The Hierarchic treatment of marine ecological information from spatial networks of benthic platforms

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.Peer ReviewedPostprint (published version

A decade of time series as produced by multiparametric ecological monitoring at the OBSEA

All biological processes, from molecular to physiology and behavioural, are essential for organisms to regulate their survival in response to the environment (e.g., irradiance and temperature) and to intra- or inter- specifc interactions (e.g. predation and competition). In the marine environment, there is a strong correlation between biological rhythms and light cycles, which varies upon the depth, with the relevance of other factors, such as current speed, still far from fully understood. Rhythmic behavioural regulation results in the massive displacement of organisms at diferent depths over diel and seasonal scales, and this may result even in bathymetric or geographic distribution shifts over the years, as a result of coping with climate change conditioning. Even if the timing of biological processes is essential for all organisms, those processes are seldom studied in the marine environments, compared to the terrestrial ones. Today, the collection of data from cabled seafoor video-observatories equipped with mobile video-platforms (e.g. crawlers) is becoming feasible. Cabled observatories enable researchers to collect environmental and biological data in a concomitant fashion, and when monitoring networks of platforms are deployed, more spatially representative long-term studies on the biases that behavioural rhythms (i.e. massive population displacements) exert on population size and biodiversity assessments are accessible. In this framework, a local coastal network of fxed and mobile video-monitoring platforms was created at the OBSEA (www.obsea.es), located at 4 km of of Vilanova i la Geltrú (Barcelona, Spain), at a depth of 20 m. The OBSEA is a cabled observatory bearing two fxed cameras (i.e. the platform one includes camera 1 and a second camera, camera 2, as a movable tripod), focusing two diferent artifcial reefs. The concomitant time-lapse imaging by diferent cameras and environmental multiparametric data acquisition would allow the analysis of diferent biodiversity indicators such as the composition of communities (i.e. richness) and relative abundance of species (i.e. evenness), as well as ecosystem functions (e.g. food-web structure, carbon and energy fuxes etc.), at diferent time scales, together with inference of potential causeand-efects principles between environmental drivers and biological variables. Here, we aim to fully present the multidisciplinary data set acquired since January 2012, at a high-frequency (30 min), continuously during the day and the night, reporting count fuctuations in 27 bony fsh species. Every photo captured each 30 min from the two installed cameras was analyzed manually by trained operators. All photos had a stamped time code to match each detected faunal entry (classifed by trained operators) to the concomitant environmental data acquired by diferent sensors. A CTD and an ADPC provided data on temperature and salinity as well as pressure and water current speed and direction, respectively. Those data were associated to turbidity and chlorophyll data. Furthermore, we used automatically recorded meteorology entries by a Catalan Meteorological Service station in Sant Pere de Ribes (6 km from the OBSEA), to derive data on the global sun irradiance, wind speed and direction, as well as rain. Difculties in data acquisition due to sensors maintenance are described along with potential examples of data treatment, in spite of the marked diel and seasonal variations in total fsh-community counts as a product of behavioural rhythms (Fig. 1). This tendency is maintained throughout the seasons with the amplitude of the total fsh counts curve following the variation in the photophase length amplitude, described through the sun irradiance (Figure 2). The comparison between the total number of fshes and the irradiance shows a consistent increase in individual counts during the day for the large majority of species. Then, the polynomial curve analysis derived from the raw total count data was introduced, to further highlight that diurnal tendency. Even so, this curve shows two up-turning tails during night time due to the presence of few active nocturnal species in the area. Furthermore, we observed that the faunal abundance curve width is larger than the irradiance curve. This could be explained by the presence of crepuscular species that avoid fully diurnal visual predators, by anticipating or dealing the timing of their activity according to a tradeof between energy gaining and mortality risks. We also introduced a diel threshold, the Midline Estimated Statistic of Rhythm (MESOR) to evidence peaks limits in terms of the onset and ofset timings of signifcant count increases within the fsh community. This has been calculated by reaveraging all the time series mean values. All the analyses were carried out with custom algorithms developed in Python.Peer Reviewe

Tele-operated ecological monitoring at the seafloor observatory (OBSEA)

The development of new cabled oceanographic observatories is becoming of extreme importance to monitor in real-time a continuously changing environment. In this context, a local coastal network of fxed and mobile videomonitoring platforms was created at the OBSEA (www.obsea.es; [1]) as European Multidisciplinary Seafoor and water column Observatory EMSO Testing-Site [2]. The cabled platform is located 4 km ofshore of Vilanova i la Geltrú coast (Barcelona, Spain), at a depth of 20 m. The observatory has been used to install a network of cameras including OBSEA fxed camera, plus a movable satellite tripod. Also, a mobile camera will be installed on an Internet Operated Vehicle (IOV), as a coastal crawler. These tele-operated vehicles are being used by marine scientists, to carry out multiparametric environmental studies (via the diversifed set of oceanographic and geochemical sensors) centered on faunal monitoring via imaging. As far as cabled seafoor observatories (and also OBSEA) are not able to move and their data collection capability is limited, it was decided to expand the monitoring capacity of the OBSEA, by connecting it to a new costal crawler. This crawler is a modifed prototype of the “Wally” platform series, which is operating at the Ocean Networks Canada (ONC; www.oceannetworks. ca) since 2010 [3]. This coastal crawler will be used to perform back and forth video transects between the fxed OBSEA camera and its satellite tripod camera (80 m away), to analyze the possible efect of environmental heterogeneity on the perceived fsh community abundance and composition. This will also allow scaling the biodiversity gathered data over a larger and more ecologicallyrepresentative area. In this scenario, we aim to present the technological design and specifcations of the modifed coastal crawler (Fig. 1). A mobile camera (1) in a glass sphere (rated for 3000 m depth) with 360° pan and 180° tilt operability has been installed, to allow the operator to perform SCUBA divers as visual census transects, by looking forward during transect progression, widening the visual feld with panoramic sweeps when needed. The tracks (2) are independent parts allowing to scale the inner part of the vehicle simply by mounting a broader main plait. The chains are made of rubber with embedded steel. Each track is driven by a powerful DC motor with a reduction gear of 989:1. The motor housings are pressure compensated by fuid flling. The junction cylinder (3) contents the driving electronics and an Ethernet switch to connect the camera and the control cylinder to the main communication cable. This housing can variate in material and dimensions to allow its use at diferent depths. The main cable (4) is a of special underwater Ethernet foating type to avoid problems like seabed abrasion and platform entanglement. A control cylinder (5) is used for controlling the crawler and the camera, providing power from the junction cylinder to supply motors. Finally, there are two 12V, 3W lights (6) that can turn on for flming at night.Peer Reviewe

The video-based EGIM development

Peer Reviewe

Cubic and Hexagonal Mesophases for Protein Encapsulation: Structural Effects of Insulin Confinement

Monoolein-based cubic and hexagonal mesophases were investigated as matrices for insulin loading, at low pH, as a function of temperature and in the presence of increasing amounts of oleic acid, as a structural stabilizer for the hexagonal phase. Synchrotron small angle X-ray diffraction, rheological measurements, and attenuated total reflection-Fourier transform infrared spectroscopy were used to study the effects of insulin loading on the lipid mesophases and of the effect of protein confinement in the 2D-and 3D-lipid matrix water channels on its stability and unfolding behavior. We found that insulin encapsulation has only little effects both on the mesophase structures and on the viscoelastic properties of lipid systems, whereas protein confinement affects the response of the secondary structure of insulin to thermal changes in a different manner according to the specific mesophase: in the cubic structure, the unfolding toward an unordered structure is favored, while the prevalence of parallel β-sheets, and nuclei for fibril formation, is observed in hexagonal structures

Deep-sea litter in the Gulf of Cadiz (Northeastern Atlantic, Spain)

This study describes the distribution and composition of litter from the Gulf of Cadiz (Northeastern Atlantic, Spain), a region of confluence between the Atlantic and Mediterranean, with intense maritime traffic. Several geological features, such as canyons, open slopes and contourite furrows and channels, were surveyed by remotely operated vehicle (ROV) observations between depths of 220 and 1000 m. Marine litter was quantified by grouping the observations into six categories. Our results indicate the presence of markedly different habitats in which a complex collection of different types of litter accumulate in relation to bottom current flows and maritime and fishing routes. This result justifies a seascape approach in further anthropogenic impact studies within deep-sea areas.Postprint (author's final draft

Multisensor acoustic tracking benthic landers to evaluate connectivity of fishes in marine protected areas

Deep-sea fishing has been carried out on an industrial scale since the 1950s, and this has had a variety of effects on the environment and its biota. Most benthic species experience a decline in abundance or a constant decline in abundance as a result of direct disturbance of the seafloor, such as its plowing and scraping by hauled nets, with overall impacts on regional biodiversity [1]. Sediment has lost some of its biogenic habitat complexity, and sessile epifauna-provided microhabitat has been destroyed or disrupted [2] and marine protected areas (MPAs) have been widely implemented to address this decline. Marine fish mobility, which is crucial for ecosystem function and is increasingly being researched with acoustic telemetry, has an impact on how well no-take MPAs (i.e., marine reserves) work in terms of protecting and repopulating fish populations [3], [4] Therefore, it is necessary to continuously monitor periodic changes in commercially exploited deep-sea ecosystems in order to gather baseline information, give accurate environmental impact assessments, and derive sound biological indicators for restoration. Using a fixed acoustic ultra-short baseline (USBL) receiver on benthic lander and miniature bidirectional acoustic tags [5], we address three key questions: How far can fish move? Does connectivity exist between adjacent MPAs? Does existing MPA size match the spatial scale of fish movements?Peer Reviewe

A New Coastal Crawler Prototype to Expand the Ecological Monitoring Radius of OBSEA Cabled Observatory

The use of marine cabled video observatories with multiparametric environmental data collection capability is becoming relevant for ecological monitoring strategies. Their ecosystem surveying can be enforced in real time, remotely, and continuously, over consecutive days, seasons, and even years. Unfortunately, as most observatories perform such monitoring with fixed cameras, the ecological value of their data is limited to a narrow field of view, possibly not representative of the local habitat heterogeneity. Docked mobile robotic platforms could be used to extend data collection to larger, and hence more ecologically representative areas. Among the various state-of-the-art underwater robotic platforms available, benthic crawlers are excellent candidates to perform ecological monitoring tasks in combination with cabled observatories. Although they are normally used in the deep sea, their high positioning stability, low acoustic signature, and low energetic consumption, especially during stationary phases, make them suitable for coastal operations. In this paper, we present the integration of a benthic crawler into a coastal cabled observatory (OBSEA) to extend its monitoring radius and collect more ecologically representative data. The extension of the monitoring radius was obtained by remotely operating the crawler to enforce back-and-forth drives along specific transects while recording videos with the onboard cameras. The ecological relevance of the monitoring-radius extension was demonstrated by performing a visual census of the species observed with the crawler’s cameras in comparison to the observatory’s fixed cameras, revealing non-negligible differences. Additionally, the videos recorded from the crawler’s cameras during the transects were used to demonstrate an automated photo-mosaic of the seabed for the first time on this class of vehicles. In the present work, the crawler travelled in an area of 40 m away from the OBSEA, producing an extension of the monitoring field of view (FOV), and covering an area approximately 230 times larger than OBSEA’s camera. The analysis of the videos obtained from the crawler’s and the observatory’s cameras revealed differences in the species observed. Future implementation scenarios are also discussed in relation to mission autonomy to perform imaging across spatial heterogeneity gradients around the OBSEA

Understanding the Distributions of Benthic Foraminifera in the Adriatic Sea with Gradient Forest and Structural Equation Models

Abstract: In the last three decades, benthic foraminiferal ecology has been intensively investigated to improve the potential application of these marine organisms as proxies of the effects of climate change and other global change phenomena. It is still challenging to define the most important factors affecting foraminiferal communities and derived faunistic parameters. In this study, we examined the abiotic-biotic relationships of foraminiferal communities in the central-southern area of the Adriatic Sea using modern machine learning techniques. We combined gradient forest (Gf) and structural equation modeling (SEM) to test hypotheses about determinants of benthic foraminiferal assemblages. These approaches helped determine the relative effect of sizes of different environmental variables responsible for shaping living foraminiferal distributions. Four major faunal turnovers (at 13–28 m, 29–58 m, 59–215 m, and >215 m) were identified along a large bathymetric gradient (13–703 m water depth) that reflected the classical bathymetric distribution of benthic communities. Sand and organic matter (OM) contents were identified as the most relevant factors influencing the distribution of foraminifera either along the entire depth gradient or at selected bathymetric ranges. The SEM supported causal hypotheses that focused the factors that shaped assemblages at each bathymetric range, and the most notable causal relationships were direct effects of depth and indirect effects of the Gf-identified environmental parameters (i.e., sand, pollution load Index–PLI, organic matter–OM and total nitrogen–N) on foraminifera infauna and diversity. These results are relevant to understanding the basic ecology and conservation of foraminiferal communitie

Automatic detection and classification of coastal Mediterranean fish from underwater images: Good practices for robust training

11 pages, 3 figures, 5 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmars.2023.1151758/full#supplementary-material.-- Data availability statement: The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary MaterialFurther investigation is needed to improve the identification and classification of fish in underwater images using artificial intelligence, specifically deep learning. Questions that need to be explored include the importance of using diverse backgrounds, the effect of (not) labeling small fish on precision, the number of images needed for successful classification, and whether they should be randomly selected. To address these questions, a new labeled dataset was created with over 18,400 recorded Mediterranean fish from 20 species from over 1,600 underwater images with different backgrounds. Two state-of-the-art object detectors/classifiers, YOLOv5m and Faster RCNN, were compared for the detection of the ‘fish’ category in different datasets. YOLOv5m performed better and was thus selected for classifying an increasing number of species in six combinations of labeled datasets varying in background types, balanced or unbalanced number of fishes per background, number of labeled fish, and quality of labeling. Results showed that i) it is cost-efficient to work with a reduced labeled set (a few hundred labeled objects per category) if images are carefully selected, ii) the usefulness of the trained model for classifying unseen datasets improves with the use of different backgrounds in the training dataset, and iii) avoiding training with low-quality labels (e.g., small relative size or incomplete silhouettes) yields better classification metrics. These results and dataset will help select and label images in the most effective way to improve the use of deep learning in studying underwater organismsProject DEEP-ECOMAR. 10.13039/100018685-Comunitat Autonoma de les Illes Balears through the Direcció General de Política Universitària i Recerca with funds from the Tourist Stay Tax law ITS 2017-006 (Grant Number: PRD2018/26). [...] The present research was carried out within the framework of the activities of the Spanish Government through the “María de Maeztu Centre of Excellence” accreditation to IMEDEA (CSIC-UIB) (CEX2021-001198-M) and the “Severo Ochoa Centre Excellence” accreditation to ICM-CSIC (CEX2019-000928-S) and the Research Unit Tecnoterra (ICM-CSIC/UPC)Peer reviewe