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Paxton AB, McGonigle C, Damour M, Holly G, Caporaso A, Campbell PB, Meyer-Kaiser KS, Hamdan LJ, Mires CH, Taylor JC. Shipwreck ecology: Understanding the function and processes from microbes to megafauna. Bioscience 2024; 74:12-24. [PMID: 38313562 PMCID: PMC10831220 DOI: 10.1093/biosci/biad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 02/06/2024] Open
Abstract
An estimated three million shipwrecks exist worldwide and are recognized as cultural resources and foci of archaeological investigations. Shipwrecks also support ecological resources by providing underwater habitats that can be colonized by diverse organisms ranging from microbes to megafauna. In the present article, we review the emerging ecological subdiscipline of shipwreck ecology, which aims to understand ecological functions and processes that occur on shipwrecks. We synthesize how shipwrecks create habitat for biota across multiple trophic levels and then describe how fundamental ecological functions and processes, including succession, zonation, connectivity, energy flow, disturbance, and habitat degradation, manifest on shipwrecks. We highlight future directions in shipwreck ecology that are ripe for exploration, placing a particular emphasis on how shipwrecks may serve as experimental networks to address long-standing ecological questions.
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Affiliation(s)
- Avery B Paxton
- National Centers for Coastal Ocean Science, National Ocean Service, National Oceanic and Atmospheric Administration, Beaufort, North Carolina, United States
| | - Christopher McGonigle
- School of Geography and Environmental Science, Ulster University, Coleraine, Northern Ireland
| | - Melanie Damour
- Bureau of Ocean Energy Management, New Orleans, Louisiana, United States
| | - Georgia Holly
- Edinburgh Marine Archaeology, School of History, Classics, and Archaeology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Alicia Caporaso
- Bureau of Ocean Energy Management, New Orleans, Louisiana, United States
| | - Peter B Campbell
- Cranfield Forensic Institute, Cranfield University, Defence Academy of the United Kingdom, Shrivenham, England, United Kingdom
| | | | - Leila J Hamdan
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, United States
| | - Calvin H Mires
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States
| | - J Christopher Taylor
- National Centers for Coastal Ocean Science, National Ocean Service, National Oceanic and Atmospheric Administration, Beaufort, North Carolina, United States
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Rovellini A, Mortimer CL, Dunn MR, Fulton EA, Jompa J, Haris A, Bell JJ. Reduced small-scale structural complexity on sponge-dominated areas of Indo-Pacific coral reefs. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106254. [PMID: 37979404 DOI: 10.1016/j.marenvres.2023.106254] [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: 08/26/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/20/2023]
Abstract
Corals provide a complex 3D framework that offers habitat to diverse coral reef fauna. However, future reefs are likely to experience reduced coral abundance. Sponges have been proposed as one potential winner on future coral reefs, but little is known of how they contribute to reef 3D structure. Given the ecological importance of structural complexity, it is critical to understand how changes in the abundance of structure-building organisms will affect the three-dimensional properties of coral reefs. To investigate the potentially important functional role of coral reef sponges as providers of structural complexity, we compared the structural complexity of coral- and sponge-dominated areas of an Indonesian coral reef, using 3D photogrammetry at a 4 m2 spatial scale. Structural complexity of 31 4 m2 quadrats was expressed as rugosity indicating reef contour complexity (R), vector dispersion indicating heterogeneity of angles between reef surfaces (1/k), and fractal dimension indicating geometrical complexity at five different spatial scales between 1 and 120 cm (D1-5). Quadrats were identified as high- or low-complexity using hierarchical clustering based on the complexity metrics. At high structural complexity, coral- and sponge-dominated quadrats were similar in terms of R and 1/k. However, smallest-scale refuge spaces (1-5 cm) were more abundant in coral-dominated quadrats, whereas larger scale refuge spaces (30-60 cm) were more abundant in sponge-dominated quadrats. Branching and massive corals contributed the most to structural complexity in coral-dominated quadrats, and barrel sponges in sponge-dominated quadrats. We show that smaller-scale refugia (1-5 cm) are reduced on sponge-dominated reefs at the spatial scale considered here (4 m2), with potential negative implications for smaller reef fauna.
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Affiliation(s)
- Alberto Rovellini
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
| | - Charlotte L Mortimer
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
| | - Matthew R Dunn
- National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand.
| | | | - Jamaluddin Jompa
- Universitas Hasanuddin, Department of Marine Science, Makassar, Indonesia.
| | - Abdul Haris
- Universitas Hasanuddin, Department of Marine Science, Makassar, Indonesia.
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
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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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Moser S, Sugano Y, Wengi A, Fisi V, Lindtoft Rosenbaek L, Mariniello M, Loffing‐Cueni D, McCormick JA, Fenton RA, Loffing J. A five amino acids deletion in NKCC2 of C57BL/6 mice affects analysis of NKCC2 phosphorylation but does not impact kidney function. Acta Physiol (Oxf) 2021; 233:e13705. [PMID: 34114742 PMCID: PMC8384713 DOI: 10.1111/apha.13705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 12/24/2022]
Abstract
Aim The phosphorylation level of the furosemide‐sensitive Na+‐K+‐2Cl− cotransporter (NKCC2) in the thick ascending limb (TAL) is used as a surrogate marker for NKCC2 activation and TAL function. However, in mice, analyses of NKCC2 phosphorylation with antibodies against phosphorylated threonines 96 and 101 (anti‐pT96/pT101) give inconsistent results. We aimed (a) to elucidate these inconsistencies and (b) to develop a phosphoform‐specific antibody that ensures reliable detection of NKCC2 phosphorylation in mice. Methods Genetic information, molecular biology, biochemical techniques and mouse phenotyping was used to study NKCC2 and kidney function in two commonly used mouse strains (ie 129Sv and in C57BL/6 mice). Moreover, a new phosphoform‐specific mouse NKCC2 antibody was developed and characterized. Results Amino acids sequence alignment revealed that C57BL/6 mice have a strain‐specific five amino acids deletion (ΔF97‐T101) in NKCC2 that diminishes the detection of NKCC2 phosphorylation with previously developed pT96/pT101 NKCC2 antibodies. Instead, the antibodies cross‐react with the phosphorylated thiazide‐sensitive NaCl cotransporter (NCC), which can obscure interpretation of results. Interestingly, the deletion in NKCC2 does not impact on kidney function and/or expression of renal ion transport proteins as indicated by the analysis of the F2 generation of crossbred 129Sv and C57BL/6 mice. A newly developed pT96 NKCC2 antibody detects pNKCC2 in both mouse strains and shows no cross‐reactivity with phosphorylated NCC. Conclusion Our work reveals a hitherto unappreciated, but essential, strain difference in the amino acids sequence of mouse NKCC2 that needs to be considered when analysing NKCC2 phosphorylation in mice. The new pNKCC2 antibody circumvents this technical caveat.
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Affiliation(s)
- Sandra Moser
- Institute of Anatomy University of Zurich Zurich Switzerland
| | - Yuya Sugano
- Institute of Anatomy University of Zurich Zurich Switzerland
| | - Agnieszka Wengi
- Institute of Anatomy University of Zurich Zurich Switzerland
| | - Viktoria Fisi
- Institute of Anatomy University of Zurich Zurich Switzerland
| | | | | | | | - James A. McCormick
- Division of Nephrology and Hypertension Oregon Health & Science University Portland OR USA
| | | | - Johannes Loffing
- Institute of Anatomy University of Zurich Zurich Switzerland
- Swiss National Centre for Competence in Research “Kidney control of homeostasis” Zurich Switzerland
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Roscian M, Herrel A, Cornette R, Delapré A, Cherel Y, Rouget I. Underwater photogrammetry for close-range 3D imaging of dry-sensitive objects: The case study of cephalopod beaks. Ecol Evol 2021; 11:7730-7742. [PMID: 34188847 PMCID: PMC8216959 DOI: 10.1002/ece3.7607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 11/11/2022] Open
Abstract
Technical advances in 3D imaging have contributed to quantifying and understanding biological variability and complexity. However, small, dry-sensitive objects are not easy to reconstruct using common and easily available techniques such as photogrammetry, surface scanning, or micro-CT scanning. Here, we use cephalopod beaks as an example as their size, thickness, transparency, and dry-sensitive nature make them particularly challenging. We developed a new, underwater, photogrammetry protocol in order to add these types of biological structures to the panel of photogrammetric possibilities.We used a camera with a macrophotography mode in a waterproof housing fixed in a tank with clear water. The beak was painted and fixed on a colored rotating support. Three angles of view, two acquisitions, and around 300 pictures per specimen were taken in order to reconstruct a full 3D model. These models were compared with others obtained with micro-CT scanning to verify their accuracy.The models can be obtained quickly and cheaply compared with micro-CT scanning and have sufficient precision for quantitative interspecific morphological analyses. Our work shows that underwater photogrammetry is a fast, noninvasive, efficient, and accurate way to reconstruct 3D models of dry-sensitive objects while conserving their shape. While the reconstruction of the shape is accurate, some internal parts cannot be reconstructed with photogrammetry as they are not visible. In contrast, these structures are visible using reconstructions based on micro-CT scanning. The mean difference between both methods is very small (10-5 to 10-4 mm) and is significantly lower than differences between meshes of different individuals.This photogrammetry protocol is portable, easy-to-use, fast, and reproducible. Micro-CT scanning, in contrast, is time-consuming, expensive, and nonportable. This protocol can be applied to reconstruct the 3D shape of many other dry-sensitive objects such as shells of shellfish, cartilage, plants, and other chitinous materials.
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Affiliation(s)
- Marjorie Roscian
- Centre de Recherche en Paléontologie‐Paris (CR2P)Muséum National d'Histoire NaturelleCNRSSorbonne UniversitéParisFrance
- Mécanismes Adaptatifs et Evolution (Mecadev)Muséum National d'Histoire NaturelleCNRSBâtiment d'Anatomie ComparéeParisFrance
| | - Anthony Herrel
- Mécanismes Adaptatifs et Evolution (Mecadev)Muséum National d'Histoire NaturelleCNRSBâtiment d'Anatomie ComparéeParisFrance
| | - Raphaël Cornette
- Institut de Systématique, Évolution, Biodiversité (ISYEB)Muséum national d'Histoire naturelleCNRSSorbonne UniversitéEPHEUniversité des AntillesParisFrance
| | - Arnaud Delapré
- Institut de Systématique, Évolution, Biodiversité (ISYEB)Muséum national d'Histoire naturelleCNRSSorbonne UniversitéEPHEUniversité des AntillesParisFrance
| | - Yves Cherel
- Centre d'Etudes Biologiques de ChizéUMR7372CNRS‐La Rochelle UniversitéVilliers‐en‐BoisFrance
| | - Isabelle Rouget
- Centre de Recherche en Paléontologie‐Paris (CR2P)Muséum National d'Histoire NaturelleCNRSSorbonne UniversitéParisFrance
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3D Fine-scale Terrain Variables from Underwater Photogrammetry: A New Approach to Benthic Microhabitat Modeling in a Circalittoral Rocky Shelf. REMOTE SENSING 2020. [DOI: 10.3390/rs12152466] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The relationship between 3D terrain complexity and fine-scale localization and distribution of species is poorly understood. Here we present a very fine-scale 3D reconstruction model of three zones of circalittoral rocky shelf in the Bay of Biscay. Detailed terrain variables are extracted from 3D models using a structure-from-motion (SfM) approach applied to ROTV images. Significant terrain variables that explain species location were selected using general additive models (GAMs) and micro-distribution of the species were predicted. Two models combining BPI, curvature and rugosity can explain 55% and 77% of the Ophiuroidea and Crinoidea distribution, respectively. The third model contributes to explaining the terrain variables that induce the localization of Dendrophyllia cornigera. GAM univariate models detect the terrain variables for each structural species in this third zone (Artemisina transiens, D. cornigera and Phakellia ventilabrum). To avoid the time-consuming task of manual annotation of presence, a deep-learning algorithm (YOLO v4) is proposed. This approach achieves very high reliability and low uncertainty in automatic object detection, identification and location. These new advances applied to underwater imagery (SfM and deep-learning) can resolve the very-high resolution information needed for predictive microhabitat modeling in a very complex zone.
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