Remote Sensing and GIS

Between a Reef and a Hard Place: Capacity to Map the Next Coral Reef Catastrophe

Hickey SM, Radford B, Roelfsema CM, Joyce KE, Wilson SK, Marrable D, Barker K, Wyatt M, Davies HN, Leon JX, et al. Between a Reef and a Hard Place: Capacity to Map the Next Coral Reef Catastrophe. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.544290/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1452864_45_Marine_20201008_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Increasing sea surface temperature and extreme heat events pose the greatest threat to coral reefs globally, with trends exceeding previous norms. The resultant mass bleaching events, such as those evidenced on the Great Barrier Reef in 2016, 2017, and 2020 have substantial ecological costs in addition to economic and social costs. Advancing remote (nanosatellites, rapid revisit traditional satellites) and in-field (drones) technological capabilities, cloud data processing, and analysis, coupled with existing infrastructure and in-field monitoring programs, have the potential to provide cost-effective and timely information to managers allowing them to better understand changes on reefs and apply effective remediation. Within a risk management framework for monitoring coral bleaching, we present an overview of how remote sensing can be used throughout the whole risk management cycle and highlight the role technological advancement has in earth observations of coral reefs for bleaching events.

A high-resolution remotely sensed benthic habitat map of the Qatari coastal zone

Butler JD, Purkis SJ, Yousif R, Al-Shaikh I, Warren C. A high-resolution remotely sensed benthic habitat map of the Qatari coastal zone. Marine Pollution Bulletin [Internet]. 2020 ;160:111634. Available from: https://www.sciencedirect.com/science/article/pii/S0025326X20307529?dgcid=raven_sd_search_email
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

A comprehensive, high resolution, ground truthed benthic habitat map has been completed for Qatar's coastal zone and Halul Island. The objectives of this research were to; 1. Systematically compare and contrast pixel- and object-based classifiers for benthic mapping in a limited focus area and then to, 2. Apply these learnings to develop an accurate high resolution benthic habitat map for the entirety of the Qatari coastal zone. Results indicate object-based methods proved more efficient and accurate when compared to pixel based classifiers. The developed country-wide map covers 4500 km2 and underscores the complex interplay of seagrass, macroalgal, and reefal habitats, as well as areas of expansive mangrove forests and microbial mats. The map developed here is a first of its kind in the region. Many potential applications exist for the datasets collected to provide fundamental information that can be used for ecosystem-based management decision making.

Can we locate shrimp aquaculture areas from space? – A case study for Thailand

Dorber M, Verones F, Nakaoka M, Sudo K. Can we locate shrimp aquaculture areas from space? – A case study for Thailand. Remote Sensing Applications: Society and Environment [Internet]. 2020 ;20:100416. Available from: https://www.sciencedirect.com/science/article/pii/S2352938520301415?dgcid=raven_sd_search_email
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Globally, shrimp aquaculture has undergone a rapid development in the last decades, as it can help to satisfy the increasing food demand of a growing population. However, shrimp production can be accompanied by environmental impacts, such as land cover changes associated with pond construction, or the degradation of coastal areas through pollution. Environmental footprinting, has proven to be a valuable tool for tracing environmental impacts from human consumption back to their location and sector of origin. Here, we focus on the land footprint, which quantifies the area of required land resources to satisfy human consumption (of shrimp production). However, today’s footprinting tools often lack spatially explicit land cover information for land footprint assessments. In this study we developed a new method, which allows us to identify the land cover change caused by shrimp pond construction in Thailand without using sample shrimp pond shape polygons as input data. We use the global water surface explorer (using globally 3 million Landsat 5 TM, Landsat 7 ETM and Landsat 8 OLI images, acquired between 1984 and 2015), aerial photographs and land cover maps in combination with known aquaculture locations, to identify water areas in Thailand that have a high likelihood to be a shrimp pond and to assess the corresponding land cover change. We estimated that in 2015 an area of 377 km2 had a high likelihood of being shrimp pond water area. Further, we show that the construction of shrimp ponds in Thailand was responsible for the transformation of 552 km2 primary habitat, such as mangrove areas. Our results support the environmental footprint assessment of shrimp ponds in Thailand, while our proposed method allows identifying possible shrimp pond areas on a global scale.

Using GIS and stakeholder involvement to innovate marine mammal bycatch risk assessment in data-limited fisheries

Verutes GM, Johnson AF, Caillat M, Ponnampalam LS, Peter C, Vu L, Junchompoo C, Lewison RL, Hines EM. Using GIS and stakeholder involvement to innovate marine mammal bycatch risk assessment in data-limited fisheries. PLOS ONE [Internet]. 2020 ;15(8):e0237835. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0237835
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Fisheries bycatch has been identified as the greatest threat to marine mammals worldwide. Characterizing the impacts of bycatch on marine mammals is challenging because it is difficult to both observe and quantify, particularly in small-scale fisheries where data on fishing effort and marine mammal abundance and distribution are often limited. The lack of risk frameworks that can integrate and visualize existing data have hindered the ability to describe and quantify bycatch risk. Here, we describe the design of a new geographic information systems tool built specifically for the analysis of bycatch in small-scale fisheries, called Bycatch Risk Assessment (ByRA). Using marine mammals in Malaysia and Vietnam as a test case, we applied ByRA to assess the risks posed to Irrawaddy dolphins (Orcaella brevirostris) and dugongs (Dugong dugon) by five small-scale fishing gear types (hook and line, nets, longlines, pots and traps, and trawls). ByRA leverages existing data on animal distributions, fisheries effort, and estimates of interaction rates by combining expert knowledge and spatial analyses of existing data to visualize and characterize bycatch risk. By identifying areas of bycatch concern while accounting for uncertainty using graphics, maps and summary tables, we demonstrate the importance of integrating available geospatial data in an accessible format that taps into local knowledge and can be corroborated by and communicated to stakeholders of data-limited fisheries. Our methodological approach aims to meet a critical need of fisheries managers: to identify emergent interaction patterns between fishing gears and marine mammals and support the development of management actions that can lead to sustainable fisheries and mitigate bycatch risk for species of conservation concern.

Current and Future Remote Sensing of Harmful Algal Blooms in the Chesapeake Bay to Support the Shellfish Industry

Wolny JL, Tomlinson MC, Uz SSchollaert, Egerton TA, McKay JR, Meredith A, Reece KS, Scott GP, Stumpf RP. Current and Future Remote Sensing of Harmful Algal Blooms in the Chesapeake Bay to Support the Shellfish Industry. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00337/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1348443_45_Marine_20200609_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Harmful algal bloom (HAB) species in the Chesapeake Bay can negatively impact fish, shellfish, and human health via the production of toxins and the degradation of water quality. Due to the deleterious effects of HAB species on economically and environmentally important resources, such as oyster reef systems, Bay area resource managers are seeking ways to monitor HABs and water quality at large spatial and fine temporal scales. The use of satellite ocean color imagery has proven to be a beneficial tool for resource management in other locations around the world where high-biomass, nearly monospecific HABs occur. However, remotely monitoring HABs in the Chesapeake Bay is complicated by the presence of multiple, often co-occurring, species and optically complex waters. Here we present a summary of common marine and estuarine HAB species found in the Chesapeake Bay, Alexandrium monilatumKarlodinium veneficumMargalefidinium polykrikoides, and Prorocentrum minimum, that have been detected from space using multispectral data products from the Ocean and Land Colour Imager (OLCI) sensor on the Sentinel-3 satellites and identified based on in situ phytoplankton data and ecological associations. We review how future hyperspectral instruments will improve discrimination of potentially harmful species from other phytoplankton communities and present a framework in which satellite data products could aid Chesapeake Bay resource managers with monitoring water quality and protecting shellfish resources.

150 shades of green: Using the full spectrum of remote sensing reflectance to elucidate color shifts in the ocean

Vandermeulen RA, Mannino A, Craig SE, P. Werdell J. 150 shades of green: Using the full spectrum of remote sensing reflectance to elucidate color shifts in the ocean. Remote Sensing of Environment [Internet]. 2020 ;247:111900. Available from: https://www.sciencedirect.com/science/article/pii/S0034425720302704
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

This article proposes a simple and intuitive classification system by which to define full spectral remote sensing reflectance (Rrs(λ)) data with a quantitative output that enables a more manageable handling of spectral information for aquatic science applications. The weighted harmonic mean of the Rrs(λ) wavelengths outputs an Apparent Visible Wavelength (in units of nanometers), representing a one-dimensional geophysical metric of color that is inherently correlated to spectral shape. This dimensionality reduction of spectral information combined with the output along a continuum of wavelength values offers a robust and user-friendly means to describe and analyze spectral Rrs(λ) in terms of spatial and temporal trends and variability. The uncertainty in the algorithm's estimation of spectral shape is demonstrated on a global scale, in addition to the utility of the algorithm to discern spectral-spatial-temporal trends in the ocean, on a per-pixel basis for the entire 22 year continuous ocean color (SeaWiFS and MODIS-Aqua) time-series. This technique can be applied to datasets of varying multi- and hyper-spectral resolutions, providing continuity between heritage and future satellite sensors, and further enabling an effective means of elucidating similarities or differences in complex spectral signatures within the constraints of two dimensions. This straightforward means of conceptualizing multi-dimensional variability can help maximize the potential of the spectral information embedded in remote sensing data.

Applications of Spatial Autocorrelation Analyses for Marine Aquaculture Siting

Jossart J, Theuerkauf SJ, Wickliffe LC, Jr. JAMorris. Applications of Spatial Autocorrelation Analyses for Marine Aquaculture Siting. Frontiers in Marine Science [Internet]. 2020 ;6. Available from: https://www.frontiersin.org/article/10.3389/fmars.2019.00806/ful
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Interest and growth in marine aquaculture are increasing around the world, and with it, advanced spatial planning approaches are needed to find suitable locations in an increasingly crowded ocean. Standard spatial planning approaches, such as a Multi-Criteria Decision Analysis (MCDA), may be challenging and time consuming to interpret in heavily utilized ocean spaces. Spatial autocorrelation, a statistical measure of spatial dependence, may be incorporated into the planning framework, which provides objectivity and assistance with the interpretation of spatial analysis results. Here, two case studies highlighting applications of spatial autocorrelation analyses in the northeast region of the United States of America are presented. The first case study demonstrates the use of a local indicator of spatial association analysis within a relative site suitability analysis – a variant of a MCDA – for siting a mussel longline farm. This case study statistically identified 17% of the area as highly suitable for a mussel longline farm, relative to other locations in the area of interest. The use of a clear, objective, and efficient analysis provides improved confidence for industry, coastal managers, and stakeholders planning marine aquaculture. The second case study presents an incremental spatial autocorrelation analysis with Moran’s I that is performed on modeled and remotely sensed oceanographic data sets (e.g., chlorophyll a, sea surface temperature, and current speed). The results are used to establish a maximum area threshold for each oceanographic variable within the online decision support tool, OceanReports, which performs an automated spatial analysis for a user-selected area (i.e., drawn polygon) of ocean space. These thresholds provide users guidance and summary statistics of relevant oceanographic information for aquaculture planning. These two case studies highlight practical uses and the value of spatial autocorrelation analyses to improve the siting process for marine aquaculture.

Estimating Mangrove Tree Biomass and Carbon Content: A Comparison of Forest Inventory Techniques and Drone Imagery

Jones AR, Segaran RRaja, Clarke KD, Waycott M, Goh WSH, Gillanders BM. Estimating Mangrove Tree Biomass and Carbon Content: A Comparison of Forest Inventory Techniques and Drone Imagery. Frontiers in Marine Science [Internet]. 2020 ;6. Available from: https://www.frontiersin.org/article/10.3389/fmars.2019.00784/full
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Mangroves provide many ecosystem services including a considerable capacity to sequester and store large amounts of carbon, both in the sediment and in the above-ground biomass. Assessment of mangrove above-ground carbon stock relies on accurate measurement of tree biomass, which traditionally involves collecting direct measurements from trees and relating these to biomass using allometric relationships. We investigated the potential to predict tree biomass using measurements derived from unmanned aerial vehicle (UAV), or drone, imagery. This approach has the potential to dramatically reduce time-consuming fieldwork, providing greater spatial survey coverage and return for effort, and may enable data to be collected in otherwise hazardous or inaccessible areas. We imaged an Avicennia marina (grey mangrove) stand using an RGB camera mounted on a UAV. The imaged trees were subsequently felled, enabling physical measurements to be taken for traditional biomass estimation techniques, as well as direct measurements of biomass and tissue carbon content. UAV image-based tree height measurements were highly accurate (R2 = 0.98). However, the variables that could be measured from the UAV imagery (tree height and canopy area) were poor predictors of tree biomass. Using the physical measurement data, we identified that trunk diameter is a key predictor of A. marina biomass. Unfortunately, trunk diameter cannot be directly measured from the UAV imagery, but it can be predicted (with some error) using models that incorporate other UAV image-based measurements, such as tree height and canopy area. However, reliance on second-order estimates of trunk diameter leads to increased uncertainty in the subsequent predictions of A. marina biomass, compared to using physical measurements of trunk diameter taken directly from the trees. Our study demonstrates that there is potential to use UAV-based imagery to measure mangrove A. marina tree structural characteristics and biomass. Further refinement of the relationship between UAV image-based measurements and tree diameter is needed to reduce error in biomass predictions. UAV image-based estimates can be made far more quickly and over extensive areas when compared to traditional data collection techniques and, with improved accuracy through further model-calibration, have the potential to be a powerful tool for mangrove biomass and carbon storage estimation.

Sea Surface Temperature Imagery Elucidates Spatiotemporal Nutrient Patterns for Offshore Kelp Aquaculture Siting in the Southern California Bight

Snyder JN, Bell TW, Siegel DA, Nidzieko NJ, Cavanaugh KC. Sea Surface Temperature Imagery Elucidates Spatiotemporal Nutrient Patterns for Offshore Kelp Aquaculture Siting in the Southern California Bight. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/article/10.3389/fmars.2020.00022/full
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Offshore aquaculture of giant kelp (Macrocystis pyrifera) has been proposed by the US Department of Energy for large scale biofuel production along the west coast of California. The Southern Californian Bight provides an ideal area for offshore kelp aquaculture as the upwelling and advection of cool, nutrient-rich waters supports the growth of vast native giant kelp populations. However, concentrations of nutrients vary greatly across space, can be limiting for kelp growth over seasonal to interannual time scales, and inputs of nutrients to surface waters may be subject to local circulation processes. Therefore, it is important to understand both the spatiotemporal variability of seawater nitrate concentrations and the appropriate scale of observation in order for offshore kelp aquaculture to be successful. Here, we use a combination of satellite sea surface temperature imagery, in situ measurements, and modeling to determine seawater nitrate fields across multiple spatial and temporal scales. We then combine this information with known giant kelp physiological traits to develop a kelp stress index (KSI) for the optimal siting of offshore kelp aquaculture over seasonal to decadal scales. Temperature to nitrate relationships were determined from in situ measurements using generalized additive models and validated with buoy data. Summer and winter relationships were significantly different, and satellite-derived products compared well to buoy validations. Surface nitrate patterns, as derived from satellite temperature products, reveal the spatial variability in nitrate concentrations, and indicate areas that that may cause nutrient stress seasonally and during the negative phase of the North Pacific Gyre Oscillation. As the spatial scale of the surface nitrate product decreased, the negative bias increased and fine scale spatial variability was lost. Similarly, the averaging of daily nitrate concentration determinations over longer time scales increased the negative bias. We found that daily, 1 km spatial resolution nitrate products were most sufficient for identifying localized upwelling and areas of consistently high surface nitrate concentrations, and that areas in the northern and western-most portions of the Southern California Bight are the most suitable for sustained offshore kelp aquaculture.

Finding Crush: Environmental DNA Analysis as a Tool for Tracking the Green Sea Turtle Chelonia mydas in a Marine Estuary

Harper KJ, Goodwin KD, Harper LR, LaCasella EL, Frey A, Dutton PH. Finding Crush: Environmental DNA Analysis as a Tool for Tracking the Green Sea Turtle Chelonia mydas in a Marine Estuary. Frontiers in Marine Science [Internet]. 2020 ;6. Available from: https://www.frontiersin.org/article/10.3389/fmars.2019.00810/full
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Environmental DNA (eDNA) analysis is a rapid, non-invasive method for species detection and distribution assessment using DNA released into the surrounding environment by an organism. eDNA analysis is recognised as a powerful tool for detecting endangered or rare species in a range of ecosystems. Although the number of studies using eDNA analysis in marine systems is continually increasing, there appears to be no published studies investigating the use of eDNA analysis to detect sea turtles in natural conditions. We tested the efficacy of two primer pairs known to amplify DNA fragments of differing lengths (488 and 253 bp) from Chelonia mydas tissues for detecting C. mydas eDNA in water samples. The capture, extraction, and amplification of C. mydas eDNA from aquaria (Sea World, San Diego, CA, United States) and natural water (San Diego Bay, CA, United States) were successful using either primer set. The primer pair providing the shorter amplicon, LCMint2/H950g, demonstrated the ability to distinguish cross-reactive species by melt curve analysis and provided superior amplification metrics compared to the other primer set (LTCM2/HDCM2); although primer dimer was observed, warranting future design refinement. Results indicated that water samples taken from deeper depths might improve detection frequency, consistent with C. mydas behaviour. Overall, this pilot study suggests that with refinement of sampling methodology and further assay optimisation, eDNA analysis represents a promising tool to monitor C. mydas. Potential applications include rapid assessment across broad geographical areas to pinpoint promising locations for further evaluation with traditional methods.

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