1
|
Nester GM, Suter L, Kitchener JA, Bunce M, Polanowski AM, Wasserman J, Deagle B. Long-distance Southern Ocean environmental DNA (eDNA) transect provides insights into spatial marine biota and invasion pathways for non-native species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175657. [PMID: 39173769 DOI: 10.1016/j.scitotenv.2024.175657] [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: 04/04/2024] [Revised: 08/04/2024] [Accepted: 08/18/2024] [Indexed: 08/24/2024]
Abstract
The Southern Ocean surrounding Antarctica harbours some of the most pristine marine environments remaining, but is increasingly vulnerable to anthropogenic pressures, climate change, and invasion by non-native species. Monitoring biotic responses to cumulative impacts requires temporal and spatial baselines and ongoing monitoring - traditionally, this has been obtained by continuous plankton recorder (CPR) surveys. Here, we conduct one of the longest environmental DNA (eDNA) transects yet, spanning over 3000 nautical miles from Hobart (Australia) to Davis Station (Antarctica). We evaluate eDNA sampling strategies for long-term open ocean biomonitoring by comparing two water volume and filter pore size combinations: large (12 l with 20 μm) and small (2 l with 0.45 μm). Employing a broad COI metabarcoding assay, we found the large sample/pore combination was better suited to open ocean monitoring, detecting more target DNA and rare or low abundance species. Comparisons with four simultaneously conducted CPR transects revealed that eDNA detections were more diverse than CPR, with 7 (4 unique) and 4 (1 unique) phyla detections respectively. While both methods effectively delineated biodiversity patterns across the Southern Ocean, eDNA enables surveys in the presence of sea-ice where CPR cannot be conducted. Accordingly, 16 species of concern were detected along the transect using eDNA, notably in the Antarctic region (south of 60°S). These were largely attributed to hull biofouling, a recognized pathway for marine introductions into Antarctica. Given the vulnerability of Antarctic environments to potential introductions in a warming Southern Ocean, this work underscores the importance of continued biosecurity vigilance. We advocate integrating eDNA metabarcoding with long-term CPR surveys in the Southern Ocean, emphasising the urgency of its implementation. We anticipate temporal and spatial interweaving of CPR, eDNA, and biophysical data will generate a more nuanced picture of Southern Ocean ecosystems, with significant implications for the conservation and preservation of Antarctic ecosystems.
Collapse
Affiliation(s)
- Georgia M Nester
- TrEnD Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
| | - Leonie Suter
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia.
| | - John A Kitchener
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia.
| | - Michael Bunce
- TrEnD Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia; Department of Conservation, New Zealand
| | - Andrea M Polanowski
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia.
| | - Johan Wasserman
- Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Perth, WA 6150, Australia
| | - Bruce Deagle
- Australian National Fish Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation, Tasmania, Battery Point, Australia.
| |
Collapse
|
2
|
Iguchi A, Nishijima M, Ikeuchi E, Yokooka H, Sugishima H, Ikeda K, Miwa R, Sekido Y, Iwasaki N, Suzumura M, Tsukasaki A, Tanaka Y, Kato S, Minatoya J, Okamoto N, Kunishima T, Ise Y, Suzuki A. Utilizing environmental DNA and imaging to study the deep-sea fish community of Takuyo-Daigo Seamount. NPJ BIODIVERSITY 2024; 3:14. [PMID: 39242887 PMCID: PMC11331990 DOI: 10.1038/s44185-024-00042-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/29/2024] [Indexed: 09/09/2024]
Abstract
The increase in interest of mining at seamounts means there is a critical need to establish baseline inventories through environmental survey, with the aim of promoting the conservation and stewardship of these remote habitats. To efficiently evaluate fish biodiversity around a seamount, we compared environmental DNA (eDNA) methods using seawater and sponge samples against methods using imagery obtained with a remotely operated vehicle (ROV) and a free-fall deep-sea camera lander called the Edokko Mark I on the Takuyo-Daigo Seamount (153.0°E, 23.5°N) in the northwestern Pacific Ocean. We detected a total of 18 fish families by these methods. The fish fauna detected on the seamount included many families commonly found in deep-sea areas and were similar to the fish fauna of other seamounts located at similar latitudes in the northwestern Pacific. Significant differences in the patterns of detection of fish families between the eDNA and imaging methods is attributed to the differing powers of detection of some fish groups between methods (related to primer compatibility and fish size). For deep-sea fish, the difference in fish composition at the family level between seawater and sponge eDNA methods was not significant, but the difference between Edokko Mark I and ROV methods was significant; the latter difference is likely due to whether or not bait is used to attract fish. Although the eDNA workflow implemented here requires improvements, the use of eDNA and imaging methods in combination provided better insight into the biodiversity of deep-sea fishes in the deep-sea around a seamount, where our knowledge of the fish fauna has been extremely limited. Our recovery of eDNA from seawater and sponge samples around the seamount demonstrates the potential of these methods for facilitating environmental baseline surveys and impact assessments of mining activities to obtain results not previously possible with the use of visual methods only.
Collapse
Affiliation(s)
- Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
- Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan.
| | - Miyuki Nishijima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Eri Ikeuchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Hiroyuki Yokooka
- IDEA Consultants, Inc., 1334-5 Riemon, Yaizu, Shizuoka, 421-0212, Japan
| | - Hideki Sugishima
- IDEA Consultants, Inc., 1334-5 Riemon, Yaizu, Shizuoka, 421-0212, Japan
| | - Kazumasa Ikeda
- Okamoto Glass Co., Ltd., 380 Toyofuta, Kashiwa, Chiba, 277-0872, Japan
| | - Ryuichi Miwa
- Kaiyo Engineering Co., Ltd., 4-28-11 Taito, Taito, Tokyo, 110-0016, Japan
| | - Yoshiro Sekido
- Marine Biological Research Institute of Japan Co., Ltd., 4-28-11 Taito, Taito, Tokyo, 110-0016, Japan
| | - Nozomu Iwasaki
- Faculty of Geo-Environmental Science, Rissho University, 1700 Magechi, Kumagaya, Saitama, 360-0194, Japan
| | - Masahiro Suzumura
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Ayumi Tsukasaki
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Yuichiro Tanaka
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Shogo Kato
- IDEA Consultants, Inc., 1334-5 Riemon, Yaizu, Shizuoka, 421-0212, Japan
| | - Jumpei Minatoya
- Marine Biological Research Institute of Japan Co., Ltd., 4-28-11 Taito, Taito, Tokyo, 110-0016, Japan
| | - Nobuyuki Okamoto
- Deep Ocean Resources Development CO., Ltd., 2-3-5, Nihonbashi Horidome-cho, Chuoh-ku, Tokyo, 103-0012, Japan
| | - Taiga Kunishima
- Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Yuji Ise
- Kuroshio Biological Research Foundation, 560 Nishidomari, Otsuki, Kochi, 788-0333, Japan
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
- Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan.
| |
Collapse
|
3
|
Lin CP, Huang CH, Padgett T, Bucay MAC, Chen CW, Shen ZY, Chiu L, Tseng YC, Yu JK, Wang J, Wang MC, Hoh DZ. Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan. Biodivers Data J 2024; 12:e116921. [PMID: 38694844 PMCID: PMC11061556 DOI: 10.3897/bdj.12.e116921] [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: 12/06/2023] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
Background This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 incertae sedis, accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios. New information The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.
Collapse
Affiliation(s)
- Chieh-Ping Lin
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, TaiwanGenome and Systems Biology Degree Program, Academia Sinica and National Taiwan UniversityTaipeiTaiwan
- Biodiversity Research Center, Academia Sinica, Taipei, TaiwanBiodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Chung-Hsin Huang
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- International Graduate Degree Program for Biodiversity, Tunghai University, Taichung, TaiwanInternational Graduate Degree Program for Biodiversity, Tunghai UniversityTaichungTaiwan
| | - Trevor Padgett
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- International Graduate Degree Program for Biodiversity, Tunghai University, Taichung, TaiwanInternational Graduate Degree Program for Biodiversity, Tunghai UniversityTaichungTaiwan
| | - Mark Angelo C. Bucay
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Cheng-Wei Chen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Zong-Yu Shen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Ling Chiu
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Institute of Oceanography, National Taiwan University, Taipei, TaiwanInstitute of Oceanography, National Taiwan UniversityTaipeiTaiwan
| | - Yung-Che Tseng
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
| | - Jr-Kai Yu
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, TaiwanInstitute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, TaiwanBiodiversity Research Center, Academia SinicaTaipeiTaiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
| | - Min-Chen Wang
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Zoological Institute, Christian-Albrechts University of Kiel, Kiel, GermanyZoological Institute, Christian-Albrechts University of KielKielGermany
| | - Daphne Z. Hoh
- Taiwan Biodiversity Information Facility, Biodiversity Research Centre, Academia Sinica, Taipei, TaiwanTaiwan Biodiversity Information Facility, Biodiversity Research Centre, Academia SinicaTaipeiTaiwan
| |
Collapse
|
4
|
Madgett AS, Elsdon TS, Marnane MJ, Schramm KD, Harvey ES. The functional diversity of fish assemblages in the vicinity of oil and gas pipelines compared to nearby natural reef and soft sediment habitats. MARINE ENVIRONMENTAL RESEARCH 2023; 187:105931. [PMID: 36966683 DOI: 10.1016/j.marenvres.2023.105931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/27/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
As the offshore hydrocarbon industry matures and decommissioning activities are expected to increase, there is a requirement to assess the environmental consequences of different pipeline decommissioning options. Previous research on fish and other ecological components associated with pipelines has focused on examining species richness, abundance and biomass surrounding structures. The extent to which subsea pipelines mimic or alter ecosystem function compared with nearby natural habitats is unknown. We analyse differences in fish assemblage biological trait composition and the functional diversity at exposed shallow-water subsea pipelines, nearby natural reef and soft sediment habitats, using mini stereo-video remotely operated vehicles (ROV). Habitats significantly differed in assemblage trait composition. The pipeline and reef habitats shared a more similar functional composition and had the presence of key functional groups required for the development and maintenance of healthy coral reef systems. The reef habitat had the greatest functional diversity, followed by the pipeline habitat and soft sediment habitat respectively.
Collapse
Affiliation(s)
- Alethea S Madgett
- The National Decommissioning Centre, Main Street, Newburgh, Aberdeenshire, AB41 6AA, United Kingdom; University of Aberdeen, School of Engineering, Fraser Noble Building, Kings College, Aberdeen, AB24 3UE, United Kingdom.
| | - Travis S Elsdon
- Chevron Energy Technology Pty Ltd, 250 St Georges Terrace, Perth, WA, 6000, Australia; Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
| | - Michael J Marnane
- Chevron Energy Technology Pty Ltd, 250 St Georges Terrace, Perth, WA, 6000, Australia
| | - Karl D Schramm
- Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
| | - Euan S Harvey
- Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
| |
Collapse
|
5
|
Measuring the Impact of Conservation: The Growing Importance of Monitoring Fauna, Flora and Funga. DIVERSITY 2022. [DOI: 10.3390/d14100824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Many stakeholders, from governments to civil society to businesses, lack the data they need to make informed decisions on biodiversity, jeopardising efforts to conserve, restore and sustainably manage nature. Here we review the importance of enhancing biodiversity monitoring, assess the challenges involved and identify potential solutions. Capacity for biodiversity monitoring needs to be enhanced urgently, especially in poorer, high-biodiversity countries where data gaps are disproportionately high. Modern tools and technologies, including remote sensing, bioacoustics and environmental DNA, should be used at larger scales to fill taxonomic and geographic data gaps, especially in the tropics, in marine and freshwater biomes, and for plants, fungi and invertebrates. Stakeholders need to follow best monitoring practices, adopting appropriate indicators and using counterfactual approaches to measure and attribute outcomes and impacts. Data should be made openly and freely available. Companies need to invest in collecting the data required to enhance sustainability in their operations and supply chains. With governments soon to commit to the post-2020 global biodiversity framework, the time is right to make a concerted push on monitoring. However, action at scale is needed now if we are to enhance results-based management adequately to conserve the biodiversity and ecosystem services we all depend on.
Collapse
|