Tools and Data

Supporting the essential - Recommendations for the development of accessible and interoperable marine biological data products

Lear D, Herman P, Van Hoey G, Schepers L, Tonné N, Lipizer M, Muller-Karger FE, Appeltans W, Kissling WD, Holdsworth N, et al. Supporting the essential - Recommendations for the development of accessible and interoperable marine biological data products. Marine Policy [Internet]. 2020 ;117:103958. Available from: https://www.sciencedirect.com/science/article/pii/S0308597X19301915
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

In this paper we outline the stakeholder-led approaches in the development of biological data products to support effective conservation, management and policy development. The requirements of a broad range of stakeholders and iterative, structured processes framed the development of tools, models and maps that support the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. By structuring the resultant data products around the emerging biological Essential Ocean Variables, and through the engagement with a broad range of end-users, the EMODnet (European Marine Observation and Data Network) Biology project has delivered a suite of demonstration data products. These products are presented in the European Atlas of Marine Life, an online resource demonstrating the value of open marine biodiversity data and help to answer fundamental and policy-driven questions related to managing the natural and anthropogenic impacts in European waters.

Use of public Earth observation data for tracking progress in sustainable management of coastal forest ecosystems in Belize, Central America

Cherrington EA, Griffin RE, Anderson ER, Sandoval BEHernand, Flores-Anderson AI, Muench RE, Markert KN, Adams EC, Limaye AS, Irwin DE. Use of public Earth observation data for tracking progress in sustainable management of coastal forest ecosystems in Belize, Central America. Remote Sensing of Environment [Internet]. 2020 ;245:111798. Available from: https://www.sciencedirect.com/science/article/pii/S0034425720301681
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Sustainable Development Goal (SDG) no. 15 addresses the protection of terrestrial ecosystems and sustainable forest management, and Target 15.2 encourages countries to sustainably manage forests, and halt deforestation by 2020. SDG indicator 15.1.1 proposes tracking forest area as an indicator for achieving that SDG. Though mangrove forests represent only about 5% of Belize's overall forest cover, the critical ecosystem services they provide are recognized in the country's Forests Act, which regulates the modification of mangrove ecosystems. Preceding the SDGs, from 2008 to 2009, the Government of Belize piloted a complete moratorium on mangrove removal, building on the Forests Act. As Earth Observation (EO) systems provide a means to track effectiveness of Belize's management of its mangrove forests, this paper examines historic and recent changes in mangrove cover across all of Belize, applying statistical adjustments to rates of change derived from Landsat satellite data. Particular attention was paid to the country's only World Heritage Site, the Belize Barrier Reef Reserve System (BBRRS), where mangrove clearing was prohibited since the site's designation in December 1996. The data indicate that within the BBRRS, approximately 89 ha of mangroves were lost from 1996 to 2017, compared to the estimated loss of 2703 ha outside the BBRRS during the same period, and nationwide loss of almost 4100 ha from 1980 to 2017. Thus, compared to the mangroves outside of the BBRRS, the annual rate of mangrove loss within the BBRRS over the period 1996–2017 was merely 4.24 ha per year, versus 129.11 ha per year outside the BBRRS. Furthermore, almost 75% of the 1996–2017 mangrove loss outside the BBRRS were concentrated in three particular geographic zones associated with tourism infrastructure. It was also estimated that Belize's overall mangrove cover declined 5.4% over 36 years, from 76,250 ha in 1980 to 72,169 ha in 2017. In terms of its implications, in addition to contributing to SDG 15, this work also addresses SDG Target 14.2 regarding sustainable management of marine and coastal ecosystems. This study serves as a use case of how EO data can contribute to monitoring changes in baseline data and thus tracking of progress toward SDG Targets.

Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish

Takahashi S, Sakata MK, Minamoto T, Masuda R. Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish Kalendar R. PLOS ONE [Internet]. 2020 ;15(4):e0231718. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0231718
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Water sampling and filtration of environmental DNA (eDNA) analysis have been performed by several different methods, and each method may yield a different species composition or eDNA concentration. Here, we investigated the eDNA of seawater samples directly collected by SCUBA to compare two widely used filtration methods: open filtration with a glass filter (GF/F) and enclosed filtration (Sterivex). We referred to biomass based on visual observation data collected simultaneously to clarify the difference between organism groups. Water samples were collected at two points in the Sea of Japan in May, September and December 2018. The respective samples were filtered through GF/F and Sterivex for eDNA extraction. We quantified the eDNA concentration of five fish and two cnidarian species by quantitative polymerase chain reaction (qPCR) using species-specific primers/probe sets. A strong correlation of eDNA concentration was obtained between GF/F and Sterivex; the intercepts and slopes of the linear regression lines were slightly different in fish and jellyfish. The amount of eDNA detected using the GF/F filtration method was higher than that detected using Sterivex when the eDNA concentration was high; the opposite trend was observed when the eDNA concentration was relatively low. The concentration of eDNA correlated with visually estimated biomass; eDNA concentration per biomass in jellyfish was approximately 700 times greater than that in fish. We conclude that GF/F provides an advantage in collecting a large amount of eDNA, whereas Sterivex offers superior eDNA sensitivity. Both filtration methods are effective in estimating the spatiotemporal biomass size of target marine species.

The MacKinnon Lists Technique: An efficient new method for rapidly assessing biodiversity and species abundance ranks in the marine environment

Bach LLuise, Bailey DM, Harvey ES, MacLeod R. The MacKinnon Lists Technique: An efficient new method for rapidly assessing biodiversity and species abundance ranks in the marine environment Hewitt J. PLOS ONE [Internet]. 2020 ;15(4):e0231820. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0231820
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Widespread and ever-increasing anthropogenic impacts in the marine environment are driving a need to develop more efficient survey methods for monitoring changes in marine biodiversity. There is a particular urgent need for survey methods that could more rapidly and effectively detect change in species richness, abundance and community composition. Here, test the suitability of the Mackinnon Lists Technique for use in the marine environment by testing its effectiveness for rapid assessment of fish communities. The MacKinnon Lists Technique is a time-efficient and cost-effective sampling method developed for studying avian tropical biodiversity, in which several list samples of species can be collected from a single survey. Using the well-established MaxN approach on data from deployments of a Baited Remote Underwater Video Systems for comparison, we tested the suitability of the MacKinnon Lists Technique for use in marine environments by analysing tropical reef fish communities. Using both methods for each data set, differences in community composition between depths and levels of protection were assessed. Both methods were comparable for diversity and evenness indices with similar ranks for species. Multivariate analysis showed that the MacKinnon Lists Technique and MaxN detected similar differences in community composition at different depths and protection status. However, the MacKinnon Lists Technique detected significant differences between factors when fewer videos (representing reduced survey effort) were used. We conclude that the MacKinnon Lists Technique is at least as effective as the widely used MaxN method for detecting differences between communities in the marine environment and suggest can do so with lower survey effort. The MacKinnon Lists Technique has the potential to be widely used as an effective new tool for rapid conservation monitoring in marine ecosystems.

Finding Plastic Patches in Coastal Waters using Optical Satellite Data

Biermann L, Clewley D, Martinez-Vicente V, Topouzelis K. Finding Plastic Patches in Coastal Waters using Optical Satellite Data. Scientific Reports [Internet]. 2020 ;10(1). Available from: https://www.nature.com/articles/s41598-020-62298-z
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Satellites collecting optical data offer a unique perspective from which to observe the problem of plastic litter in the marine environment, but few studies have successfully demonstrated their use for this purpose. For the first time, we show that patches of floating macroplastics are detectable in optical data acquired by the European Space Agency (ESA) Sentinel-2 satellites and, furthermore, are distinguishable from naturally occurring materials such as seaweed. We present case studies from four countries where suspected macroplastics were detected in Sentinel-2 Earth Observation data. Patches of materials on the ocean surface were highlighted using a novel Floating Debris Index (FDI) developed for the Sentinel-2 Multi-Spectral Instrument (MSI). In all cases, floating aggregations were detectable on sub-pixel scales, and appeared to be composed of a mix of seaweed, sea foam, and macroplastics. Building first steps toward a future monitoring system, we leveraged spectral shape to identify macroplastics, and a Naïve Bayes algorithm to classify mixed materials. Suspected plastics were successfully classified as plastics with an accuracy of 86%.

High-Resolution Reef Bathymetry and Coral Habitat Complexity from Airborne Imaging Spectroscopy

Asner GP, Vaughn NR, Balzotti C, Brodrick PG, Heckler J. High-Resolution Reef Bathymetry and Coral Habitat Complexity from Airborne Imaging Spectroscopy. Remote Sensing [Internet]. 2020 ;12(2):310. Available from: https://www.mdpi.com/2072-4292/12/2/310
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Coral reef ecosystems are rapidly changing, and a persistent problem with monitoring changes in reef habitat complexity rests in the spatial resolution and repeatability of measurement techniques. We developed a new approach for high spatial resolution (<1 m) mapping of nearshore bathymetry and three-dimensional habitat complexity (rugosity) using airborne high-fidelity imaging spectroscopy. Using this new method, we mapped coral reef habitat throughout two bays to a maximum depth of 25 m and compared the results to the laser-based SHOALS bathymetry standard. We also compared the results derived from imaging spectroscopy to a more conventional 4-band multispectral dataset. The spectroscopic approach yielded consistent results on repeat flights, despite variability in viewing and solar geometries and sea state conditions. We found that the spectroscopy-based results were comparable to those derived from SHOALS, and they were a major improvement over the multispectral approach. Yet, spectroscopy provided much finer spatial information than that which is available with SHOALS, which is valuable for analyzing changes in benthic composition at the scale of individual coral colonies. Monitoring temporal changes in reef 3D complexity at high spatial resolution will provide an improved means to assess the impacts of climate change and coastal processes that affect reef complexity

Considerations for transferring an operational dynamic ocean management tool between ocean color products

Welch H, Brodie S, Jacox MG, Robinson D, Wilson C, Bograd SJ, Oliver MJ, Hazen EL. Considerations for transferring an operational dynamic ocean management tool between ocean color products. Remote Sensing of Environment [Internet]. 2020 ;242:111753. Available from: https://www.sciencedirect.com/science/article/pii/S0034425720301231
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

Satellite remote sensing data are critical for assessing ecosystem state and evaluating long-term trends and shifts in ecosystem components. Many operational tools rely on continuous streams of remote sensing data, and when a satellite sensor reaches the end of its designed lifespan, these tools must be transferred to a more reliable data stream. Transferring between data streams can produce discontinuities in tool products, and it is important to quantify these downstream impacts and understand the mechanisms that cause discontinuity. To illustrate the complexities of tool transfer, we compare five products for ocean chlorophyll-a, which is a proxy for phytoplankton biomass and an important input for tools that monitor marine biophysical processes. The five chlorophyll-a products included three blended products and two single sensor products from MODIS and VIIRS. We explored the downstream impacts of tool transfer using EcoCast: an operational dynamic ocean management tool that combines real-time predictions from target and bycatch species distribution models to produce integrated surfaces of fishing suitability. EcoCast was operationalized using MODIS chlorophyll-a, and we quantify the impacts of transferring to the intended replacement of MODIS, VIIRS, and test if impacts can be minimized by using a blended chlorophyll-a product instead. Differences between chlorophyll products did not linearly propagate through to the species model predictions and the integrated fishing suitability surfaces. Instead, differences in species model predictions were determined by the shape of chlorophyll-a response curves in the species models relative to chlorophyll-a differences between sensors. However, differences in the integrated fishing suitability surfaces were reduced by canceling of differences from individual species model predictions. Differences in the integrated fishing suitability surfaces were not reduced by transferring to a blended product, highlighting the complexity of transferring operational tools between different remote sensing data products. These results contribute to our general understanding of the mechanisms by which transferring between data streams impacts downstream products. To aid decision-making regarding tool transfer, we developed an interactive web application that allows end-users to explore differences in chlorophyll products within times period and regions of interest.

A Data-Informed Approach for Identifying Move-on Encounter Thresholds for Vulnerable Marine Ecosystem Indicator Taxa

Geange SW, Rowden AA, Nicol S, Bock T, Cryer M. A Data-Informed Approach for Identifying Move-on Encounter Thresholds for Vulnerable Marine Ecosystem Indicator Taxa. Frontiers in Marine Science [Internet]. 2020 ;7. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2020.00155/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1286267_45_Marine_20200331_arts_A
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

The United Nations General Assembly has called for the adoption of conservation management measures to protect vulnerable marine ecosystems (VMEs) from significant adverse impacts outside of areas of national jurisdiction. In response, many regional fisheries management organizations (RFMOs) have implemented move-on rules triggered by encounter threshold levels for the biomass of VME indicator taxa retained as bycatch. However, due to uncertainty of the relationships between catch, catch efficiency and the in situ biomass of VME indicator taxa, move-on rules alone may not be enough to prevent significant adverse impacts on VMEs. Although spatial management measures present one possible solution to these concerns, a lack of empirical data on the distribution of VMEs within the high seas means spatial management is often informed by model predictions of the spatial distribution of VME indicator taxa. Given the uncertainty associated with predicted distributions, move-on rules can provide immediate responses when spatial management measures may not be providing the expected conservation benefits. Using bycatch data from 9,771 New Zealand bottom trawls within the South Pacific RFMO Convention Area, we illustrate a data-informed approach for selecting high move-on encounter thresholds that may suggest the predicted distributions of VME taxa used to underpin spatial management are highly inaccurate. The reasoning that high thresholds act as a safeguard against uncertainty in the performance of spatial management measures requires untested assumptions regarding the level of permissible bycatch before further management action is required, with the acceptance of those assumptions a management decision balancing the sensitivity of the move-on rule with uncertainty regarding the effectives of the spatial management measures. Additional work is required to support these management decisions, including the determination of taxa-specific catchability estimates, and the seafloor density/biomass of VME indicator taxa that represents a VME. Obtaining this information will allow for the identification of encounter thresholds that are more ecologically meaningful. In the interim, the choice of thresholds should be re-evaluated as more experience with their application is gathered.

Modelling regional futures at decadal scale: application to the Kimberley region

Boschetti F, Lozano-Montes H, Stelfox B. Modelling regional futures at decadal scale: application to the Kimberley region. Scientific Reports [Internet]. 2020 ;10(1). Available from: https://www.nature.com/articles/s41598-019-56646-x
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

We address the question of how to provide meaningful scientific information to support environmental decision making at the regional scale and at the temporal scale of several decades in a network of marine parks in the Kimberley region of Western Australia. Where environmental sustainability is affected by slow-dynamics climate change processes and one-off investments in large infrastructure which can affect a region for decades to come, both strategic and reactive planning is necessary and prediction becomes as urgent as standard adaptive management. At the interface between future studies, socio-economic modelling and environmental modelling, we define 18 scenarios of economic development and climate change impacts and five management strategies. We explore these potential futures using coupled models of terrestrial and marine ecosystem dynamics. We obtain a projection of the Kimberley marine system to the year 2050, conditional on the chosen scenarios and management strategies. Our results suggest that climate change, not economic development, is the largest factor affecting the future of marine ecosystems in the Kimberley region, with site-attached species such as reef fish at greatest risk. These same species also benefit most from more stringent management strategies, especially expansion of sanctuary zones and Marine Protected Areas.

GliderTools: A Python Toolbox for Processing Underwater Glider Data

Gregor L, Ryan-Keogh TJ, Nicholson S-A, Plessis Mdu, Giddy I, Swart S. GliderTools: A Python Toolbox for Processing Underwater Glider Data. Frontiers in Marine Science [Internet]. 2019 ;6. Available from: https://www.frontiersin.org/articles/10.3389/fmars.2019.00738/full
Freely available?: 
Yes
Summary available?: 
No
Type: Journal Article

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.

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