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McCauley M, Koda SA, Loesgen S, Duffy DJ. Multicellular species environmental DNA (eDNA) research constrained by overfocus on mitochondrial DNA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169550. [PMID: 38142009 DOI: 10.1016/j.scitotenv.2023.169550] [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: 09/22/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Environmental DNA (eDNA) is becoming an established tool across the biological and medical sciences. Despite the evident successes and wide adoption of eDNA approaches, some fundamental questions remain. For instance, there is almost a dogma in the field around the superiority of mitochondrial DNA for use in eDNA studies, however robust comparison with nuclear eDNA is widely lacking. The dominance of mitochondrial-based eDNA for animal and plant studies appears to be largely settled, despite a widespread lack of rigorous nuclear eDNA testing. Outside of the source organism the protections conferred on eDNA by the cell, mitochondrial and nuclear membranes are poorly understood, including the contribution of each to eDNA persistence and degradation. Utilizing shotgun sequencing to unbiasedly assess the level of nuclear and mitochondrial eDNA across samples, we reveal stark differences in nuclear versus mitochondrial eDNA persistence and abundance. By focusing too heavily on mitochondrial DNA alone the field is underutilizing eDNA's full potential.
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Affiliation(s)
- Mark McCauley
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
| | - Samantha A Koda
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA
| | - Sandra Loesgen
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - David J Duffy
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL 32611, USA
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Guo Y, Chen H, Liu P, Wang F, Li L, Ye M, Zhao W, Chen J. Microbial composition of carapace, feces, and water column in captive juvenile green sea turtles with carapacial ulcers. Front Vet Sci 2022; 9:1039519. [PMID: 36590814 PMCID: PMC9797667 DOI: 10.3389/fvets.2022.1039519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Green sea turtles are endangered marine reptiles. Carapacial ulcers will develop on juvenile green sea turtles during artificial rescue, seriously affecting their health and potentially leading to death. Methods To determine the pathogens causing ulcerative carapacial disease, we performed 16S and ITS high-throughput sequencing, and microbial diversity analysis on samples from carapacial ulcers, healthy carapaces, feces, and seawater of juvenile green sea turtles. Results Our analysis showed that changes in microbial diversity of green sea turtle feces and seawater were not significantly associated with ulcerative carapacial disease. Discussion Psychrobacter sp. is the dominant species in the carapacial ulcers of green sea turtles. The bacterium is present in both healthy turtles and seawater where carapacial ulcers did not occur and decreasing seawater temperatures are likely responsible for the infection of juvenile green turtles with Psychrobacter sp. This is the first study on carapacial ulcers in captive juvenile green sea turtles. Our research provides theoretical guidance for the prevention and control of carapacial ulcers in captive juvenile green sea turtles.
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Affiliation(s)
- Yide Guo
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province, China
| | - Hualing Chen
- Huidong Sea Turtle National Reserve Management Bureau, Sea Turtle Bay, Huidong, Guangdong, China
| | - Ping Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province, China
| | - Fumin Wang
- Huidong Sea Turtle National Reserve Management Bureau, Sea Turtle Bay, Huidong, Guangdong, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province, China
| | - Mingbin Ye
- Huidong Sea Turtle National Reserve Management Bureau, Sea Turtle Bay, Huidong, Guangdong, China
| | - Wenge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China,*Correspondence: Wenge Zhao
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province, China,Jinping Chen
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Cáceres-Farias L, Reséndiz E, Espinoza J, Fernández-Sanz H, Alfaro-Núñez A. Threats and Vulnerabilities for the Globally Distributed Olive Ridley (Lepidochelys olivacea) Sea Turtle: A Historical and Current Status Evaluation. Animals (Basel) 2022; 12:ani12141837. [PMID: 35883384 PMCID: PMC9311662 DOI: 10.3390/ani12141837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/08/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
The olive ridley (Lepidochelys olivacea) is the most abundant of all seven sea turtles, found across the tropical regions of the Atlantic, Pacific, and Indian Oceans in over 80 different countries all around the globe. Despite being the most common and widely distributed sea turtle, olive ridley populations have been declining substantially for decades. Worldwide, olive ridleys have experienced a 30–50% decline, putting their populations at risk and being considered an Endangered Species by the IUCN. Natural habitat degradation, pollution, bycatch, climate change, predation by humans and animals, infectious diseases and illegal trade are the most notorious threats to explain olive ridley populations rapidly decline. The present review assesses the numerous dangers that the olive ridley turtle has historically faced and currently faces. To preserve olive ridleys, stronger conservation initiatives and strategies must continue to be undertaken. Policies and law enforcement for the protection of natural environments and reduction in the effects of climate change should be implemented worldwide to protect this turtle species.
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Affiliation(s)
- Lenin Cáceres-Farias
- AquaCEAL Corporation, Urb. Las Palmeras, Ave. Capitán Byron Palacios & General Quisquis, Santo Domingo de los Colorados 230101, Ecuador;
- Grupo de Investigación en Biología y Cultivo de Moluscos, Departamento de Acuicultura, Pesca y Recursos Naturales Renovables, Facultad de Ciencias Veterinarias, Universidad Técnica de Manabí, Bahía de Caráquez, Manabí 131101, Ecuador
| | - Eduardo Reséndiz
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz 23080, Mexico; (E.R.); (J.E.); (H.F.-S.)
- Health Assessments in Sea Turtles from BCS, La Paz 23085, Mexico
| | - Joelly Espinoza
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz 23080, Mexico; (E.R.); (J.E.); (H.F.-S.)
- Health Assessments in Sea Turtles from BCS, La Paz 23085, Mexico
| | - Helena Fernández-Sanz
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz 23080, Mexico; (E.R.); (J.E.); (H.F.-S.)
- Health Assessments in Sea Turtles from BCS, La Paz 23085, Mexico
| | - Alonzo Alfaro-Núñez
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
- Department of Clinical Biochemistry, Naestved Hospital, Ringstedgade 57a, 4700 Naestved, Denmark
- Correspondence:
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Manes C, Pinton D, Canestrelli A, Capua I. Occurrence of Fibropapillomatosis in Green Turtles ( Chelonia mydas) in Relation to Environmental Changes in Coastal Ecosystems in Texas and Florida: A Retrospective Study. Animals (Basel) 2022; 12:1236. [PMID: 35625082 PMCID: PMC9137486 DOI: 10.3390/ani12101236] [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: 04/04/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022] Open
Abstract
Fibropapillomatosis is a neoplastic disease of marine turtles, with green turtles (Chelonia mydas) being the most affected species. Fibropapillomatosis causes debilitating tumor growths on soft tissues and internal organs, often with lethal consequences. Disease incidence has been increasing in the last few decades and the reason is still uncertain. The potential viral infectious agent of Fibropapillomatosis, chelonid herpesvirus 5, has been co-evolving with its sea turtle host for millions of years and no major mutation linked with increased disease occurrence has been detected. Hence, frequent outbreaks in recent decades are likely attributable to external drivers such as large-scale anthropogenic changes in the green turtle coastal marine ecosystem. This study found that variations in sea surface temperature, salinity, and nutrient effluent discharge from nearby rivers were correlated with an increased incidence of the disease, substantiating that these may be among the significant environmental drivers impacting Fibropapillomatosis prevalence. This study offers data and insight on the need to establish a baseline of environmental factors which may drive Fibropapillomatosis and its clinical exacerbation. We highlight the multifactorial nature of this disease and support the inclusion of interdisciplinary work in future Fibropapillomatosis research efforts.
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Affiliation(s)
- Costanza Manes
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, USA
- One Health Center of Excellence, University of Florida, Gainesville, FL 32611, USA;
| | - Daniele Pinton
- Department of Civil and Coastal Engineering, University of Florida, Gainesville, FL 32611, USA; (D.P.); (A.C.)
| | - Alberto Canestrelli
- Department of Civil and Coastal Engineering, University of Florida, Gainesville, FL 32611, USA; (D.P.); (A.C.)
| | - Ilaria Capua
- One Health Center of Excellence, University of Florida, Gainesville, FL 32611, USA;
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Farrell JA, Whitmore L, Mashkour N, Rollinson Ramia DR, Thomas RS, Eastman CB, Burkhalter B, Yetsko K, Mott C, Wood L, Zirkelbach B, Meers L, Kleinsasser P, Stock S, Libert E, Herren R, Eastman S, Crowder W, Bovery C, Anderson D, Godfrey D, Condron N, Duffy DJ. Detection and population genomics of sea turtle species via non-invasive environmental DNA analysis of nesting beach sand tracks and oceanic water. Mol Ecol Resour 2022; 22:2471-2493. [PMID: 35377560 DOI: 10.1111/1755-0998.13617] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/12/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022]
Abstract
Elusive aquatic wildlife, such as endangered sea turtles, are difficult to monitor and conserve. As novel molecular and genetic technologies develop, it is possible to adapt and optimize them for wildlife conservation. One such technology is environmental (e)DNA - the detection of DNA shed from organisms into their surrounding environments. We developed species-specific green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtle probe-based qPCR assays, which can detect and quantify sea turtle eDNA in controlled (captive tank water and sand samples) and free ranging (oceanic water samples and nesting beach sand) settings. eDNA detection complemented traditional in-water sea turtle monitoring by enabling detection even when turtles were not visually observed. Furthermore, we report that high throughput shotgun sequencing of eDNA sand samples enabled sea turtle population genetic studies and pathogen monitoring, demonstrating that non-invasive eDNA techniques are viable and efficient alternatives to biological sampling (e.g. biopsies and blood draws). Genetic information was obtained from sand many hours after nesting events, without having to observe or interact with the target individual. This greatly reduces the sampling stress experienced by nesting mothers and emerging hatchlings, and avoids sacrificing viable eggs for genetic analysis. The detection of pathogens from sand indicates significant potential for increased wildlife disease monitoring capacity and viral variant surveillance. Together, these results demonstrate the potential of eDNA approaches to ultimately help understand and conserve threatened species such as sea turtles.
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Affiliation(s)
- Jessica A Farrell
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Liam Whitmore
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Narges Mashkour
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Devon R Rollinson Ramia
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Rachel S Thomas
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Catherine B Eastman
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Brooke Burkhalter
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Kelsey Yetsko
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, Florida International University, Miami, FL, 33181, USA
| | - Cody Mott
- Inwater Research Group Inc, Jensen Beach, FL, 34957, USA
| | - Larry Wood
- Florida Hawksbill Project, National Save The Sea Turtle Foundation, Ft. Lauderdale, FL, 33308, USA
| | - Bette Zirkelbach
- The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Lucas Meers
- Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - Pat Kleinsasser
- Crescent Beach Turtle Patrol, Crescent Beach, FL, 32080, USA
| | - Sharon Stock
- Flagler Turtle Patrol, Marineland Beach, FL, 32080, USA
| | | | | | - Scott Eastman
- Florida Department of Environmental Protection, St Augustine, FL, 32080, USA
| | | | | | | | - David Godfrey
- The Sea Turtle Conservancy, Gainesville, FL, 32609, USA
| | - Nancy Condron
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - David J Duffy
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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