Limnology and Oceanography: Methods最新文献

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.

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.

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.

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 cm² 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.

Autonomous underwater vehicles provide water column observations of phytoplankton biomass using chlorophyll a (Chl a) fluorometers. However, under high incident light, phytoplankton fluorescence yield decreases in a process known as non-photochemical quenching, resulting in a reduced Chl a 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 a fluorescence data across shelf sea ecosystems.

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 ExStream 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.

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 nifH 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, nifH amplicon sequencing, and shotgun metagenomic sequencing.

Mono- and dimethylmercury (MMHg and DMHg, respectively) are the two primary organic forms of mercury (Hg) found in natural waters. While experimental approaches to characterize the environmental behavior of MMHg and inorganic forms of Hg are widely used today, few laboratories conduct experimental studies entailing the use of DMHg. In this paper, we have evaluated and developed different analytical and experimental approaches to quantify and use DMHg in laboratory studies. We demonstrate that DMHg can be analyzed from samples where MMHg is derivatized using sodium tetraethyl borate and where the matrix effects of dissolved sulfide are masked using copper sulfate. Tests, where the calibration curves of MMHg and DMHg were used, showed that MMHg may be used to calibrate for DMHg. For the pre-concentration of DMHg, both traps filled with Tenax® TA and Bond Elut ENV were found suitable. We observed good recoveries of DMHg added to different types of natural waters or purified water containing aquarium salt, sodium chloride and dissolved sulfide, iron sulfide, and cadmium sulfide at DMHg : sulfide molar ratios > 10⁻⁶. In addition to evaluating these analytical aspects, we present suitable subsampling techniques for DMHg-containing solutions, the recovery of DMHg when filtering DMHg through different types of filters, and experimental data on the long-term stability of DMHg added to different types of waters and stored at different temperatures. Finally, we present and discuss a new synthetization protocol for preparing aqueous solutions containing DMHg free of organic solvents and where handling DMHg in a pure form is prevented.

A key assumption in trophic position (TP) estimation using stable isotope analysis is that consumers are in isotopic equilibrium with their resources. Here, we assess the degree to which time-varying resource dynamics and isotope incorporation rates of consumers influence consumer TP estimates across multiple trophic levels and aquatic ecosystems. We constructed a first-order kinetics model to explore consumer stable isotope incorporation rates and modeled the effect on TP calculations using bulk and compound-specific stable isotope data from previous experimental and observational studies. We found TP estimates of higher trophic level consumers are less accurate than lower trophic level consumers when applying bulk stable isotope analysis (BSIA) and using particulate organic matter as the stable isotope baseline. The accuracy of TP estimates depended on the time-varying dynamics of the stable isotope baseline. Tertiary consumers had the highest TP estimation error, and this error was not eliminated by sampling tissues with fast incorporation rates (i.e., blood) in the tertiary consumer. Compound-specific stable isotope analysis (CSIA) of individual amino acids was more accurate in estimating TP for all consumers and ecosystems compared to BSIA. Our analysis confirms that consideration for the dynamic nature of stable isotope ratios is necessary for accurate TP estimates. Finally, we show how first-order kinetics models can provide a useful framework for integrating prey and consumer incorporation rates in stable isotope studies to improve TP estimates.

This work assesses the effectiveness of sample preservation techniques for measurements of pH_T (total scale), total dissolved inorganic carbon (C_T), and total alkalinity (A_T) in organic-rich estuarine waters as well as the internal consistency of measurements and calculations (e.g., A_T, pH_T, and C_T) in these waters. Using mercuric chloride (HgCl₂)-treated and untreated water samples, measurements of these carbonate system parameters were examined over a period of 3 months. Respiration of dissolved organic matter in untreated samples created large discrepancies in C_T concentrations (~37 μmol kg⁻¹ increase, p < 0.0001), while C_T was effectively constant in treated samples (3095.0 ± 1.14 μmol kg⁻¹). A_T changes were observed for both treated and untreated samples, with HgCl₂-treated samples showing the greatest variation (~ 26 μmol kg⁻¹ decrease, p < 0.001). In response to changing A_T/C_T ratios, pH_T changes occurred in both treated and untreated samples but were relatively small in treated samples. Results in organic-rich estuarine waters that reflect the in situ carbonate system characteristics of the samples at the time of collection can be improved when samples obtained for C_T and A_T analysis are collected and stored separately. Accurate analyses of C_T can be obtained by filtration and preservation with HgCl₂. Accuracy of A_T analyses can be improved by filtration and storage without adding HgCl₂. The quality of pH_T measurements can be improved by prompt analysis in the field and, if this cannot be accomplished, then samples can be preserved with HgCl₂ and measured in the laboratory within 1 week.