Limnology and Oceanography: Methods最新文献

{"title":"Applicability of the steady-state oxygen stable isotope method for estimating metabolism in low-productivity Arctic lakes","authors":"Fredrik Alriksson,&nbsp;Marcus Klaus,&nbsp;Cristian Gudasz,&nbsp;Matthew Bogard,&nbsp;Gerard Rocher-Ros,&nbsp;Dominic Vachon,&nbsp;Jan Karlsson","doi":"10.1002/lom3.70048","DOIUrl":"https://doi.org/10.1002/lom3.70048","url":null,"abstract":"<p>Metabolism is a key property of lake ecosystem functioning, but logistical challenges make it difficult to estimate across remote regions. The steady-state dissolved oxygen (DO) stable isotope method (¹⁸O method) estimates metabolism from discrete water samples and thus enables large-scale surveys. However, this method relies on the assumptions that the upper mixed layer DO saturation (DO_%) relative to its isotopic composition (δ¹⁸O_DO) is at a steady state and that an increase in DO_% results in a proportional decrease in δ¹⁸O_DO. The applicability of these assumptions has not been broadly assessed for small, low-productivity lakes with predominantly benthic metabolism. We evaluated the ¹⁸O method in these types of systems by surveying 184 Arctic lakes in Sweden and found that the method consistently produces realistic estimates of metabolism in well-mixed conditions and when water temperatures were relatively stable. Under such conditions, results from the ¹⁸O method agreed with those from the free-water diel DO method, and rates derived from both methods responded similarly to environmental drivers. In contrast, we found that the ¹⁸O method frequently generated unrealistic metabolic rates when temperatures were rising. Increasing temperatures may increase DO_% irrespective of δ¹⁸O_DO in the upper mixed layer and promote lake stratification, both violating the assumptions of the ¹⁸O method and preventing benthic metabolism from being integrated by surface water samples. We conclude that the ¹⁸O method is a powerful tool for studying metabolism in Arctic lakes across large spatial gradients, provided that temperature dynamics and vertical stratification are considered.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 6","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Red, green, blue color indices as proxy for Symbiodiniaceae cell density and chlorophyll content during coral bleaching","authors":"Erik Francesco Ferrara,&nbsp;Lavinia Bauer,&nbsp;Giulia Puntin,&nbsp;Friederike Bautz,&nbsp;Sibel Celayir,&nbsp;Marie-Sa Do,&nbsp;Frederik Eck,&nbsp;Melissa Heider,&nbsp;Pia Wissel,&nbsp;Angelina Arnold,&nbsp;Thomas Wilke,&nbsp;Jessica Reichert,&nbsp;Maren Ziegler","doi":"10.1002/lom3.70047","DOIUrl":"https://doi.org/10.1002/lom3.70047","url":null,"abstract":"<p>Coral bleaching, the breakdown of the symbiosis between the coral host and endosymbiotic microalgae, is the main cause of widespread coral reef degradation. Current visual assessment methods for coral health, including color reference cards, are constrained by subjective human color perception and limited resolution. Red, green, blue (RGB) color channel analysis through digital photography provides a rapid, noninvasive, and standardized approach for estimating key physiological parameters. While image analysis is extensively used in plant studies, the relationship between coral color and physiological parameters during bleaching requires further attention. In this study, we analyzed the correlation between Symbiodiniaceae cell density and total chlorophyll content across three coral species (<i>Acropora muricata</i>, <i>Pocillopora verrucosa</i>, and <i>Stylophora pistillata</i>) with 19 color indices currently established as predictors of chlorophyll content in plants. We exposed corals to three bleaching treatments (short-term and long-term heat stress and menthol bleaching) and correlated physiological parameters with color indices to identify the index with the strongest linear correlation. We found that the red channel had the strongest and most consistent linear correlation with Symbiodiniaceae cell density and chlorophyll content across species (<i>R</i>² values up to 0.97), enabling a direct interpretation of relative changes in channel intensity values as changes in tissue parameters. Additionally, training a model with 10–12 samples allows for accurate predictions of Symbiodiniaceae densities, achieving over 95% accuracy, compared to models trained on larger datasets. This research improves image analysis as a reliable, non-invasive tool for monitoring coral health using RGB data.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 6","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70047","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Demonstration, validation, and application of hyperspectral microscopy for the collection of cyanobacterial spectral signatures","authors":"Natalie C. Hall,&nbsp;Adam C. Mumford,&nbsp;Aaron M. Goldfain,&nbsp;David W. Allen,&nbsp;E. Terrence Slonecker,&nbsp;Alisa Shtabnoy,&nbsp;Carl J. Legleiter,&nbsp;Sarah A. Spaulding","doi":"10.1002/lom3.70038","DOIUrl":"https://doi.org/10.1002/lom3.70038","url":null,"abstract":"<p>Cyanobacterial and other algal blooms are an environmental concern in waterbodies worldwide. While these blooms are a nuisance for recreational activities, they can also be harmful to human and wildlife health when the algae produce and release toxins. Algal community composition can be monitored and analyzed by acquiring hyperspectral images that provide information on various photosynthetic and accessory pigments. Validated, traceable measurements are needed to compare data collected by different hyperspectral instruments. In this proof-of-concept study, we detail the development and validation of a custom hyperspectral microscopy imaging system and assess whether this technology can differentiate between cyanobacteria genera based on differences in their reflectance characteristics. As not all cyanobacteria produce toxins, the ability to distinguish among taxa could be used to identify potential toxin-producers and guide field sampling and further research. Spectral characterization of these taxa contributes to remote sensing efforts to characterize and identify cyanobacterial genera at larger spatial scales.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 6","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sampling effort to characterize estuarine macroinfaunal communities in patchy habitats","authors":"Paul A. Montagna","doi":"10.1002/lom3.70045","DOIUrl":"https://doi.org/10.1002/lom3.70045","url":null,"abstract":"<p>Estuarine benthic macroinfauna have aggregated, patchy distributions, making accurate community measurements dependent upon sampling scales. The purpose of this study is to determine the appropriate core sizes and sampling effort needed to characterize benthic infaunal communities in Corpus Christi Bay, Texas, USA. Macroinfauna were sampled with small (6.7 cm) and large cores (15 cm) at two sites to determine if different sampling sizes characterized different spatial scales. Vertical distribution was sampled from 0 to 20 cm (0–3 cm, 3–10 cm, and 10–20 cm) to determine appropriate sampling depths. Eleven replicates of small cores were collected to assess species accumulation with area sampled. The log-area to log-diversity relationship was used to determine which core size and number of replicates accurately estimated abundance, biomass, and diversity of macrofauna. Seven replicates of small cores captured 100% of species richness. In the same area sampled, small cores found 25% more species diversity than large cores in one station and 58% more in the other. Three to five replicates of small (6.7 cm) cores provided sufficient precision to estimate abundance, biomass, and diversity. In Corpus Christi Bay, small scale patch dynamics regulate community structure and sampling with three replicate small cores to a depth of 10 cm can accurately characterize the small-scale patches.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 6","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70045","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance of a glider-mounted multifrequency echosounder for measuring the vertical distribution and abundance of large pelagic copepods","authors":"Delphine Mossman,&nbsp;Joseph D. Warren,&nbsp;Natasha J. Hynes,&nbsp;Kimberley T. A. Davies","doi":"10.1002/lom3.70042","DOIUrl":"https://doi.org/10.1002/lom3.70042","url":null,"abstract":"<p>The difficulty of sampling zooplankton communities in situ has driven advancements in autonomous, remote sensing technology. The goal of this paper was to perform a gear comparison study testing the performance of one such piece of technology—a glider-mounted four-frequency echosounder—against traditional shipboard methods of measuring zooplankton, with a particular focus on stage C5 <i>Calanus finmarchicus</i> distribution. Abundance data from concurrent vessel (nets, optical plankton counter) and glider-mounted acoustic backscatter were collected over a 9-d period in two deep basins in the outer Bay of Fundy, Canada. Zooplankton were generally found in depth-stratified layers, with <i>C. finmarchicus</i> in particular being concentrated near the bottom of both basins, and smaller copepods near the surface. The echosounder was typically able to discriminate between the presence and absence of <i>C.finmarchicus</i> layers vertically in the water column and resolve patchiness within the deep layer. The echosounder was unable to detect layers of small copepods. We found moderate correlation between expected and observed backscatter that depended primarily on echosounder frequency. <i>C. finmarchicus</i> concentration was best predicted (<i>R</i>² = 0.26) by observed backscatter using the 455 kHz frequency filtered using the dB difference between the 200 and 455 kHz frequencies. Absolute concentration estimates from the echosounder after correction with the derived linear model remained consistently lower than net-derived estimates by approximately one order of magnitude. Overall, the glider-mounted instrument performed well at its given objectives, and we recommend its use in other areas where patch location is an important attribute to determine.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 6","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 5","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148069883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PNNL-TUNAMELT: Toward automating the detection of interactions with marine energy devices using acoustic camera sensors","authors":"Theodore Nowak,&nbsp;Garrett Staines,&nbsp;Blerim Abdullai","doi":"10.1002/lom3.70024","DOIUrl":"https://doi.org/10.1002/lom3.70024","url":null,"abstract":"<p>Acoustic cameras, or imaging sonars, are often used to monitor marine energy sites in regions where the water is too dark or turbid for optical sensing. To do so more effectively, scientists are investigating automated detection methodologies to use on these data. However, prior work has found that existing automated detection approaches struggle with the dynamic image background around marine energy devices—such as moving turbine blades. While open-access datasets, methods, and standard evaluation metrics are needed to quickly develop and compare novel automated detection methods, none yet exist for this domain. Using previously collected data, in this work we created a labeled dataset of possible marine life interactions in acoustic camera video around an operating tidal turbine. We call this dataset the Pacific Northwest National Laboratory dataset for Tracking Underwater Nautical Activity around Marine Energy LocaTions or PNNL TUNAMELT dataset. In addition to this dataset, we developed an automated detection pipeline which filters noise from the acoustic camera imagery and then performs object detection to identify possible targets. To analyze our automated detection pipeline, we used a series of common detection and classification metrics. In doing so, we found that our pipeline detected 98% of targets and removed 70% of target-less frames in our dataset. These results illustrate our method's potential utility as an aid to a human analyst tasked with extracting targets of interest from the dataset. Finally, we openly release our labeled dataset and all associated code to support and encourage future work in this domain.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 4","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148048544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of very short-term formalin fixation on coral carbon and nitrogen stable isotopes, total lipids, and chlorophyll a and c2 concentrations","authors":"Shannon L. Dixon,&nbsp;Ann Marie Hulver,&nbsp;Christopher R. Suchocki,&nbsp;Claire E. Bardin,&nbsp;Claire J. Lewis,&nbsp;R3D Consortium,&nbsp;Robert J. Toonen,&nbsp;Andréa G. Grottoli","doi":"10.1002/lom3.70027","DOIUrl":"https://doi.org/10.1002/lom3.70027","url":null,"abstract":"<p>The type of tissue preservation used in coral studies determines the type and quantity of downstream analyses that can be conducted on a given sample. Formalin is often used as a tissue preservative, but its effect on downstream analyses is unknown in coral specimens. We evaluated the effects of very short-term (up to 3 h) formalin fixation on carbon and nitrogen stable isotopes (δ¹³C and δ¹⁵N) of the coral host and algal endosymbiont, total lipid concentration, and chlorophyll <i>a</i> and <i>c2</i> (Chl <i>a</i> and Chl <i>c2</i>) concentrations in two coral species, <i>Montipora capitata</i> and <i>Porites compressa</i>. δ¹³C and δ¹⁵N values were unaffected by formalin fixation when all data from both coral species were pooled. However, when examined at the species level, <i>P. compressa</i> host δ¹⁵N was lower when fixed with formalin. Total lipid, Chl <i>a</i>, and Chl <i>c2</i> concentrations were not altered by formalin fixation. Contrary to previous thinking, our study demonstrates that some physiological and isotopic analyses can be reliably performed on very short-term formalin preserved coral tissue samples.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 4","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148050571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A systematic framework for automated rip current detection from numerically modeled flow data","authors":"Yuli Liu,&nbsp;Changming Dong,&nbsp;Xiang Li,&nbsp;Fan Yang","doi":"10.1002/lom3.70022","DOIUrl":"https://doi.org/10.1002/lom3.70022","url":null,"abstract":"<p>Rip currents are strong, offshore-directed water jets that pose severe safety concerns to bathers at recreational beaches. While numerical modeling has been increasingly used in studying rip current dynamics and forecasting nearshore hydrodynamics, automatically detecting rip currents from model data remains challenging due to variable spatiotemporal characteristics and complex flow patterns associated with different types of rip currents. In this paper, a systematic framework for automated rip current detection was developed and validated across a range of bathymetries and wave conditions using data from the Boussinesq model FUNWAVE simulations. Specifically, the framework integrates physics-based criteria, considering both rip current kinematics and structural characteristics, along with multi-step identification and tracking procedures that account for spatiotemporal dynamics. Manual validation shows over 95% accuracy in locating rip currents and over 90% accuracy in detecting their occurrence times across different rip current types. Additionally, complex evolutionary behaviors, including the coexistence of multiple rips in close proximity and significant structural changes in individual rip currents, can be effectively detected. Furthermore, the method's potential for real-world applications is demonstrated by its successful implementation under a realistic bathymetry and observed wave conditions at Habin Beach, Zhuhai, where rip currents lasting from a few minutes to hours at multiple locations were detected over a 5-d period. Overall, the systematic and automated framework for rip current detection demonstrates promising outcomes for enhancing the analysis of numerically modeled data, with possible benefits from both scientific and hazard mitigation perspectives.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 4","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148049515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 4","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148072340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}