Limnology and Oceanography: Methods最新文献

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Lotic-SIPCO2: Adaptation of an open-source CO2 sensor system and examination of associated emission uncertainties across a range of stream sizes and land uses Lotic-SIPCO2:调整开放源码二氧化碳传感器系统,并在一系列溪流大小和土地利用情况下检查相关排放的不确定性
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2024-02-26 DOI: 10.1002/lom3.10600
Andrew L. Robison, Lauren E. Koenig, Jody D. Potter, Lisle E. Snyder, Christopher W. Hunt, William H. McDowell, Wilfred M. Wollheim
{"title":"Lotic-SIPCO2: Adaptation of an open-source CO2 sensor system and examination of associated emission uncertainties across a range of stream sizes and land uses","authors":"Andrew L. Robison,&nbsp;Lauren E. Koenig,&nbsp;Jody D. Potter,&nbsp;Lisle E. Snyder,&nbsp;Christopher W. Hunt,&nbsp;William H. McDowell,&nbsp;Wilfred M. Wollheim","doi":"10.1002/lom3.10600","DOIUrl":"10.1002/lom3.10600","url":null,"abstract":"<p>River networks play a crucial role in the global carbon cycle, as relevant sources of carbon dioxide (CO<sub>2</sub>) to the atmosphere. Advancements in high-frequency monitoring in aquatic environments have enabled measurement of dissolved CO<sub>2</sub> concentration at temporal resolutions essential for studying carbon variability and evasion from these dynamic ecosystems. Here, we describe the adaptation, deployment, and validation of an open-source and relatively low-cost in situ <i>p</i>CO<sub>2</sub> sensor system for lotic ecosystems, the lotic-SIPCO2. We tested the lotic-SIPCO2 in 10 streams that spanned a range of land cover and basin size. Key system adaptations for lotic environments included prevention of biofouling, configuration for variable stage height, and reduction of headspace equilibration time. We then examined which input parameters contribute the most to uncertainty in estimating CO<sub>2</sub> emission rates and found scaling factors related to the gas exchange velocity were the most influential when CO<sub>2</sub> concentration was significantly above saturation. Near saturation, sensor measurement of <i>p</i>CO<sub>2</sub> contributed most to uncertainty in estimating CO<sub>2</sub> emissions. We also found high-frequency measurements of <i>p</i>CO<sub>2</sub> were not necessary to accurately estimate median emission rates given the CO<sub>2</sub> regimes of our streams, but daily to weekly sampling was sufficient. High-frequency measurements of <i>p</i>CO<sub>2</sub> remain valuable for exploring in-stream metabolic variability, source partitioning, and storm event dynamics. Our adaptations to the SIPCO2 offer a relatively affordable and robust means of monitoring dissolved CO<sub>2</sub> in lotic ecosystems. Our findings demonstrate priorities and related considerations in the design of monitoring projects of dissolved CO<sub>2</sub> and CO<sub>2</sub> evasion dynamics more broadly.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 4","pages":"191-207"},"PeriodicalIF":2.7,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10600","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139968681","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 temperature-controlled, circular maintenance system for studying growth and development of pelagic tunicates (salps) 用于研究浮游鳞栉水母(鲑鱼)生长发育的温控循环维护系统
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2024-02-24 DOI: 10.1002/lom3.10605
Svenja J. Müller, Wiebke Wessels, Sara Driscoll, Evgeny A. Pakhomov, Lutz Auerswald, Katharina Michael, Bettina Meyer
{"title":"A temperature-controlled, circular maintenance system for studying growth and development of pelagic tunicates (salps)","authors":"Svenja J. Müller,&nbsp;Wiebke Wessels,&nbsp;Sara Driscoll,&nbsp;Evgeny A. Pakhomov,&nbsp;Lutz Auerswald,&nbsp;Katharina Michael,&nbsp;Bettina Meyer","doi":"10.1002/lom3.10605","DOIUrl":"10.1002/lom3.10605","url":null,"abstract":"<p>Salps have attracted attention as zooplankton organisms that may be able to expand their habitat range and increase their ecological importance in the face of ongoing global warming. Due to their gelatinous nature, unique feeding strategy, and reproductive ecology such changes could have profound impacts on regional marine ecosystems. While their role in the regional carbon cycle is receiving attention, our knowledge of their physiology and life cycle is still limited. This knowledge gap is mainly due to their fragile gelatinous nature, which makes it difficult to capture and maintain intact specimen in the laboratory. We present here a modified kreisel tank system that has been tested onboard a research vessel with the Southern Ocean salp <i>Salpa thompsoni</i> and at a research station with <i>Salpa fusiformis</i> and <i>Thalia democratica</i> from the Mediterranean Sea. Successful maintenance over days to weeks allowed us to obtain relative growth and developmental rates comparable to in situ field samples of <i>S. thompsoni</i> and <i>S. fusiformis</i>, and provided insights into previously unknown features of their life cycle (e.g., testes development). Our results show that traditional methods of estimating growth, such as cohort analysis, may lead to a general overestimation of growth rates and neglect individual strategies (e.g., shrinkage), which can affect the results and conclusions drawn from population dynamic models. By providing a starting point for the successful maintenance of different species, comparable experiments on the physiology of salps is made possible. This will contribute to refining model parameters and improving the reliability of the predictions.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 5","pages":"281-294"},"PeriodicalIF":2.7,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10605","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139952297","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
Toward a synthesis of phytoplankton community composition methods for global-scale application 综合浮游植物群落组成方法,促进全球尺度应用
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2024-02-23 DOI: 10.1002/lom3.10602
Sasha J. Kramer, Luis M. Bolaños, Dylan Catlett, Alison P. Chase, Michael J. Behrenfeld, Emmanuel S. Boss, E. Taylor Crockford, Stephen J. Giovannoni, Jason R. Graff, Nils Haëntjens, Lee Karp-Boss, Emily E. Peacock, Collin S. Roesler, Heidi M. Sosik, David A. Siegel
{"title":"Toward a synthesis of phytoplankton community composition methods for global-scale application","authors":"Sasha J. Kramer,&nbsp;Luis M. Bolaños,&nbsp;Dylan Catlett,&nbsp;Alison P. Chase,&nbsp;Michael J. Behrenfeld,&nbsp;Emmanuel S. Boss,&nbsp;E. Taylor Crockford,&nbsp;Stephen J. Giovannoni,&nbsp;Jason R. Graff,&nbsp;Nils Haëntjens,&nbsp;Lee Karp-Boss,&nbsp;Emily E. Peacock,&nbsp;Collin S. Roesler,&nbsp;Heidi M. Sosik,&nbsp;David A. Siegel","doi":"10.1002/lom3.10602","DOIUrl":"10.1002/lom3.10602","url":null,"abstract":"<p>The composition of the marine phytoplankton community has been shown to impact many biogeochemical processes and marine ecosystem services. A variety of methods exist to characterize phytoplankton community composition (PCC), with varying degrees of taxonomic resolution. Accordingly, the resulting PCC determinations are dependent on the method used. Here, we use surface ocean samples collected in the North Atlantic and North Pacific Oceans to compare high-performance liquid chromatography pigment-based PCC to four other methods: quantitative cell imaging, flow cytometry, and 16S and 18S rRNA amplicon sequencing. These methods allow characterization of both prokaryotic and eukaryotic PCC across a wide range of size classes. PCC estimates of many taxa resolved at the class level (e.g., diatoms) show strong positive correlations across methods, while other groups (e.g., dinoflagellates) are not well captured by one or more methods. Since variations in phytoplankton pigment concentrations are related to changes in optical properties, this combined dataset expands the potential scope of ocean color remote sensing by associating PCC at the genus- and species-level with group- or class-level PCC from pigments. Quantifying the strengths and limitations of pigment-based PCC methods compared to PCC assessments from amplicon sequencing, imaging, and cytometry methods is the first step toward the robust validation of remote sensing approaches to quantify PCC from space.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 4","pages":"217-240"},"PeriodicalIF":2.7,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10602","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139952270","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
Hit or miss? Impact of time series resolution on resolving phytoplankton dynamics at hourly, weekly, and satellite remote sensing frequencies 命中还是失误?时间序列分辨率对以小时、周和卫星遥感频率解析浮游植物动态的影响
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2024-02-21 DOI: 10.1002/lom3.10604
Virginie Sonnet, Colleen B. Mouw, Audrey B. Ciochetto, Jessica Carney-Almeida
{"title":"Hit or miss? Impact of time series resolution on resolving phytoplankton dynamics at hourly, weekly, and satellite remote sensing frequencies","authors":"Virginie Sonnet,&nbsp;Colleen B. Mouw,&nbsp;Audrey B. Ciochetto,&nbsp;Jessica Carney-Almeida","doi":"10.1002/lom3.10604","DOIUrl":"10.1002/lom3.10604","url":null,"abstract":"<p>Characterizing marine phytoplankton community variability is crucial to designing sampling strategies and interpreting time series. Satellite remote sensing, microscopy sampling, and flow through imaging systems have widely different resolutions: from weekly or monthly with microscopy sampling to daily when no cloud cover or glint is present with polar-orbiting satellites, and hourly for autonomous imaging instruments. To improve our understanding of data robustness against sampling resolution at different taxonomic levels, we analyze 2 yr of data from an Imaging FlowCytobot with hourly resolution and resample it to daily, satellite-temporal, and weekly microscopy sampling resolution. We show that weekly and satellite-temporal resolutions are sufficient to resolve general community composition but that the randomness of satellite-temporal resolution can result in overrepresenting or underrepresenting certain categories. While the yearly phytoplankton biomass bloom is detected in late winter by all four resolutions, category-specific yearly blooms are generally consistent in timing but often underestimated or missed by the weekly and satellite-temporal resolutions, introducing a bias in year-to-year comparisons. A minimum of biweekly sampling, particularly during known bloom periods, would lower the bias in such categories. Similarly, sampling time should be considered as daily variations are category-specific. Overall, morning and low tide sampling tended to have higher biomass. We provide tables for categories detected by the IFCB in Narragansett Bay with their major bloom characteristics and recorded daily variability to inform future sampling designs. These results provide tools to interpret past and future time series, including possible detection of specific taxonomic groups with targeted satellite algorithms.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 4","pages":"254-267"},"PeriodicalIF":2.7,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10604","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139952215","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
Combined benthic and stream edge sampling better represent macroinvertebrate assemblages than benthic sampling alone along an aridity gradient 在干旱梯度上,底栖生物和溪流边缘取样相结合比单独进行底栖生物取样更能代表大型无脊椎动物的集合体
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2024-02-15 DOI: 10.1002/lom3.10601
Brian A. Gill, Daniel C. Allen, Meryl C. Mims, Thomas M. Neeson, Albert Ruhi, Carla L. Atkinson, Arial J. Shogren, Travis M. Apgar, Zacchaeus G. Compson, Stephen Cook, Daryl R. Trumbo, Michelle H. Busch, Kelsey D. Hollien, Kyle Leathers, Megan C. Malish, Grace L. O'Malley, Samuel Silknetter, Chelsea R. Smith, Howard Dunleavy, Michael T. Bogan
{"title":"Combined benthic and stream edge sampling better represent macroinvertebrate assemblages than benthic sampling alone along an aridity gradient","authors":"Brian A. Gill,&nbsp;Daniel C. Allen,&nbsp;Meryl C. Mims,&nbsp;Thomas M. Neeson,&nbsp;Albert Ruhi,&nbsp;Carla L. Atkinson,&nbsp;Arial J. Shogren,&nbsp;Travis M. Apgar,&nbsp;Zacchaeus G. Compson,&nbsp;Stephen Cook,&nbsp;Daryl R. Trumbo,&nbsp;Michelle H. Busch,&nbsp;Kelsey D. Hollien,&nbsp;Kyle Leathers,&nbsp;Megan C. Malish,&nbsp;Grace L. O'Malley,&nbsp;Samuel Silknetter,&nbsp;Chelsea R. Smith,&nbsp;Howard Dunleavy,&nbsp;Michael T. Bogan","doi":"10.1002/lom3.10601","DOIUrl":"10.1002/lom3.10601","url":null,"abstract":"<p>Studies of stream macroinvertebrates traditionally use sampling methods that target benthic habitats. These methods could underestimate biodiversity if important assemblage components exist outside of the benthic zone. To test the efficacy of different sampling methods, we collected paired reach-wide benthic and edge samples from up to 10 study reaches in nine basins spanning an aridity gradient across the United States. Edge sampling targeted riparian-adjacent microhabitats not typically sampled, including submerged vegetation, roots, and overhanging banks. We compared observed richness, asymptotic richness, and assemblage dissimilarity between benthic samples alone and different combinations of benthic and edge samples to determine the magnitude of increased diversity and assemblage dissimilarity values with the addition of edge sampling. We also examined how differences in richness and assemblage composition varied across an aridity gradient. The addition of edge sampling significantly increased observed richness (median increase = 29%) and asymptotic richness (median increase = 173%). Similarly, median Bray–Curtis dissimilarity values increased by as much as 0.178 when benthic and edge samples were combined. Differences in richness metrics were generally higher in arid basins, but assemblage dissimilarity either increased or decreased across the aridity gradient depending on how benthic and edge samples were combined. Our results suggest that studies that do not sample stream edges may significantly underestimate reach diversity and misrepresent assemblage compositions, with effects that can vary across climates. We urge researchers to carefully consider sampling methods in field studies spanning climatic zones and the comparability of existing data sets when conducting data synthesis studies.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 4","pages":"208-216"},"PeriodicalIF":2.7,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139835423","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
The Ellrott grab: A small, lightweight sediment sampler for collecting undisturbed sandy sediments 埃尔罗特抓斗一种小型、轻便的沉积物取样器,用于采集未受扰动的沙质沉积物
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2024-01-15 DOI: 10.1002/lom3.10598
Chyrene Moncada, Andreas Ellrott, Dirk de Beer, Rudolf Amann, Katrin Knittel
{"title":"The Ellrott grab: A small, lightweight sediment sampler for collecting undisturbed sandy sediments","authors":"Chyrene Moncada,&nbsp;Andreas Ellrott,&nbsp;Dirk de Beer,&nbsp;Rudolf Amann,&nbsp;Katrin Knittel","doi":"10.1002/lom3.10598","DOIUrl":"10.1002/lom3.10598","url":null,"abstract":"<p>Sampling sandy surface sediments is an important first step in understanding biogeochemical processes in these dynamic environments. However, sampling such sediments poses several challenges, especially when undisturbed samples with porewater are required. Several grab samplers are commercially available, but they are either prone to sample loss, too heavy or bulky for use in small vessels, or those with spring-loaded mechanisms present safety issues. Here, we present the Ellrott grab, a lightweight sediment sampler designed for collecting undisturbed surface sediments including porewater and overlying bottom seawater. The sampler consists of a frame and a rotating bowl that can collect 370 cm<sup>2</sup> of surface sediments up to 10 cm deep (2.5 liters total volume). The instrument is 40 × 60 cm in size, has a basic weight of 10 kg, with up to 20 kg additional weights for stability in sandy sediments. Two persons can operate the grab and it can be used on small boats with a crane and winch system or a hand winch. The grab is now in routine use in the Wadden Sea and in Isfjorden, Svalbard. The samples obtained from the grab were suitable for various geochemical and microbial analyses. Using microelectrodes, we found that in situ oxygen profiles were similar to ex situ profiles in cores subsampled from the grab, confirming that the grab causes minimal disturbance to the sample. Although the grab was designed for collecting sandy sediments, it could also be applied to silty sediments, allowing straightforward and efficient sampling of various sediment types.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 3","pages":"159-169"},"PeriodicalIF":2.7,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10598","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139475501","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 chlorophyll a, non-photochemical fluorescence quenching correction method for autonomous underwater vehicles in shelf sea environments 陆架海环境中自主潜水器的叶绿素 a 非光化学荧光淬灭校正方法
IF 2.7 3区 地球科学
Limnology and Oceanography: Methods Pub Date : 2024-01-11 DOI: 10.1002/lom3.10597
Catherine Mitchell, David Drapeau, Sunny Pinkham, William M Balch
{"title":"A chlorophyll a, non-photochemical fluorescence quenching correction method for autonomous underwater vehicles in shelf sea environments","authors":"Catherine Mitchell,&nbsp;David Drapeau,&nbsp;Sunny Pinkham,&nbsp;William M Balch","doi":"10.1002/lom3.10597","DOIUrl":"10.1002/lom3.10597","url":null,"abstract":"<p>Autonomous underwater vehicles provide water column observations of phytoplankton biomass using chlorophyll <i>a</i> (Chl <i>a</i>) fluorometers. However, under high incident light, phytoplankton fluorescence yield decreases in a process known as non-photochemical quenching, resulting in a reduced Chl <i>a</i> fluorescence signal. Methods have been developed to identify and remove the quenched signal from observations by autonomous underwater vehicles. These existing methods rely on assumptions of the homogeneity of the system, both in terms of time (i.e., between day and night observations) and space (i.e., within the water column or between neighboring profiles). These assumptions are not valid in shallow shelf seas or when sampling across different water masses. Thus, we evaluate six new quenching correction methods based on an existing ocean-based method, but adapted for a continental shelf sea environment where the water mass changes between night and day observations. We have included two main changes to the existing method. First, we interpolate the unquenched, nighttime signal across the daytime observations and use this as a reference for correcting the quenched, daytime signal. Second, we explore the inclusion of a fluorescence quenching depth limit. By interpolating nighttime observations across daytime periods, the diel changes in non-photochemical quenching were separated from the phytoplankton population changes. The proposed methods all show improved performance compared to existing approach. The methods presented here, and the approach used to evaluate them, are applicable in other shelf sea environments, enabling studies using autonomous Chl <i>a</i> fluorescence data across shelf sea ecosystems.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"22 3","pages":"149-158"},"PeriodicalIF":2.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10597","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139422183","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
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
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