Underwater gliders have become widely used in the last decade. This has led to a proliferation of data and the concomitant development of tools to process the data. These tools are focused primarily on converting the data from its raw form to more accessible formats and often rely on proprietary programing languages. This has left a gap in the processing of glider data for academics, who often need to perform secondary quality control (QC), calibrate, correct, interpolate and visualize data. Here, we present GliderTools, an open-source Python package that addresses these needs of the glider user community. The tool is designed to change the focus from the processing to the data. GliderTools does not aim to replace existing software that converts raw data and performs automatic first-order QC. In this paper, we present a set of tools, that includes secondary cleaning and calibration, calibration procedures for bottle samples, fluorescence quenching correction, photosynthetically available radiation (PAR) corrections and data interpolation in the vertical and horizontal dimensions. Many of these processes have been described in several other studies, but do not exist in a collated package designed for underwater glider data. Importantly, we provide potential users with guidelines on how these tools are used so that they can be easily and rapidly accessible to a wide range of users that span the student to the experienced researcher. We recognize that this package may not be all-encompassing for every user and we thus welcome community contributions and promote GliderTools as a community-driven project for scientists.
Remote Sensing and GIS
Tomorrow’s smart lakes and oceans will be able to, among other things, predict changes in the water environment and produce information critical to proper management and planning. Smart Lake Erie – a proof of concept – will integrate data from distributed sensors using resilient networks to feed adaptive, predictive analytics that define and perhaps even perform necessary management actions. This paper presents the Smart Lake Erie pilot as a series of steps that include convening innovation competitions, engaging stakeholders, securing the core observation system, and designing then building a sustainable early warning system for harmful algal blooms. The pilot’s data platform will show what is needed to serve new data contributors, service providers, stakeholders and consumers of the data and information service paradigm. Lessons learned from the early implementation of the pilot will be applicable to the overall Great Lakes region, other regional associations within the U.S. Integrated Ocean Observing System (IOOS), and the Global Ocean Observing System (GOOS).
Multidisciplinary ocean observing activities provide critical ocean information to satisfy ever-changing socioeconomic needs and require coordinated implementation. The upper oxycline (transition between high and low oxygen waters) is fundamentally important for the ecosystem structure and can be a useful proxy for multiple observing objectives connected to eastern boundary systems (EBSs) that neighbor oxygen minimum zones (OMZs). The variability of the oxycline and its impact on the ecosystem (VOICE) initiative demonstrates how societal benefits drive the need for integration and optimization of biological, biogeochemical, and physical components of regional ocean observing related to EBS. In liaison with the Global Ocean Oxygen Network, VOICE creates a roadmap toward observation-model syntheses for a comprehensive understanding of selected oxycline-dependent objectives. Local to global effects, such as habitat compression or deoxygenation trends, prompt for comprehensive observing of the oxycline on various space and time scales, and for an increased awareness of its impact on ecosystem services. Building on the Framework for Ocean Observing (FOO), we present a first readiness level assessment for ocean observing of the oxycline in EBS. This was to determine current ocean observing design and future needs in EBS regions (e.g., the California Current System, the Equatorial Eastern Pacific off Ecuador, the Peru–Chile Current system, the Northern Benguela off Namibia, etc.) building on the FOO strategy. We choose regional champions to assess the ocean observing design elements proposed in the FOO, namely, requirement processes, coordination of observational elements, and data management and information products and the related best practices. The readiness level for the FOO elements was derived for each EBS through a similar and very general ad hoc questionnaire. Despite some weaknesses in the questionnaire design and its completion, an assessment was achievable. We found that fisheries and ecosystem management are a societal requirement for all regions, but maturity levels of observational elements and data management and information products differ substantially. Identification of relevant stakeholders, developing strategies for readiness level improvements, and building and sustaining infrastructure capacity to implement these strategies are fundamental milestones for the VOICE initiative over the next 2–5 years and beyond.
Sea-surface temperature (SST) was one of the first ocean variables to be studied from earth observation satellites. Pioneering images from infrared scanning radiometers revealed the complexity of the surface temperature fields, but these were derived from radiance measurements at orbital heights and included the effects of the intervening atmosphere. Corrections for the effects of the atmosphere to make quantitative estimates of the SST became possible when radiometers with multiple infrared channels were deployed in 1979. At the same time, imaging microwave radiometers with SST capabilities were also flown. Since then, SST has been derived from infrared and microwave radiometers on polar orbiting satellites and from infrared radiometers on geostationary spacecraft. As the performances of satellite radiometers and SST retrieval algorithms improved, accurate, global, high resolution, frequently sampled SST fields became fundamental to many research and operational activities. Here we provide an overview of the physics of the derivation of SST and the history of the development of satellite instruments over half a century. As demonstrated accuracies increased, they stimulated scientific research into the oceans, the coupled ocean-atmosphere system and the climate. We provide brief overviews of the development of some applications, including the feasibility of generating Climate Data Records. We summarize the important role of the Group for High Resolution SST (GHRSST) in providing a forum for scientists and operational practitioners to discuss problems and results, and to help coordinate activities world-wide, including alignment of data formatting and protocols and research. The challenges of burgeoning data volumes, data distribution and analysis have benefited from simultaneous progress in computing power, high capacity storage, and communications over the Internet, so we summarize the development and current capabilities of data archives. We conclude with an outlook of developments anticipated in the next decade or so.
Seagrass meadows play a key ecological role as nursery and feeding grounds for multiple fish species. Underwater Visual Census (UVC) has been historically used as the non-extractive method to characterize seagrass fish communities, however, less intrusive methodologies such as Remote Underwater Video (RUV) are gaining interest and could be particularly useful for seagrass habitats, where juvenile fish camouflage among the vegetation and could easily hide or flee from divers. Here we compared the performance of UVC and RUV methodologies in assessing the fish communities of two seagrass meadows with low and high canopy density. We found that RUV detected more species and fish individuals than UVC, particularly on the habitat with higher seagrass density, which sheltered more juveniles, especially herbivorous, and adult piscivorous of commercial importance, evidencing significant differences in energy flow from macrophytes to predators between seagrass habitats, and also differences in the ecosystem services they can provide. Considering the ongoing worldwide degradation of seagrass ecosystems, our results strongly suggest that fish surveys using RUV in ecologic and fisheries programs would render more accurate information and would be more adequate to inform the conservation planning of seagrass meadows around the world.
Harmful Algal Blooms (HABs) are of global concern, as their presence is often associated with socio-economic and environmental issues including impacts on public health, aquaculture and fisheries. Therefore, monitoring the occurrence and succession of HABs is fundamental for managing coastal regions around the world. Yet, due to the lack of adequate in situmeasurements, the detection of HABs in coastal marine ecosystems remains challenging. Sensors on-board satellite platforms have sampled the Earth synoptically for decades, offering an alternative, cost-effective approach to routinely detect and monitor phytoplankton. The Red Sea, a large marine ecosystem characterised by extensive coral reefs, high levels of biodiversity and endemism, and a growing aquaculture industry, is one such region where knowledge of HABs is limited. Here, using high-resolution satellite remote sensing observations (1km, MODIS-Aqua) and a second-order derivative approach, in conjunction with available in situ datasets, we investigate for the first time the capability of a remote sensing model to detect and monitor HABs in the Red Sea. The model is able to successfully detect and generate maps of HABs associated with different phytoplankton functional types, matching concurrent in situdata remarkably well. We also acknowledge the limitations of using a remote-sensing based approach and show that regardless of a HAB’s spatial coverage, the model is only capable of detecting the presence of a HAB when the Chl-a concentrations exceed a minimum value of ~ 1 mg m-3. Despite the difficulties in detecting HABs at lower concentrations, and identifying species toxicity levels (only possible through in situ measurements), the proposed method has the potential to map the reported spatial distribution of several HAB species over the last two decades. Such information is essential for the regional economy (i.e., aquaculture, fisheries & tourism), and will support the management and sustainability of the Red Sea’s coastal economic zone.
Barrier islands are dynamic ecosystems that change gradually from coastal processes, including currents and tides, and rapidly from episodic events, such as storms. These islands provide many important ecosystem services, including storm protection and erosion control to the mainland, habitat for fish and wildlife, and tourism. Habitat maps, developed by scientists, provide a critical tool for monitoring changes to these dynamic ecosystems. Barrier island monitoring often requires custom habitat maps due to several factors, including island size and the classification of unique geomorphology-based habitats, such as beach, dune, and barrier flats. In this study, we reviewed barrier-island-specific habitat mapping efforts and highlighted common habitat class types, source data, and mapping approaches. We also developed a framework for mapping geomorphology-based barrier island habitats using a rule-based, geographic object-based image analysis approach, which included the use of field data, tide data, high-resolution orthophotography, and lidar data. This framework integrates several barrier island mapping advancements with regard to the use of landscape position information for automated dune extraction and the use of Monte Carlo analyses for the treatment of elevation uncertainty for elevation-dependent habitats. Specifically, we used the uncertainty analyses to refine automated dune delineation based on elevation relative to extreme storm water levels and to increase the accuracy of intertidal and supratidal/upland habitat delineation. We found that dune extraction results were enhanced when elevation relative to storm water levels and visual interpretation were also applied. This framework could also be applied to beach–dune systems found along a mainland.
Global elasmobranch populations have declined dramatically over the past 50 years, and continued research into the drivers of their habitats and distributions is vital for improved conservation and management. How environmental factors influence elasmobranch behavior, habitat use, and movement patterns is still relatively poorly understood, in part because of the scale over which many of these animals roam and the remote nature of the marine ecosystems they inhabit. In the last decade there has been an explosion of satellite remote sensing (SRS) technologies that can cover these vast spatial scales for the marine environment. Consequentially, SRS presents an opportunity to analyze important environmental drivers in elasmobranch ecology and to aid management decisions for the conservation of declining populations. A systematic literature review was undertaken to synthesize the current use of SRS environmental data in elasmobranch research. In addition, to facilitate the use of SRS in this field moving forward, we have compiled a list of popular SRS data sources and sensors for common environmental variables in marine science. Our review of 71 papers (55 published in the last 10 years) identified ten SRS-derived environmental variables that have been used in elasmobranch studies, from a range of satellite sensors and data sources. Sea surface temperature and ocean productivity were the most frequently used variables. Articles primarily analyzed variables individually or in pairs, with few studies looking at a suite of interacting variables. Here, we present a summary of the current state of knowledge on the application of SRS, current gaps and limitations, and discuss some of the potential future directions in which we envisage this field developing. Threatened elasmobranch populations inhabit some of the world’s most remote marine ecosystems. With often global coverage, SRS presents an opportunity to analyze the important environmental drivers of elasmobranch ecology to aid management decisions for the conservation of declining and threatened populations.
Accurate estimates of fishing effort are necessary in order to assess interactions with the wider ecosystem and for defining and implementing appropriate management. In intertidal and inshore fisheries in which vessel monitoring systems (VMS) or logbook programmes may not be implemented, quantifying the distribution and intensity of fishing can be difficult. The most obvious effects of bottom-contact fishing are often physical changes to the habitat, such as scarring of the sediment following dredging or trawling. We explored the potential of applying remote sensing techniques to aerial imagery collected by an unmanned aerial vehicle, or drone, in an area of intertidal mud flat (0.52 km2) in Poole Harbour, UK, where shellfish dredging is widely carried out and conflicts between commercial fishing interests and the conservation of internationally important shorebird populations are a concern. Image classification and image texture analysis were performed on imagery collected during the open dredge season in November 2015, in order to calculate measures of fishing intensity across three areas of the harbour subject to different management measures. We found a significant correlation between results of the image texture analysis and official sightings records collected during the dredging season, indicating that this method most accurately quantified dredging disturbance. The relationship between shorebird densities and food intake rates and the results of this analysis method were then investigated to assess the potential for using remotely sensed measures of fishing effort to assess responses of overwintering shorebird populations to intertidal shellfish dredging. Our work highlights the application of such methods, providing a low-cost tool for quantifying fishing effort and predicting wildlife conflicts.
As petroleum development and other activities move further north, the potential for oil spills in ice-covered waters is of great concern. As a tool for contingency planning and forecasting during response, oil spill models play a key role. With the development of new, high-resolution coupled ice-ocean models, better predictions of sea ice are becoming available. We have updated the OSCAR oil spill model to use sea-ice velocity and coverage fields from coupled ice-ocean models to improve simulation of oil fate and transport in ice-covered waters.
We describe the implementation of oil transport in the presence of ice, and demonstrate the improvement by considering three case studies. We find clear improvement when taking ice velocity from a coupled ice-ocean model into account, compared to a heuristic model that uses surface current and wind velocity. The difference is found to be especially important in a response situation near the marginal ice zone.