Tools and Data

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.

On the interplay between horizontal resolution and wave drag and their effect on tidal baroclinic mode waves in realistic global ocean simulations

Buijsman MC, Stephenson GR, Ansong JK, Arbic BK, Green JAMattias, Richman JG, Shriver JF, Vic C, Wallcraft AJ, Zhao Z. On the interplay between horizontal resolution and wave drag and their effect on tidal baroclinic mode waves in realistic global ocean simulations. Ocean Modelling [Internet]. 2020 :101656. Available from: https://www.sciencedirect.com/science/article/pii/S146350032030158X
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

The effects of horizontal resolution and wave drag damping on the semidiurnal M2 tidal energetics are studied for two realistically-forced global HYbrid Coordinate Ocean Model (HYCOM) simulations with 41 layers and horizontal resolutions of 8 km (1∕12.5∘; H12) and 4 km (1∕25∘; H25). In both simulations, the surface tidal error is minimized by tuning the strength of the linear wave drag, which is a parameterization of the surface-tide energy conversion to the unresolved baroclinic wave modes. In both simulations the M2 surface tide error with TPXO8-atlas, an altimetry constrained model, is 2.6 cm. Compared to H12, the surface tide energy conversion to the resolved vertical modes is increased by 50% in H25. This coincides with an equivalent reduction in the tuned loss of energy from the surface tide to the wave drag. For the configurations studied here, the horizontal and not the vertical resolution is the factor limiting the number of vertical modes that are resolved in most of the global ocean: modes 1–2 in H12 and modes 1–5 in H25. The wave drag also dampens the resolved internal tides. The 40% reduction in wave-drag strength does not result in a proportional increase in the mode-1 energy density in H25. In the higher-resolution simulations, topographic mode-scattering and wave–wave interactions are better resolved. This allows for an energy flux out of mode 1 to the higher modes, mitigating the need for an internal tide damping term. The HYCOM simulations are validated with analytical conversion models and altimetry-inferred sea-surface height, fluxes, and surface tide dissipation. H25 agrees best with these data sets to within ∼10%. To facilitate the comparison of stationary tide signals extracted from time series with different durations, we successfully apply a spatially-varying correction factor.

Establishing the links between marine ecosystem components, functions and services: An ecosystem service assessment tool

Armoškaitė A, Puriņa I, Aigars J, Strake S, Pakalniete K, Frederiksen P, Schrøder L, Hansen HSten. Establishing the links between marine ecosystem components, functions and services: An ecosystem service assessment tool. Ocean & Coastal Management [Internet]. 2020 ;193:105229. Available from: https://www.sciencedirect.com/science/article/pii/S0964569120301393
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Although the concept of ecosystem services has been in use for many decades, its application for policy support is limited, particularly with respect to marine ecosystems. Gaps in the assessments of ecosystem services supply prevent its empirical application. We advance these assessments by providing an assessment tool, which links marine ecosystem components, functions and services, and graphically represents the assessment process and its results. The tool consists of two parts: (i) a matrix following the ecosystem services cascade structure for quantifying the contribution of ecosystem components in the provision of ecosystem services; (ii) and a linkage diagram for visualising the interactions between the elements. With the aid of the Common International Classification of Ecosystem Services (CICES), the tool was used to assess the relative contribution of a wide range of marine ecosystem components in the supply of ecosystem services in the Latvian marine waters. Results indicate that the tool can be used to assess the impacts of environmental degradation in terms of ecosystem service supply. These impacts could further be valued in socioeconomic terms, as change in the socioeconomic values derived from the use of ecosystem services. The tool provides an opportunity for conducting a holistic assessment of the ecosystem service supply and communicating the results to marine spatial planning practitioners, and increasing their understanding and use of the ecosystem service concept.

Meta-Analysis Reveals Artificial Reefs Can Be Effective Tools for Fish Community Enhancement but Are Not One-Size-Fits-All

Paxton AB, Shertzer KW, Bacheler NM, G. Kellison T, Riley KL, J. Taylor C. Meta-Analysis Reveals Artificial Reefs Can Be Effective Tools for Fish Community Enhancement but Are Not One-Size-Fits-All. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00282/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1334659_45_Marine_20200521_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Approaches toward habitat conservation and restoration often include supplementing or enhancing existing, degraded, or lost natural habitats. In aquatic environments, a popular approach toward habitat enhancement is the introduction of underwater human-made structures or artificial reefs. Despite the nearly global prevalence of artificial reefs deployed to enhance habitat, it remains debated whether these structures function similarly to comparable natural reefs. To help resolve this question, we conducted a literature review and accompanying meta-analysis of fish community metrics on artificial reefs within the coastal ocean and made comparisons with naturally-occurring reference reefs (rocky reefs and coral reefs). Our findings from a synthesis of 39 relevant studies revealed that, across reef ecosystems, artificial reefs support comparable levels of fish density, biomass, species richness, and diversity to natural reefs. Additional analyses demonstrated that nuances in these patterns were associated with the geographic setting (ocean basin, latitude zone) and artificial reef material. These findings suggest that, while artificial reefs can mimic natural reefs in terms of the fish assemblages they support, artificial reefs are not one-size-fits-all tools for habitat enhancement. Instead, artificial reefs should be considered strategically based on location-specific scientific assessments and resource needs to maximize benefits of habitat enhancement.

A Comparison of the Diagnostic Accuracy of in-situ and Digital Image-Based Assessments of Coral Health and Disease

Burns JHR, Weyenberg G, Mandel T, Ferreira SB, Gotshalk D, Kinoshita CK, Marshall MJ, Del Moral NAV, Murphy SJ, Pascoe KH, et al. A Comparison of the Diagnostic Accuracy of in-situ and Digital Image-Based Assessments of Coral Health and Disease. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00304/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1334659_45_Marine_20200521_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

The prevalence of coral disease is steadily increasing throughout the global ocean, and there is a growing need for efficient methods for detecting and monitoring coral health. At present, coral health assessments are primarily conducted using in-situ surveys, which record visual observations of disease in the field. Recent technological advancements allow researchers to instead collect high-resolution imagery of benthic habitats, and these images can be used in conjunction with digital tools to assess the health of coral colonies at a later time. However, little is known about the relative efficacy or diagnostic accuracy of these two approaches. This study contrasts the diagnostic accuracy of in-situ and digital methodologies for detecting diseases and adverse health conditions affecting corals. Multiple 1 m2 plots are surveyed on coral reefs located on both the windward and leeward side of Hawaii Island. For each plot, an in-situ visual analysis of coral health is conducted by a diver and images are collected and rendered into a high-resolution orthomosaic for subsequent digital analysis. Both methods assess the same coral colonies, resulting in paired health diagnoses for multiple health conditions. Lacking a gold-standard diagnosis of health conditions, a latent class model is used to estimate the sensitivity (true positive rate) and specificity (true negative rate) of both methods. We find that in-situ assessments of coral health have a higher sensitivity and lower specificity in detecting health conditions when compared to digital analyses based on orthomosaics. However, the effect size is relatively modest, indicating that while the in-situ method provides a more sensitive diagnostic approach, the techniques are of comparable accuracy, and should both be considered viable methods of characterizing and monitoring coral health.

Estimating marine survival of Atlantic salmon using an inverse matrix approach

Pardo SA, Hutchings JA. Estimating marine survival of Atlantic salmon using an inverse matrix approach Patterson HM. PLOS ONE [Internet]. 2020 ;15(5):e0232407. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232407
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

The marine phase of anadromous Atlantic salmon (Salmo salar) is the least known yet one of the most crucial with regards to population persistence. Recently, declines in many salmon populations in eastern Canada have been attributed to changes in the conditions at sea, thus reducing their survival. However, marine survival estimates are difficult to obtain given that many individuals spend multiple winters in the ocean before returning to freshwater to spawn; therefore, multiple parameters need to be estimated. We develop a model that uses an age-structured projection matrix which, coupled with yearly smolt and return abundance estimates, allows us to resample a distribution of matrices weighted by how close the resulting return estimates match the simulated returns, using a sample-importance-resampling algorithm. We test this model by simulating a simple time series of salmon abundances, and generate six different scenarios of varying salmon life histories where we simulate data for one-sea-winter (1SW)-dominated and non-1SW dominated populations, as well as scenarios where the proportion returning as 1SW is stable or highly variable. We find that our model provides reasonable estimates of marine survival for the first year at sea (S1), but highly uncertain estimates of proportion returning as 1SW (Pr) and survival in the second year at sea (S2). Our exploration of variable scenarios suggests the model is able to detect temporal trends in S1 for populations that have a considerable 1SW component in the returns; the ability of the model to detect trends in S1 diminishes as the proportion of two-sea-winter fish increases. Variability in the annual proportion of fish returning as 1SW does not seem to impact model accuracy. Our approach provides an instructive stepping-stone towards a model that can be applied to empirical abundance estimates of Atlantic salmon, and anadromous fishes in general, and therefore improve our knowledge of the marine phase of their life cycles as well as examining spatial and temporal trends in their variability.

Optimal soak times for Baited Remote Underwater Video Station surveys of reef-associated elasmobranchs

Currey-Randall LM, Cappo M, Simpfendorfer CA, Farabaugh NF, Heupel MR. Optimal soak times for Baited Remote Underwater Video Station surveys of reef-associated elasmobranchs Januchowski-Hartley FAndrew. PLOS ONE [Internet]. 2020 ;15(5):e0231688. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0231688
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Effective sampling of marine communities is essential to provide robust estimates of species richness and abundance. Baited Remote Underwater Video Stations (BRUVS) are a useful tool in assessment of fish assemblages, but research on the optimal sampling period required to record common and rare elasmobranch species is limited. An appropriate ‘soak time’ (time elapsed between settlement of the BRUVS on the seabed and when it is hauled off the seabed) requires consideration, since longer soak times may be required to record species rare in occurrence, or sightings in areas of generally low elasmobranch abundance. We analysed 5352 BRUVS deployments with a range of soak times across 21 countries in the Coral Triangle and Pacific Ocean, to determine the optimal soak time required for sampling reef-associated elasmobranchs, considering species rarity, and community abundance at each site. Species were categorised into 4 ‘rarity’ groups (very rare to common), by their relative occurrence in the dataset, defined simply by the proportion of BRUVS on which they occurred. Individual BRUVS were categorised into 3 ‘abundance’ groups (low to high) by overall relative elasmobranch abundance, defined as total number of all elasmobranchs sighted per unit of sampling effort. The effects of BRUVS soak times, and levels of rarity and abundance groupings, on the time to first sighting (TFS) and time to maximum number of elasmobranchs observed (tMaxN) were examined. We found that TFS occurred earlier for species groups with high occurrence, and on BRUVS with high elasmobranch abundance, yet longer soak times were not essential to observe rarer species. Our models indicated an optimum of 95% of both sighting event types (TFStMaxN) was recorded within 63–77 minutes, and a soak time of 60 minutes recorded 78–94% of the elasmobranch sighting events recorded (78–94% of TFS events and 82–90% of tMaxN events), when species rarity and abundance on BRUVS was accounted for. Our study shows that deployments of ~ 77 minutes are optimal for recording all species we observed, although 60 minutes soak time effectively samples the majority of elasmobranch species in shallow coral reef habitats using BRUVS.

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