surface texture (intensity variance) and compactness (derived from particle perimeter and area) proving most relevant to detritus classification. This classifier achieved 81% accuracy using a training dataset of approximately 7300 observations, reducing the workload compared to other classification methods. The reconstructed particle size spectra closely matched the observed spectra for detritus and phytoplankton. Binary classifiers like this offer a fast, effective alternative for detritus screening, aiding the pre-processing and re-analysis of FlowCAM datasets.

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Primary production dynamics during the decline phase of the North Atlantic annual spring bloom

Meyer, M. G.; Brzezinski, M.; Cohn, M. R.; Kramer, S. J.; Paul, N.; Sharpe, G. C.; Niebergall, A. K.; Gifford, S. M.; Cassar, N.; Marchetti, A.

2023-05-18 ecology 10.1101/2023.05.18.541304 medRxiv
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The second field campaign of the NASA EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) program was conducted in the late spring of 2021 within the vicinity of the Porcupine Abyssal Plain (49.0{degrees}N, 16.5{degrees}W) in the North Atlantic Ocean. Observations from EXPORTS support previous characterizations of this system as highly productive and organic matter rich, with the majority of primary production occurring in large cells ([&ge;] 5 {micro}m) such as diatoms that are primarily utilizing nitrate. Rates of total euphotic zone depth-integrated net primary production ranged from 36.4 to 146.6 mmol C m- 2 d-1, with an observational period average f-ratio of 0.74, indicating predominantly new production. Substantial variability in the contribution of small (<5 {micro}m) and large cells occurred over the observation period, coinciding with the end of the annual spring phytoplankton bloom. Physical changes associated with storms appear to have impacted the integrated production rates substantially, enhancing rates by [~]10%. These disturbances altered the balance between contributions of the different phytoplankton size fractions, thus highlighting the important role of mixed layer variability in nutrient entrainment into the upper water column and production dynamics. In diatoms, inputs of silicic acid related to deepening of the mixed layer increased silicic acid uptake rates yet concomitant increases in NPP in large cells was not observed. This campaign serves as the high productivity endmember within the EXPORTS program and as such, elucidates how nutrient concentrations and size class play key roles in both low and high productivity systems, but in differing ways.

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Phytoplankton phenology through gene expression during the North Atlantic spring bloom decline

Meyer, M. G.; Torano, O.; Llopis-Monferrer, N. L.; Cassar, N.; Cohn, M. R.; Brzezinski, M. A.; Marchetti, A.

2025-10-15 ecology 10.1101/2025.10.15.682395 medRxiv
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While phytoplankton dynamics in the annual North Atlantic spring bloom have been well characterized, the physiological underpinnings driving these changes and their net impact on the biogeochemistry of the region are less understood. Phytoplankton metabolism is both affected by, and influences the regions nutrient cycling, primary production, and ultimately, the fate of carbon export. Thus, developing an understanding of these processes is critical. Phytoplankton biomass, biological rates, and gene expression data along with associated environmental parameters were measured as part of the NASA EXport Processes in the Ocean from RemoTe Sensing programs campaign to the North Atlantic to evaluate the relationships amongst these processes within the four most dominant phytoplankton groups (diatoms, dinoflagellates, haptophytes, and chlorophytes) during the spring bloom. We observe a transition from a period dominated by active diatom growth (defined as Phase I) to a period dominated by non-diatom phytoplankton groups (Phase II). Silicic acid depletion appears to limit overall production and reduce competition from diatoms, likely leading to enhanced contributions of haptophytes in Phase II. Expression of key protein-encoding genes involved in cell maintenance, photosynthesis, and nitrogen and vitamin metabolisms varied amongst the taxa throughout the observation period. Expression patterns of diatom genes involved in silicon transport suggest an apparent uncoupling between genes involved in nitrate uptake and photosynthesis, resulting in an increase in silicification independent growth. Our analysis demonstrates the utility in combining gene expression with biological rate processes to provide a more holistic view of phytoplankton bloom dynamics and phenology.

6
A method for correcting systematic error in PO2 measurement to improve measures of oxygen supply capacity

Timpe, A. W.; Seibel, B. A.

2024-02-28 physiology 10.1101/2024.02.25.581970 medRxiv
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An organisms oxygen supply capacity () can be measured as a ratio of the metabolic rate (MR) and the critical oxygen partial pressure (Pc). However, this metric is sensitive to errors in the measurement of PO2, especially at low PO2 where the ratio of instrument error to environmental oxygen is magnified. Consequently, the oxygen supply capacity of animals, particularly those that evolved in low-oxygen environments, may appear unnaturally high and variable. Here, we present a method to correct for instrumental calibration error and use simulated and literature datasets to demonstrate how it can be used post hoc to diagnose error in, correct the magnitude of, and reduce the variability in repeat measures of the oxygen supply capacity.

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A novel method for characterising the inter- and intra-lake variability of CH4 emissions: validation and application across a latitudinal transect in the Alpine region

Tomelleri, E.; Scholz, K.; Pighini, S.; Carotenuto, F.; Gioli, B.; Miglietta, F.; Sommaruga, R.; Tonon, G.; Zaldei, A.; Wohlfahrt, G.

2023-01-21 ecology 10.1101/2023.01.19.524063 medRxiv
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Lakes in the Alpine region are recognised as critical CH4 emitters, but a robust characterisation of the magnitude and variability of CH4 fluxes is still needed. We developed a mobile platform for CH4 eddy covariance (EC) flux measurements to tackle this gap. Our approach was shown to be well suited to catch all CH4 emission pathways and overcome the limitations of other methods (e.g., gradient-based). This is by surpassing their local nature and thus being suited for characterising the variability of the within-lake emissions, primarily because of CH4 emissions by ebullition stochasticity. The mobile system was deployed at nine lakes across a latitudinal transect in the Alps and validated by comparing the measured fluxes with a fixed EC station and to chambers and boundary layer estimates. Methane fluxes were explained by water turbidity, dissolved organic carbon, dissolved nitrogen, elevation, particulate organic carbon, and total phosphorus. The highest fluxes and most substantial seasonal variability were found in a shallow low-altitude lake in the Southern Alps. Additionally, the mobile EC permitted to resolve the spatial structure of fluxes at the selected lakes. Finally, we demonstrated the usability of our novel mobile system to characterise intra- and inter-lake variability of fluxes. We suggest that characterising the intra-lake emission heterogeneity and a deeper understanding of inter-lake emission magnitude differences is fundamental for a solid estimate of freshwater CH4 budgets. Key PointsO_LICH4 emissions from alpine lakes are recognised to be an important component to the global methane budget but they are poorly characterized C_LIO_LIWe developed and validated a mobile eddy covariance platform for capturing CH4 fluxes across lakes in the alpine region for two years C_LIO_LIA robust statistical model based on a few in-situ physicochemical and biological parameters can be generally used to predict CH4 fluxes C_LI

8
Comparing fluorometric methods (in vivo vs extracted) for cyanoHAB monitoring in six Rhode Island ponds

Shivers, S.; Hollister, J. W.; Fournier, S.; Stankoski, J. A.; Kreakie, B. J.

2025-06-23 ecology 10.1101/2025.06.17.660268 medRxiv
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Harmful algal blooms caused by cyanobacteria (cyanoHABs) are detrimental to human and environmental health and can be difficult to monitor without specialized training and equipment. A variety of instruments have been developed to measure cyanoHAB indicators (i.e., chlorophyll a or phycocyanin) that do not require advanced laboratory processes (e.g., pigment extraction). We compared measurements from five in vivo fluorometers (Turner Trilogy in-vivo module, Turner Fluorosense, Turner Cyanofluor, bbe AlgaeTorch, and bbe Phycoprobe) to results from solvent-based extractions for chlorophyll a and phycocyanin at six different waterbodies in Rhode Island. We found a strong relationship between extracted phycocyanin and in vivo fluorometers (R2 ranging from 0.78-0.96). We found less consistency between in vivo measurements of chlorophyll a and the extracted results (R2 between 0.34 and 0.82). Some variability in the chlorophyll a results can be explained by differences in the phytoplankton community across the different sampling sites. Phycocyanin results from in vivo fluorometry were also strongly related with cell counts, which implies that phycocyanin measurements from these instruments can be a good proxy for cell counts. Many federal, state, and local entities use cell counts of cyanobacteria to determine when to issue health or contact advisories for waterbodies. Producing accurate cell counts requires highly specialized training/equipment, processing time, and counts can vary greatly between technicians. The results from this study encourage further adoption of in vivo fluorometry and phycocyanin for cyanoHAB monitoring efforts.

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Monitoring Lake Okeechobee Harmful Algal Bloom populations and dynamics with a long-duration Autonomous Surface Vehicle

Ruiz-Xomchuk, V.; Duncan, S.; McFarland, M. N.; Beckler, J. S.

2023-08-23 ecology 10.1101/2023.08.23.554529 medRxiv
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This article describes the main findings of a full year of continuous operation of a 2-meter Autonomous Sail and Solar Surface Drone, the Nav2 (Navocean Inc.), as part of a Harmful Algal Bloom (HAB) monitoring program in Lake Okeechobee. The Nav2 was equipped with a set of water quality and atmospheric sensors, that recorded high frequency measurements ({inverted exclamation} 1 min) and transmitted near real-time information to allow reporting through a web portal for assessment and operation responses. Major findings include detection of HABs early in the year through chlorophyll (chl-a) and phycocyanin (phyco) fluorometric measurements, as well as different spatial scales of variability in the algal patches. The 24/7 high resolution monitoring allowed detection of patch motion and discrimination between growth and motion along a transect. Furthermore, the platform can potentially fingerprint specific HAB species based on the relatively fine-scale spatial expression of the phyco to chl-a ratio, which essentially captures the bloom macrostructure (e.g. surface scums versus more uniform sub-surface waves over 0.1 - 1 km scale). Sensor outputs, when converted to concentrations based on calibrated with pure laboratory standards, did not accurately yield true chl-a or phyco values when compared to validation samples, likely due to the high turbidity of the lake. However, routine solid-state validations of fluorometric measurements proved useful for assessing consistency in optical sensors to check for sensor drift (e.g. to due biofouling), which was not significant. Overall this demonstration shows that the Nav2 can uniquely and reliably provide in situ HAB and environmental monitoring capabilities in a large, turbid, shallow lake. We envision that platform as an innovative technology for water resource managers by providing turn-key long-duration baseline environmental data (hands-off waypoint navigation), early warnings of HABs for protecting human health, and for HAB mitigation monitoring.

10
Complete zooplankton size spectra re-constructed from in situ imaging and Multinet data in the global ocean

SOVIADAN, Y. D.; Dugenne, M.; Drago, L.; Biard, T.; Trudnowska, E.; Romagnan, J.-B.; Jamet, J.-L.; Kiko, R.; Gorsky, G.; Stemmann, L.

2023-06-29 ecology 10.1101/2023.06.29.547051 medRxiv
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Plankton size spectra are important indicators of the ecosystem state, as they illustrate the quantity of organisms available for higher marine food web and reflect multiple size-dependent processes. Yet, such measurements are typically biased by the available sampling methods, either disrupting fragile organisms or lacking good resolution (in size and/or time and space). In this study, we combined two of the most common approaches to measure zooplankton Normalized Biomass/Biovolume Size Spectra (NBSS) to calculate a complete zooplankton distribution for organisms larger than 1 mm. The reconstructed NBSS slopes appeared steeper and closer to those measured by the UVP5 (+7.6%) and flatter than those of the Multinet (- 20%) particularly in tropics and temperate latitudes. The overall gain in polar biomass was relatively small for reconstructed biomass compared to bulk estimates from Multinet (+0.24 mgC/m3 or +4.25%) and high from the UVP5 (+2.0 mgC/m3 or +53%). In contrast, in the tropical and temperate ecosystems, the gain in biomass was small for UVP5 (+0.67 mgC/m3 or +30.44% and +0.74 mgC/m3 or +19.59% respectively) and high for Multinet (+1.66 mgC/m3 or +136% and +3.4 mgC/m3 or +309% respectively). Given these differences, we suggest here to combine in situ imaging sensors and net data in any comprehensive study exploring key living players in the ocean ecosystem and their contributions to the biological pump.

11
Laboratory application of the Aquascope approach of automated imaging and classification for long-term plankton monitoring

Merkli, S.; Reyes, M.; Pomati, F.

2024-02-24 ecology 10.1101/2024.02.23.581739 medRxiv
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Anthropogenic changes such as climate change and pollution have strong effects on plankton and its ecosystem services. In freshwater, phytoplankton forms the basis of the food web and plays a key role in water quality. It is therefore important to monitor the plankton community. In Switzerland, lake plankton has been monitored for decades by cantonal authorities. But in the future, there will be a limitation in the availability of trained taxonomists that are able to count plankton samples under the microscope as well as time and budget constraints. New technologies will be needed to fulfil the federal requirements on the monitoring of lakes in the future. Here we focus on two such instruments, both based on plankton automated imaging: the FlowCam and the Aquascope. The first is a commercially available instrument, the second is custom made. They are the only automated imaging instruments that can track freshwater plankton across the desired size range (phytoplankton and zooplankton). Their design makes them the state of the art technologies to make quantitative observations of plankton. While the FlowCam is a laboratory instrument, the Aquascope is originally designed for field deployment. In this report, we focus the empirical work on the laboratory application of the Aquascope approach of automated imaging and classification for long term plankton monitoring. We find that there are major advantages of the Aquascope approach but the application as a laboratory instrument still needs further development. The major advantages of the Aquascope approach compared to traditional, human-supervised, microscopy methods are the automation and the speed of the data processing, the availability of individual level traits and the management of the data generated. One of the major drawbacks is the lack of taxonomic resolution (mostly at the genus level). Nevertheless, we show that with a larger benchmarking project, it might be possible to continue the long term time series on a coarse taxonomic level as usually reported by cantonal authorities to the general public. We discuss advantages and limitations of Aquascope relative to traditional microscopy and FlowCam, and propose ways forward for future development and application of this approach.

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Sea butterflies in a pickle: Reliable biomarkers and seasonal sensitivity of pteropods to ocean acidification in the Gulf of Maine

Maas, A. E.; Lawson, G. L.; Bergan, A. J.; Wang, Z. A.; Tarrant, A. M.

2023-08-02 physiology 10.1101/2023.07.31.551235 medRxiv
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The passive dissolution of anthropogenically produced CO2 into the ocean system is reducing ocean pH and changing a suite of chemical equilibria, with negative consequences for some marine organisms, in particular those that bear calcium carbonate shells. Although our monitoring of these chemical changes has improved, we have not developed effective tools to translate observations, which are typically of the pH and carbonate saturation state, into ecologically relevant predictions of biological risks. One potential solution is to develop bioindicators: biological variables with a clear relationship to environmental risk factors that can be used for assessment and management. Thecosomatous pteropods, a group of pelagic shelled marine gastropods, whose biological responses to CO2 have been suggested as potential bioindicators of OA owing to their sensitivity to acidification in both laboratory and the natural environment. Using five CO2 exposure experiments, occurring across 4 seasons and running for up to 15 days, we describe a consistent relationship between saturation state, shell transparency, and duration of exposure, as well as identify a suite of genes that could be used for biological monitoring. We clarify variations in thecosome responses due to seasonality, resolving prior uncertainties and demonstrating the range of their phenotypic plasticity. These biomarkers of acidification stress can be implemented into ecosystem models and monitoring programs in regions where pteropods are found, while the approach will serve as an example for other regions on how to bridge the gap between point-based chemical monitoring and biologically relevant assessments of ecosystem health. Summary StatementDespite seasonal variability, pteropods exposed to acidification over multiple seasons reveal consistent patterns in gene expression and shell condition that can be used as bioindicators of ocean acidification stress.

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Microalgal pigments and their relation with phytoplankton carbon biomass on the northeastern Mediterranean Sea shore, with special emphasis on nanophytoplankton

Eker-Develi, E.; Konucu, M.; Örek, H.; Basduvar, S.

2019-08-23 ecology 10.1101/745588 medRxiv
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Summary Marker pigments are used as a proxy for biomass of distinct phytoplankton classes in different oceanic regions. However, sometimes disagreements are observed between microscopy and accessory-pigment based approaches in distinct regions mainly due to changing environmental factors governing diversity and structure of community composition. In this study, concordance between microscopy and HPLC-CHEMTAX methods were investigated first time in coastal waters of Erdemli, Turkey, in the Levantin Basin of the northeastern Mediterranean Sea by weekly intervals during 2015-2016. According to our results, marker pigment of diatoms, fucoxanthin, which was the most prominent pigment in the study area during most of the year, was a better indicator of diatom abundance than diatom carbon biomass. CHEMTAX derived values of diatom chlorophyll a (Chl a) were not in concert with either abundance or carbon biomass of this group. Contribution of dinoflagellates and cryptophytes to the phytoplankton community was underestimated with pigment based approach. Accessory pigment of cyanophytes, zeaxanthin, was also an important pigment in the samples. Biomass of haptophytes seemed to be overestimated by HPLC-CHEMTAX analysis. In contrast to diatoms, CHEMTAX derived chlorophyll a values of cryptophytes were correlated with abundance of this group but not with alloxanthin. Inclusion of live counts of nanoplanktic cryptophytes, haptophytes and prasinophytes provided a better correlation between microscopy and pigment based results. According to CHEMTAX analysis, nanoplankton and picoplankton constituted [~]55% of Chl a in the region.

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Blooms like it hot, but mussels do not: Influence of invasive quagga mussels on cyanobacteria during summer

Mauch, J.; Erize Gardoki, M.; Neiling, R.; Koehler, J.; Facey, J.; Hilt, S.

2026-02-23 ecology 10.64898/2026.02.21.707163 medRxiv
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Quagga mussels (Dreissena rostriformis bugensis) are among the most impactful invaders in freshwaters of the Northern Hemisphere. As filter-feeders, they can reduce harmful algal blooms (HABs), but their effects are expected to be dependent on cyanobacteria species and water temperature. However, conclusive studies on these traits and their combination are lacking. Here, we combined laboratory experiments with an analysis of long-term data from a temperate shallow lake 10 years before and after quagga mussel invasion, respectively. We tested the hypotheses that quagga mussel filtration rates in the laboratory would 1) vary among common cyanobacteria species and 2) decrease above a critical temperature. Regarding the field data, we expected that 3) quagga mussels can reduce the summer biovolume of palatable cyanobacteria, but that 4) this effect disappears above a critical temperature. Our results support all four hypotheses. In laboratory experiments, Dolichospermum flos-aquae was classified as palatable to quagga mussels, while Aphanizomenon flos-aquae, Anabaenopsis elenkinii and Microcystis aeruginosa were less-palatable cyanobacteria. Filtration rates decreased above 28.9{degrees}C (CI: 27.6-30.2{degrees}C) with mussels dying at 32{degrees}C. Our long-term lake data show that cyanobacteria biovolumes were lower after quagga mussel invasion, but only below 27.7{degrees}C (CI: 26.9-28.4{degrees}C), confirming a critical thermal window for quagga mussel filtration. Global warming will therefore facilitate HABs by increasing the growth rates of cyanobacteria and reducing the filtration rates of quagga mussels above critical summer water temperatures, which are increasingly being reached in invaded lakes. This critical thermal window must be considered when making HAB predictions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/707163v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@175851eorg.highwire.dtl.DTLVardef@76a481org.highwire.dtl.DTLVardef@12a3965org.highwire.dtl.DTLVardef@11e3e7d_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Variability in the relationship between ocean phytoplankton diversity and carbon biomass across methods and scales

Kramer, S. J.

2026-02-24 ecology 10.64898/2026.02.19.706895 medRxiv
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More diverse ecosystems on land and in the ocean are thought to be more productive, stable, and resistant to change, but these relationships are highly variable across systems and scales. Although the productivity-diversity relationship (PDR) has been extensively explored on land, there are limited in-water observations of the PDR in marine ecosystems. In this work, the relationship between phytoplankton diversity and carbon biomass (as a proxy for productivity) was examined using a global in situ dataset. The shape of this relationship was evaluated for three metrics of phytoplankton diversity: pigment concentrations modeled from hyperspectral remote sensing reflectance (Rrs({lambda})), pigment concentrations measured by high performance liquid chromatography (HPLC), and 18S rRNA gene sequences. While gene sequencing methods provide higher resolution taxonomic information about phytoplankton communities, remote sensing methods collect higher resolution spatiotemporal information on global scales. By comparing these methods (Rrs({lambda})-modeled pigments vs. measured HPLC pigments vs. 18S rRNA gene sequences), this work demonstrates the variability in the relationship between phytoplankton diversity and carbon biomass based on the method of assessing these parameters, and establishes a baseline for in situ observations that has the potential to be extended to global observations from NASAs Plankton Aerosol Cloud ocean Ecosystem (PACE) satellite.

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Hyperspectral Remote Sensing for Harmful Algal Bloom Detection: Pseudo-nitzschia in the Northeast Pacific

Bailess, A.; Baetge, N.; Barnard, A.; Tufillaro, N.; Behrenfeld, M.; Bill, B.; Kudela, R.; Graff, J.; Kavanaugh, M.

2026-02-26 ecology 10.64898/2026.02.24.707776 medRxiv
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1Diatoms are microscopic marine algae that are critical for global primary production, carbon sequestration, and fisheries productivity. However, select diatoms may form harmful algal blooms, which threaten marine ecosystems and the fisheries they sustain. Rapidly identifying harmful blooms is necessary to effectively manage marine resources, yet current identification methods are limited by expensive and labor-intensive in situ point sampling. Hyperspectral remote sensing enables scalable monitoring, but its ability to resolve taxonomic shifts within phytoplankton groups (e.g. diatoms) is largely unknown. To investigate this uncertainty, we cultured four dominant diatom genera from the California Current upwelling system, including this systems most abundant harmful algae, Pseudo-nitzschia. The hyperspectral absorption and backscatter of these taxa were measured and used to model spectral reflectances that remote sensing platforms (satellites/drones) might detect. Differences between fingerprints of these taxa were quantified using vector-based and statistical analyses. Mean spectral differences of 48% were observed between the most dominant diatom, Thalassiosira, and the most toxic diatom, Pseudo-nitzschia. Differences of approximately 30% were found between Pseudo-nitzschia and the second and third most abundant diatoms, Chaetoceros and Asterionellopsis. Successful identification of Pseudo-nitzschias reflectance fingerprint was driven by the presence of a unique feature around 560 nm. The distinct spectral fingerprint of Pseudo-nitzschia indicates that it can be distinguished from benign diatom blooms using hyperspectral remote sensing platforms.

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Glucose Uptake as an Alternative to Stop-Flow Respirometry for Measuring Metabolic Rate in Danio rerio Larvae

Evans, B. L.; Shiels, H. A.; Hurlstone, A. F.; Stevens, A.; Clayton, P. E.

2021-04-30 physiology 10.1101/2021.04.30.442098 medRxiv
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Respirometry is the current gold-standard for measuring metabolic rate. However, there is a growing need for metabolic rate measurements suitable for developmental studies, particularly in Danio rerio, where many important developmental stages occur at < 4 mm. While many metabolic studies rely on respirometry, the cost and complexity of the equipment limits its appeal in non-specialist labs, and background respiration becomes increasingly problematic as the size of the organism reduces. Here, glucose uptake was compared to stop-flow respirometry as an alternative measure of metabolic rate more suitable to the small scale required for developmental studies. A Passing-Bablok regression revealed the rate of glucose uptake can be considered equivalent to oxygen consumption as a measure of metabolic rate in Danio rerio larvae within a 95% limit of agreement. Therefore, glucose uptake is a valid alternative to the gold-standard in small organisms where conventional respirometry is problematic. Summary statementThe rate of glucose uptake is a valid alternative to respirometry for metabolic rate measurements in small larval fish.

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From Blue to Pink: Resazurin as a High-Throughput Proxy for Metabolic Rate in Oysters

Huffmyer, A. S.; Ozguner, N.; Baird, M.; Elvrum, C.; Kounellas, C.; Dicksion, D.; White, S. J.; Plough, L.; Gavery, M. R.; Krebs, N.; Walton, W.; Small, J.; Pitsenbarger, M.; Ealy-Whitfield, H.; Roberts, S.

2025-11-07 physiology 10.1101/2025.11.06.686367 medRxiv
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Metabolic rate assays are critical tools for assessing organismal stress and resilience, yet their widespread application in aquaculture and ecological monitoring is limited. Improving these assays is essential for hatchery managers, farmers, and scientists seeking to identify resilient stocks and monitor stress in shellfish populations. Resazurin, a redox-sensitive dye commonly used in cell viability assays, offers a promising, high-throughput assay for metabolic rate assessment, but its application at the whole-organism level remains under explored. This study evaluates the efficacy of a resazurin-based metabolic assay in oysters (Crassostrea gigas and Crassostrea virginica) through four experimental approaches: (1) adaptation of the resazurin assay to measure oyster metabolism, (2) examination of temperature effects on oyster metabolism, (3) characterization of acute thermal stress responses, (4) examination of genetic variability in metabolism, and (5) correlations between metabolism and predicted performance in a selective breeding case study. Our findings confirm that resazurin fluorescence is correlated with oxygen consumption, validating its use as a measure of metabolism. Thermal performance assays reveal expected metabolic responses to temperature, including identification of optima and tipping points where metabolic stimulation shifts to depression under temperature stress. Acute thermal stress experiments demonstrate that oysters exhibiting greater metabolic depression are more likely to survive, supporting metabolism as a predictor of mortality. Further, genetic variation in stress responses is detected as family-level variation in metabolism. Metabolism of 50 families (C. virginica) selectively bred for performance in varying environments was measured and significantly correlated with predicted performance. By establishing resazurin as an additional reliable and scalable method for metabolic assessment, this study lays the groundwork for its broader adoption in aquaculture and conservation. Implementing this approach may provide a tool to enhance stock selection, improve hatchery management practices, and support adaptive strategies in the face of climate variability and increased environmental stress in coastal oceans.

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Simultaneous collection of 87Sr/86Sr and trace-element data in otoliths and other sclerochronological hard structures

Hegg, J. C.; Fisher, C. M.

2020-04-25 ecology 10.1101/2020.04.24.060640 medRxiv
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Chronological data from hard structures have been instrumental in reconstructing information about the past across numerous disciplines. Isotopic and trace elemental chronologies from the depositional layers of speleothems, corals, bivalve shells, fish otoliths and other structures are routinely used to reconstruct climate, growth, temperature, geological, archeological and migratory histories. Recent in situ analytical advances have revolutionized the use of these structures. This is particularly true of fish, in which detailed origin, life-history, and migration history can be reconstructed from their otoliths. Specifically, improvements in laser ablation-inductively coupled plasma mass spectrometry (LA-ICPMS) have allowed increases in temporal resolution, precision, and sample throughput. Many studies now combine multiple chemical and isotopic tracers, taking advantage of multivariate statistical methods and multiple trace-elements and isotope systems to glean further information from individual samples. This paper describes a novel laser ablation split-stream (LASS) methodology which allows simultaneous collection of the Sr isotope composition (87Sr/86Sr) and trace-elemental data from chronologically deposited carbonate samples. The study investigates the accuracy and precision of varying laser spot sizes on a marine shell standard and fish otoliths using LASS and presents a comparison to traditional "single stream methods" using pre-existing otolith data on the same samples. Our results indicate that LASS techniques can be used to provide accurate and precise data at the same laser spot sizes as previous otolith studies, thereby doubling analytical throughput, while also providing improved spatially and temporally-matched data reduction using newly developed features for the Iolite data reduction platform.

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The effects of elevated seawater pH and total alkalinity following dosing of sodium hydroxide in Calanus finmarchicus

Murray, C. S.; Marx, L.; Aluru, N.; Wang, Z. A.; Chen, K.; Kim, H. H.; Michel, A.; McCorkle, D. C.; Rheuban, J. E.; Subhas, A.

2026-02-05 ecology 10.64898/2026.02.03.700700 medRxiv
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Ocean Alkalinity Enhancement (OAE) is a marine carbon dioxide removal (mCDR) strategy that involves adding alkaline substances to surface waters to enhance CO2 uptake and storage. The dispersal of alkaline materials such as sodium hydroxide (NaOH) into seawater can cause rapid increases in pH and total alkalinity (TA) that substantially exceeds natural variability in marine environments. Such fluctuations may negatively affect marine life, especially small animals like copepods who cannot avoid OAE plumes and whose physiological processes could be disrupted by large and rapid shifts in seawater pH. To address knowledge gaps regarding potential biological impacts of OAE, we studied these effects in Calanus finmarchicus, a keystone copepod species in the Northwest Atlantic Ocean. We exposed C. finmarchicus from the late juvenile copepodite stages and adult females to NaOH-dosed seawater at pH 10.5 ([~]5,000 {micro}mol kg-1 TA) and pH 9.0 ([~]3,150 {micro}mol kg-1 TA) for durations that reflect expected short-term exposure times during field OAE deployments (pH 10.5: 1, 5, 10 minutes; pH 9.0: 1, 15, 30 minutes). None of the treatment combinations resulted in mortality immediately after the initial exposure. Individuals were monitored for survival for 72 hours post-exposure (hpe), and only one treatment group (juveniles exposed to pH 10.5 for 10 minutes) showed a significant reduction in final survival; no other pH-duration combination showed increased mortality. Effects on the ability to initiate an escape response were more substantial. Adult females treated with pH 10.5 for 5 or 10 minutes showed a significant reduction in escape response immediately after exposure. In contrast, juveniles showed no immediate change in escape response following exposure to pH 10.5 or pH 9.0, although juveniles exposed to pH 10.5 for 10 minutes exhibited reduced escape response at 24 hpe. Using microrespirometry, we measured oxygen consumption following a 10-minute exposure to pH 10.5 and detected no effect on routine metabolic rate immediately post-exposure or at 12 hpe. Overall, our results suggest that C. finmarchicus is relatively tolerant to short-term exposures to very high pH and alkalinity. Future work should prioritize longer-term exposure under more moderate ocean OAE conditions.