Limnology and Oceanography: Methods最新文献

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An automated modular heating solution for experimental flow-through stream mesocosm systems 流经流介观实验系统的自动化模块加热解决方案
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-12-08 DOI: 10.1002/lom3.10596
Iris Madge Pimentel, Philipp M. Rehsen, Arne J. Beermann, Florian Leese, Jeremy J. Piggott, Sebastian Schmuck
{"title":"An automated modular heating solution for experimental flow-through stream mesocosm systems","authors":"Iris Madge Pimentel,&nbsp;Philipp M. Rehsen,&nbsp;Arne J. Beermann,&nbsp;Florian Leese,&nbsp;Jeremy J. Piggott,&nbsp;Sebastian Schmuck","doi":"10.1002/lom3.10596","DOIUrl":"10.1002/lom3.10596","url":null,"abstract":"<p>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 effects in stream ecosystems have mostly been tested in recirculating experimental systems, which can neither capture diurnal and seasonal variability in other environmental variables nor allow for entrainment of stream organisms. In contrast, open flow-through systems, which are constantly supplied with stream water, offer a more realistic setting for stream ecological experiments, yet are difficult to implement. Here, we outline a heating module for the purpose of differential temperature regulation in a flow-through mesocosm system by automatic control of warm water supply. We validated the functionality of the module in indoor trials as well as in an outdoor <i>ExStream</i> experimental mesocosm system. Furthermore, we tested the implications of different warm water temperatures for the survival of invertebrates drifting through the heating module to derive recommendations for the maximum warm water temperature for mixing with the natural water inflow. The module allows for controlled open flow-through experiments in the field and the key components are flexible and scalable. Therefore, the module can be easily integrated into existing experimental flow-through setups.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 3","pages":"135-148"},"PeriodicalIF":2.7,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10596","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138573694","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
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 利用NanoString nCounter快速定量评估多种海洋环境中微生物氮循环关键功能基因的时空变化
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-12-01 DOI: 10.1002/lom3.10594
Jennifer Tolman, Dhwani Desai, Julie LaRoche
{"title":"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","authors":"Jennifer Tolman,&nbsp;Dhwani Desai,&nbsp;Julie LaRoche","doi":"10.1002/lom3.10594","DOIUrl":"10.1002/lom3.10594","url":null,"abstract":"<p>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 of marine diazotrophs within known <i>nifH</i> phylogenetic clades. The OceansN CodeSet provided direct hybridization-based quantitation of 48 probes in a single sample, presenting advantages in terms of reduced sample handling, elimination of amplification bias, minimal DNA sample requirements, and the ability to assess targets ranging from relatively rare to abundant, with a reliable quantitation limit of ~ 1000 gene copies per target per sample. As such, our approach fills a unique methodological niche between the scale of high-throughput amplicon sequencing (a compositional method) and quantitative polymerase chain reaction (qPCR) (a targeted method with generally lower throughput). When applied to North Atlantic environmental DNA samples, the OceansN CodeSet revealed temporal and spatial patterns in nitrogen assimilation, nitrification, and denitrification, as well as the abundance and distribution of various nitrogen-fixing microorganisms (diazotrophs). Data from the nCounter was validated via internal and external controls, and by comparison to qPCR, <i>nifH</i> amplicon sequencing, and shotgun metagenomic sequencing.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 2","pages":"103-117"},"PeriodicalIF":2.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10594","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138540375","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
Dimethylmercury in natural waters—analytical and experimental considerations 天然水体中的二甲基汞——分析和实验考虑
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-11-30 DOI: 10.1002/lom3.10586
Johannes West, Diana Babi, Alyssa Azaroff, Sofi Jonsson
{"title":"Dimethylmercury in natural waters—analytical and experimental considerations","authors":"Johannes West,&nbsp;Diana Babi,&nbsp;Alyssa Azaroff,&nbsp;Sofi Jonsson","doi":"10.1002/lom3.10586","DOIUrl":"10.1002/lom3.10586","url":null,"abstract":"<p>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 and experimental approaches to quantify and use DMHg in laboratory studies. We demonstrate that DMHg can be analyzed from samples where MMHg is derivatized using sodium tetraethyl borate and where the matrix effects of dissolved sulfide are masked using copper sulfate. Tests, where the calibration curves of MMHg and DMHg were used, showed that MMHg may be used to calibrate for DMHg. For the pre-concentration of DMHg, both traps filled with Tenax® TA and Bond Elut ENV were found suitable. We observed good recoveries of DMHg added to different types of natural waters or purified water containing aquarium salt, sodium chloride and dissolved sulfide, iron sulfide, and cadmium sulfide at DMHg : sulfide molar ratios &gt; 10<sup>−6</sup>. In addition to evaluating these analytical aspects, we present suitable subsampling techniques for DMHg-containing solutions, the recovery of DMHg when filtering DMHg through different types of filters, and experimental data on the long-term stability of DMHg added to different types of waters and stored at different temperatures. Finally, we present and discuss a new synthetization protocol for preparing aqueous solutions containing DMHg free of organic solvents and where handling DMHg in a pure form is prevented.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 12","pages":"837-846"},"PeriodicalIF":2.7,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10586","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138540379","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
The influence of dynamic resources and stable isotope incorporation rates on aquatic consumer trophic position estimation 动态资源和稳定同位素掺入率对水生消费者营养位置估算的影响
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-11-28 DOI: 10.1002/lom3.10595
Megan L. Feddern, Jens M. Nielsen, Timothy E. Essington, Gordon W. Holtgrieve
{"title":"The influence of dynamic resources and stable isotope incorporation rates on aquatic consumer trophic position estimation","authors":"Megan L. Feddern,&nbsp;Jens M. Nielsen,&nbsp;Timothy E. Essington,&nbsp;Gordon W. Holtgrieve","doi":"10.1002/lom3.10595","DOIUrl":"10.1002/lom3.10595","url":null,"abstract":"<p>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 consumer stable isotope incorporation rates and modeled the effect on TP calculations using bulk and compound-specific stable isotope data from previous experimental and observational studies. We found TP estimates of higher trophic level consumers are less accurate than lower trophic level consumers when applying bulk stable isotope analysis (BSIA) and using particulate organic matter as the stable isotope baseline. The accuracy of TP estimates depended on the time-varying dynamics of the stable isotope baseline. Tertiary consumers had the highest TP estimation error, and this error was not eliminated by sampling tissues with fast incorporation rates (i.e., blood) in the tertiary consumer. Compound-specific stable isotope analysis (CSIA) of individual amino acids was more accurate in estimating TP for all consumers and ecosystems compared to BSIA. Our analysis confirms that consideration for the dynamic nature of stable isotope ratios is necessary for accurate TP estimates. Finally, we show how first-order kinetics models can provide a useful framework for integrating prey and consumer incorporation rates in stable isotope studies to improve TP estimates.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 3","pages":"119-134"},"PeriodicalIF":2.7,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138540382","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
An assessment of HgII to preserve carbonate system parameters in organic-rich estuarine waters 富有机质河口水体碳酸盐体系参数保护的HgII评价
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-11-27 DOI: 10.1002/lom3.10593
Christopher S. Moore, Robert H. Byrne, Kimberly K. Yates
{"title":"An assessment of HgII to preserve carbonate system parameters in organic-rich estuarine waters","authors":"Christopher S. Moore,&nbsp;Robert H. Byrne,&nbsp;Kimberly K. Yates","doi":"10.1002/lom3.10593","DOIUrl":"10.1002/lom3.10593","url":null,"abstract":"<p>This work assesses the effectiveness of sample preservation techniques for measurements of pH<sub>T</sub> (total scale), total dissolved inorganic carbon (C<sub>T</sub>), and total alkalinity (A<sub>T</sub>) in organic-rich estuarine waters as well as the internal consistency of measurements and calculations (e.g., A<sub>T</sub>, pH<sub>T</sub>, and C<sub>T</sub>) in these waters. Using mercuric chloride (HgCl<sub>2</sub>)-treated and untreated water samples, measurements of these carbonate system parameters were examined over a period of 3 months. Respiration of dissolved organic matter in untreated samples created large discrepancies in C<sub>T</sub> concentrations (~37 <i>μ</i>mol kg<sup>−1</sup> increase, <i>p</i> &lt; 0.0001), while C<sub>T</sub> was effectively constant in treated samples (3095.0 ± 1.14 <i>μ</i>mol kg<sup>−1</sup>). A<sub>T</sub> changes were observed for both treated and untreated samples, with HgCl<sub>2</sub>-treated samples showing the greatest variation (~ 26 <i>μ</i>mol kg<sup>−1</sup> decrease, <i>p</i> &lt; 0.001). In response to changing A<sub>T</sub>/C<sub>T</sub> ratios, pH<sub>T</sub> changes occurred in both treated and untreated samples but were relatively small in treated samples. Results in organic-rich estuarine waters that reflect the in situ carbonate system characteristics of the samples at the time of collection can be improved when samples obtained for C<sub>T</sub> and A<sub>T</sub> analysis are collected and stored separately. Accurate analyses of C<sub>T</sub> can be obtained by filtration and preservation with HgCl<sub>2</sub>. Accuracy of A<sub>T</sub> analyses can be improved by filtration and storage without adding HgCl<sub>2</sub>. The quality of pH<sub>T</sub> measurements can be improved by prompt analysis in the field and, if this cannot be accomplished, then samples can be preserved with HgCl<sub>2</sub> and measured in the laboratory within 1 week.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 2","pages":"93-102"},"PeriodicalIF":2.7,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10593","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138540370","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 new, global optical sediment trap calibration 一种新的全球光学沉积物捕获器校准方法
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-11-23 DOI: 10.1002/lom3.10592
Margaret L. Estapa, Colleen Andrea Durkin, Wayne H. Slade, Christine L. Huffard, Sean P. O'Neill, Melissa M. Omand
{"title":"A new, global optical sediment trap calibration","authors":"Margaret L. Estapa,&nbsp;Colleen Andrea Durkin,&nbsp;Wayne H. Slade,&nbsp;Christine L. Huffard,&nbsp;Sean P. O'Neill,&nbsp;Melissa M. Omand","doi":"10.1002/lom3.10592","DOIUrl":"10.1002/lom3.10592","url":null,"abstract":"<p>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, and complementary to, other autonomous, sensor-derived estimates of BCP fluxes. However, limited intercalibrations of OSTs with traditional sediment traps and uncharacterized, potential biases have limited their broad adoption. A global field data set spanning three orders of magnitude in carbon flux was compiled and used to develop empirical models predicting particulate organic carbon flux from OST observations, and intercalibrating different sensor designs. These data provided valuable constraints on the uncertainty in the predicted carbon flux and showed a quantitative, theoretically consistent relationship between observations from OSTs with collimated and diffuse optical geometries. While not designed for this purpose, commercial beam transmissometers have been used as OSTs, so two models were developed quantifying the biases arising from the transmissometer's housing geometry and optical beam diameter. Finally, an algorithm for the quality control of beam transmissometer-derived OST data was optimized using sensitivity tests. The results of this study support the expansion of OST-based gravitational carbon flux measurements and provide a framework for interpretation of OST measurements alongside other gravitational particle flux observations. These findings also suggest key features that should be included in designs of future, purpose-built OST sensors.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 2","pages":"77-92"},"PeriodicalIF":2.7,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10592","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138540381","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
Classification of suspended particles in seawater using an in situ polarized light scattering prototype 利用原位偏振光散射原型对海水中悬浮粒子进行分类
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-11-17 DOI: 10.1002/lom3.10580
Hanbo Deng, Hongjian Wang, Zhiming Guo, Jiajin Li, Ran Liao, Hening Li, Qiang Li, Hui Ma
{"title":"Classification of suspended particles in seawater using an in situ polarized light scattering prototype","authors":"Hanbo Deng,&nbsp;Hongjian Wang,&nbsp;Zhiming Guo,&nbsp;Jiajin Li,&nbsp;Ran Liao,&nbsp;Hening Li,&nbsp;Qiang Li,&nbsp;Hui Ma","doi":"10.1002/lom3.10580","DOIUrl":"10.1002/lom3.10580","url":null,"abstract":"<p>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 prototype can classify the sediments, microplastics, and phytoplankton in seawater with an accuracy larger than 85%, and further calculate their relative proportion in water. In the summer and winter of 2020, the prototype was deployed three times in Daya Bay and lasted for dozens of hours each time, along with the additional commercial sensors, that is, Environment X Observation (EXO) and Acoustic Doppler Current Profiler (ADCP). The chlorophyll content measured by EXO and the acoustic backscatter intensity measured by ADCP are respectively related to the number of algal cells and sediments in the water, which helps to interpret the data of the prototype. The results of field data show that the prototype can effectively classify phytoplankton and sediment particles in seawater and monitor their temporal variations. Besides, the retrieved information of the suspended particles is consistent with the analysis from the flow dynamics and season variations in Daya Bay. These results indicate the ability of this prototype to classify the suspended particles in seawater, which promises its potential contribution to particulate oceanography in the future.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 12","pages":"775-789"},"PeriodicalIF":2.7,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10580","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138543618","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 bold new purpose for an old method: Using invertebrate kick-netting to improve monitoring of microplastic pollution in running waters 旧方法的大胆新用途:使用无脊椎动物踢网来改善自来水中微塑料污染的监测
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-11-16 DOI: 10.1002/lom3.10585
Aidan Mora-Teddy, Gerry P. Closs, Christoph D. Matthaei
{"title":"A bold new purpose for an old method: Using invertebrate kick-netting to improve monitoring of microplastic pollution in running waters","authors":"Aidan Mora-Teddy,&nbsp;Gerry P. Closs,&nbsp;Christoph D. Matthaei","doi":"10.1002/lom3.10585","DOIUrl":"10.1002/lom3.10585","url":null,"abstract":"<p>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 a novel method, adapted from stream invertebrate kick-net sampling, which can be employed for long-term, standardized microplastic monitoring. We hypothesized that invertebrate kick-net sampling would be effective at collecting microplastics, capturing higher microplastic concentrations than standard microplastic sampling, due to collecting suspended and benthic microplastics simultaneously. We sampled 28 streams for microplastics using standard drift and sediment microplastic collection methods and invertebrate kick-netting. As predicted, kick-netting captured microplastics at higher concentrations than conventional sampling, regardless of whether values were expressed per volume of water (as in drift samples), per kg of sediment or per area sampled (as in benthic samples). Consequently, kick-net sampling has the potential to be a time- and cost-efficient tool for monitoring microplastic pollution. We recommend the employment of invertebrate kick-netting as a new, standardized means to investigate and routinely monitor microplastic concentrations worldwide. This would generate a more robust dataset of global freshwater microplastic pollution, making it possible to answer unresolved questions pertaining to changes in microplastic pollution profiles. Standardized, long-term records of microplastic concentrations in freshwaters would also allow a more accurate assessment of the ecological risks of microplastic pollution. Finally, long-term microplastic data could be used to inform much-needed regulatory decisions pertaining to microplastic pollution.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 2","pages":"65-76"},"PeriodicalIF":2.7,"publicationDate":"2023-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10585","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138540369","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
Taming the data deluge: A novel end-to-end deep learning system for classifying marine biological and environmental images 驯服数据洪流:用于海洋生物和环境图像分类的新型端到端深度学习系统
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-11-10 DOI: 10.1002/lom3.10591
Hongsheng Bi, Yunhao Cheng, Xuemin Cheng, Mark C. Benfield, David G. Kimmel, Haiyong Zheng, Sabrina Groves, Kezhen Ying
{"title":"Taming the data deluge: A novel end-to-end deep learning system for classifying marine biological and environmental images","authors":"Hongsheng Bi,&nbsp;Yunhao Cheng,&nbsp;Xuemin Cheng,&nbsp;Mark C. Benfield,&nbsp;David G. Kimmel,&nbsp;Haiyong Zheng,&nbsp;Sabrina Groves,&nbsp;Kezhen Ying","doi":"10.1002/lom3.10591","DOIUrl":"10.1002/lom3.10591","url":null,"abstract":"<p>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 has limitations in handling high concentrations of biotic and abiotic particles, rapid changes in dominant taxa, and highly variable target sizes. To address these challenges, we introduce a new framework that starts with a scene classifier to capture large within-image variation, such as disparities in the layout of particles and dominant taxa. After scene classification, scene-specific Mask regional convolutional neural network (Mask R-CNN) models are trained to separate target objects into different groups. The procedure allows information to be extracted from different image types, while minimizing potential bias for commonly occurring features. Using in situ coastal plankton images, we compared the scene-specific models to the Mask R-CNN model encompassing all scene categories as a single full model. Results showed that the scene-specific approach outperformed the full model by achieving a 20% accuracy improvement in complex noisy images. The full model yielded counts that were up to 78% lower than those enumerated by the scene-specific model for some small-sized plankton groups. We further tested the framework on images from a benthic video camera and an imaging sonar system with good results. The integration of scene classification, which groups similar images together, can improve the accuracy of detection and classification for complex marine biological images.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 1","pages":"47-64"},"PeriodicalIF":2.7,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135138405","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
A novel method to sample individual marine snow particles for downstream molecular analyses 用于下游分子分析的单个海洋雪粒子采样新方法
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2023-11-10 DOI: 10.1002/lom3.10590
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
{"title":"A novel method to sample individual marine snow particles for downstream molecular analyses","authors":"Chloé M.J. Baumas,&nbsp;Fatima-Ezzahra Ababou,&nbsp;Marc Garel,&nbsp;Mina Bizic,&nbsp;Danny Ionescu,&nbsp;Arthur Puzenat,&nbsp;Frederic A.C. Le Moigne,&nbsp;Hans-Peter Grossart,&nbsp;Christian Tamburini","doi":"10.1002/lom3.10590","DOIUrl":"10.1002/lom3.10590","url":null,"abstract":"<p>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 communities. This limits our mechanistic understanding of the biological carbon pump (BCP) and its feedback on the global carbon cycle. We established a method to sample individual particles while preserving their shape, structure, and nucleic acids by placing a jellified RNA-fixative at the bottom of drifting sediment traps. Coupling imaging of individual particles with associated 16S rRNA analysis reveals that active bacterial communities are highly heterogenous from one particles origin to another. In contrast to lab-made particles, we found that complex in situ conditions lead to heterogeneity even within the same particle type. Our new method allows to associate patterns of active prokaryotic and functional diversity to particle features, enabling the detection of potential remineralization niches. This new approach will therefore improve our understanding of the BCP and numerical representation in the context of a rapidly changing ocean.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 1","pages":"34-46"},"PeriodicalIF":2.7,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10590","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135136586","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
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