Limnology and Oceanography: Methods最新文献

Phytoplankton functional types (PFTs) found in natural aquatic environments play different roles in the biogeochemical cycles of different elements. However, commonly used methods for identifying PFTs have inherent limitations. In this study, based on a large dataset (1747 samples) collected from 2004 to 2019 in the South China Sea and adjacent Taiwan Strait, which had concurrent measurements of the spectral absorption coefficient of phytoplankton and chlorophyll a concentration of nine PFTs (PFTs_Chla), along with depth and time information, a reliable support vector regression (SVR) model was developed to retrieve these nine PFTs_Chla in the water column. These PFTs included diatoms, dinoflagellates, haptophytes_8, haptophytes_6, chlorophytes, cryptophytes, Prochlorococcus, Synechococcus, and prasinophytes. The independent validation results indicated that the SVR model outperformed the traditional PFTs_Chla retrieval algorithms, with an average mean bias of −14.2%, an average mean absolute unbiased relative difference of 60.3%, and an average coefficient of determination of 0.56. The predicted PFTs_Chla values and their error distributions in the water column were subsequently analyzed. Finally, the SVR model was found to be applicable to most PFTs_Chla retrieval in the East China Sea.

Accessing the metabolic functioning of deep-sea animals in situ remains a technological challenge as the recovery time of samples is incompatible with the short lifespan of such molecules as mRNAs. Tools able to preserve RNA in situ exist, but they are incompatible with the study of mobile fauna. Here, we describe a new sampling tool, named FISH (fixer in situ of homogenized substrates), implemented on a submersible and equipped with a number of new specific features to collect and preserve in situ tissue of mobile fauna. Connected to the suction pump of a submersible, the FISH sampler incorporates a sampling bowl to which two bottles of a preservative reagent are attached, a suction hose, and a support containing a motor connected to the sampling bowl by a magnetic coupling system. We used the deep-sea hydrothermal shrimp Rimicaris exoculata from the Mid-Atlantic Ridge as a model to test the suitability of our new tool. The FISH sampler was compared to two other sampling methods, which use a metatranscriptomic approach targeting microbial communities associated with cephalothorax symbionts. RNA quality, gene assignment, and taxonomic and gene function diversity showed differences between in situ and on-board preservation of tissues. Of the alternative sampling methods tested, the suction sampler was clearly not suitable for RNA-based studies, while pressurized recovery showed results closer to the sample quality obtained with FISH sampling. The FISH sampler has therefore demonstrated to be a cost-effective and reliable tool to efficiently preserve RNA recovered from deep-sea environments.

Pulse amplitude modulation (PAM) fluorometry provides high-resolution and high-frequency primary production (PP) estimates, crucial for understanding and managing dynamic ecosystems such as estuaries. However, traditional PAM-derived PP estimations often overlook the variability of the photosynthetic quotient and the dynamics of chlorophyll a, leading to uncertainties. This study introduced an innovative method for estimating the PP of natural phytoplankton communities using the rapid light curve of PAM measurements. Validation using ¹⁴C incorporation and oxygen techniques in two subtropical estuaries demonstrated a strong linear relationship between PAM-derived PP and measured oxygen evolution rates (R² = 0.76, p < 0.001) and carbon fixation rates (R² = 0.94, p < 0.001). While the dynamics of chlorophyll a had minimal impact on hourly PAM-derived PP estimations, they caused significant deviations on daily time scales, influenced by sampling times. Predicting photosynthetic quotient values based on salinity (R² = 0.34, p < 0.05) allowed for expanded temporal and spatial PP estimations. Seasonal PP patterns in the Jiulong River Estuary, Xiamen Bay, Zhangjiang Estuary, and Dongshan Bay revealed the highest PP in summer, followed by spring, with similar levels in autumn and winter. Using these surface measurements, annual phytoplankton carbon fixation fluxes were estimated through the entire water column across the four regions. This method provides a more comprehensive understanding of PP dynamics, highlighting its potential for frequent application in small-scale valuable ecosystems like estuaries and bays to better assess their ecological functions and biogeochemical cycles.

The performance of a single commercial accelerometer-based underwater acoustic vector sensor (AVS) in resolving acoustic azimuth was evaluated. The method involves calculating the active intensity of an acoustic signal to determine the dominant directionality of an acoustic pressure field as a function of time and frequency. While this method efficiently displays azimuth bearings for specific frequencies, there are very few assessments of its performance in resolving all possible bearings using a single AVS. Field experiments were conducted with an AVS placed on the sea bottom and an active source suspended from a research vessel. A 600 Hz signal was transmitted from 16 positions covering a 360° azimuth to the AVS. During the transmissions, the vessel maintained its position and heading by using a dynamic positioning system. The acoustic azimuths were compared with the transmission bearings obtained via Global Positioning System. This study demonstrates that a commercial AVS system can effectively resolve acoustic bearings across a full 360° azimuth at high signal-to-noise ratios using the active intensity method. Our results support the use of AVS systems in research on sound directionality, including bioacoustics studies on how marine organisms respond to natural underwater sound and anthropogenic noise.

In traditional grain-size separation of marine sediment using the sieve technique, the majority of organic matter (OM) in the ultrafine sediment is yet hardly further separated. In this study, we suggest an inertial sieving method that utilizes an ultrafine particle separator (UPS), which consists of a suspended particle generator (SPG) combined with a particle size separating device (PSSD), to separate ultrafine particles from marine sediments. Specifically, our method can fractionate ultrafine particles (< 10 μm) into eight different grain size categories: 0.43–0.65, 0.65–1.10, 1.10–2.10, 2.10–3.30, 3.30–4.70, 4.70–5.80, 5.80–9.00, and 9.00–10.00 μm. We evaluate the effectiveness of this method in fractionating ultrafine marine sediment from the China Marginal Sea. Our study find that the inertial sieving method achieved a high mass recovery rate of 77.7–88.7% and a sieving accuracy of 75–94% for sediment samples. Additionally, we measure total organic carbon (OC) and stable carbon isotopes of OM associated with these eight ultrafine sediments. Overall, we suggest that the inertial sieving method has a high potential to effectively fractionate the marine sediments with particle sizes below 10 μm for further organic geochemical analysis on these grain size fractionated sediments.

In recent years, optical imaging has emerged as a promising tool for in situ observations of plankton. In this study, we aimed to compare the plankton community estimates obtained from a Video Plankton Recorder (VPR) imaging device with net-based approaches. By collecting VPR and net samples in clear waters with large-sized plankton and eutrophic waters with small-sized plankton, spatial and temporal patterns in plankton densities and community composition were compared. Furthermore, it allowed the evaluation of the performance of imaging methods under diverse hydrographic conditions. We observed pronounced spatial differences in density estimates. In the eutrophic site, the WP2 net densities consistently surpassed those from a VPR, while in the clear water site the observed densities of the VPR and a MultiNet were more similar. Variations in water column turbidity, plankton body size, plankton nets and their mesh size, and the total sampled water volume were found to likely play a role in the observed inconsistencies between the sampling sites. The results suggested that a VPR is particularly well-suited for use in clear waters inhabited by large-sized plankton. The VPR demonstrated potential in enhancing density estimates of fragile (Phaeocystis) and gelatinous taxa (Cnidaria and Ctenophora) in specific environments being non-invasive. Overall, the VPR and other optical imaging devices show valuable insights into zooplankton ecology and distribution, complementing density estimates of traditional net sampling methods, and enhancing our understanding of the role of zooplankton in marine ecosystems.

Seabed gas and oil emissions appear as bubble plumes ascending through the water column in various environments. Understanding bubble characteristics—size, rise speed—is important for estimating escape rates of fluids like methane, oil, and carbon dioxide. However, measuring underwater gas bubbles is challenging, often requiring expensive specialized equipment. This study presents a novel methodology using two calibrated consumer-grade cameras to estimate bubble size distribution, rise velocities, and corresponding gas or oil flow rates. Our approach, named BURST (Bubble Rise and Size Tracking), uses a trained neural network for automated bubble detection in diverse camera footage, effectively analyzing under varying lighting conditions and visibility, without requiring a uniform backlit background for bubble identification. Post-detection, bubbles are tracked and synchronized between the cameras, with three-dimensional triangulation used to deduce sizes and rise speeds, enabling flow rate calculations. We demonstrate the efficacy of our methodology through basin experiments capturing methane bubble plumes with controlled flow rates. Additionally, we successfully apply this methodology to existing footage from natural methane emission sites in the Hopendjupet seeps within the central Barents Sea, measuring methane flow rates of approximately 46 and 24 mmol CH₄ min⁻¹ at water depths of 327 and 341 m, respectively. These results underscore the practical applicability of BURST in complex underwater environments without disrupting natural bubble flow. By utilizing readily available equipment, BURST enables reliable bubble measurements in challenging real-world conditions, including the analysis of legacy footage not initially intended for bubble flow rate quantification. The BURST python script is available at https://github.com/BUbbleRST/BURST/.

Coral resilience to heat stress is higher in corals that eat more zooplankton. In addition, coral feeding on zooplankton increases as zooplankton concentrations increase. To leverage the advantage that zooplankton feeding has on coral resilience, we developed the Underwater Zooplankton Enhancement Light Array (UZELA). UZELA is a patented autonomous, submersible, and programmable underwater light that is deployable for 6 months on a single battery. With 1 h of operation per night, it locally concentrates naturally occurring zooplankton, providing corals with greater feeding opportunities. Field tests show that UZELA increases local zooplankton concentrations by sevenfold compared to adjacent non-UZELA controls and coral feeding rates by 10 to 50-fold in both healthy and bleached Montipora capitata and Porites compressa corals compared to conspecifics without UZELA. With the continuing decline of coral reefs, technologies that can enhance coral feeding could play a critical role in coral resilience for coral in restoration nurseries and on the reef.

Measuring microalgae density in soft-sediment benthos has challenges for even the most sophisticated methods. If the goal is to assess the photosynthetic potential of epipelon, then microalgae should be sampled only at the surface of the benthos to the depth of light penetration. Furthermore, microalgae density may show spatial and temporal variability that can only be captured by using many point samples and nondestructive sampling. Here, we use simple near-infrared (NIR) imagery to assess surface density of microalgae in soft underwater sediments and to infer their photosynthetic capacity. In lab studies, NIR imagery gives estimates of epipelon density that are strongly correlated with standard chlorophyll a (Chl a) assays using pigment extraction and fluorometry ($��R_{\mathrm{adj}}^2�$  = 0.70), but NIR imagery is better able to separate experimental treatments. In analyses of sediment samples from a lake, NIR imagery gives estimates of epipelon Chl a density that are strongly correlated to net ecosystem production (NEP). Near-infrared imagery also gives a fine-grained assessment of the spatial distribution of epipelon that helps to explain the relationship between epipelon density and NEP. Finally, images from an underwater NIR camera over the course of a wind disturbance event give estimates of the relative density of microalgae that is buried and is likely to be, at least temporarily, photosynthetically inactive. These results show that NIR imagery provides an easy and nondestructive method for sampling surface densities of microalgae which is particularly suitable for remote field locations and for educational settings in which students can generate results with cheap and robust equipment.