Limnology and Oceanography: Methods最新文献

{"title":"Simultaneous preconcentration of 9Be and cosmogenic 10Be for determination of the 10Be/9Be ratio in (coastal) seawater","authors":"Chenyu Wang,&nbsp;Daniel A. Frick,&nbsp;Friedhelm von Blanckenburg,&nbsp;Martin Frank,&nbsp;Ergang Lian,&nbsp;Shouye Yang,&nbsp;Hella Wittmann","doi":"10.1002/lom3.10587","DOIUrl":"10.1002/lom3.10587","url":null,"abstract":"<p>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 ⁹Be and ¹⁰Be from (coastal) seawater based on the iron co-precipitation method. The concentrations of ⁹Be, ¹⁰Be, and the resulting ¹⁰Be/⁹Be ratio for Changjiang Estuary water derived from the new procedure agree well with those obtained from the conventional procedure requiring separate preconcentration for ⁹Be and ¹⁰Be determinations. By avoiding the separate preconcentration, our newly developed procedure contributes toward more time-efficient handling of samples, less sample cross-contamination, and a more reliable ¹⁰Be/⁹Be ratio. Prior to this, we validated the iron co-precipitation method using artificial seawater and natural water samples from the Amazon Estuary regarding: (1) the “matrix effect” for Be analysis, (2) its extraction efficiency for pg g⁻¹ levels Be in the presence and absence of organic matter, and (3) the data comparability with another preconcentration method. We calculated that for the determination of ⁹Be and ¹⁰Be in most open ocean seawater with typical ¹⁰Be concentrations of &gt; 500 atoms g⁻¹, good precisions (&lt; 5%) can be achieved using less than 3 liters of seawater compared to more than 20 liters routinely used previously. Even for coastal seawater with extremely low ¹⁰Be concentration (e.g., 100 atoms g⁻¹), we estimate a maximum amount of 10 liters to be adequate.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 1","pages":"14-24"},"PeriodicalIF":2.7,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10587","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135390466","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":"Lab-based multispectral photography for approximating chlorophyll content in Zostera marina","authors":"Katherine Ann Haviland,&nbsp;Melanie Hayn,&nbsp;Robert Warren Howarth","doi":"10.1002/lom3.10589","DOIUrl":"10.1002/lom3.10589","url":null,"abstract":"<p>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 <i>Zostera marina</i>. Using near-infrared and red wavelength cameras in the lab environment, we measured normalized difference vegetation index (NDVI) in photographs of sampled seagrass leaves. In samples taken from three different environments, we found a positive correlation between lab-based NDVI and chlorophyll content, with variation attributable to leaf age. In samples grown under different light conditions, we found high levels of NDVI associated with lower light possibly due to seagrass photoacclimation. This method may be used in addition to existing seagrass monitoring methods to collect data on seagrass photic status and estimate chlorophyll content, and detect possible light limitation due to turbidity or high epibiota cover. The relatively low cost and time required for this method may make it useful where researchers are already collecting and imaging seagrass as part of routine monitoring.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 1","pages":"25-33"},"PeriodicalIF":2.7,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135341747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HOTFLOOR: A benthic chamber system to simulate warming on the seafloor","authors":"Norman Göbeler,&nbsp;Laura Kauppi,&nbsp;Robin Gottberg,&nbsp;Göran Lundberg,&nbsp;Alf Norkko,&nbsp;Joanna Norkko","doi":"10.1002/lom3.10581","DOIUrl":"10.1002/lom3.10581","url":null,"abstract":"<p>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 days. The system consists of a commercially available electric boiler, usually applied in domestic underfloor heating, and custom-designed benthic acrylic glass chambers connected to individual thermostats. Furthermore, the chambers are semi-open, allowing constant water exchange, maintaining otherwise near-natural conditions, including oxygen concentrations, while the temperature is elevated. The water exchange can be stopped to facilitate incubations measuring changes in benthic fluxes. We conducted a 15-d trial study in July 2021 on a bare-sediment habitat at 2.5 m depth, exposing five chambers to water temperatures 5°C above ambient temperatures for 6 d and comparing with five control chambers. In this assessment, we demonstrate that the temperature control and stability were reliable while maintaining natural oxygen conditions. The modular character of the system permits adaptations for various benthic habitats, facilitating the investigation of elevated temperatures in situ for future climate change scenarios.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"21 12","pages":"790-799"},"PeriodicalIF":2.7,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10581","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135636461","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":"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}