Tools and Data

Dynamic Satellite Seascapes as a Biogeographic Framework for Understanding Phytoplankton Assemblages in the Florida Keys National Marine Sanctuary, United States

Montes E, Djurhuus A, Muller-Karger FE, Otis D, Kelble CR, Kavanaugh MT. Dynamic Satellite Seascapes as a Biogeographic Framework for Understanding Phytoplankton Assemblages in the Florida Keys National Marine Sanctuary, United States. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00575/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1391749_45_Marine_20200730_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Physical, chemical, geological, and biological factors interact in marine environments to shape complex but recurrent patterns of organization of life on multiple spatial and temporal scales. These factors define biogeographic regions in surface waters that we refer to as seascapes. We characterize seascapes for the Florida Keys National Marine Sanctuary (FKNMS) and southwest Florida shelf nearshore environment using multivariate satellite and in situ measurements of Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs). The study focuses on three periods that cover separate oceanographic expeditions (March 11–18, May 9–13, and September 12–19, 2016). We collected observations on bio-optical parameters (particulate and dissolved spectral absorption coefficients), phytoplankton community composition, and hydrography from a ship. Phytoplankton community composition was evaluated using (1) chemotaxonomic analysis (CHEMTAX) based on high-performance liquid chromatography (HPLC) pigment measurements, and (2) analysis of spectral phytoplankton absorption coefficients (aphy). Dynamic seascapes were derived by combining satellite time series of sea surface temperature, chlorophyll-a concentration, and normalized fluorescent line height (nFLH) using a supervised thematic classification. The seascapes identified areas of different salinity and nutrient concentrations where different phytoplankton communities were present as determined by hierarchical cluster analyses of HPLC pigments and aphy spectra. Oligotrophic, Mesotrophic, and Transition seascape classes of deeper offshore waters were dominated by small phytoplankton (<2 μm; ∼ 40–60% of total cell abundance). In eutrophic, optically shallow coastal seascapes influenced by fresh water discharge, the phytoplankton was dominated by larger taxa (>60%). Spectral analysis of aphy indicated higher absorption levels at 492 and 550 nm wavelengths in seascapes carrying predominantly small phytoplankton than in classes dominated by larger taxa. Seascapes carrying large phytoplankton showed absorption peaks at the 673 nm wavelength. The seascape framework promises to be a tool to detect different biogeographic domains quickly, providing information about the changing environmental conditions experienced by coral reef organisms including coral, sponges, fish, and higher trophic levels. The effort illustrates best practices developed under the Marine Biodiversity Observation Network (MBON) demonstration project, in collaboration with the South Florida Ecosystem Restoration Research (SFER) project managed by the Atlantic Oceanographic and Meteorological Laboratory of NOAA (AOML-NOAA).

Acoustic Telemetry: A Tool to Monitor Fish Swimming Behavior in Sea-Cage Aquaculture

Muñoz L, Aspillaga E, Palmer M, Saraiva JL, Arechavala-Lopez P. Acoustic Telemetry: A Tool to Monitor Fish Swimming Behavior in Sea-Cage Aquaculture. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00645/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1406443_45_Marine_20200818_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Acoustic telemetry techniques are very useful tools to monitor in detail the swimming behavior and spatial use of fish in artificial rearing environments at individual and group levels. We evaluated the feasibility of using passive acoustic telemetry to monitor fish welfare in sea-cage aquaculture at an industrial scale, characterizing for the first time the diel swimming and distribution patterns of gilthead seabream (Sparus aurata) at fine-scale. Ten fish were implanted with acoustic tags equipped with pressure and acceleration sensors, and monitored in a commercial-size sea-cage for a period of 1 month. Overall, fish exhibited clear differences in day vs. night patterns both on swimming activity and vertical distribution throughout the experiment. Space use increased at night after the implementation of structural environmental enrichment in the sea-cage. Acoustic telemetry may represent an advancement to monitor fish farming procedures and conditions, helping to promote fish welfare and product quality.

Gear-Induced Concept Drift in Marine Images and Its Effect on Deep Learning Classification

Langenkämper D, van Kevelaer R, Purser A, Nattkemper TW. Gear-Induced Concept Drift in Marine Images and Its Effect on Deep Learning Classification. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00506/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1391749_45_Marine_20200730_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

In marine research, image data sets from the same area but collected at different times allow seafloor fauna communities to be monitored over time. However, ongoing technological developments have led to the use of different imaging systems and deployment strategies. Thus, instances of the same class exhibit slightly shifted visual features in images taken at slightly different locations or with different gear. These shifts are referred to as concept drift in the domains computational image analysis and machine learning as this phenomenon poses particular challenges for these fields. In this paper, we analyse four different data sets from an area in the Peru Basin and show how changes in imaging parameters affect the classification of 12 megafauna morphotypes with a 34-layer ResNet. Images were captured using the ocean floor observation system, a traditional sled-based system, or an autonomous underwater vehicle, which is used as an imaging platform capable of surveying larger regions. ResNet applied on separate individual data sets, i.e., without concept drift, showed that changing object distance was less important than the amount of training data. The results for the image data acquired with the ocean floor observation system showed higher performance values than data collected with the autonomous underwater vehicle. The results from this concept drift studies indicate that collecting image data from many dives with slightly different gear may result in training data well-suited for learning taxonomic classification tasks and that data volume can compensate for light concept drift.

Accurate Bathymetric Maps From Underwater Digital Imagery Without Ground Control

Hatcher GA, Warrick JA, Ritchie AC, Dailey ET, Zawada DG, Kranenburg C, Yates KK. Accurate Bathymetric Maps From Underwater Digital Imagery Without Ground Control. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00525/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1376892_45_Marine_20200714_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Structure-from-Motion (SfM) photogrammetry can be used with digital underwater photographs to generate high-resolution bathymetry and orthomosaics with millimeter-to-centimeter scale resolution at relatively low cost. Although these products are useful for assessing species diversity and health, they have additional utility for quantifying benthic community structure, such as coral growth and fine-scale elevation change over time, if accurate length scales and georeferencing are included. This georeferencing is commonly provided with “ground control,” such as pre-installed seafloor benchmarks or identifiable “static” features, which can be difficult and time consuming to install, survey, and maintain. To address these challenges, we developed the SfM Quantitative Underwater Imaging Device with Five Cameras (SQUID-5), a towed surface vehicle with an onboard survey-grade Global Navigation Satellite System (GNSS) and five rigidly mounted downward-looking cameras with overlapping views of the seafloor. The cameras are tightly synchronized with both the GNSS and each other to collect quintet photo sets and record the precise location of every collection event. The system was field tested in July 2019 in the U.S. Florida Keys, in water depths ranging from 3 to 9 m over a variety of bottom types. Surveying accuracy was assessed using pre-installed stations with known coordinates, machined scale bars, and two independent surveys of a site to evaluate repeatability. Under a range of sea conditions, ambient lighting, and water clarity, we were able to map living and senile coral reef habitats and sand waves at mm-scale resolution. Data were processed using best practice SfM techniques without ground control and local measurement errors of horizontal and vertical scales were consistently sub-millimeter, equivalent to 0.013% RMSE relative to water depth. Survey-to-survey repeatability RMSE was on the order of 3 cm without georeferencing but could be improved to several millimeters with the incorporation of one or more non-surveyed marker points. We demonstrate that the SQUID-5 platform can map complex coral reef and other seafloor habitats and measure mm-to-cm scale changes in the morphology and location of seafloor features over time without pre-existing ground control.

Efficient Modeling of Complex Sandy Coastal Evolution at Monthly to Century Time Scales

Roelvink D, Huisman B, Elghandour A, Ghonim M, Reyns J. Efficient Modeling of Complex Sandy Coastal Evolution at Monthly to Century Time Scales. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00535/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1376892_45_Marine_20200714_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

With large-scale human interventions and climate change unfolding as they are now, coastal changes at decadal timescales are not limited to incremental modifications of systems that are fixed in their general geometry, but often show significant changes in layout that may be catastrophic for populations living in previously safe areas. This poses severe challenges that are difficult to meet for existing models. A new free-form coastline model, ShorelineS, is presented that is able to describe large coastal transformations based on relatively simple principles of alongshore transport gradient driven changes as a result of coastline curvature, including under highly obliquely incident waves, and consideration of splitting and merging of coastlines, and longshore transport disturbance by hard structures. An arbitrary number of coast sections is supported, which can be open or closed and can interact with each other through relatively straightforward merging and splitting mechanisms. Rocky parts or structures may block wave energy and/or longshore sediment transport. These features allow for a rich behavior including shoreline undulations and formation of spits, migrating islands, merging of coastal shapes, salients and tombolos. The main formulations of the (open-source) model, which is freely available at www.shorelines.nl, are presented. Test cases show the capabilities of the flexible, vector-based model approach, while field validation cases for a large-scale sand nourishment (the Sand Engine; 21 million m3) and an accreting groin scheme at Al-Gamil (Egypt) show the model’s capability of computing realistic rates of coastline change as well as a good representation of the shoreline shape for real situations.

Assessing Northwest Pacific Fishery Stocks Using Two New Methods: The Monte Carlo Catch-MSY (CMSY) and the Bayesian Schaefer Model (BSM)

Ren Q-qiang, Liu M. Assessing Northwest Pacific Fishery Stocks Using Two New Methods: The Monte Carlo Catch-MSY (CMSY) and the Bayesian Schaefer Model (BSM). Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00430/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1376892_45_Marine_20200714_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

The CMSY and Bayesian Schaefer model (BSM) methods were applied to assess data-limited fishery stocks in the Japan Sea and surrounding areas of the Northwest Pacific. Ten stocks including 4 fish species and 5 cephalopod species were assessed; the CMSY method was used in 3 stocks with catch data only, and the BSM method in 7 stocks with both catch time series and catch per unit effort (CPUE) data available. The two methods estimated the maximum intrinsic rate of population increase (r) and carrying capacity of each stock, which allowed the computation of maximum sustainable yield (MSY), and exploited biomass relative to the biomass at maximum sustainable yield (B/BMSY). All 10 stocks were overfished, if to a different extent, and one, the spear squid (Heterololigo bleekeri) has collapsed. The reference points estimated here may be used as indicator for fishery management in this ecoregion.

The use of Unmanned Aerial Vehicles (UAVs) to sample the blow microbiome of small cetaceans

Centelleghe C, Carraro L, Gonzalvo J, Rosso M, Esposti E, Gili C, Bonato M, Pedrotti D, Cardazzo B, Povinelli M, et al. The use of Unmanned Aerial Vehicles (UAVs) to sample the blow microbiome of small cetaceans Caballero S. PLOS ONE [Internet]. 2020 ;15(7):e0235537. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0235537
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Recent studies describe the use of UAVs in collecting blow samples from large whales to analyze the microbial and viral community in exhaled air. Unfortunately, attempts to collect blow from small cetaceans have not been successful due to their swimming and diving behavior. In order to overcome these limitations, in this study we investigated the application of a specific sampling tool attached to a UAV to analyze the blow from small cetaceans and their respiratory microbiome. Preliminary trials to set up the sampling tool were conducted on a group of 6 bottlenose dolphins (Tursiops truncatus) under human care, housed at Acquario di Genova, with approximately 1 meter distance between the blowing animal and the tool to obtain suitable samples. The same sampling kit, suspended via a 2 meter rope assembled on a waterproof UAV, flying 3 meters above the animals, was used to sample the blows of 5 wild bottlenose dolphins in the Gulf of Ambracia (Greece) and a sperm whale (Physeter macrocephalus) in the southern Tyrrhenian Sea (Italy), to investigate whether this experimental assembly also works for large whale sampling. In order to distinguish between blow-associated microbes and seawater microbes, we pooled 5 seawater samples from the same area where blow samples’ collection were carried out. The the respiratory microbiota was assessed by using the V3-V4 region of the 16S rRNA gene via Illumina Amplicon Sequencing. The pooled water samples contained more bacterial taxa than the blow samples of both wild animals and the sequenced dolphin maintained under human care. The composition of the bacterial community differed between the water samples and between the blow samples of wild cetaceans and that under human care, but these differences may have been mediated by different microbial communities between seawater and aquarium water. The sperm whale’s respiratory microbiome was more similar to the results obtained from wild bottlenose dolphins. Although the number of samples used in this study was limited and sampling and analyses were impaired by several limitations, the results are rather encouraging, as shown by the evident microbial differences between seawater and blow samples, confirmed also by the meta-analysis carried out comparing our results with those obtained in previous studies. Collecting exhaled air from small cetaceans using drones is a challenging process, both logistically and technically. The success in obtaining samples from small cetacean blow in this study in comparison to previous studies is likely due to the distance the sampling kit is suspended from the drone, which reduced the likelihood that the turbulence of the drone propeller interfered with successfully sampling blow, suggested as a factor leading to poor success in previous studies.

A mini ROV-based method for recovering marine instruments at depth

Tarnecki JH, Patterson WF. A mini ROV-based method for recovering marine instruments at depth Hewitt J. PLOS ONE [Internet]. 2020 ;15(7):e0235321. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0235321
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Instruments are often deployed at depth for weeks to years for a variety of marine applications. In many cases, divers can be deployed to retrieve instruments, but divers are constrained by depth limitations and safety concerns. Acoustic release technology can also be employed but can add considerable expense and acoustic releases will at times fail. Here, we report a simple method that utilizes a commercially available mooring hook integrated with a mini remotely operated vehicle to attach lines to instruments deployed on the sea floor, which can then be winched to the surface. The mooring hook apparatus was tested in a pool setting and then used to retrieve acoustic telemetry receiver bases (50 kg) or fish traps (30–50 kg) from the northern Gulf of Mexico continental shelf at depths between 28 and 80 m. During 2013–2019, 539 retrievals (100% success rate) were made of receiver bases (n = 239) and traps (n = 300) on 30 sea days using this approach. This method could easily be applied to other types of instruments, or recovery and salvage of objects that are too deep for standard diving operations.

Toward elimination of unwanted catches using a 100 mm T90 extension and codend in demersal mixed fisheries

Robert M, Morandeau F, Scavinner M, Fiche M, Larnaud P. Toward elimination of unwanted catches using a 100 mm T90 extension and codend in demersal mixed fisheries Patterson HM. PLOS ONE [Internet]. 2020 ;15(7):e0235368. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0235368
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Most European fishing fleets will need to drastically reduce their unwanted catches to comply with new rules of the common fisheries policy. A more practical way to avoid increasing on-board sorting time and issues linked to storage capacity is to prevent unwanted catches in the first place. We assessed the selectivity properties of an experimental fishing gear that combined a 100 mm T90 cylinder with 130 meshes in the extension and a 100 mm T90 codend of 33 meshes (experimental gear) compared to a 100 mm diamond mesh extension and codend (control gear) during commercial trips using twin trawls. Analysis of the relative size composition of catches indicated a significantly higher escapement of small fish of several target species (e.g. Lepidorhombus whiffiagonisMelanogrammus aeglefinusRaja spp, and Lophius spp) and non-target species (e.g. Capros aper and Gurnards spp) from the T90 experimental trawl compared to the control trawl (n = 49 hauls), resulting in a significant reduction of unwanted catches of Gadidae, Triglidae, and Caproidae. In contrast, non-negligible commercial losses of small grade target gadoid species were observed. Mixed general linear models showed that the proportion of ray, haddock and anglerfish retained per length class decreased with increased tow duration. The T90 experimental gear will perform at a commercial level when targeting monkfish, megrim, rays and large haddock, however fishers are not likely to use this gear when targeting smaller-bodied species such as cephalopods, small haddock, whiting (Merlangius merlangus) and hake (Merluccius merluccius), because the gear is likely to allow large numbers to escape. Selectivity studies often focus on a short list of target species; however, catches of non-target species under quota can be problematic for some fisheries. For example, under the implementation of the Landing Obligation catches of boarfish could choke the French whitefish demersal fisheries in the Celtic sea, as France has no national quota for that species. The device tested constitutes an efficient solution to mitigate catches for such non-target schooling fish.

New insights into the hydrogeology and groundwater flow in the Great Barrier Reef catchment, Australia, revealed through 3D modelling

Shishaye HA, Tait DR, Befus KM, Maher DT, Reading MJ. New insights into the hydrogeology and groundwater flow in the Great Barrier Reef catchment, Australia, revealed through 3D modelling. Journal of Hydrology: Regional Studies [Internet]. 2020 ;30:100708. Available from: https://www.sciencedirect.com/science/article/pii/S2214581820301828
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Study region

The Great Barrier Reef catchment is located adjacent to the world's largest coral reef system, the Great Barrier Reef, in eastern Queensland, Australia.

Study focus

This study characterized the geologic and hydrogeologic settings and evaluated the influence of regional faults on groundwater flow. 3D geological models of six regions within the catchment were constructed using drill-log data from >49,000 wells, digital elevation models and surface geological maps. The 3D models were then integrated with potentiometric surface maps and faults data to conceptualize the hydraulic relationships of aquifer units and estimate groundwater development potentials. Potentiometric surfaces and fault orientations were used to conceptualize groundwater flow directions.

New hydrological insights for the region

The 3D geological and hydrogeological characterizations revealed previously unknown faults and aquifer units in the study area. The study found that the central regions consisted of fractured and porous-unconfined aquifers, while confined aquifers, which extend to the coast and likely beyond, were also found in the northern and southern most regions. The orientations of the faults trended in NW-SE directions and could form conduits for south-easterly groundwater flow as opposed to the predominate easterly flow in the porous-unconfined and confined aquifers. The 3D models, aquifer connectivities and geometries provided crucial information to determine groundwater development potentials and offer a first step in developing local and regional groundwater flow and contaminant transport models.

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