Limnology and Oceanography: Methods最新文献

{"title":"Resolving phytoplankton pigments from spectral images using convolutional neural networks","authors":"Pauliina Salmi,&nbsp;Ilkka Pölönen,&nbsp;Daniel Atton Beckmann,&nbsp;Marco L. Calderini,&nbsp;Linda May,&nbsp;Justyna Olszewska,&nbsp;Laura Perozzi,&nbsp;Salli Pääkkönen,&nbsp;Sami Taipale,&nbsp;Peter Hunter","doi":"10.1002/lom3.10588","DOIUrl":"10.1002/lom3.10588","url":null,"abstract":"<p>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 <i>a</i> (Chl <i>a</i>), carotenoids, and phycocyanin. The protocol was demonstrated with samples from 20 lakes across Scotland, with special emphasis on Loch Leven where blooms of cyanobacteria are frequent. In parallel, samples were prepared for reference observations of Chl <i>a</i> and carotenoids by high-performance liquid chromatography and of phycocyanin by spectrophotometry. Robustness of the CNNs were investigated by excluding each lake from model trainings one at a time and using the excluded data as independent test data. For Loch Leven, median absolute percentage difference (MAPD) was 15% for Chl <i>a</i> and 36% for carotenoids. MAPD in estimated phycocyanin concentration was high (102%); however, the system was able to indicate the possibility of a cyanobacteria bloom. In the leave-one-out tests with the other lakes, MAPD was 26% for Chl <i>a</i>, 27% for carotenoids, and 75% for phycocyanin. The higher error for phycocyanin was likely due to variation in the data distribution and reference observations. It was concluded that this protocol could support phytoplankton monitoring by using Chl <i>a</i> and carotenoids as proxies for biomass. Greater focus on the distribution and volume of the training data would improve the phycocyanin estimates.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 1","pages":"1-13"},"PeriodicalIF":2.7,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10588","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135635374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small microplastic particles in Lake Superior: A preliminary study coupling Nile red staining, flow cytometry and pyrolysis gas chromatography–mass spectrometry","authors":"Elizabeth C. Minor,&nbsp;Uttam D. Gomes,&nbsp;Kathryn M. Schreiner,&nbsp;Nicole J. Poulton,&nbsp;Erik Hendrickson,&nbsp;Melissa A. Maurer-Jones","doi":"10.1002/lom3.10582","DOIUrl":"10.1002/lom3.10582","url":null,"abstract":"<p>Microplastic particles (&lt; 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 (&lt; 10 <i>μ</i>m), and 1–20 <i>μ</i>m particles are difficult to quantify with existing techniques. This study presents a method using Nile red (NR) staining and flow cytometry (FCM) to quantify and isolate small microplastic particles for subsequent identification by pyrolysis gas chromatography–mass spectrometry (pyGCMS). Results using standard plastic particles showed that FCM sorting can provide sufficient material for pyGCMS analyses; the polymer composition remains identifiable after the processing steps. The post-sorting concentration step yielded recovery of 58%–83% of the original plastic polymer mass. Analysis of a mixed plastic standard solution showed no significant difference in plastic counts obtained by microscopy and FCM, although blank correction reduces the FCM counts to 62% of the microscopy counts. The applicability of NR staining and FCM was demonstrated through analysis of small microplastic particles (5–45 <i>μ</i>m) from Lake Superior surface water samples, which showed particle abundances two to three orders of magnitude higher than particles &gt; 100 <i>μ</i>m that were counted using FTIR microscopy. PyGCMS analysis of a test lake sample showed the presence of polyethylene in this small size fraction. Careful attention to blanks and longer FCM sorting times (&gt; 2 h) are recommended for successful analysis of natural aquatic samples processed by this approach.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 12","pages":"800-813"},"PeriodicalIF":2.7,"publicationDate":"2023-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10582","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135819772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Flaws in the methodologies for organic carbon analysis in seagrass blue carbon soils","authors":"Oscar Serrano,&nbsp;Ines Mazarrasa,&nbsp;James W. Fourqurean,&nbsp;Eduard Serrano,&nbsp;Jeffrey Baldock,&nbsp;Jonathan Sanderman","doi":"10.1002/lom3.10583","DOIUrl":"10.1002/lom3.10583","url":null,"abstract":"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 pre‐treatments for determination of OC in sediments and soils containing CaCO3 based on the analyses of artificial soil mixtures made of different OC and CaCO3 contents, and multiple soils from Australian seagrass cores. The results obtained showed that methods involving acidification pre‐treatment entailed −17 ± 0.2% (mean ± SE) underestimation of OC content (ranging from −8% to −26%), whereas the combustion‐based method was accurate for samples with high CaCO3 content but entailed 32–47% overestimation in samples with low CaCO3 content. The Heanes method (wet oxidation method) showed <5% deviation from the known OC content, but this method is not suitable for soil samples containing reduced iron, sulfur and potentially manganese compounds. The differences observed among methods have significant impacts on local, regional, and global Blue Carbon storage calculations. We provide key methodological guidelines for the analysis of OC in soils with high and low CaCO3 contents, aiming at improving accuracy in current Blue Carbon science.","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 12","pages":"814-827"},"PeriodicalIF":2.7,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10583","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135973374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A simple and low-cost open dynamic chamber for the versatile determination of methane emissions from aquatic surfaces","authors":"Víctor Germán Rodríguez-García,&nbsp;Leobardo Ottmar Palma-Gallardo,&nbsp;Francisco Silva-Olmedo,&nbsp;Frederic Thalasso","doi":"10.1002/lom3.10584","DOIUrl":"10.1002/lom3.10584","url":null,"abstract":"<p>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 expensive and heavy CH₄ analyzers with high sensitivity, as well as a carrier gas system that comprises a gas cylinder and a gas flow controller, among other components. This system involves significant weight and cost challenges, limiting method implementation in certain settings and hindering its wider adoption. To address these limitations, we developed a simplified ODC configuration using atmospheric air as the carrier gas and a light and relatively less expensive detector. We applied this method to a 450-ha urban lake with CH₄ emissions ranging from moderate diffusive to high ebullitive fluxes. Concurrent measurements using a high-sensitivity CH₄ analyzer allowed us to compare the accuracy of the simplified ODC method and to assess its advantages and disadvantages. Results show that our method provides accurate CH₄ flux measurements with a spatial resolution comparable to high-sensitivity analyzers. This offers a more cost-effective, straightforward, and lightweight alternative to high-sensitivity detectors and carrier gas systems, simplifying ODC deployment in aquatic ecosystems.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 12","pages":"828-836"},"PeriodicalIF":2.7,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10584","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135934872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel boat-based field application of a high-frequency conductometric ammonium analyzer to characterize spatial variation in aquatic ecosystems","authors":"Emily T. Richardson,&nbsp;Angela M. Hansen,&nbsp;Tamara E. C. Kraus,&nbsp;Bryan D. Downing,&nbsp;Don Forsberg,&nbsp;John Stillian,&nbsp;Katy O'Donnell,&nbsp;Crystal L. Sturgeon,&nbsp;Brian A. Bergamaschi","doi":"10.1002/lom3.10579","DOIUrl":"10.1002/lom3.10579","url":null,"abstract":"&lt;p&gt;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 in surface waters, allowing for the formation of steep spatial gradients and patchiness. Documenting nutrient variability is also necessary to identify sources, quantify transformation rates, and understand drivers. Because of logistical and cost constraints, it is often unfeasible to measure concentrations of nutrients in surface waters using discrete sampling followed by laboratory analysis at a resolution high enough to identify steep spatial gradients and patchiness. Because of these constraints, data generated from discrete sampling are limited in space and time, often missing key variabilities. Recent advancements of in situ nitrate plus nitrite (&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;NO&lt;/mi&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt; and &lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;NO&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt;) sensor technology have enabled highly temporally and spatially resolved &lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;NO&lt;/mi&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt; concentration measurements in aquatic ecosystems. However, comparable information about ammonium (&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;NH&lt;/mi&gt;\u0000 &lt;mn&gt;4&lt;/mn&gt;\u0000 &lt;mo&gt;+&lt;/mo&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt;) concentrations remains unavailable. To address this need, US Geological Survey collaborated with Timberline Instruments to modify their commercially available benchtop TL-2800 ammonia analyzer to operate in flow-through mode, enabling rapid continuous &lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;NH&lt;/mi&gt;\u0000 &lt;mn&gt;4&lt;/mn&gt;\u0000 &lt;mo&gt;+&lt;/mo&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt; concentration measurements at a micromolar (0.5 &lt;i&gt;μ&lt;/i&gt;M) resolution while receiving water pumped from a moving boat. Although the utility of this method is described for spatial surveys, we anticipate that it would be adaptable to installation at a fixed station for continuous monitoring of &lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;NH&lt;/mi&gt;\u0000 &lt;mn&gt;4&lt;/mn&gt;\u0000 &lt;mo&gt;+","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 12","pages":"761-774"},"PeriodicalIF":2.7,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10579","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135872038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Studying bioluminescence flashes with the ANTARES deep-sea neutrino telescope","authors":"Nico Reeb,&nbsp;Sebastian Hutschenreuter,&nbsp;Philipp Zehetner,&nbsp;Torsten Ensslin,&nbsp;A. Albert,&nbsp;S. Alves,&nbsp;M. André,&nbsp;M. Anghinolfi,&nbsp;G. Anton,&nbsp;M. Ardid,&nbsp;J.-J. Aubert,&nbsp;J. Aublin,&nbsp;B. Baret,&nbsp;S. Basa,&nbsp;B. Belhorma,&nbsp;M. Bendahman,&nbsp;V. Bertin,&nbsp;S. Biagi,&nbsp;M. Bissinger,&nbsp;J. Boumaaza,&nbsp;M. Bouta,&nbsp;M. C. Bouwhuis,&nbsp;H. Brânzaş,&nbsp;R. Bruijn,&nbsp;J. Brunner,&nbsp;J. Busto,&nbsp;B. Caiffi,&nbsp;A. Capone,&nbsp;L. Caramete,&nbsp;J. Carr,&nbsp;V. Carretero,&nbsp;S. Celli,&nbsp;M. Chabab,&nbsp;T. N. Chau,&nbsp;R. Cherkaoui El Moursli,&nbsp;T. Chiarusi,&nbsp;M. Circella,&nbsp;A. Coleiro,&nbsp;M. Colomer-Molla,&nbsp;R. Coniglione,&nbsp;P. Coyle,&nbsp;A. Creusot,&nbsp;A. F. Díaz,&nbsp;G. de Wasseige,&nbsp;A. Deschamps,&nbsp;C. Distefano,&nbsp;I. Di Palma,&nbsp;A. Domi,&nbsp;C. Donzaud,&nbsp;D. Dornic,&nbsp;D. Drouhin,&nbsp;T. Eberl,&nbsp;T. van Eeden,&nbsp;N. El Khayati,&nbsp;A. Enzenhöfer,&nbsp;P. Fermani,&nbsp;G. Ferrara,&nbsp;F. Filippini,&nbsp;L. Fusco,&nbsp;Y. Gatelet,&nbsp;P. Gay,&nbsp;H. Glotin,&nbsp;R. Gozzini,&nbsp;R. Gracia Ruiz,&nbsp;K. Graf,&nbsp;C. Guidi,&nbsp;S. Hallmann,&nbsp;H. van Haren,&nbsp;A. J. Heijboer,&nbsp;Y. Hello,&nbsp;J. J. Hernández-Rey,&nbsp;J. Hößl,&nbsp;J. Hofestädt,&nbsp;F. Huang,&nbsp;G. Illuminati,&nbsp;C. W. James,&nbsp;B. Jisse-Jung,&nbsp;M. de Jong,&nbsp;P. de Jong,&nbsp;M. Jongen,&nbsp;M. Kadler,&nbsp;O. Kalekin,&nbsp;U. Katz,&nbsp;N. R. Khan-Chowdhury,&nbsp;A. Kouchner,&nbsp;I. Kreykenbohm,&nbsp;V. Kulikovskiy,&nbsp;R. Lahmann,&nbsp;R. Le Breton,&nbsp;D. Lefèvre,&nbsp;E. Leonora,&nbsp;G. Levi,&nbsp;M. Lincetto,&nbsp;D. Lopez-Coto,&nbsp;S. Loucatos,&nbsp;L. Maderer,&nbsp;J. Manczak,&nbsp;M. Marcelin,&nbsp;A. Margiotta,&nbsp;A. Marinelli,&nbsp;J. A. Martínez-Mora,&nbsp;K. Melis,&nbsp;P. Migliozzi,&nbsp;A. Moussa,&nbsp;R. Muller,&nbsp;L. Nauta,&nbsp;S. Navas,&nbsp;E. Nezri,&nbsp;B. Ó Fearraigh,&nbsp;M. Organokov,&nbsp;G. E. Păvălaş,&nbsp;C. Pellegrino,&nbsp;M. Perrin-Terrin,&nbsp;P. Piattelli,&nbsp;C. Pieterse,&nbsp;C. Poirè,&nbsp;V. Popa,&nbsp;T. Pradier,&nbsp;N. Randazzo,&nbsp;S. Reck,&nbsp;G. Riccobene,&nbsp;A. Romanov,&nbsp;A. Sánchez-Losa,&nbsp;F. Salesa Greus,&nbsp;D. F. E. Samtleben,&nbsp;M. Sanguineti,&nbsp;P. Sapienza,&nbsp;J. Schnabel,&nbsp;J. Schumann,&nbsp;F. Schüssler,&nbsp;M. Spurio,&nbsp;Th. Stolarczyk,&nbsp;M. Taiuti,&nbsp;Y. Tayalati,&nbsp;S.J. Tingay,&nbsp;B. Vallage,&nbsp;V. Van Elewyck,&nbsp;F. Versari,&nbsp;S. Viola,&nbsp;D. Vivolo,&nbsp;J. Wilms,&nbsp;S. Zavatarelli,&nbsp;A. Zegarelli,&nbsp;J. D. Zornoza,&nbsp;J. Zúñiga,&nbsp;(ANTARES Collaboration)","doi":"10.1002/lom3.10578","DOIUrl":"https://doi.org/10.1002/lom3.10578","url":null,"abstract":"<p>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 of individual organisms, as well as their location and movement. A mathematical model is built to describe the measurement process of underwater neutrino telescopes and the signal generation of the biological organisms. The Metric Gaussian Variational Inference algorithm is used to reconstruct the model parameters using photon counts recorded by photomultiplier tubes. We apply this method to synthetic data sets and data collected by the ANTARES neutrino telescope. The telescope is located 40 km off the French coast and fixed to the sea floor at a depth of 2475 m. The runs with synthetic data reveal that we can model the emitted bioluminescent flashes of the organisms. Furthermore, we find that the spatial resolution of the localization of light sources highly depends on the configuration of the telescope. Precise measurements of the efficiencies of the detectors and the attenuation length of the water are crucial to reconstruct the light emission. Finally, the application to ANTARES data reveals the first localizations of bioluminescent organisms using neutrino telescope data.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 11","pages":"734-760"},"PeriodicalIF":2.7,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10578","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134805101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extracting proteins from microscopic biominerals: A reproducible method development using oyster larvae","authors":"Alessia Carini,&nbsp;Juan Diego Gaitán-Espitia,&nbsp;Vengatesen Thiyagarajan","doi":"10.1002/lom3.10574","DOIUrl":"https://doi.org/10.1002/lom3.10574","url":null,"abstract":"<p>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 methodological constraints that limit the overall insight, particularly in small organisms. Therefore, we propose this straightforward and reproducible method development for preparing microscopic biominerals before proteome extraction. The method development can be tailored to other microscopic biominerals, and, importantly, it aims to integrate biomineral cleanliness and integrity without sacrificing proteome completeness. First, we suggest running an in-depth sample exploration to identify key sample characteristics and determine the magnitude of the sodium hypochlorite (NaOCl) treatment. Then, we recommend running a multiple time points experiment for biomineral cleaning treatment with a fixed NaOCl concentration. The time points are evaluated using qualitative (visual assessment) and quantitative methods (biomineral loss, elemental composition, and organic structural components removal). Finally, critical time points are identified for method validation using shotgun proteomics. This approach was tested using Hong Kong oyster larval shells as a model organism. Our study discovered that surprisingly, longer treatments and partial biomineral damage are preferred for Hong Kong oyster larvae and do not lead to protein diversity loss but enrichment. This microscopic biomineral cleaning method development can facilitate harnessing information from increasingly diverse biomineral proteomes.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 11","pages":"673-686"},"PeriodicalIF":2.7,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10574","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134804907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new index for the rapid generation of chlorophyll time series from hyperspectral imaging of sediment cores","authors":"Hamid Ghanbari,&nbsp;David R. Zilkey,&nbsp;Irene Gregory-Eaves,&nbsp;Dermot Antoniades","doi":"10.1002/lom3.10576","DOIUrl":"https://doi.org/10.1002/lom3.10576","url":null,"abstract":"<p>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 chlorophyll inferences but it requires more extensive vetting. Despite recent advances in model development, there is still a knowledge gap about the reliability of chlorophyll models when applied in lakes with diverse properties, as well as the potential confounding effects of physical sediment properties on these models. We assessed the performance of 23 chlorophyll indices based on paired measurements collected via hyperspectral imaging and spectrophotometry for 202 samples spread across seven Canadian lake sediment cores. The best performance was by a new index based on the wavelength of the red-edge minimum point (λREMP). We tested the applicability of λREMP to a broad range of sediment cores using a database of 116 cores, and found the index to provide reliable reconstructions of ƩChl (i.e., chlorophyll <i>a</i> and <i>b</i> and their degradation products) trends in 84% of sites. Further analyses indicated that sediment characteristics including particle size, organic matter content, water content, and density had no systematic impact on ƩChl, but greater sediment brightness did increase ƩChl inferences from hyperspectral images. Hyperspectral core scanning is poised to facilitate the generation of high-resolution chlorophyll time series data, which could greatly improve our understanding of trajectories of change from the local to global scales.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 11","pages":"703-717"},"PeriodicalIF":2.7,"publicationDate":"2023-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10576","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134815725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ZooScan and the ZooCAM zooplankton imaging systems are intercomparable: A benchmark on the Bay of Biscay zooplankton","authors":"Nina Grandremy,&nbsp;Christine Dupuy,&nbsp;Pierre Petitgas,&nbsp;Sophie Le Mestre,&nbsp;Paul Bourriau,&nbsp;Antoine Nowaczyk,&nbsp;Bertrand Forest,&nbsp;Jean-Baptiste Romagnan","doi":"10.1002/lom3.10577","DOIUrl":"https://doi.org/10.1002/lom3.10577","url":null,"abstract":"<p>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 the ZooScan, a commercially available, laboratory-based scanner, which analyses zooplankton preserved samples, and the ZooCAM, an in-flow imaging system designed for on-board live zooplankton imaging. Sixty-one zooplankton samples collected over the Bay of Biscay in environments ranging from estuarine to offshore blue waters were imaged with both instruments. Zooplankton Normalized Biovolume-Size Spectra slopes, mean sizes, abundances, and zooplankton community biogeographical patterns were computed for each instrument and compared at the taxonomic group, the sampling stations and the Bay of Biscay scales. Both instruments produced similar zooplankton variables by stations and by taxa and described similar zooplankton community compositions and biogeographical patterns, on the large mesozooplankton size range, i.e., [0.3–3.39] mm ESD. We conclude that the ZooCAM and the ZooScan data can be combined to generate long term or spatially resolved zooplankton time series. Our study shows that benchmarking imaging instruments or techniques (1) offers a robust assessment of interoperability between instruments, mitigating possible instrumental biases, and (2) may be of great interest in the case of instrumental obsolescence or breakdown, to choose the most conservative replacement solution in a long term time series framework.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 11","pages":"718-733"},"PeriodicalIF":2.7,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10577","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134815396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of advanced methodologies for diatom identification within dynamic coastal communities","authors":"Emily Pierce,&nbsp;Olivia Torano,&nbsp;YuanYu Lin,&nbsp;Astrid Schnetzer,&nbsp;Adrian Marchetti","doi":"10.1002/lom3.10575","DOIUrl":"https://doi.org/10.1002/lom3.10575","url":null,"abstract":"<p>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 rapid advancements. This study aims to compare diatom taxonomic composition results within natural assemblages derived from rapidly advancing methods, FlowCam imaging and metabarcoding of the V4 region of the 18S rRNA gene, with traditional light microscopy cell counting techniques. All three methods were implemented in tandem to analyze changes in dynamic diatom assemblages within simulated upwelling experiments conducted in the California upwelling zone. The results of this study indicate that, summed across all samples, DNA sequencing detected four times as many genera as morphology-based methods, thus supporting previous findings that DNA sequencing is the most powerful method for analyzing species richness. Results indicate that all three methods returned comparable relative abundance for the most abundant genera. However, the three methods did not return comparable absolute abundance, primarily due to barriers in deriving quantities in equal units. Overall, this study indicates that at the semi-quantitative level of relative abundance measurements, FlowCam imaging and metabarcoding of the V4 region of the 18S rRNA gene yield comparable results with light microscopy but at the qualitative and quantitative levels, enumeration metrics diverge, and thus method selection and cross-method comparison should be performed with caution.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 11","pages":"687-702"},"PeriodicalIF":2.7,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134814880","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}