Limnology and Oceanography: Methods最新文献

Intertidal habitats are shaped by the actions of tides and waves which are difficult to monitor in shallow water. To address this challenge, the “Mini Buoy” and associated open-source App were recently developed for the low-cost and long-term monitoring of tidal inundation and current velocities simultaneously. The Mini Buoy is a bottom-mounted float that measures tilt to infer near-bed hydrodynamics. Here, we present significant updates to the Mini Buoy and App. Two new Mini Buoy designs were calibrated: the “Pendant” that requires minimal assembly for deployment, and the “B4+” that can also measure wave orbital velocity. Comparisons against industry-standard water-level and velocity sensors deployed in the field showed that each new design was effective at detecting tidal inundation (overall accuracy of 86–97%) and current velocities (R² = 0.73–0.91; accuracies of ± 0.14–0.22 m s⁻¹; detection limits between 0.02 and 0.8 m s⁻¹). The B4+ could reasonably measure wave orbital velocities (R² = 0.56; accuracies of ± 0.18 m s⁻¹; detection limits between 0.02 and 0.8 m s⁻¹). Reducing the sampling rate to prolong survey durations did not markedly reduce the precision of velocity measurements, except in the original Mini Buoy design (uncertainty increased by ± 2.11 m s⁻¹ from 1 to 10 s sampling). The updated App enhances user experience, accepts data from any Mini Buoy design, is suitable for generic use across any tidal setting, and presents multiple options to understand and contrast local hydrodynamic regimes. Improvements to the Mini Buoy designs and App offer greater opportunities in monitoring hydrodynamics for purposes including ecosystem restoration and flood risk management.

Methods that supplement optical instruments with bait, such as baited remote underwater video (BRUV), are used worldwide to detect and quantify marine life. Optical instruments only detect targets within visible range, such that BRUVs may underestimate fishes in light-limited habitats, especially fishes that respond to the bait at ranges beyond visibility. Alternatively, light-independent instruments (e.g., imaging sonars) can detect and quantify fishes regardless of visibility. This study presents the first application of a baited imaging sonar (BISON), deployed to survey fishes around a small, shallow artificial habitat in a turbid embayment in southern Florida. To establish the influence of bait on fish detection, BISON trials were alternately conducted alongside deployments of an unbaited control, with a high-definition camera integrated to ascertain visibility and inform species composition. For fishes of two size classes, larger (> 30 cm) and smaller (10–30 cm), maximum density (MaxD) and range of detection were quantified. Although the densities of larger and smaller fishes quantified by the BISON and unbaited control did not differ, over 55% of larger fishes were detected at ranges beyond maximum visibility, with asymptotes in fish density on the BISON identified at 15–20 min and 5–10 min for larger and smaller fishes, respectively. Overall, this study demonstrates the potential of BISONs as both a complementary and alternative method to BRUVs for quantifying fishes, especially in habitats of limited visibility. Future applications of BISONs in other habitats will further demonstrate its value as a tool to detect and enumerate aquatic assemblages.

Methane (CH₄) dissolved in water is readily consumed by CH₄-oxidizing bacteria, so the possibility of the dissolved CH₄ concentration (dCH₄) in sampled water changing before analysis is a concern. To determine the accurate in situ dCH₄ level, mercury chloride (HgCl₂) or sodium azide (NaN₃) is traditionally used for sample preservation. However, these preservatives are very toxic and great care must be taken when adding them to samples. Benzalkonium chloride (BAC), a quaternary ammonium salt cationic surfactant, is a readily available disinfectant that is less harmful to the human body than HgCl₂, NaN₃, and other preservatives. In this study, we investigated the usefulness of BAC in preserving dCH₄ in swamp water, which is a critical terrestrial source of CH₄. The dCH₄ in samples without BAC decreased immediately after sample collection, whereas the dCH₄ in the samples with added BAC did not change significantly for at least 15 d. In addition, when BAC was added to 18 water samples with different water chemistries, the dCH₄ did not change significantly from immediately after sampling to 1 week after sampling (average difference: 3%). Thus, in the water samples used in this study, BAC effectively preserved dCH₄ in the samples for at least 1 week. Further testing of the effect of BAC on the preservation of dCH₄ in different types of water samples worldwide will help to establish a more complete, simple, and safe method.

To face the current downward trajectory of freshwater biodiversity loss, the implementation of effective biodiversity monitoring programs is of utmost importance. Environmental DNA offers unprecedented opportunities for this aim but several challenges still need to be addressed before implementing efficient species monitoring using eDNA. One of them is optimizing the eDNA sampling scheme to maximize the eDNA detection probability. For instance, in flowing freshwaters, the transport of eDNA downstream from its source can impact the eDNA detection probability, and blur the link between eDNA detection and the local occurrence of the species. Here, we investigated the eDNA spatial range of Harttiella lucifer (Siluriformes, Loricariidae), a threatened neotropical siluriform fish inhabiting French Guianese mountain streams, and confined to waterfalls and fast-flowing environments. Environmental samples were collected at 11 sites from the H. lucifer population to 2000 m downstream. A species-specific dPCR approach was applied to quantify the amount of DNA present in each sample and evaluate the eDNA detection probability of H. lucifer according to the distance from its source. Results showed an accumulation of eDNA at 50 and 100 m downstream from H. lucifer population. The evaluation of detection probabilities revealed that 300 m downstream from H. lucifer population, the probability of detection drops to 50%. This study suggests that eDNA drift in neotropical small streams is limited to a few tens meters downstream. These findings demonstrate that in neotropical small streams, eDNA provides a picture of the local fish fauna rather than integrating information over large spatial scales.

Salinization threatens freshwater resources and freshwater-dependent wetlands in coastal areas worldwide. Many research efforts focus on gradual or chronic salinization, but the phenomenon is also episodic in nature, particularly in small streams and artificial waterways. In surface waters, salinization events may coincide with storms, droughts, wind tides, and other episodic events. A lack of standardized quantitative methods and metrics for describing and discussing episodic salinization hinders cross-disciplinary efforts by scientists and others to analyze, discuss, and make recommendations concerning these events. Here, we present a set of metrics that use statistics which describe flow characteristics in rivers and streams as a template for empirically describing and characterizing salinization events. We developed a set of metrics to quantify the duration, magnitude, and other characteristics of episodic salinization, and we apply the metrics to extensive time-series data from a field site in coastal North Carolina. We then demonstrate the utility of these metrics by coupling them with ancillary data to perform an unsupervised classification that groups individual salinization events by their primary meteorological driver. We provide simple and flexible code needed to compute metrics in any environment experiencing salinization events in hopes that it will facilitate more standardized approaches to the quantification and study of widespread freshwater salinization.

In vitro incubations using natural marine communities can provide insight into community structure and function in ways that are challenging through field observations alone. We have designed a minimal metal incubation system for controlled and repeatable experimentation of microbial communities. The systems, dubbed Pelagic Ecosystem Research Incubators (PERIcosms), are 115 L, conical tanks designed to sample suspended, settled, and wall associated material for month long periods. PERIcosms combine some of the ecological advantages of large volume mesocosm incubations with the experimental ease and replication of bottle incubations, and their design is accessible for use by researchers without specialized training or travel to a designated incubation facility. Here, we provide a detailed description for the construction and implementation of PERIcosms and demonstrate their potential to promote replicable, diverse communities for several weeks under clean conditions using time-series results from two field experiments. One field experiment utilized coastal waters collected from Santa Catalina Island, CA and the other oligotrophic waters collected offshore of Honolulu, HI. Biomass metrics (chlorophyll a and particulate carbon) along with 16S/18S DNA based community composition assessments were conducted to show that communities contained within PERIcosms remained alive and diverse for several weeks using a semi-continuous culturing approach. We detail trace metal clean techniques that can be used to minimize external contamination, particularly for low dissolved iron environments. PERIcosms have the potential to facilitate natural community incubations which are needed to continue advancing our understanding of microbial ecology and geochemistry.

Freshwater cyanobacterial harmful algal blooms (CHABs) are a well-known global public health threat. Monitoring and early detection of CHAB toxins are currently accomplished using labor-intensive sampling techniques and subsequent shore-based analyses, with results typically reported 24–48 h after sample collection. We have developed and implemented an uncrewed, autonomous mobile sampler-analytical system capable of conducting targeted in situ toxin measurements in < 2 h. A surface plasmon resonance (SPR) instrument was combined with the environmental sample processor (ESP) to fully automate detection and quantification of particle-associated cyanobacterial microcystins (pMC). This sensor-sampler system was integrated with a long-range autonomous underwater vehicle (LRAUV) and deployed in western Lake Erie for field trials in the summer of 2021. The LRAUV was remotely piloted to acquire samples at selected locations within and adjacent to a CHAB. Sixteen pMC measurements ranging from 0.09 to 0.55 μg/L lake water were obtained over a 14-day period without recovery of the LRAUV. The SPR/ESP/LRAUV system complements existing satellite, aerial, and manual sampling CHAB survey techniques, and could be used to enhance predictive models that underpin bloom and toxicity forecasts. This system is also extensible to detection of other algal toxins in freshwater and marine environments, with its near real-time assessment of bloom toxin levels potentially offering additional socioeconomic benefits and public health protection in a variety of settings.

Hydrographic data, nutrient data and bulk rates of nitrate uptake and primary production were determined in the Amazon River plume (ARP) in the Western Tropical North Atlantic (WTNA) during three cruises in May 2018, June/July 2019, with RV Endeavor and April/May 2021 with RV Meteor. Using daily quasi-geostrophic surface velocity data from satellite observations, the geographical positions of the stations of observations were transformed onto Lagrangian coordinates to obtain a dynamically coherent and consistent spatial distribution. After the transformation, the observed surface salinity and temperature fields were consistent with the flow fields, the ARP formed a coherent structure and the retroflection of the North Brazil Current became visible. By transforming other surface variables such as nitrate concentration, photosynthetically available radiation, turbidity, bulk rates of nitrate uptake, and primary production onto Lagrangian coordinates, patterns became consistent with the physical variables at the surface. The use of “synchronous” fields as done here by transformation onto Lagrangian coordinates is essential for spatially structured analyses of data collected over tens of days in a highly dynamic region characterized by complex flow fields with low persistence such as the WTNA. Therefore, the use of the Lagrangian method provides a powerful tool for exploring spatial distributions of biologically relevant factors in regions with complex and dynamic flow patterns. These spatial distributions are qualitatively in agreement with satellite images of daily sea surface temperature and composites of monthly mean Chlorophyll a distributions.

In freshwater systems, δ¹³C and δ¹⁵N stable isotopes can be used to differentiate between pelagic and littoral energy sources and to quantify trophic position. In these ecosystems, crustacean zooplankton are frequently used to characterize the pelagic baseline. Zooplankton samples are often preserved prior to processing and analysis, which can affect isotopic signatures. Variability in preservation effects across studies make it difficult to determine if and how to correct for preservation effects. Here, we develop a correction factor for ethanol preservation and present a flexible statistical method that can be updated with additional data to increase its applicability. We collected zooplankton from five lakes in Minnesota, USA encompassing wide isotopic ranges (δ¹³C from −37.23‰ to −23.96‰; δ¹⁵N from 3.07‰ to 14.44‰). Changes in zooplankton δ¹³C and δ¹⁵N signatures were quantified using a Bayesian hierarchical model predicting fresh values from ethanol-preserved values. Ethanol preservation increased δ¹³C by a factor of 1.158 (95% CI 0.866–1.441) and had a negligible effect on δ¹⁵N (slope = 1.077; 95% CI 0.833–1.359). Lake-specific values did not differ from the overall relationship. K-fold and leave-one-out cross validation tests verified that both models were accurate; RMSE of predicted δ¹³C = 0.701 and RMSE of predicted δ¹⁵N = 0.590. Our correction factors could be applied to other systems in which baseline δ¹³C and δ¹⁵N values fall within the range of our study, and this approach also enables the inclusion of data from additional lakes to estimate new corrections.

Owing to the high cost of commercial optical sensors, there is a need to develop low-cost optical sensing packages to expand monitoring of aquatic environments, particularly in under-resourced regions. Visual methods to monitor the optical properties of water, like the Secchi disk and Forel-Ule color scale, remain in use in the modern era owing to their simplicity, low-cost and long history of use. Yet, recent years have seen advances in low-cost, electronic-based optical sensing. Here, the designs of a miniaturized hand-held device (mini-Secchi disk) that measures the Secchi depth and Forel-Ule color are updated. We then extend the device by integrating a small electronic sensing package (Arduino-based) into the Secchi disk, for vertical profiling, combining historic and modern methods for monitoring the optical properties of water into a single, low-cost sensing device, that measures positioning (GPS), light spectra, temperature, and pressure. It is charged and transfers data wirelessly, is encased in epoxy resin, and can be used to derive vertical profiles of spectral light attenuation and temperature, in addition to Secchi depth and Forel-Ule color. We present data from a series of deployments of the package, compare its performance with commercially available instruments, and demonstrate its use for validation of satellite remotely sensed data. Our designs are made openly available to promote community-based development and have potential in communicating and teaching science, participatory science, and low-cost monitoring of aquatic environments.