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Carneiro IM, Sá JA, Chiroque-Solano PM, Cardoso FC, Castro GM, Salomon PS, Bastos AC, Moura RL. Precision and accuracy of common coral reef sampling protocols revisited with photogrammetry. MARINE ENVIRONMENTAL RESEARCH 2024; 194:106304. [PMID: 38142582 DOI: 10.1016/j.marenvres.2023.106304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/26/2023]
Abstract
The rapid decline of coral reefs calls for cost-effective benthic cover data to improve reef health forecasts, policy building, management responses and evaluation. Reef monitoring has been largely based on divers' observations along transects, and secondarily on quadrat-based protocols, video and photographic records. However, the accuracy and precision of the most common sampling approaches are not yet fully understood. Here, we compared benthic cover estimates from three common sampling protocols: Reef Check (RC), Atlantic and Gulf Rapid Reef Assessment (AGRRA) and photoquadrats (PQ). The reef cover of two contrasting sites was reconstructed with ∼450 m2 orthomosaics built with high resolution Structure-from-Motion (SfM) photogrammetry, which were used as references for comparisons among protocols. In addition, we explored sample size requirements for each protocol and provided cost-effectiveness comparisons. Our results evidenced between-reef differences in the accuracy and precision of estimates with the different protocols. The three protocols performed similarly in the reef with low macroalgal cover (<0.5%), but PQ were more accurate and precise in the reef with relatively high (∼20%) macroalgal cover. The sample size for estimating coral cover with a 20% error margin and a 0.05 significance level was lower for PQ, followed by AGRRA and RC. Considering performance, cost surrogates and equipment needs, cost-effectiveness was higher for PQ. We also discuss costs, limitations and advantages/disadvantages of SfM photogrammetry as a sampling approach for coral reef monitoring.
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Affiliation(s)
- Ivan M Carneiro
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - João A Sá
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Pamela M Chiroque-Solano
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernando C Cardoso
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Guilherme M Castro
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Paulo S Salomon
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Alex C Bastos
- Departamento de Oceanografia, Universidade Federal do Espirito Santo, Vitória, ES, Brazil
| | - Rodrigo L Moura
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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2
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Martínez-Quintana Á, Lasker HR, Wilson AM. Three-dimensional species distribution modelling reveals the realized spatial niche for coral recruitment on contemporary Caribbean reefs. Ecol Lett 2023; 26:1497-1509. [PMID: 37380335 DOI: 10.1111/ele.14281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/06/2023] [Accepted: 05/05/2023] [Indexed: 06/30/2023]
Abstract
The three-dimensional structure of habitats is a critical component of species' niches driving coexistence in species-rich ecosystems. However, its influence on structuring and partitioning recruitment niches has not been widely addressed. We developed a new method to combine species distribution modelling and structure from motion, and characterized three-dimensional recruitment niches of two ecosystem engineers on Caribbean coral reefs, scleractinian corals and gorgonians. Fine-scale roughness was the most important predictor of suitable habitat for both taxa, and their niches largely overlapped, primarily due to scleractinians' broader niche breadth. Crevices and holes at mm scales on calcareous rock with low coral cover were more suitable for octocorals than for scleractinian recruits, suggesting that the decline in scleractinian corals is facilitating the recruitment of octocorals on contemporary Caribbean reefs. However, the relative abundances of the taxa were independent of the amount of suitable habitat on the reef, emphasizing that niche processes alone do not predict recruitment rates.
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Affiliation(s)
| | - Howard R Lasker
- Department of Environment and Sustainability, University at Buffalo, Buffalo, New York, USA
- Department of Geology, University at Buffalo, Buffalo, New York, USA
| | - Adam M Wilson
- Department of Geography, University at Buffalo, Buffalo, New York, USA
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3
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Pulido Mantas T, Roveta C, Calcinai B, Coppari M, Di Camillo CG, Marchesi V, Marrocco T, Puce S, Cerrano C. Photogrammetry as a promising tool to unveil marine caves' benthic assemblages. Sci Rep 2023; 13:7587. [PMID: 37165208 PMCID: PMC10172382 DOI: 10.1038/s41598-023-34706-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Traditionally, monitoring approaches to survey marine caves have been constrained by equipment limitations and strict safety protocols. Nowadays, the rise of new approaches opens new possibilities to describe these peculiar ecosystems. The current study aimed to explore the potential of Structure from Motion (SfM) photogrammetry to assess the abundance and spatial distribution of the sessile benthic assemblages inside a semi-submerged marine cave. Additionally, since impacts of recent date mussel Lithophaga lithophaga illegal fishing were recorded, a special emphasis was paid to its distribution and densities. The results of SfM were compared with a more "traditional approach", by simulating photo-quadrats deployments over the produced orthomosaics. A total of 22 sessile taxa were identified, with Porifera representing the dominant taxa within the cave, and L. lithophaga presenting a density of 88.3 holes/m2. SfM and photo-quadrats obtained comparable results regarding species richness, percentage cover of identified taxa and most of the seascape metrics, while, in terms of taxa density estimations, photo-quadrats highly overestimated their values. SfM resulted in a suitable non-invasive technique to record marine cave assemblages. Seascape indexes proved to be a comprehensive way to describe the spatial pattern of distribution of benthic organisms, establishing a useful baseline to assess future community shifts.
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Affiliation(s)
- Torcuato Pulido Mantas
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Camilla Roveta
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Barbara Calcinai
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Martina Coppari
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Cristina Gioia Di Camillo
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Veronica Marchesi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Teo Marrocco
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Stefania Puce
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Carlo Cerrano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Fano Marine Center, Viale Adriatico 1/N, 61032, Fano, Italy
- Stazione Zoologica di Napoli Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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4
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Apprill A, Girdhar Y, Mooney TA, Hansel CM, Long MH, Liu Y, Zhang WG, Kapit J, Hughen K, Coogan J, Greene A. Toward a New Era of Coral Reef Monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5117-5124. [PMID: 36930700 PMCID: PMC10077584 DOI: 10.1021/acs.est.2c05369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 06/18/2023]
Abstract
Coral reefs host some of the highest concentrations of biodiversity and economic value in the oceans, yet these ecosystems are under threat due to climate change and other human impacts. Reef monitoring is routinely used to help prioritize reefs for conservation and evaluate the success of intervention efforts. Reef status and health are most frequently characterized using diver-based surveys, but the inherent limitations of these methods mean there is a growing need for advanced, standardized, and automated reef techniques that capture the complex nature of the ecosystem. Here we draw on experiences from our own interdisciplinary research programs to describe advances in in situ diver-based and autonomous reef monitoring. We present our vision for integrating interdisciplinary measurements for select "case-study" reefs worldwide and for learning patterns within the biological, physical, and chemical reef components and their interactions. Ultimately, these efforts could support the development of a scalable and standardized suite of sensors that capture and relay key data to assist in categorizing reef health. This framework has the potential to provide stakeholders with the information necessary to assess reef health during an unprecedented time of reef change as well as restoration and intervention activities.
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Affiliation(s)
- Amy Apprill
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Yogesh Girdhar
- Department
of Applied Ocean Sciences and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - T. Aran Mooney
- Biology
Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Colleen M. Hansel
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Matthew H. Long
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Yaqin Liu
- Marine
Policy Center, Woods Hole Oceanographic
Institution, Woods Hole, Massachusetts 02543, United States
| | - W. Gordon Zhang
- Department
of Applied Ocean Sciences and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Jason Kapit
- Department
of Applied Ocean Sciences and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Konrad Hughen
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Jeff Coogan
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Austin Greene
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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Gámez S, Harris NC. Conceptualizing the 3D niche and vertical space use. Trends Ecol Evol 2022; 37:953-962. [PMID: 35872027 DOI: 10.1016/j.tree.2022.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/24/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022]
Abstract
Spatial partitioning in ecological communities has predominantly been described in two dimensions, yet habitat is complex and 3D. Complex space use mediates community structure and interaction strength by expanding spatial, temporal, and dietary dimensions. Vertical stratification of resources provides opportunities for novel specializations, creating a 3D niche. Competition and predation are mediated by 3D space use, as individuals use the vertical axis to access prey, flee predators, or avoid competitors. The 3D niche is important for long-term conservation strategies as species must navigate tradeoffs in habitat use between strata-specific threats and suboptimal habitat patches. Ultimately, elucidating the 3D niche has implications for protected area management and corridor design that directly influence species persistence and ecosystem function in a rapidly changing world.
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Affiliation(s)
- Siria Gámez
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University 195 Prospect Street, New Haven, CT 06511, USA.
| | - Nyeema C Harris
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University 195 Prospect Street, New Haven, CT 06511, USA
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Ventura D, Mancini G, Casoli E, Pace DS, Lasinio GJ, Belluscio A, Ardizzone G. Seagrass restoration monitoring and shallow-water benthic habitat mapping through a photogrammetry-based protocol. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 304:114262. [PMID: 34923414 DOI: 10.1016/j.jenvman.2021.114262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Seagrasses rank among the most productive yet highly threatened ecosystems on Earth. Loss of seagrass habitat because of anthropogenic disturbances and evidence of their limited resilience have provided the impetus for investigating and monitoring habitat restoration through transplantation programmes. Although Structure from Motion (SfM) photogrammetry is becoming a more and more relevant technique for mapping underwater environments, no standardised methods currently exist to provide 3-dimensional high spatial resolution and accuracy cartographic products for monitoring seagrass transplantation areas. By synthesizing various remote sensing applications, we provide an underwater SfM-based protocol for monitoring large seagrass restoration areas. The data obtained from consumer-grade red-green-blue (RGB) imagery allowed the fine characterization of the seabed by using 3D dense point clouds and raster layers, including orthophoto mosaics and Digital Surface Models (DSM). The integration of high spatial resolution underwater imagery with object-based image classification (OBIA) technique provided a new tool to count transplanted Posidonia oceanica fragments and estimate the bottom coverage expressed as a percentage of seabed covered by such fragments. Finally, the resulting digital maps were integrated into Geographic Information Systems (GIS) to run topographic change detection analysis and evaluate the mean height of transplanted fragments and detect fine-scale changes in seabed vector ruggedness measure (VRM). Our study provides a guide for creating large-scale, replicable and ready-to-use products for a broad range of applications aimed at standardizing monitoring protocols in future seagrass restoration actions.
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Affiliation(s)
- Daniele Ventura
- Department of Environmental Biology and Ecology, University of Rome 'La Sapienza', V. le dell'Università 32, 00185, Rome, Italy.
| | - Gianluca Mancini
- Department of Environmental Biology and Ecology, University of Rome 'La Sapienza', V. le dell'Università 32, 00185, Rome, Italy
| | - Edoardo Casoli
- Department of Environmental Biology and Ecology, University of Rome 'La Sapienza', V. le dell'Università 32, 00185, Rome, Italy
| | - Daniela Silvia Pace
- Department of Environmental Biology and Ecology, University of Rome 'La Sapienza', V. le dell'Università 32, 00185, Rome, Italy
| | - Giovanna Jona Lasinio
- Department of Statistics Sciences, University of Rome 'La Sapienza', V. le dell'Università 32, 00185, Rome, Italy
| | - Andrea Belluscio
- Department of Environmental Biology and Ecology, University of Rome 'La Sapienza', V. le dell'Università 32, 00185, Rome, Italy
| | - Giandomenico Ardizzone
- Department of Environmental Biology and Ecology, University of Rome 'La Sapienza', V. le dell'Università 32, 00185, Rome, Italy
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7
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Assessing Geomorphic Change in Restored Coastal Dune Ecosystems Using a Multi-Platform Aerial Approach. REMOTE SENSING 2021. [DOI: 10.3390/rs13030354] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Uncrewed aerial systems (UAS) provide an effective method to examine geomorphic and vegetation change in restored coastal dune ecosystems. Coupling structure-from-motion (SfM) photogrammetry with RGB orthomosaic imagery allows researchers to characterize spatial-temporal geomorphic responses associated with differences in vegetation cover. Such approaches provide quantitative data on landscape morphodynamics and sediment erosion and deposition responses that allow scientists and land managers to assess the efficacy of dynamic restoration efforts and, in turn, make informed decisions for future restoration projects. Two different restored coastal foredune sites in Humboldt County, California were monitored between 2016–20 with UAS (quadcopter and fixed-wing), kite aerial photogrammetry (KAP), and terrestrial laser scanning (TLS) platforms. We compared our KAP- and UAS-SfM elevation models to concurrently collected TLS bare earth models for five of our fifteen collections. The goal of this study was to inform on the potential of a multi-platform aerial approach for calculating geomorphic differences (i.e., topographic differencing), in order to quantify sediment erosion and deposition, and vegetation change over a coastal dune ecosystem. While UAS-SfM datasets were relatively well fit to their TLS counterparts (2.1–12.2% area of difference), the KAP-SfM surfaces exhibited higher deviations (23.6–27.6%) and suffered from systematic collection inconsistencies related to methods and susceptibility to external factors (e.g., the influence of wind speed and direction on variable altitude, image overlap, and coverage extent). Finally, we provide commentary on the logistical considerations regarding KAP and UAS data collection and the construction of uncertainty budgets for geomorphic change detection (GCD), while providing suggestions for standardizing methods for uncertainty budgeting. While we propose an approach that incorporates multiple levels of collection- and processing-based uncertainty, we also recognize that uncertainty is often project-specific and outline the development of potential standards for incorporating uncertainty budgets in SfM projects.
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