Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats
Abstract Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding th...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2024-02-01
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| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.10999 |
| _version_ | 1827572820177059840 |
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| author | Pablo Saenz‐Agudelo Paula Ramirez Ricardo Beldade Ana N. Campoy Vladimir Garmendia Francesca V. Search Miriam Fernández Evie A. Wieters Sergio A. Navarrete Mauricio F. Landaeta Alejandro Pérez‐Matus |
| author_facet | Pablo Saenz‐Agudelo Paula Ramirez Ricardo Beldade Ana N. Campoy Vladimir Garmendia Francesca V. Search Miriam Fernández Evie A. Wieters Sergio A. Navarrete Mauricio F. Landaeta Alejandro Pérez‐Matus |
| author_sort | Pablo Saenz‐Agudelo |
| collection | DOAJ |
| description | Abstract Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better‐studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better‐resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region. |
| first_indexed | 2024-03-07T19:29:02Z |
| format | Article |
| id | doaj.art-7bb20c225ce747b7b5636835febd8b5f |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-03-07T19:29:02Z |
| publishDate | 2024-02-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-7bb20c225ce747b7b5636835febd8b5f2024-02-29T08:56:40ZengWileyEcology and Evolution2045-77582024-02-01142n/an/a10.1002/ece3.10999Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitatsPablo Saenz‐Agudelo0Paula Ramirez1Ricardo Beldade2Ana N. Campoy3Vladimir Garmendia4Francesca V. Search5Miriam Fernández6Evie A. Wieters7Sergio A. Navarrete8Mauricio F. Landaeta9Alejandro Pérez‐Matus10Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia ChileInstituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia ChileMillennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces ChileCenter of Marine Sciences (CCMAR‐CIMAR) University of the Algarve Faro PortugalMillennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces ChileMillennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces ChileMillennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces ChileMillennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces ChileMillennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces ChileMillennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces ChileMillennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces ChileAbstract Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better‐studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better‐resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.https://doi.org/10.1002/ece3.10999biodiversity surveyeDNAeukaryotesfishesmetabarcoding |
| spellingShingle | Pablo Saenz‐Agudelo Paula Ramirez Ricardo Beldade Ana N. Campoy Vladimir Garmendia Francesca V. Search Miriam Fernández Evie A. Wieters Sergio A. Navarrete Mauricio F. Landaeta Alejandro Pérez‐Matus Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats Ecology and Evolution biodiversity survey eDNA eukaryotes fishes metabarcoding |
| title | Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats |
| title_full | Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats |
| title_fullStr | Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats |
| title_full_unstemmed | Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats |
| title_short | Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats |
| title_sort | environmental dna reveals temporal variation in mesophotic reefs of the humboldt upwelling ecosystems of central chile toward a baseline for biodiversity monitoring of unexplored marine habitats |
| topic | biodiversity survey eDNA eukaryotes fishes metabarcoding |
| url | https://doi.org/10.1002/ece3.10999 |
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