Evaluating biodiversity for coral reef reformation and monitoring on complex 3D structures using environmental DNA (eDNA) metabarcoding

Levy, Natalie; Simon‐Blecher, Noa; Ben-Ezra, Shachaf; Yuval, Matan; Doniger, Tirza; Leray, Matthieu; Lampert-Karako, Sarit; Tarazi, Ezri; Levy, Oren

doi:10.1016/j.scitotenv.2022.159051

Cited by 15 publications

(23 citation statements)

References 49 publications

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“…We expect that in the near future 3D instance-segmentation (a deep-learning task that segments every object in a model) together with geometric deep-learning will enable studies that include taxonomic information together with geometry and reef structure. Altogether, computer-vision with advances in scalable conservation technologies such as sound recordings (Williams et al 2022) and metagenomics (Levy et al 2023) will enable a new generation of multi-modal studies in coral reef ecology.…”

Section: Discussionmentioning

confidence: 99%

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Assessment of Storm Impact on Coral Reef Structural Complexity

Yuval

Pearl

Tchernov

et al. 2022

Preprint

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Extreme weather events are increasing in frequency and magnitude. Consequently, it is important to understand their effects and remediation. We studied the impact of a powerful storm on coral reef structural complexity using novel computational tools and detailed 3D reconstructions captured at seven sites in three time-points over three years. We employed six geometrical metrics, two of which are new algorithms for calculating fractal-dimension of reefs in full 3D. Three metrics showed a significant difference between time-points, i.e., decline and subsequent recovery in structural complexity. We also explored the changes in fractal dimension per size category and found a similar trend. A multivariate analysis helped us to reveal which sites were affected the most and their relative recovery. The full picture suggests that the reef has not gone through a phase-shift and is returning to its prior state w.r.t. structural complexity.

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Section: Discussionmentioning

confidence: 99%

“…Altogether, computer-vision with advances in scalable conservation technologies such as sound recordings(Williams et al 2022) and metagenomics(Levy et al 2023) will enable a new generation of multi-modal studies in coral reef ecology. • Author Contributions: All authors: Conceptualization, Writing-Review and Editing.…”

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confidence: 99%

Assessment of Storm Impact on Coral Reef Structural Complexity

Yuval

Pearl

Tchernov

et al. 2022

Preprint

Self Cite

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“…Furthermore, eDNA metabarcoding has been demonstrated to be an effective assessment tool for restoration efforts. Levy et al (2023) showcased the significance of eDNA metabarcoding as a crucial tool for assessing biodiversity linked to artificial reefs. This study demonstrated the effectiveness of eDNA metabarcoding in assessing the metazoan diversity associated with artificial reefs in the Gulf of Eilat/Aqaba located in the Red Sea by targeting the COI gene.…”

Section: Application In Ecologymentioning

confidence: 99%

Advancing ecological assessment of the Arabian Gulf through eDNA metabarcoding: opportunities, prospects, and challenges

Joydas,

Manokaran,

Gopi

et al. 2024

Front. Mar. Sci.

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The Arabian Gulf (hereafter ‘the Gulf’) is renowned for its unique ecological characteristics and distinct marine life. It offers a diverse range of ecosystems that have adapted to the impacts posed by natural stress and human activities. Regular biomonitoring and diversity assessments are necessary to document the health of the Gulf ecosystem and to implement appropriate measures for effective conservation and management. Recently, environmental DNA (eDNA), a total pool of DNA isolated from environmental samples, has emerged as a highly effective tool for ecological studies. This review explores the opportunities, prospects, and challenges associated with employing eDNA metabarcoding in the ecological assessment and biomonitoring of the Gulf. It provides an overview of the status of the Gulf ecosystem and discusses the potential applications of eDNA metabarcoding in assessing biodiversity, monitoring invasive species, and evaluating ecosystem health. Additionally, the investigation addresses the challenges inherent in implementing this technique, considering environmental complexities, methodological intricacies, and data interpretation. Overall, this review emphasizes the immense potential of eDNA metabarcoding in advancing ecological assessment in the Gulf and calls for further research and collaboration to harness its benefits in this unique marine ecosystem.

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“…Economic analysis determines the viability and benefit of projects, and can also assess the value placed on healthy ecosystems by local residents and their ‘willingness to pay’ for proposed restoration activities (e.g., mangrove forest restoration in India and Bangladesh [ 9 ]). Genetic analysis is of growing importance to understand the remaining genetic diversity of populations, to determine the optimal source populations for species introductions, and for monitoring ongoing projects - both of the target species themselves, and also of general community biodiversity through environmental DNA analyses (e.g., assessment of biodiversity associated with artificial coral reefs [ 10 ]). Incorporation of engineering principles is also critical for many restoration projects, for example, the inclusion of breakwalls to alleviate boat wake disturbance to facilitate shellfish reef recovery [ 11 ].…”

Section: Main Textmentioning

confidence: 99%

Ecosystem restoration, regeneration and rewilding

Shackelford,

McDougall

2023

BMC Ecol Evo

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Anthropomorphic activities have caused major damage to ecosystems worldwide. Although documenting this damage is important, implementing measures to halt and reverse ecosystem decline is critical and is now being prioritised globally. To support global goals to protect and restore nature, BMC Ecology and Evolution has launched a new article collection to encourage contributions from the multifaceted ecosystem restoration community.

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Evaluating biodiversity for coral reef reformation and monitoring on complex 3D structures using environmental DNA (eDNA) metabarcoding

Cited by 15 publications

References 49 publications

Assessment of Storm Impact on Coral Reef Structural Complexity

Assessment of Storm Impact on Coral Reef Structural Complexity

Advancing ecological assessment of the Arabian Gulf through eDNA metabarcoding: opportunities, prospects, and challenges

Ecosystem restoration, regeneration and rewilding

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