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Long‐term culture system for deep‐sea mussels Gigantidas childressi Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-04-18 Claas Hiebenthal, Finn‐Ole Gehlert, Mark Schmidt, Thorsten B. H. Reusch, Frank Melzner
The simulation of deep‐sea conditions in laboratories is technically challenging but necessary for experiments that aim at a deeper understanding of physiological mechanisms or host‐symbiont interactions of deep‐sea organisms. In a proof‐of‐concept study, we designed a recirculating system for long‐term culture (>2 yr) of deep‐sea mussels Gigantidas childressi (previously Bathymodiolus childressi)
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Simple and affordable colorimetric sensing strips for quantitative determination of total manganese in porewater samples Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-04-18 Ignacio Pedre, Nico Fröhberg, Hannelore Waska, Andrea Koschinsky, Katharina Pahnke
Simple and economical colorimetric strips for measuring manganese (Mn) in natural waters are described. For their construction, leucomalachite green (LMG) embedded in a Nafion® polymeric matrix was immobilized on a polyvinylchloride surface. Upon immersing the strips in the sample, any soluble manganese(II/III) present catalyzed the oxidation of the LMG base to malachite green by adding sodium periodate
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Development and use of a novel diver‐operated ski for surveying nearshore rocky reef habitats Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-04-11 Carol S. Thornber, Giancarlo Cicchetti, Lindsay Green‐Gavrielidis, Niels‐Viggo S. Hobbs, Gabrielle Pantoni, David L. Taylor
The use of camera and video technologies for conducting underwater surveys has rapidly expanded over the past several decades. However, the utility of these systems can be significantly hampered by numerous logistical factors, including limited underwater visibility, rough bottom topography, and ease of use for the operator. Video studies can be difficult to compare when methods and terminologies differ
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From seasonal field study to surrogate modeling: Investigating the biomechanical dynamics of Elymus sp. in salt marshes Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-04-11 Kara Keimer, Felix Kind, Inga Prüter, Viktoria Kosmalla, Oliver Lojek, David Schürenkamp, Markus Prinz, Stephan Niewerth, Jochen Aberle, Nils Goseberg
Salt marshes have been studied in the context of ecosystem services they can provide for coastal protection. In this study, monthly field campaigns focusing on Elymus spp. and its biomechanical properties were conducted from December 2021 to December 2022 on the German Barrier Island Spiekeroog. A total of 1390 specimens were investigated to determine their growth length, out of which 418 specimens
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First application of one‐class support vector machine algorithms for detecting abnormal behavior of marine medaka Oryzias javanicus exposed to the harmful alga Karenia mikimotoi Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-04-11 Abrianna Elke Chairil, Yuki Takai, Yosuke Koba, Shinya Kijimoto, Yukinari Tsuruda, Ik‐Joon Kang, Yuji Oshima, Yohei Shimasaki
It is empirically known that fish exposed to harmful algal blooms (HABs) exhibit abnormal behavior. This might serve as a method for early detection of HABs. There has been no report of the detection of behavioral abnormalities of fish exposed to harmful algae using machine learning. In this study, the behavior of Oryzias javanicus (Java medaka) exposed in a stepwise manner to the HAB species Karenia
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Developing a hybrid model with multiview learning for acoustic classification of Atlantic herring schools Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-04-10 Yawen Zhang, Carrie C. Wall, J. Michael Jech, Qin Lv
Advances in active acoustic technology have outpaced the ability to process and analyze the data in a timely manner. Currently, scientists rely on manual scrutiny or limited automation to translate acoustic backscatter to biologically meaningful metrics useful for fisheries and ecosystem management. The National Oceanic and Atmospheric Administration Northeast Fisheries Science Center has monitored
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An improved method to quantify bulk carbohydrate in marine planktonic samples Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-03-28 Ying-Yu Hu, Andrew J. Irwin, Zoe V. Finkel
The TPTZ (2,4,6-tripyridyl-s-triazine) method is used to detect monosaccharides from seawater and particulate matter samples because it is sensitive, precise, rapid and easy to perform. Contrary to mechanisms proposed in the literature, we provide evidence that the TPTZ method detects hydroxyl as well as aldehyde groups in monosaccharides when all reducing groups are fully deprotonated in alkaline
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In vivo injection of exogenous molecules into octocorals: Application to the study of calcification Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-04-01 Clémence Forin, Guillaume Loentgen, Denis Allemand, Sylvie Tambutté, Philippe Ganot
In vivo studies of the effects of molecules of interest, such as hormones or xenobiotics on corals, are essential to uncover their effects on coral biological processes. However, exposure to such molecules is very challenging in aquarium systems due to the duration of exposure, the high cost of the compounds, their quantity, and their diffusion in seawater. In this study, we provide a durable alternative
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Development of a fast‐response system with integrated calibration for high‐resolution mapping of dissolved methane concentration in surface waters Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-04-01 Jesse T. Dugan, Thomas Weber, John D. Kessler
Dissolved gas concentrations in surface waters can have sharp gradients across marine and freshwater environments, which often prove challenging to capture with analytical measurement. Collecting discrete samples for laboratory analysis provides accurate results, but suffers from poor spatial resolution. To overcome this limitation, water equilibrators and gas membrane contactors (GMCs) have been used
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Interpreting biogeochemical processes through the relationship between total alkalinity and dissolved inorganic carbon: Theoretical basis and limitations Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-03-14 Hang Yin, Lei Jin, Xinping Hu
The marine carbonate system is influenced by anthropogenic CO2 uptake, biogeochemical processes, and physical changes that involve freshwater input and removal. Two frequently used parameters to quantify seawater carbonate system are total alkalinity (TA) and total dissolved inorganic carbon (DIC). To account for the physical changes, both TA and DIC are usually normalized to a reference salinity (i
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A video monitoring and computational system for estimating migratory juvenile fish abundance in river systems Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-03-14 Meghna N. Marjadi, Sidney Batchelder, Ryan Govostes, Allison H. Roy, John J. Sheppard, Meghan‐Grace Slocombe, Joel K. Llopiz
Diadromous fishes migrate between marine and fresh waters for reproduction. For anadromous species, which spawn in freshwater, improved access to freshwater spawning and nursery habitats and ability of juveniles to emigrate to the ocean may support population recovery. Despite the potentially enormous influence of early life stage survival on adult population size, managers and scientists have limited
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A new framework for estimating abundance of animals using a network of cameras Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-03-01 Camille Magneville, Capucine Brissaud, Valentine Fleuré, Nicolas Loiseau, Thomas Claverie, Sébastien Villéger
While many ecology studies require estimations of species abundance, doing so for mobile animals in an accurate, non‐invasive manner remains a challenge. One popular stopgap method involves the use of remote video‐based surveys using several cameras, but abundance estimates derived from this method are computed with conservative metrics (e.g., maxN computed as the maximum number of individuals seen
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Automated monitoring of early life-stage development in Atlantic cod (Gadus morhua) embryos exposed to a reference toxicant Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-02-29 David R. Williamson, Ron R. Togunov, Emlyn J. Davies, Martin Ludvigsen, Bjørn Henrik Hansen
Early life stages of fish are widely used for regulatory toxicity testing, and marine fish display high sensitivity to pollutant exposure. Exposure to pollutants during embryogenesis causes acute effects on embryonic development and survival, but also sub-lethal impacts manifested as maldeveloped larvae. Acquiring time- and exposure-dependent responses to pollutant exposure and other stressors in small
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Investigating the impacts of solid phase extraction on dissolved organic matter optical signatures and the pairing with high‐resolution mass spectrometry data across a freshwater stream network Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-02-28 J. Alan Roebuck Jr, Allison N. Myers‐Pigg, Vanessa Garayburu‐Caruso, James Stegen
Advancing our understanding of dissolved organic matter (DOM) chemistry in aquatic systems necessitates the integration of data streams from multiple analytical platforms. Some measurements require pretreatment with solid phase extraction (SPE), while others are performed directly on whole water samples. Evidence has suggested that SPE will be biased against select DOM fractions, leading to concerns
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Lotic‐SIPCO2: Adaptation of an open‐source CO2 sensor system and examination of associated emission uncertainties across a range of stream sizes and land uses Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-02-26 Andrew L. Robison, Lauren E. Koenig, Jody D. Potter, Lisle E. Snyder, Christopher W. Hunt, William H. McDowell, Wilfred M. Wollheim
River networks play a crucial role in the global carbon cycle, as relevant sources of carbon dioxide (CO2) to the atmosphere. Advancements in high‐frequency monitoring in aquatic environments have enabled measurement of dissolved CO2 concentration at temporal resolutions essential for studying carbon variability and evasion from these dynamic ecosystems. Here, we describe the adaptation, deployment
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A temperature‐controlled, circular maintenance system for studying growth and development of pelagic tunicates (salps) Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-02-24 Svenja J. Müller, Wiebke Wessels, Sara Driscoll, Evgeny A. Pakhomov, Lutz Auerswald, Katharina Michael, Bettina Meyer
Salps have attracted attention as zooplankton organisms that may be able to expand their habitat range and increase their ecological importance in the face of ongoing global warming. Due to their gelatinous nature, unique feeding strategy, and reproductive ecology such changes could have profound impacts on regional marine ecosystems. While their role in the regional carbon cycle is receiving attention
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Toward a synthesis of phytoplankton communities composition methods for global‐scale application Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-02-23 Sasha J. Kramer, Luis M. Bolaños, Dylan Catlett, Alison P. Chase, Michael J. Behrenfeld, Emmanuel S. Boss, E. Taylor Crockford, Stephen J. Giovannoni, Jason R. Graff, Nils Haëntjens, Lee Karp‐Boss, Emily E. Peacock, Collin S. Roesler, Heidi M. Sosik, David A. Siegel
The composition of the marine phytoplankton community has been shown to impact many biogeochemical processes and marine ecosystem services. A variety of methods exist to characterize phytoplankton community composition (PCC), with varying degrees of taxonomic resolution. Accordingly, the resulting PCC determinations are dependent on the method used. Here, we use surface ocean samples collected in the
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Hit or miss? Impact of time series resolution on resolving phytoplankton dynamics at hourly, weekly, and satellite remote sensing frequencies Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-02-21 Virginie Sonnet, Colleen B. Mouw, Audrey B. Ciochetto, Jessica Carney‐Almeida
Characterizing marine phytoplankton community variability is crucial to designing sampling strategies and interpreting time series. Satellite remote sensing, microscopy sampling, and flow through imaging systems have widely different resolutions: from weekly or monthly with microscopy sampling to daily when no cloud cover or glint is present with polar‐orbiting satellites, and hourly for autonomous
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Combined benthic and stream edge sampling better represent macroinvertebrate assemblages than benthic sampling alone along an aridity gradient Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-02-15 Brian A. Gill, Daniel C. Allen, Meryl C. Mims, Thomas M. Neeson, Albert Ruhi, Carla L. Atkinson, Arial J. Shogren, Travis M. Apgar, Zacchaeus G. Compson, Stephen Cook, Daryl R. Trumbo, Michelle H. Busch, Kelsey D. Hollien, Kyle Leathers, Megan C. Malish, Grace L. O'Malley, Samuel Silknetter, Chelsea R. Smith, Howard Dunleavy, Michael T. Bogan
Studies of stream macroinvertebrates traditionally use sampling methods that target benthic habitats. These methods could underestimate biodiversity if important assemblage components exist outside of the benthic zone. To test the efficacy of different sampling methods, we collected paired reach-wide benthic and edge samples from up to 10 study reaches in nine basins spanning an aridity gradient across
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The Ellrott grab: A small, lightweight sediment sampler for collecting undisturbed sandy sediments Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-01-15 Chyrene Moncada, Andreas Ellrott, Dirk de Beer, Rudolf Amann, Katrin Knittel
Sampling sandy surface sediments is an important first step in understanding biogeochemical processes in these dynamic environments. However, sampling such sediments poses several challenges, especially when undisturbed samples with porewater are required. Several grab samplers are commercially available, but they are either prone to sample loss, too heavy or bulky for use in small vessels, or those
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A chlorophyll a, non-photochemical fluorescence quenching correction method for autonomous underwater vehicles in shelf sea environments Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2024-01-11 Catherine Mitchell, David Drapeau, Sunny Pinkham, William M Balch
Autonomous underwater vehicles provide water column observations of phytoplankton biomass using chlorophyll a (Chl a) fluorometers. However, under high incident light, phytoplankton fluorescence yield decreases in a process known as non-photochemical quenching, resulting in a reduced Chl a fluorescence signal. Methods have been developed to identify and remove the quenched signal from observations
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An automated modular heating solution for experimental flow-through stream mesocosm systems Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-12-08 Iris Madge Pimentel, Philipp M. Rehsen, Arne J. Beermann, Florian Leese, Jeremy J. Piggott, Sebastian Schmuck
Water temperature is a key environmental variable in stream ecosystems determining species distribution ranges, community composition, and ecological processes. In addition to global warming, direct anthropogenic impacts, for example through the influx of power plant cooling water or due to sun exposure after the removal of riparian vegetation, result in elevated water temperatures. However, temperature
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Rapid quantitative assessment of temporal and spatial variation in key functional genes of the microbial nitrogen cycle across multiple marine environments using the NanoString nCounter Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-12-01 Jennifer Tolman, Dhwani Desai, Julie LaRoche
The marine nitrogen cycle controls oceanic productivity through enzymatic processes mediated by microbes. Here, we report the construction, evaluation, and application of the OceansN CodeSet for the NanoString nCounter, which quantifies a suite of protein-coding genes that are central to microbially mediated nitrogen cycle processes in the ocean. We also placed emphasis on quantifying a diverse set
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Dimethylmercury in natural waters—analytical and experimental considerations Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-30 Johannes West, Diana Babi, Alyssa Azaroff, Sofi Jonsson
Mono- and dimethylmercury (MMHg and DMHg, respectively) are the two primary organic forms of mercury (Hg) found in natural waters. While experimental approaches to characterize the environmental behavior of MMHg and inorganic forms of Hg are widely used today, few laboratories conduct experimental studies entailing the use of DMHg. In this paper, we have evaluated and developed different analytical
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The influence of dynamic resources and stable isotope incorporation rates on aquatic consumer trophic position estimation Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-28 Megan L. Feddern, Jens M. Nielsen, Timothy E. Essington, Gordon W. Holtgrieve
A key assumption in trophic position (TP) estimation using stable isotope analysis is that consumers are in isotopic equilibrium with their resources. Here, we assess the degree to which time-varying resource dynamics and isotope incorporation rates of consumers influence consumer TP estimates across multiple trophic levels and aquatic ecosystems. We constructed a first-order kinetics model to explore
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An assessment of HgII to preserve carbonate system parameters in organic-rich estuarine waters Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-27 Christopher S. Moore, Robert H. Byrne, Kimberly K. Yates
This work assesses the effectiveness of sample preservation techniques for measurements of pHT (total scale), total dissolved inorganic carbon (CT), and total alkalinity (AT) in organic-rich estuarine waters as well as the internal consistency of measurements and calculations (e.g., AT, pHT, and CT) in these waters. Using mercuric chloride (HgCl2)-treated and untreated water samples, measurements of
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A new, global optical sediment trap calibration Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-23 Margaret L. Estapa, Colleen Andrea Durkin, Wayne H. Slade, Christine L. Huffard, Sean P. O'Neill, Melissa M. Omand
Autonomous sensors for gravitational carbon flux in the ocean are critically needed, because of uncertainties in the projected response of the biological carbon pump (BCP) to climate change, and the proposed, engineered acceleration of the BCP to sequester carbon dioxide in the ocean. Optical sediment trap (OST) sensors directly sense fluxes of sinking particles in a manner that is independent of,
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Classification of suspended particles in seawater using an in situ polarized light scattering prototype Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-17 Hanbo Deng, Hongjian Wang, Zhiming Guo, Jiajin Li, Ran Liao, Hening Li, Qiang Li, Hui Ma
Classification of suspended particles characterizes the composition of seawater, which helps the interpretation of remote sensing data and promotes the researches of the matter exchanges in ocean processes. In this article, an in situ prototype based on polarized light scattering is introduced, and its ability to classify the suspended particles is demonstrated. The experimental results show that the
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A bold new purpose for an old method: Using invertebrate kick-netting to improve monitoring of microplastic pollution in running waters Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-16 Aidan Mora-Teddy, Gerry P. Closs, Christoph D. Matthaei
Freshwaters are impacted by many pollutants. Scientists and resource managers need to reliably detect and monitor these pollutants by employing appropriate sampling techniques to quantify and mitigate their impacts. Emerging freshwater contaminants such as microplastics are difficult to monitor as effective sampling techniques have not been fully developed and lack standardization. Here, we propose
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Taming the data deluge: A novel end-to-end deep learning system for classifying marine biological and environmental images Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-10 Hongsheng Bi, Yunhao Cheng, Xuemin Cheng, Mark C. Benfield, David G. Kimmel, Haiyong Zheng, Sabrina Groves, Kezhen Ying
Underwater imaging enables nondestructive plankton sampling at frequencies, durations, and resolutions unattainable by traditional methods. These systems necessitate automated processes to identify organisms efficiently. Early underwater image processing used a standard approach: binarizing images to segment targets, then integrating deep learning models for classification. While intuitive, this infrastructure
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A novel method to sample individual marine snow particles for downstream molecular analyses Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-10 Chloé M.J. Baumas, Fatima-Ezzahra Ababou, Marc Garel, Mina Bizic, Danny Ionescu, Arthur Puzenat, Frederic A.C. Le Moigne, Hans-Peter Grossart, Christian Tamburini
The ocean–atmosphere exchange of carbon largely depends on the balance between carbon export of particulate organic carbon (POC) as sinking marine particles, and POC remineralization by attached microbial communities. Despite the vast spectrum of types, sources, ages, shapes, and composition of individual sinking particles, they are usually considered as a bulk together with their associated microbial
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Simultaneous preconcentration of 9Be and cosmogenic 10Be for determination of the 10Be/9Be ratio in (coastal) seawater Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-08 Chenyu Wang, Daniel A. Frick, Friedhelm von Blanckenburg, Martin Frank, Ergang Lian, Shouye Yang, Hella Wittmann
Beryllium isotopes have emerged as a quantitative tracer of continental weathering, but accurate and precise determination of the cosmogenic 10Be and stable 9Be in seawater is challenging, because seawater contains high concentrations of matrix elements but extremely low concentrations of 9Be and 10Be. In this study, we develop a new, time-efficient procedure for the simultaneous preconcentration of
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Lab-based multispectral photography for approximating chlorophyll content in Zostera marina Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-08 Katherine Ann Haviland, Melanie Hayn, Robert Warren Howarth
Reduced light is one of the primary threats to seagrass meadows in the coming decades, with reduced light reaching the benthos due to eutrophication. We assessed a multispectral photography technique using near-infrared photography to estimate chlorophyll content in the seagrass Zostera marina. Using near-infrared and red wavelength cameras in the lab environment, we measured normalized difference
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HOTFLOOR: A benthic chamber system to simulate warming on the seafloor Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-06 Norman Göbeler, Laura Kauppi, Robin Gottberg, Göran Lundberg, Alf Norkko, Joanna Norkko
The frequency of abnormally warm water events is increasing not only in surface waters, but also in subsurface layers, with major impacts on benthic ecosystems. Previous insights on heatwave effects have been obtained through field observations or manipulative laboratory experiments. Here, we introduce a system capable of inducing elevated water temperatures in benthic habitats in situ over several
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Resolving phytoplankton pigments from spectral images using convolutional neural networks Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-06 Pauliina Salmi, Ilkka Pölönen, Daniel Atton Beckmann, Marco L. Calderini, Linda May, Justyna Olszewska, Laura Perozzi, Salli Pääkkönen, Sami Taipale, Peter Hunter
Motivated by the need for rapid and robust monitoring of phytoplankton in inland waters, this article introduces a protocol based on a mobile spectral imager for assessing phytoplankton pigments from water samples. The protocol includes (1) sample concentrating; (2) spectral imaging; and (3) convolutional neural networks (CNNs) to resolve concentrations of chlorophyll a (Chl a), carotenoids, and phycocyanin
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Small microplastic particles in Lake Superior: A preliminary study coupling Nile red staining, flow cytometry and pyrolysis gas chromatography–mass spectrometry Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-03 Elizabeth C. Minor, Uttam D. Gomes, Kathryn M. Schreiner, Nicole J. Poulton, Erik Hendrickson, Melissa A. Maurer-Jones
Microplastic particles (< 5 mm) are now found throughout earth's ecosystems, with smaller microplastics often showing greater impacts on organismal health than larger ones. Unfortunately, there are no readily available analytical approaches that can couple microplastics enumeration and polymer determination for smaller microplastics (< 10 μm), and 1–20 μm particles are difficult to quantify with existing
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A simple and low-cost open dynamic chamber for the versatile determination of methane emissions from aquatic surfaces Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-02 Víctor Germán Rodríguez-García, Leobardo Ottmar Palma-Gallardo, Francisco Silva-Olmedo, Frederic Thalasso
Methane (CH4) emissions from aquatic ecosystems require accurate monitoring in the context of climate change. Among the several methods for CH4 flux measurement, open dynamic chambers (ODC) are a reliable option. This method consists of a floating chamber through which a carrier gas is constantly flowing, providing accurate flux measurement with high temporal resolution. However, this method requires
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Flaws in the methodologies for organic carbon analysis in seagrass blue carbon soils Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-11-02 Oscar Serrano, Ines Mazarrasa, James W. Fourqurean, Eduard Serrano, Jeffrey Baldock, Jonathan Sanderman
The ability to accurately measure organic carbon (OC) in marine sediments or soils is overall taken for granted in scientific communities, yet this seemingly mundane task remains a methodological challenge when the soil matrix contains calcium carbonate (CaCO3), creating inaccuracies in Blue Carbon estimates. Here, we compared five common methods combining acidification, combustion, and wet oxidation
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A novel boat-based field application of a high-frequency conductometric ammonium analyzer to characterize spatial variation in aquatic ecosystems Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-10-31 Emily T. Richardson, Angela M. Hansen, Tamara E. C. Kraus, Bryan D. Downing, Don Forsberg, John Stillian, Katy O'Donnell, Crystal L. Sturgeon, Brian A. Bergamaschi
Documenting dissolved inorganic nitrogen (DIN) concentrations and forms at appropriate temporal and spatial scales is key to understanding aquatic ecosystem health, particularly because DIN fuels primary productivity. In addition to point and nonpoint source nutrient inputs, factors such as hydrology, geomorphology, temperature, light, and biogeochemical transformations influence nutrient dynamics
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Studying bioluminescence flashes with the ANTARES deep-sea neutrino telescope Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-10-11 Nico Reeb, Sebastian Hutschenreuter, Philipp Zehetner, Torsten Ensslin, A. Albert, S. Alves, M. André, M. Anghinolfi, G. Anton, M. Ardid, J.-J. Aubert, J. Aublin, B. Baret, S. Basa, B. Belhorma, M. Bendahman, V. Bertin, S. Biagi, M. Bissinger, J. Boumaaza, M. Bouta, M. C. Bouwhuis, H. Brânzaş, R. Bruijn, J. Brunner, J. Busto, B. Caiffi, A. Capone, L. Caramete, J. Carr, V. Carretero, S. Celli, M. Chabab
We develop a novel technique to exploit the extensive data sets provided by underwater neutrino telescopes to gain information on bioluminescence in the deep sea. The passive nature of the telescopes gives us the unique opportunity to infer information on bioluminescent organisms without actively interfering with them. We propose a statistical method that allows us to reconstruct the light emission
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Extracting proteins from microscopic biominerals: A reproducible method development using oyster larvae Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-10-10 Alessia Carini, Juan Diego Gaitán-Espitia, Vengatesen Thiyagarajan
Microscopic biominerals are ubiquitous in the ocean, and several major taxa secrete them during early life stages or as adults. Organisms secrete an extracellular proteome incorporated within the biomineral to guide biomineralization remotely and enhance its material properties. This proteome has attracted the attention of extensive scientific research, but its characterization is challenging due to
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A new index for the rapid generation of chlorophyll time series from hyperspectral imaging of sediment cores Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-09-30 Hamid Ghanbari, David R. Zilkey, Irene Gregory-Eaves, Dermot Antoniades
Time series analyses of pigment concentrations are key to understanding past aquatic ecosystem dynamics. As lake sediments provide a window into longer-term changes, innovative paleolimnological chlorophyll quantification could provide impactful insights into past environmental processes. Lab-based hyperspectral imaging of sediment cores is an emerging technique to develop rapid, non-destructive, high-resolution
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The ZooScan and the ZooCAM zooplankton imaging systems are intercomparable: A benchmark on the Bay of Biscay zooplankton Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-09-29 Nina Grandremy, Christine Dupuy, Pierre Petitgas, Sophie Le Mestre, Paul Bourriau, Antoine Nowaczyk, Bertrand Forest, Jean-Baptiste Romagnan
Zooplankton analysis represents a bottleneck in marine ecology studies due to the difficulty to obtain zooplankton data. The last decades have seen the intense development of zooplankton imaging systems, to increase the zooplankton data spatio-temporal resolution as well as enabling the combination of size, taxonomy, and functional traits in aquatic ecology studies. Here, we propose a benchmark between
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Comparison of advanced methodologies for diatom identification within dynamic coastal communities Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-09-27 Emily Pierce, Olivia Torano, YuanYu Lin, Astrid Schnetzer, Adrian Marchetti
Diatom community composition has a critical influence on global ocean health and ecological processes. Developing accurate and efficient methods for diatom identification under dynamic environmental conditions is essential to understanding the implications of diatom community changes. Two developing methods for identifying and enumerating phytoplankton, cell imaging and molecular sequencing, are experiencing
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Predicting lake bathymetry from the topography of the surrounding terrain using deep learning Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-09-07 Kenneth Thorø Martinsen, Kaj Sand-Jensen, Raghavendra Selvan
Lake morphometric features like surface area, volume, mean, and maximum depth are important predictors of many physical, biological, and ecological processes. Lake bathymetric maps that present the lake basin contours are thus an integral part of limnological investigations. Accurate but cumbersome traditional bathymetric surveys measure the depth using a lead line or echosounder. Recently, airborne
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A novel fluoro-electrochemical technique for classifying diverse marine nanophytoplankton Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-09-04 Samuel Barton, Minjun Yang, Haotian Chen, Christopher Batchelor-McAuley, Richard G. Compton, Heather A. Bouman, Rosalind E. M. Rickaby
To broaden our understanding of pelagic ecosystem responses to environmental change, it is essential that we improve the spatiotemporal resolution of in situ monitoring of phytoplankton communities. A key challenge for existing methods is in classifying and quantifying cells within the nanophytoplankton size range (2–20 μm). This is particularly difficult when there are similarities in morphology,
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Preparation and quality control of in-house reference materials for marine dissolved inorganic carbon and total alkalinity measurements Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-08-21 Charly A. Moras, Lennart T. Bach, Tyler Cyronak, Renaud Joannes-Boyau, Kai G. Schulz
Accurate measurements of seawater carbonate chemistry are crucial for marine carbon cycle research. Certified reference materials (CRMs) are typically analyzed alongside samples to correct measurements for calibration drift. However, the COVID-19 pandemic led to a limited access to CRMs. In response to this shortage, we prepared and monitored in-house reference materials (IHRMs) for total alkalinity
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An in situ benthic chamber system for improved temporal and spatial resolution measurement of sediment oxygen demand Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-08-17 Kara J. Gadeken, Grant Lockridge, Kelly M. Dorgan
In shallow coastal systems, sediments are exposed to dramatic and complex variability in environmental conditions that influences sediment processes on short timescales. Sediment oxygen demand (SOD), or consumption of oxygen by sediment-dwelling organisms and chemical reactions within sediments, is one such process and an important metric of aquatic ecosystem functioning and health. The most common
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Cryptic biodiversity: A portfolio-approach to coral reef fish surveys Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-07-28 Cindy Bessey, Martial Depczynski, Jordan S. Goetze, Glenn Moore, Christopher J. Fulton, Mark Snell, Sylvia K. Parsons, Oliver Berry, Shaun Wilson
Biodiversity conservation and management requires surveillance that captures the full spectrum of taxa. Here, we showcase the potential for a portfolio of visual, extractive, and molecular methods for detecting previously hidden components of tropical fish biodiversity in an economically and culturally valuable marine site that spans a tropical-temperate ecotone—the Ningaloo Coast World Heritage Area
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Digitizing lake bathymetric data using ImageJ Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-07-25 Christopher I. Rounds, Kelsey Vitense, Gretchen J. A. Hansen
Lake morphometry is a driver of limnological processes, yet digitized bathymetry is lacking for most lakes. Here, we describe a method for efficiently extracting hypsography from bathymetric maps using ImageJ. To validate our method, we compared results generated from two independent users to those obtained from digital elevation models for 100 lakes. The mean absolute difference between hypsographic
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From two sensors to a single sensor: Better understanding of oxygen–sulfide interfaces Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-07-21 Fabian Steininger, Ramya Veerubhotla, Niels Peter Revsbech, Ugo Marzocchi, Klaus Koren
Intense biogeochemical transformations in sediments and biofilms may occur over sub-mm distances. Our current understanding of those transformations in such narrowly stratified environments has been facilitated by the introduction of microsensors. Until now most studies have been conducted using individual sensors for the various chemical species, and careful vertical alignment of the sensor tips is
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Schrödinger's fish: Examining the robotic observer effect on pelagic animals Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-07-10 Kelly J. Benoit-Bird, Chad M. Waluk, Eric J. Martin, Kim R. Reisenbichler, Robert E. Sherlock, Paul R. McGill, Bruce H. Robison
Robust sampling of animals is necessary for understanding ocean ecology, but evaluating the effectiveness of our samplers is a challenge. Scientific echosounders were added to two robotic platforms carrying video imaging systems: a remotely operated vehicle (ROV) and an autonomous underwater vehicle (AUV). The vehicles were used to quantitatively sample midwater life in Monterey Bay along horizontal
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Updated temperature correction for computing seawater nitrate with in situ ultraviolet spectrophotometer and submersible ultraviolet nitrate analyzer nitrate sensors Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-07-06 Joshua N. Plant, Carole M. Sakamoto, Kenneth S. Johnson, Tanya L. Maurer, Mariana B. Bif
Sensors that use ultraviolet (UV) light absorption to measure nitrate in seawater at in situ temperatures require a correction to the calibration coefficients if the calibration and sample temperatures are not identical. This is mostly due to the bromide molecule, which absorbs more UV light as temperature increases. The current correction applied to in situ ultraviolet spectrophotometer (ISUS) and
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DeepBryo: A web app for AI-assisted morphometric characterization of cheilostome bryozoans Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-07-04 Emanuela Di Martino, Björn Berning, Dennis P Gordon, Piotr Kuklinski, Lee Hsiang Liow, Mali H Ramsfjell, Henrique L Ribeiro, Abigail M Smith, Paul D Taylor, Kjetil L Voje, Andrea Waeschenbach, Arthur Porto
Bryozoans are becoming an increasingly popular study system in macroevolutionary, ecological, and paleobiological research. Members of this colonial invertebrate phylum display an exceptional degree of division of labor in the form of specialized modules, which allows for the inference of individual allocation of resources to reproduction, defense, and growth using simple morphometric tools. However
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The determination of dimethyl sulfoxide in natural waters using electrochemical reduction Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-06-30 Ross McCulloch, Philippe Tortell
A highly specific electrochemical reduction method has been developed that enables the trace level measurement of dimethyl sulfoxide (DMSO) concentration in natural waters. Following the sparging of native dimethyl sulfide (DMS) from the sample, DMSO is reduced to DMS using a novel electrochemical workflow that relies upon CuSO4 as a redox mediator. The DMS produced through DMSO reduction is collected
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Development and deployment of a long-term aquatic eddy covariance system Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-06-29 Jeff Coogan, Matthew H. Long
The aquatic eddy covariance (AEC) technique is a versatile tool for understanding benthic fluxes, and calculating primary production, respiration, and net ecosystem metabolism rates of benthic communities. A limitation for researchers has been the length of deployments where the major constraints have primarily been sensor breakage and degradation over time and battery consumption. This paper evaluates
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Lignin phenol quantification from machine learning-assisted decomposition of liquid chromatography-absorbance spectroscopy data Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-06-20 Anders Dalhoff Bruhn, Urban Wünsch, Christopher L. Osburn, Jacob C. Rudolph, Colin A. Stedmon
Analysis of lignin in seawater is essential to understanding the fate of terrestrial dissolved organic matter (DOM) in the ocean and its role in the carbon cycle. Lignin is typically quantified by gas or liquid chromatography, coupled with mass spectrometry (GC-MS or LC-MS). MS instrumentation can be relatively expensive to purchase and maintain. Here we present an improved approach for quantification
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Quantifying pelagic primary production and respiration via an automated in situ incubation system Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-06-16 Solomon T. Chen, Collin P. Ward, Matthew H. Long
Pelagic photosynthesis and respiration serve critical roles in controlling the dissolved oxygen (DO) concentration in seawater. The consumption and production via pelagic primary production are of particular importance in the surface ocean and in freshwater ecosystems where photosynthetically active radiation is abundant. However, the dynamic nature and large degree of heterogeneity in these ecosystems
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Self-diagnosis of model suitability for continuous measurements of stream-dissolved organic carbon derived from in situ UV–visible spectroscopy Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-06-14 Christian Gaviria Salazar, J. Alan Roebuck, Allison N. Myers-Pigg, Susan Ziegler
Application of high-frequency monitoring of dissolved organic carbon (DOC) is difficult in instances where training datasets are challenging to develop (e.g., remote locations) and the relationship between optical features and DOC concentration changes due to environmental or landscape shifts (e.g., climate or land-use change). We developed and compared three partial least squares (PLS) models using
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Quantitative and qualitative comparison of marine dissolved organic nitrogen recovery using solid phase extraction Limnol. Oceanogr. Methods (IF 2.7) Pub Date : 2023-06-12 Carlos Miranda, Rene M. Boiteau, Amy M. McKenna, Angela N. Knapp
Marine dissolved organic carbon and nitrogen (DOC and DON) are major global carbon and nutrient reservoirs, and their characterization relies on extraction methods for preconcentration and salt removal. Existing methods optimize for capturing and describing DOC. Here, we report an optimized analytical strategy to recover marine DON for subsequent molecular characterization. Retention efficiencies between