Limnology and Oceanography: Methods最新文献_第6页

Evaluation of the BenthoTorch using lake periphyton: A comparison of attached cyanobacterial biomass estimates 利用湖泊周边植物评价底栖火炬：附蓝藻生物量估算的比较

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-03-15 Epub Date: 2025-11-26 DOI: 10.1002/lom3.70017

Abby M. Webster, Trevor Massey, Lisa B. Cleckner, Gregory L. Boyer, N. Roxanna Razavi

{"title":"Evaluation of the BenthoTorch using lake periphyton: A comparison of attached cyanobacterial biomass estimates","authors":"Abby M. Webster, Trevor Massey, Lisa B. Cleckner, Gregory L. Boyer, N. Roxanna Razavi","doi":"10.1002/lom3.70017","DOIUrl":"https://doi.org/10.1002/lom3.70017","url":null,"abstract":"Simple monitoring methods for benthic cyanobacteria are lacking, especially in lentic systems. Traditional methods to estimate biomass, such as Chlorophyll-a or phycocyanin measurements, are complicated by benthic cyanobacteria's ability to adapt under variable light conditions. In response, benthic cyanobacteria adjust the phycobiliprotein (phycocyanin, phycoerythrin) content in their phycobilisome complex, leading to potential underestimation of biomass if the chosen method does not account for both pigments. Here, we assessed the utility of the BenthoTorch, an in situ fluorometric tool, against in vitro fluorometry, a common benchtop method, in estimating cyanobacterial biomass in periphyton from lakes ranging in productivity and light intensity. We propose a new change point, the first that is specific to cyanobacterial biomass, for the BenthoTorch's comparability to the benchtop method: at 0.5 μg cyanobacterial biomass cm−2 determined in vitro, above which high variability between estimates was observed. Using a larger dataset of phycoerythrin-containing periphyton than has been previously assessed, we found that the presence of phycoerythrin did not directly affect the correlation between methods, but evidence suggests higher phycoerythrin content may lead to greater discrepancy. We found that the Turner Trilogy benchtop fluorometer's phycocyanin and phycoerythrin modules are not methodologically independent, and the two pigments are not distinctly quantified by the fluorometer if existing in the same sample. We offer recommendations to consider before applying either of these methods in similar systems when direct measurements (i.e., biovolumes) are not available and suggest that researchers have preliminary knowledge of expected productivity and taxonomy of periphyton communities prior to method selection.","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 3","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147653364","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}

引用次数: 0

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-03-15

引用次数: 0

Relationships between acoustic scattering layers and ocean stratification: An acoustic approach to estimate mixed layer depth 声散射层与海洋分层之间的关系：估计混合层深度的声学方法

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-03-15 Epub Date: 2025-11-22 DOI: 10.1002/lom3.70010

Fabio Campanella, Jeroen van der Kooij, Liam Fernand

{"title":"Relationships between acoustic scattering layers and ocean stratification: An acoustic approach to estimate mixed layer depth","authors":"Fabio Campanella, Jeroen van der Kooij, Liam Fernand","doi":"10.1002/lom3.70010","DOIUrl":"https://doi.org/10.1002/lom3.70010","url":null,"abstract":"Ocean stratification, measured as mixed layer depth (MLD), is an important feature that influences many processes in the ocean; for example, by mediating the fluxes of momentum, heat and crucially key gases such as CO2 and oxygen from the atmosphere into the water column and vice versa. The conventional methods to measure stratification (e.g., Conductivity, Temperature and Depth profiling from ARGO floats) are limited in terms of spatial and temporal coverage especially in shelf sea areas and can be expensive to conduct. Several studies have highlighted the possibility of detecting water stratification using active acoustic measurements by scientific echosounders that are able to provide high spatial and temporal resolution data, which can be collected continuously, including on surveys carrying out other tasks. In this work we apply a method to detect and map the distribution of stratification by using narrowband echosounder data collected over an area that included the Western English Channel and Celtic Sea from 2012 to 2019. The approach is based on the identification of the scattering layers located at the depth of the thermocline that can be attributed to biological scattering or scattering from the oceanic microstructure. The relationship between the thermocline and the scattering layers was modeled using machine learning methods to predict the intensity and extent of the stratification. The methodology developed within this project can offer the opportunity for wide-scale routine application on surveys where acoustic data are collected for other purposes (e.g., fisheries survey) and it can also be applied to datasets already collected.","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 3","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147653325","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}

引用次数: 0

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-02-22

引用次数: 0

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-02-19

引用次数: 0

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-02-17

引用次数: 0

Simulating climate change scenarios established by the Intergovernmental Panel on Climate Change in aquatic mesocosms 在水生生态系统中模拟政府间气候变化专门委员会制定的气候变化情景

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-02-13 Epub Date: 2025-11-18 DOI: 10.1002/lom3.70014

Tauany Rodrigues, Aldo Caccavo, Saulo Jacques, Luiza O. Costa, Vinicius F. Farjalla, Aliny P. F. Pires

{"title":"Simulating climate change scenarios established by the Intergovernmental Panel on Climate Change in aquatic mesocosms","authors":"Tauany Rodrigues, Aldo Caccavo, Saulo Jacques, Luiza O. Costa, Vinicius F. Farjalla, Aliny P. F. Pires","doi":"10.1002/lom3.70014","DOIUrl":"10.1002/lom3.70014","url":null,"abstract":"Climate change poses a major threat to ecosystems worldwide, with temperature changes being a key driver of ecological disruption in aquatic environments due to the limited ability of many aquatic species to relocate in response. Despite advances in aquatic experimental approaches to temperature control, most studies rely on simplified warming models that fail to capture the temporal complexity projected in climate change scenarios. Bridging the gap between predictive modeling and realistic field simulations remains a key challenge in climate research. Here, we present a novel method for simulating projected temperature changes predicted by the Intergovernmental Panel on Climate Change in field-based aquatic mesocosms. We manipulated temperature trajectories according to three climate scenarios represented by historical baseline conditions, a mitigation (RCP 4.5), and a business-as-usual (RCP 8.5) future scenario for Rio de Janeiro, Brazil. We employed an automated temperature control system, the Nayad Limno device, designed to replicate projected temperature trajectories with high precision within a 3-h window. The Nayad Limno device achieved an overall accuracy of 95% in maintaining target temperatures across all scenarios, with low error margins (mean absolute deviation < 0.1°C; root mean squared error < 1.0°C). Time series and Autoregressive Integrated Moving Average with eXogenous variable analyses supported strong alignment between observed and modeled temperatures, despite sensor-level variability. The system can be readily adapted to diverse experimental contexts by following the methodology established here, using low-cost and commercially available components. Our approach enhances the realism of climate change simulations in aquatic environments, offering a flexible and scalable framework for investigating ecosystem responses under projected climate scenarios.","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147288310","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}

引用次数: 0

pamfit: A new R package for spatially resolved analysis of Imaging PAM photosynthesis–irradiance light curve parameters pamfit：一个用于成像PAM光合作用-辐照光曲线参数空间分辨分析的新R包

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-02-13 Epub Date: 2025-11-12 DOI: 10.1002/lom3.70011

B. Jesus, P. Cartaxana, C. Williamson

{"title":"pamfit: A new R package for spatially resolved analysis of Imaging PAM photosynthesis–irradiance light curve parameters","authors":"B. Jesus, P. Cartaxana, C. Williamson","doi":"10.1002/lom3.70011","DOIUrl":"10.1002/lom3.70011","url":null,"abstract":"Imaging Pulse Amplitude Modulation (PAM) fluorometry allows spatially resolved measurements of Photosystem II (PSII) fluorescence kinetics through time without disturbing study organisms or their environments. In particular, the use of photosynthesis–irradiance curves (P–I curves) provides detailed information on PSII quantum efficiency, electron transport rates and the overall photosynthetic performance of samples. Here, we present the R “pamfit” package developed as a Shiny application to significantly extend current analysis capabilities for Imaging PAM P–I curve datasets. Through a sequential Shiny user interface, pamfit allows to (i) import Imaging PAM TIFF P–I curve datasets, assign light levels and employ pixel smoothing; (ii) define a region of interest for subsequent modeling; (iii) derive optimal start parameters and fit one of three P–I curve models—Jassby and Platt, Platt et al., or Eilers and Peeters; and (iv) undertake pixel-wise interrogation of both initial data and derived P–I curve parameters including, light utilization (α) and saturation (Ek) coefficients, maximum electron transport rates (ETRmax), photo-inhibition coefficients (e.g., β when derived), and associated residual mean square error (RMSE) images. Outputs can be saved in GeoTIFF or CSV format and exported to the R global environment for subsequent processing. We present here example applications of pamfit to three P–I curve datasets for the photosynthetic sea slug Elysia timida, a microphytobenthic biofilm, and the coralline seaweed Corallina officinalis, chosen because they exhibit high spatial variability. The flexibility of processing images using free open-source software extends the usefulness of this technique and holds great potential for application in ecophysiological studies.","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146680441","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}

引用次数: 0

A prototype submersible sheathless flow cytometer designed for autonomous platforms 为自主平台设计的潜水式无鞘流式细胞仪原型

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-02-13 Epub Date: 2025-10-03 DOI: 10.1002/lom3.70007

J. E. Swalwell, K. Cain, E. V. Armbrust

{"title":"A prototype submersible sheathless flow cytometer designed for autonomous platforms","authors":"J. E. Swalwell, K. Cain, E. V. Armbrust","doi":"10.1002/lom3.70007","DOIUrl":"10.1002/lom3.70007","url":null,"abstract":"Development of submersible flow cytometers has allowed for continuous, in situ measurements of natural assemblages of phytoplankton cells. Here we introduce DeepCyte, a sensitive prototype submersible flow cytometer developed for deployment on autonomous platforms. DeepCyte continuously collects multidimensional characteristics of individual phytoplankton cells (~0.5–10 μm in diameter), including Prochlorococcus, and transmits this data in real-time to remote observatories via a network connection. DeepCyte utilizes a virtual sample core technology and an open flow system, enabling direct measures from the surrounding environment without the use of a clean carrier fluid. The primary surfaces of excitation and collection optics are exposed to the outside of the instrument, and the only fluid path is a 6 mm diameter length of silicon tubing. These design features allow for simple maintenance of optical surfaces and minimize sampling downtime due to clogs or air bubbles. An innovative arrangement of the optical system means the instrument fits within a volume of 0.017 m3, and our selection and design of low power electronics yield power consumption of 36 watts when operated as a standalone instrument with integrated pump. The DeepCyte is characterized by high optical sensitivity, low power consumption, compact size, and low maintenance. This technology will provide a continuous view of the dynamics and structure of the smallest phytoplankton populations, aligning with and expanding upon other continuous measurements such as chlorophyll-a fluorescence, temperature, and salinity.","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.70007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146256262","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}

引用次数: 0

Combining multibeam and single beam echosounders for quantifying gas bubble release from the seafloor 多波束与单波束相结合的海底气泡释放定量测深方法

IF 1.9 3区地球科学

Limnology and Oceanography: Methods Pub Date : 2026-02-13 Epub Date: 2025-10-06 DOI: 10.1002/lom3.10722

P. Urban, M. E. Veloso-Alarcón, J. Greinert

{"title":"Combining multibeam and single beam echosounders for quantifying gas bubble release from the seafloor","authors":"P. Urban, M. E. Veloso-Alarcón, J. Greinert","doi":"10.1002/lom3.10722","DOIUrl":"10.1002/lom3.10722","url":null,"abstract":"Marine gas bubble release is a worldwide phenomenon that impacts the local marine ecosystem and contributes to carbon fluxes with respect to global warming. It is still challenging to assess gas flow for large seep areas (tens of km2), but recent advances in calibrating and processing multibeam echosounder (MBES) data make this problem approachable. A recently published method called “echo grid integration” describes the computation of aggregated backscattering cross-sections of bubble stream layers from calibrated MBES data. Here, we use this method combined with methods for bubble stream detection, acoustic inversion, cross-calibration and dissolution modeling to create a full gas flow quantification workflow. A simultaneously recording scientific single beam echosounder (SBES) is used to acoustically (cross-) calibrate the MBES. The final result of the presented workflow is a map showing the distribution and estimated gas flow of 10 bubble seep clusters and > 50 individual seeps in a 5 × 7 km wide area on the Black Sea shelf. It is shown that the MBES gas flow estimates correlate linearly with estimates from the SBES and are consistent over depth and at different beam angles. Multibeam echosounder data thereby provided 10 times the areal coverage per survey line compared to the scientific SBES. Our results highlight a heterogeneous picture of gas release in the area, where 10% of the flares are responsible for ~ 80% of the overall gas flow (~ 260–780 tons of methane per year). According to bubble dissolution modeling, this free methane dissolves in the water before reaching the surface.","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"24 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10722","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147275033","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}

引用次数: 0