Mesopelagic crustacean habitat identification and analysis using deep learning

This paper presents a software infrastructure based on Deep Learning aimed at identifying habitats of certain species of crustacean that colonize areas of the marine Mesopelagic zone. Determining their presense is done, in this case, from the detection of holes in the sand that form sets of burrow structures. Preliminar inferencing models are obtained from images captured in the North Sea by trawled UWTV (undewater TV) stations, offering quite significant detection success ratios.Peer Reviewe

Transects in the deep: Opportunities with tele-operated resident seafloor robots

Scientific, industrial and societal needs call urgently for the development and establishment of intelligent, cost-effective and ecologically sustainable monitoring protocols and robotic platforms for the continuous exploration of marine ecosystems. Internet Operated Vehicles (IOVs) such as crawlers, provide a versatile alternative to conventional observing and sampling tools, being tele-operated, (semi-) permanent mobile platforms capable of operating on the deep and coastal seafloor. Here we present outstanding observations made by the crawler “Wally” in the last decade at the Barkley Canyon (BC, Canada, NE Pacific) methane hydrates site, as a part of the NEPTUNE cabled observatory. The crawler followed the evolution of microhabitats formed on and around biotic and/or abiotic structural features of the site (e.g., a field of egg towers of buccinid snails, and a colonized boulder). Furthermore, episodic events of fresh biomass input were observed (i.e., the mass transport of large gelatinous particles, the scavenging of a dead jellyfish and the arrival of macroalgae from shallower depths). Moreover, we report numerous faunal behaviors (i.e., sablefish rheo- and phototaxis, the behavioral reactions and swimming or resting patterns of further fish species, encounters with octopuses and various crab intra- and interspecific interactions). We report on the observed animal reactions to both natural and artificial stimuli (i.e., crawler’s movement and crawler light systems). These diverse observations showcase different capabilities of the crawler as a modern robotic monitoring platform for marine science and offshore industry. Its long deployments and mobility enable its efficiency in combining the repeatability of long-term studies with the versatility to opportunistically observe rarely seen incidents when they occur, as highlighted here. Finally, we critically assess the empirically recorded ecological footprint and the potential impacts of crawler operations on the benthic ecosystem of the Barkley Canyon hydrates site, together with potential solutions to mitigate them into the future

Deep learning based deep-sea automatic image enhancement and animal species classification

The automatic classification of marine species based on images is a challenging task for which multiple solutions have been increasingly provided in the past two decades. Oceans are complex ecosystems, difficult to access, and often the images obtained are of low quality. In such cases, animal classification becomes tedious. Therefore, it is often necessary to apply enhancement or pre-processing techniques to the images, before applying classification algorithms. In this work, we propose an image enhancement and classification pipeline that allows automated processing of images from benthic moving platforms. Deep-sea (870 m depth) fauna was targeted in footage taken by the crawler “Wally” (an Internet Operated Vehicle), within the Ocean Network Canada (ONC) area of Barkley Canyon (Vancouver, BC; Canada). The image enhancement process consists mainly of a convolutional residual network, capable of generating enhanced images from a set of raw images. The images generated by the trained convolutional residual network obtained high values in metrics for underwater imagery assessment such as UIQM (~ 2.585) and UCIQE (2.406). The highest SSIM and PSNR values were also obtained when compared to the original dataset. The entire process has shown good classification results on an independent test data set, with an accuracy value of 66.44% and an Area Under the ROC Curve (AUROC) value of 82.91%, which were subsequently improved to 79.44% and 88.64% for accuracy and AUROC respectively. These results obtained with the enhanced images are quite promising and superior to those obtained with the non-enhanced datasets, paving the strategy for the on-board real-time processing of crawler imaging, and outperforming those published in previous papers.This work was developed at Deusto Seidor S.A. (01015, Vitoria-Gasteiz, Spain) within the framework of the Tecnoterra (ICM-CSIC/UPC) and the following project activities: ARIM (Autonomous Robotic sea-floor Infrastructure for benthopelagic Monitoring); MarTERA ERA-Net Cofund; Centro para el Desarrollo Tecnológico Industrial, CDTI; and RESBIO (TEC2017-87861-R; Ministerio de Ciencia, Innovación y Universidades). This work was supported by the Centro para el Desarrollo Tecnológico Industrial (CDTI) (Grant No. EXP 00108707 / SERA-20181020)

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

5 year-long monitoring of Barkley Canyon cold-seeps with the internet operated deep-sea crawler "Wally"

Despite the technological advances of the last decades (e.g. ROVs, AUVs, cabled observatories), our knowledge of most deep-sea environments is still strongly limited by spatio-temporal sampling and observational capabilities. The novel Internet Operated Deep-Sea Crawler technology can provide high-frequency, multi-sensor data, during long-term deployments, 24/7 communication with researchers and broader spatial coverage (i.e. mobile platform) than fixed instrument installations. The crawler “Wally” is deployed at the Barkley Canyon methane hydrates site (NE Pacific, Canada; ~890 m depth) and connected to the Ocean Networks Canada NEPTUNE cabled observatory network (ONC; www. oceannetworks.ca). Here we present the environmental and biological datasets obtained from Wally instruments and cameras, during the first deployment phase (September 2010 to January 2015), as well as new features and preliminary results obtained since it was re-deployed (May 2016 – present). In addition to data provided by the standard payload of the crawler (i.e. ADCP, CTD, methane sensor, turbidity sensor and fluorometer), the hydrates community was video-monitored at different frequencies and timespans. Photomosaics were generated at two distinct locations, in order to map chemosynthetic bacterial mats and vesicomyid clam colonies covering the ~2-3 m high hydrate mounds, and document their temporal dynamics. The crawler followed the development of a deep-sea shell taphonomic experiment aiming to quantify biogenic carbon fluxes at the hydrates environment. The composition and diel activity patterns of the hydrates megafaunal community were studied with the use of linear video-transects conducted from February 2013 to April 2014. Since the summer of 2016, video-frames recorded at different locations of the site are analyzed for a biodiversity study and photomosaicing of the hydrate mounds continues, with 3D modelling of the mound structures also available as a new feature of the crawler deployed in May 2016. All data are archived in real-time and can be accessed online on the Ocean Networks Canada database. As deep-sea crawler technology and similar mobile, benthic platform technologies progress towards full operational autonomy, they will provide an even greater capacity for future monitoring and understanding of dynamic, extreme environments such as methane hydrate fields.Peer Reviewe

High-Frequency Patterns in the Abundance of Benthic Species near a Cold-Seep – An Internet Operated Vehicle Application

Three benthic megafaunal species (i.e. sablefish Anoplopoma fimbria; pacific hagfish Eptatretus stoutii and a group of juvenile crabs) were tested for diel behavioral patterns at the methane hydrates site of Barkley Canyon (890 m depth), off Vancouver Island (BC, Canada). Fluctuations of animal counts in linear video-transects conducted with the Internet Operated Deep-Sea Crawler ªWallyº in June, July and December of 2013, were used as proxy of population activity rhythms. Count time series and environmental parameters were analyzed under the hypothesis that the environmental conditioning of activity rhythms depends on the life habits of particular species (i.e. movement type and trophic level). Nonlinear least squares modeling of biological time series revealed significant diel periods for sablefish in summer and for hagfish and crabs in December. Combined cross-correlation and redundancy (RDA) analyses showed strong relationships among environmental fluctuations and detected megafauna. In particular, sablefish presence during summer months was related to flow magnitude, while the activity of pacific hagfish and juvenile crabs in December correlated with change in chemical parameters (i.e. chlorophyll and oxygen concentrations, respectively). Waveform analyses of animal counts and environmental variables confirmed the phase delay during the 24 h cycle. The timing of detection of sablefish occurred under low flow velocities, a possible behavioral adaptation to the general hypoxic conditions. The proposed effect of chlorophyll concentrations on hagfish counts highlights the potential role of phytodetritus as an alternative food source for this opportunistic feeder. The juvenile crabs seemed to display a cryptic behavior, possibly to avoid predation, though this was suppressed when oxygen levels were at a minimum. Our results highlight the potential advantages such mobile observation platforms offer in multiparametric deep-sea monitoring in terms of both spatial and temporal resolution and add to the vastly understudied field of diel rhythms of deep-sea megafauna

Physical and hydrodynamic properties of deep sea mining-generated, abyssal sediment plumes in the Clarion Clipperton Fracture Zone (eastern-central Pacific)

The anthropogenic impact of polymetallic nodule harvesting in the Clarion-Clipperton Fracture Zone is expected to strongly affect the benthic ecosystem. To predict the long-term, industrial-scale impact of nodule mining on the deep-sea environment and to improve the reliability of the sediment plume model, information about the specific characteristics of deep-sea particles is needed. Discharge simulations of mining-related fine-grained (median diameter ≈ 20 μm) sediment plumes at concentrations of 35–500 mg L–1 (dry weight) showed a propensity for rapid flocculation within 10 to 135 min, resulting in the formation of large aggregates up to 1100 μm in diameter. The results indicated that the discharge of elevated plume concentrations (500 mg L–1) under an increased shear rate (G ≥ 2.4 s–1) would result in improved efficiency of sediment flocculation. Furthermore, particle transport model results suggested that even under typical deep-sea flow conditions (G ≈ 0.1 s–1), rapid deposition of particles could be expected, which would restrict heavy sediment blanketing (several centimeters) to a smaller fall-out area near the source, unless subsequent flow events resuspended the sediments. Planning for in situ tests of these model projections is underwa

The video-based EGIM development

Peer Reviewe

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

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