Limnology and Oceanography: Methods最新文献

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.

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 > 500 atoms g⁻¹, good precisions (< 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.

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 Zostera marina. 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.

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.

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 a (Chl a), 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 a 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 a 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 a, 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 a and carotenoids as proxies for biomass. Greater focus on the distribution and volume of the training data would improve the phycocyanin estimates.

Microplastic particles (< 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 (< 10 μm), and 1–20 μm 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 μm) from Lake Superior surface water samples, which showed particle abundances two to three orders of magnitude higher than particles > 100 μm 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 (> 2 h) are recommended for successful analysis of natural aquatic samples processed by this approach.

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.

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.