1
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Nhat NH, Saito M, Onodera SI, Hamada M, Hyodo F, Nagare H. Environmental DNA Reveals the Impact of Submarine Groundwater Discharge on the Spatial Variability of Coastal Fish Diversity. BIOLOGY 2024; 13:609. [PMID: 39194547 DOI: 10.3390/biology13080609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024]
Abstract
Submarine groundwater discharge (SGD) has recently been recognized as an influential factor in coastal ecosystems; however, little research has been conducted on its effects on coastal fish diversity. To investigate the relationship between SGD and fish diversity, we conducted a survey at the coastal island scale using the environmental DNA (eDNA) method. Our findings indicate that fish species richness and functional richness peak at stations with high SGD. Environmental variables, such as salinity, dissolved inorganic nitrogen (DIN) concentration, and SGD, significantly influence fish diversity. Carnivore fish richness was negatively correlated with salinity, while planktivore fish richness was positively correlated. Additionally, SGD and DIN concentrations were found to be crucial in shaping omnivorous and pelagic communities, respectively. This study highlights the role of SGD in enhancing nutrient conditions favorable for diverse fish communities and demonstrates the effectiveness of eDNA metabarcoding for rapid marine biodiversity assessment. These findings provide valuable insights for coastal ecosystem monitoring and management.
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Affiliation(s)
- Nguyen Hong Nhat
- Graduate School of Environmental and Life Science, Okayama University, Okayama 7008530, Japan
- Faculty of Technology-Engineering-Environment, An Giang University, Vietnam National University-Ho Chi Minh City, Ho Chi Minh City 880000, Vietnam
| | - Mitsuyo Saito
- Graduate School of Advanced Science and Engineering, Hiroshima University, Higashi Hiroshima 7398521, Japan
| | - Shin-Ichi Onodera
- Graduate School of Advanced Science and Engineering, Hiroshima University, Higashi Hiroshima 7398521, Japan
| | - Mayuko Hamada
- Ushimado Marine Institute (UMI), Graduate School of Environment, Life, Natural Science and Technology, Okayama University, Okayama 7014303, Japan
| | - Fujio Hyodo
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 7008530, Japan
| | - Hideaki Nagare
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 7008530, Japan
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2
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Dan ME, Portner EJ, Bowman JS, Semmens BX, Owens SM, Greenwald SM, Choy CA. Using low volume eDNA methods to sample pelagic marine animal assemblages. PLoS One 2024; 19:e0303263. [PMID: 38748719 PMCID: PMC11095688 DOI: 10.1371/journal.pone.0303263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024] Open
Abstract
Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.
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Affiliation(s)
- Michelle E. Dan
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Elan J. Portner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Jeff S. Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Brice X. Semmens
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Sarah M. Owens
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Stephanie M. Greenwald
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - C. Anela Choy
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
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3
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Wang S, Wu D, Song Y, Wang T, Fan S, Wu E, Chen N, Xia W, Xu MN, Chen Z, Wen J, Zhang Y, Mo L, Xiang L. Application of environmental DNA metabarcoding to identify fish community characteristics in subtropical river systems. Ecol Evol 2024; 14:e11214. [PMID: 38725828 PMCID: PMC11079634 DOI: 10.1002/ece3.11214] [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: 08/04/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 05/12/2024] Open
Abstract
Fish are vital in river ecosystems; however, traditional investigations of fish usually cause ecological damage. Extracting DNA from aquatic environments and identifying DNA sequences offer an alternative, noninvasive approach for detecting fish species. In this study, the effects of environmental DNA (eDNA), coupled with PCR and next-generation sequencing, and electrofishing for identifying fish community composition and diversity were compared. In three subtropical rivers of southern China, fish specimens and eDNA in water were collected along the longitudinal (upstream-downstream) gradient of the rivers. Both fish population parameters, including species abundance and biomass, and eDNA OTU richness grouped 38 sampling sites into eight spatial zones with significant differences in local fish community composition. Compared with order-/family-level grouping, genus-/species-level grouping could more accurately reveal the differences between upstream zones I-III, midstream zones IV-V, and downstream zones VI-VIII. From the headwaters to the estuary, two environmental gradients significantly influenced the longitudinal distribution of the fish species, including the first gradient composed of habitat and physical water parameters and the second gradient composed of chemical water parameters. The high regression coefficient of alpha diversity between eDNA and electrofishing methods as well as the accurate identification of dominant, alien, and biomarker species in each spatial zone indicated that eDNA could characterize fish community attributes at a level similar to that of traditional approaches. Overall, our results demonstrated that eDNA metabarcoding can be used as an effective tool for revealing fish composition and diversity, which is important for using the eDNA technique in aquatic field monitoring.
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Affiliation(s)
- Sai Wang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Dong‐Hai Wu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
- College of Ecology and EnvironmentHainan UniversityHaikouChina
| | - Yong‐Duo Song
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Tuan‐Tuan Wang
- College of Ecology and EnvironmentHainan UniversityHaikouChina
- Key Laboratory of Agro‐Forestry Environmental Processes and Ecological Regulation of Hainan ProvinceHainan UniversityHaikouChina
| | - Shi‐Di Fan
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - En‐Ni Wu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Nan‐Lin Chen
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Wen‐Tong Xia
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Min N. Xu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Zhong‐Bing Chen
- Department of Applied·Ecology, Faculty of Environmental SciencesCzech University of Life Sciences PraguePraha‐SuchdolCzech Republic
| | - Jing Wen
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
- Hainan Qingxiao Environmental Testing Co., Ltd.SanyaChina
- Hainan Qianchao Ecological Technology Co., Ltd.SanyaChina
| | - Yang Zhang
- Shenzhen Guanghuiyuan Environment Water Co., Ltd.ShenzhenChina
| | - Ling Mo
- Hainan Research Academy of Environmental SciencesHaikouChina
| | - Lei Xiang
- Department of EcologyJinan UniversityGuangzhouChina
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4
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Fernandez S, Ardura A, Martinez JL, Rick J, Machado-Schiaffino G, Garcia-Vazquez E. Plankton assessment across the distribution of West African hake and tuna based on eDNA metabarcoding. MARINE ENVIRONMENTAL RESEARCH 2024; 194:106312. [PMID: 38150786 DOI: 10.1016/j.marenvres.2023.106312] [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: 10/20/2023] [Revised: 11/28/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023]
Abstract
The richness of plankton communities determines the fish productivity in the ocean, including important resources that rely on extractive fisheries, such as hakes (genus Merluccius) and tunas (genus Thunnus). Their preys forage on zooplankton, and the latter feed on phytoplankton. Inventories of plankton communities for scientific advice to sustainable fishing are essential in this moment of climate change. Plankton is generally inventoried using conventional methodologies based on large water volumes and visual morphological analyses of samples. In this study, we have employed metabarcoding on environmental DNA (eDNA) samples extracted from small water volumes for plankton inventory from twelve distant sampling stations in the East Atlantic Ocean. Zones rich in hake and tuna prey were detected from eDNA, and multivariate multiple regression analysis was able to predict those zones from diatom-based indices and planktonic diversity based on functional groups. Salinity was negatively correlated with the proportion of diatoms in phytoplankton, highlighting expected impacts of current global change on marine plankton communities. The results emphasise the importance of the plankton richness for fish productivity and support the utility of environmental DNA as a tool to monitor plankton composition changes.
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Affiliation(s)
- Sara Fernandez
- Department of Functional Biology, University of Oviedo, Spain
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, Spain
| | | | - Johannes Rick
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, AWI - Department of Coastal Ecology, Germany
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5
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Weinheimer AR, Aylward FO, Leray M, Scott JJ. Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems. ISME COMMUNICATIONS 2023; 3:127. [PMID: 38049529 PMCID: PMC10695958 DOI: 10.1038/s43705-023-00333-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023]
Abstract
Phages (viruses of bacteria and archaea) are a ubiquitous top-down control on microbial communities by selectively infecting and killing cells. As obligate parasites, phages are inherently linked to processes that impact their hosts' distribution and physiology, but phages can also be impacted by external, environmental factors, such as UV radiation degrading their virions. To better understand these complex links of phages to their hosts and the environment, we leverage the unique ecological context of the Isthmus of Panama, which narrowly disconnects the productive Tropical Eastern Pacific (EP) and nutrient-poor Tropical Western Atlantic (WA) provinces. We could thus compare patterns of phage and prokaryotic communities at both global scales (between oceans) and local-scales (between habitats within an ocean). Although both phage and prokaryotic communities differed sharply between the oceans, phage community composition did not significantly differ between mangroves and reefs of the WA, while prokaryotic communities were distinct. These results suggest phages are more shaped by dispersal processes than local conditions regardless of spatial scale, while prokaryotes tend to be shaped by local conditions at smaller spatial scales. Collectively, we provide a framework for addressing the co-variability between phages and prokaryotes in marine systems and identifying factors that drive consistent versus disparate trends in community shifts, essential to informing models of biogeochemical cycles that include these interactions.
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Affiliation(s)
- Alaina R Weinheimer
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061-0913, USA
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Jarrod J Scott
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.
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6
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Waters T, Gold Z, Obaza A, Ambrose RF, Eagle RA. Environmental DNA metabarcoding reveals distinct fish assemblages supported by seagrass (Zostera marina and Zostera pacifica) beds in different geographic settings in Southern California. PLoS One 2023; 18:e0286228. [PMID: 37796915 PMCID: PMC10553302 DOI: 10.1371/journal.pone.0286228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Seagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these different environments contribute to local biodiversity. This study evaluates the assemblages of fish found at five Zostera beds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.
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Affiliation(s)
- Tanner Waters
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
- Center for Diverse Leadership in Science, University of California, Los Angeles, CA, United States of America
| | - Zachary Gold
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, United States of America
| | - Adam Obaza
- Paua Marine Research Group, Long Beach, CA, United States of America
| | - Richard F. Ambrose
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
- Department of Environmental Health Sciences, Jonathan and Karen Fielding School of Public Health, University of California, Los Angeles, CA, United States of America
| | - Robert A. Eagle
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
- Center for Diverse Leadership in Science, University of California, Los Angeles, CA, United States of America
- Atmospheric and Oceanic Sciences Department, University of California, Los Angeles, CA, United States of America
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7
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Zhang M, Zou Y, Xiao S, Hou J. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects. MARINE POLLUTION BULLETIN 2023; 194:115430. [PMID: 37647798 DOI: 10.1016/j.marpolbul.2023.115430] [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: 04/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.
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Affiliation(s)
- Miaolian Zhang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yingtong Zou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Xiao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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8
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Brandl SJ, Weigt LA, Pitassy DE, Coker DJ, Patrick CJ, Luchese MH, Berumen ML, Buskey EJ, Casey JM, Di Domenico M, Soeth M, Topor ZM, Duffy JE, Baldwin CC, Hagedorn M, Parenti LR. Using standardized fish‐specific autonomous reef monitoring structures (
FARMS
) to quantify cryptobenthic fish communities. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- Simon J. Brandl
- Department of Marine Science The University of Texas at Austin, Marine Science Institute Port Aransas Texas USA
- Laboratories of Analytical Biology, National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
| | - Lee A. Weigt
- Laboratories of Analytical Biology, National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
| | - Diane E. Pitassy
- Laboratories of Analytical Biology, National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
| | - Darren J. Coker
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Christopher J. Patrick
- Department of Biological Sciences Virginia Institute of Marine Science, College of William and Mary Gloucester Point Virginia USA
| | - Matheus H. Luchese
- Center for Marine Studies Federal University of Paraná Paraná Brazil
- Postgraduate Program in Coastal and Oceanic Systems Federal University of Paraná Paraná Brazil
| | - Michael L. Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Edward J. Buskey
- Department of Marine Science The University of Texas at Austin, Marine Science Institute Port Aransas Texas USA
| | - Jordan M. Casey
- Department of Marine Science The University of Texas at Austin, Marine Science Institute Port Aransas Texas USA
| | | | - Marcelo Soeth
- Postgraduate Program in Coastal and Oceanic Systems Federal University of Paraná Paraná Brazil
- Marine Fish Ecology Laboratory North University Center of Espírito Santo, Federal University of Espírito Santo São Mateus Brazil
| | | | - J. Emmett Duffy
- Tennenbaum Marine Observatories Network and MarineGEO Program Smithsonian Environmental Research Center Edgewater Maryland USA
| | - Carole C. Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
| | - Mary Hagedorn
- Smithsonian's National Zoo and Conservation Biology Institute Smithsonian Institution Front Royal Virginia USA
- Hawai'i Institute of Marine Biology University of Hawai'i at Mānoa Kāne'ohe Hawai'i USA
| | - Lynne R. Parenti
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
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9
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Schreiber L, Castellanos‐Galindo GA, Robertson DR, Torchin M, Chavarria K, Laakmann S, Saltonstall K. Environmental DNA (eDNA) reveals potential for interoceanic fish invasions across the Panama Canal. Ecol Evol 2023; 13:e9675. [PMID: 36726876 PMCID: PMC9884569 DOI: 10.1002/ece3.9675] [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: 07/05/2022] [Revised: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 02/03/2023] Open
Abstract
Interoceanic canals can facilitate biological invasions as they connect the world's oceans and remove dispersal barriers between bioregions. As a consequence, multiple opportunities for biotic exchange arise and the resulting establishment of migrant species often causes adverse ecological and economic impacts. The Panama Canal is a key region for biotic exchange as it connects the Pacific and Atlantic Oceans in Central America. In this study, we used two complementary methods (environmental DNA (eDNA) metabarcoding and gillnetting) to survey fish communities in this unique waterway. Using COI (cytochrome oxidase subunit I) metabarcoding, we detected a total of 142 fish species, including evidence for the presence of sixteen Atlantic and eight Pacific marine fish in different freshwater sections of the Canal. Of these, nine are potentially new records. Molecular data did not capture all species caught with gillnets, but generally provided a more complete image of the known fish fauna as more small-bodied fish species were detected. Diversity indices based on eDNA surveys revealed significant differences across different sections of the Canal reflecting in part the prevailing environmental conditions. The observed increase in the presence of marine fish species in the Canal indicates a growing potential for interoceanic fish invasions. The potential ecological and evolutionary consequences of this increase in marine fishes are not only restricted to the fish fauna in the Canal as they could also impact adjacent ecosystems in the Pacific and Atlantic Oceans.
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Affiliation(s)
- Lennart Schreiber
- Smithsonian Tropical Research InstituteBalboaPanama
- Faculty of Biology & ChemistryUniversity of BremenBremenGermany
| | - Gustavo A. Castellanos‐Galindo
- Smithsonian Tropical Research InstituteBalboaPanama
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
| | | | - Mark Torchin
- Smithsonian Tropical Research InstituteBalboaPanama
| | | | - Silke Laakmann
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB)OldenburgGermany
- Alfred‐Wegener‐Institute, Helmholtz Centre for Polar and Marine ResearchBremerhavenGermany
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10
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Maslakova S, Ellison CI, Hiebert TC, Conable F, Heaphy MC, Venera-Pontón DE, Norenburg JL, Schwartz ML, Moss ND, Boyle MJ, Driskell AC, Macdonald KS, Zattara EE, Collin R. Sampling multiple life stages significantly increases estimates of marine biodiversity. Biol Lett 2022; 18:20210596. [PMID: 35414224 PMCID: PMC9039783 DOI: 10.1098/rsbl.2021.0596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Biodiversity assessments are critical for setting conservation priorities, understanding ecosystem function and establishing a baseline to monitor change. Surveys of marine biodiversity that rely almost entirely on sampling adult organisms underestimate diversity because they tend to be limited to habitat types and individuals that can be easily surveyed. Many marine animals have planktonic larvae that can be sampled from the water column at shallow depths. This life stage often is overlooked in surveys but can be used to relatively rapidly document diversity, especially for the many species that are rare or live cryptically as adults. Using DNA barcode data from samples of nemertean worms collected in three biogeographical regions—Northeastern Pacific, the Caribbean Sea and Eastern Tropical Pacific—we found that most species were collected as either benthic adults or planktonic larvae but seldom in both stages. Randomization tests show that this deficit of operational taxonomic units collected as both adults and larvae is extremely unlikely if larvae and adults were drawn from the same pool of species. This effect persists even in well-studied faunas. These results suggest that sampling planktonic larvae offers access to a different subset of species and thus significantly increases estimates of biodiversity compared to sampling adults alone. Spanish abstract is available in the electronic supplementary material.
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Affiliation(s)
- Svetlana Maslakova
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Christina I Ellison
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Terra C Hiebert
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Frances Conable
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Maureen C Heaphy
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | | | - Jon L Norenburg
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Megan L Schwartz
- University of Washington, 1900 Commerce Avenue, Tacoma, WA 98420, USA
| | - Nicole D Moss
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Michael J Boyle
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
| | - Amy C Driskell
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Eduardo E Zattara
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,INIBIOMA, Universidad Nacional del Comahue-CONICET, Bariloche, Río Negro, 8400, Argentina
| | - Rachel Collin
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
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11
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Shelton AO, Ramón-Laca A, Wells A, Clemons J, Chu D, Feist BE, Kelly RP, Parker-Stetter SL, Thomas R, Nichols KM, Park L. Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean. Proc Biol Sci 2022; 289:20212613. [PMID: 35317670 PMCID: PMC8941408 DOI: 10.1098/rspb.2021.2613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86 000 km2 to depths of 500 m) to understand the abundance and distribution of Pacific hake (Merluccius productus), the target of the largest finfish fishery along the west coast of the USA. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data- or resource-limited contexts.
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Affiliation(s)
- Andrew Olaf Shelton
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Ana Ramón-Laca
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington at Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, WA 98112, USA
| | - Abigail Wells
- Lynker Technologies, Under Contract to Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Julia Clemons
- Fisheries Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Dezhang Chu
- Fisheries Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Blake E Feist
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Ave NE, Seattle, WA 98105, USA
| | - Sandra L Parker-Stetter
- Fisheries Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA.,Resource Assessment and Conservation Engineering Division, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - Rebecca Thomas
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Linda Park
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
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12
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Marques V, Castagné P, Polanco A, Borrero-Pérez GH, Hocdé R, Guérin PÉ, Juhel JB, Velez L, Loiseau N, Letessier TB, Bessudo S, Valentini A, Dejean T, Mouillot D, Pellissier L, Villéger S. Use of environmental DNA in assessment of fish functional and phylogenetic diversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1944-1956. [PMID: 34224158 DOI: 10.1111/cobi.13802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/19/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species' phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.
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Affiliation(s)
- Virginie Marques
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valery Montpellier 3, Montpellier, France
| | - Paul Castagné
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Andréa Polanco
- Instituto de Investigaciones Marinas y Costeras-INVEMAR, Colombia, Museo de Historia Natural Marina de Colombia (MHNMC), Programa de Biodiversidad y Ecosistemas Marinos, Santa Marta, Colombia
| | - Giomar Helena Borrero-Pérez
- Instituto de Investigaciones Marinas y Costeras-INVEMAR, Colombia, Museo de Historia Natural Marina de Colombia (MHNMC), Programa de Biodiversidad y Ecosistemas Marinos, Santa Marta, Colombia
| | - Régis Hocdé
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Pierre-Édouard Guérin
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valery Montpellier 3, Montpellier, France
| | | | - Laure Velez
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Nicolas Loiseau
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | - Sandra Bessudo
- Fundación Malpelo y Otros Ecosistemas Marinos, Bogotá, Colombia
| | | | | | - David Mouillot
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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13
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Stauffer S, Jucker M, Keggin T, Marques V, Andrello M, Bessudo S, Cheutin M, Borrero‐Pérez GH, Richards E, Dejean T, Hocdé R, Juhel J, Ladino F, Letessier TB, Loiseau N, Maire E, Mouillot D, Mutis Martinezguerra M, Manel S, Polanco Fernández A, Valentini A, Velez L, Albouy C, Pellissier L, Waldock C. How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? Ecol Evol 2021; 11:14630-14643. [PMID: 34765130 PMCID: PMC8571620 DOI: 10.1002/ece3.8150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 01/22/2023] Open
Abstract
Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one another. As a result, non-saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false-negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.
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Affiliation(s)
- Salomé Stauffer
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | - Meret Jucker
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | - Thomas Keggin
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Virginie Marques
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
- CEFEUniv. MontpellierCNRSEPHE‐PSL UniversityIRDUniv. Paul Valéry Montpellier 3MontpellierFrance
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine EnvironmentNational Research CouncilRomeItaly
| | - Sandra Bessudo
- Fundación Malpelo y otros ecosistemas marinosBogotáColombia
| | | | - Giomar Helena Borrero‐Pérez
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Eilísh Richards
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | | | - Régis Hocdé
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
| | | | - Felipe Ladino
- Fundación Malpelo y otros ecosistemas marinosBogotáColombia
| | - Tom B. Letessier
- Institute of ZoologyZoological Society of LondonLondonUK
- Marine Futures LabUniversity of Western AustraliaCrawleyWAAustralia
| | | | - Eva Maire
- Lancaster Environment CentreLancaster UniversityLancasterUK
| | | | - Maria Mutis Martinezguerra
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Stéphanie Manel
- CEFEUniv. MontpellierCNRSEPHE‐PSL UniversityIRDUniv. Paul Valéry Montpellier 3MontpellierFrance
| | - Andrea Polanco Fernández
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | | | - Laure Velez
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
| | - Camille Albouy
- IFREMERunité Écologie et Modèles pour l’HalieutiqueNantesFrance
| | - Loïc Pellissier
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Conor Waldock
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
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14
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Bravo H, Cheng CLY, Iannucci A, Natali C, Quadros A, Rhodes M, Yip MML, Cannicci S, Fratini S. A DNA barcode library for mangrove gastropods and crabs of Hong Kong and the Greater Bay Area reveals an unexpected faunal diversity associated with the intertidal forests of Southern China. BMC Ecol Evol 2021; 21:180. [PMID: 34556035 PMCID: PMC8459539 DOI: 10.1186/s12862-021-01914-6] [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: 06/08/2021] [Accepted: 09/15/2021] [Indexed: 11/30/2022] Open
Abstract
Background Mangroves are tropical and subtropical intertidal forests colonising sheltered coasts across the world. They host a unique faunal community, dominated by brachyuran crabs and gastropods. These invertebrates strongly contribute to the functionality of the entire forest. The reliable assessment of mangrove faunal diversity is, thus, a crucial step for efficient management and conservation plans, but it is hindered by difficulties in species identification. Here we provide a verified DNA barcode library for brachyuran crabs and gastropods inhabiting the mangroves of the Greater Bay Area, Southern China. In particular, we collected and morphologically identified 1100 specimens of mangrove associated brachyuran crabs and gastropods. The partial sequences of the mtDNA cytochrome oxidase subunit I gene were obtained from 275 specimens. Barcode sequences were then used to delineate Molecular Operational Taxonomic Units (MOTUs), employing three different delimitation methods: the automatic barcode gap discovery (ABGD) method, the general mixed Yule coalescent (GMYC) model and a Bayesian implementation of the Poisson tree processes (bPTP) model. Results By integrating DNA barcodes with morphology, we identified 44 gastropod species and 58 brachyuran species associated with Hong Kong mangroves, with five and seven new records, for gastropods and crabs, respectively, for the Greater Bay Area. The delineation of MOTUs based on barcode sequences revealed a strong congruence between morphological and molecular identification for both taxa, showing the high reliability of the barcode library. Conclusions This study provides the first reference barcode library for mangrove-associated macrobenthic fauna in the Greater Bay Area and represents a reliable tool to management and conservation plans. Our molecular analyses resolved long lasting taxonomic misidentifications and inconsistencies and updated the knowledge on the geographical distribution of Asian mangrove associated fauna, ultimately highlighting a level of biodiversity higher than previously thought for Southern China. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01914-6.
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Affiliation(s)
- Henrique Bravo
- The Swire Institute of Marine Science and Division for Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong S.A.R., People's Republic of China.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC, Groningen, The Netherlands
| | - Christine L Y Cheng
- The Swire Institute of Marine Science and Division for Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong S.A.R., People's Republic of China
| | - Alessio Iannucci
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Chiara Natali
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Aline Quadros
- The Swire Institute of Marine Science and Division for Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong S.A.R., People's Republic of China
| | - Martin Rhodes
- The Swire Institute of Marine Science and Division for Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong S.A.R., People's Republic of China
| | - Matthew M L Yip
- The Swire Institute of Marine Science and Division for Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong S.A.R., People's Republic of China
| | - Stefano Cannicci
- The Swire Institute of Marine Science and Division for Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong S.A.R., People's Republic of China. .,Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy.
| | - Sara Fratini
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
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15
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Drinkwater R, Williamson J, Clare EL, Chung AYC, Rossiter SJ, Slade E. Dung beetles as samplers of mammals in Malaysian Borneo-a test of high throughput metabarcoding of iDNA. PeerJ 2021; 9:e11897. [PMID: 34447624 PMCID: PMC8366524 DOI: 10.7717/peerj.11897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespread, with most terrestrial studies relying on DNA derived from the gut contents of blood-feeding invertebrates, such as leeches and mosquitoes. Dung beetles (superfamily Scarabaeoidea) primarily feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps, are globally distributed, and occur in a wide range of habitats. To build on the few existing studies demonstrating the potential of dung beetles as sources of mammalian DNA, we subjected the large-bodied, Bornean dung beetle (Catharsius renaudpauliani) to a controlled feeding experiment. We analysed DNA from gut contents at different times after feeding using qPCR techniques. Here, we first describe the window of DNA persistence within a dung beetle digestive tract. We found that the ability to successfully amplify cattle DNA decayed over relatively short time periods, with DNA copy number decreasing by two orders of magnitude in just 6 h. In addition, we sampled communities of dung beetles from a lowland tropical rainforest in Sabah, Malaysia, in order to test whether it is possible to identify vertebrate sequences from dung beetle iDNA. We sequenced both the gut contents from large dung beetle species, as well as whole communities of smaller beetles. We successfully identified six mammalian species from our samples, including the bearded pig (Sus barbatus) and the sambar deer (Rusa unicolor)—both vulnerable species on the IUCN red list. Our results represent the first use of dung beetle iDNA to sample Southeast Asian vertebrate fauna, and highlight the potential for dung beetle iDNA to be used in future biodiversity monitoring surveys.
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Affiliation(s)
- Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Joseph Williamson
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Arthur Y C Chung
- Sabah Forestry Department, Forest Research Centre, Sandakan, Malaysia
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Eleanor Slade
- Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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16
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Johnson MD, Scott JJ, Leray M, Lucey N, Bravo LMR, Wied WL, Altieri AH. Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. Nat Commun 2021; 12:4522. [PMID: 34312399 PMCID: PMC8313580 DOI: 10.1038/s41467-021-24777-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic community composition and microbial assemblages in a shallow tropical reef ecosystem. Conditions associated with the event precipitated coral bleaching and mass mortality, causing a 50% loss of live coral and a shift in the benthic community that persisted a year later. Conversely, the unique taxonomic and functional profile of hypoxia-associated microbes rapidly reverted to a normoxic assemblage one month after the event. The decoupling of ecological trajectories among these major functional groups following an acute event emphasizes the need to incorporate deoxygenation as an emerging stressor into coral reef research and management plans to combat escalating threats to reef persistence.
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Affiliation(s)
- Maggie D Johnson
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.
- Tennenbaum Marine Observatories Network, MarineGEO, Smithsonian Institution, Edgewater, MD, USA.
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Jarrod J Scott
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Noelle Lucey
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Lucia M Rodriguez Bravo
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - William L Wied
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Department of Biological Sciences, Center for Coastal Oceans Research, Florida International University, Miami, FL, USA
| | - Andrew H Altieri
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
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17
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Ely T, Barber PH, Man L, Gold Z. Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky reef environment. PLoS One 2021; 16:e0245314. [PMID: 34086697 PMCID: PMC8177635 DOI: 10.1371/journal.pone.0245314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/21/2021] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) is increasingly used to measure biodiversity of marine ecosystems, yet key aspects of the temporal dynamics of eDNA remain unknown. Of particular interest is in situ persistence of eDNA signals in dynamic marine environments, as eDNA degradation rates have predominantly been quantified through mesocosm studies. To determine in situ eDNA residence times, we introduced an eDNA signal from a non-native fish into a protected bay of a Southern California rocky reef ecosystem, and then measured changes in both introduced and background eDNA signals across a fixed transect over 96 hours. Foreign eDNA signal was no longer detected only 7.5 hours after introduction, a time substantially shorter than the multi-day persistence times in laboratory studies. Moreover, the foreign eDNA signal spread along the entire 38 m transect within 1.5 hours after introduction, indicating that transport and diffusion play a role in eDNA detectability even in protected low energy marine environments. Similarly, native vertebrate eDNA signals varied greatly over the 96 hours of observation as well as within two additional nearby fixed transects sampled over 120 hours. While community structure did significantly change across time of day and tidal direction, neither accounted for the majority of observed variation. Combined, results show that both foreign and native eDNA signatures can exhibit substantial temporal heterogeneity, even on hourly time scales. Further work exploring eDNA decay from lagrangian perspective and quantifying effects of sample and technical replication are needed to better understand temporal variation of eDNA signatures in nearshore marine environments.
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Affiliation(s)
- Taylor Ely
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lauren Man
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
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18
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Boulanger E, Loiseau N, Valentini A, Arnal V, Boissery P, Dejean T, Deter J, Guellati N, Holon F, Juhel JB, Lenfant P, Manel S, Mouillot D. Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves. Proc Biol Sci 2021; 288:20210112. [PMID: 33906403 PMCID: PMC8080007 DOI: 10.1098/rspb.2021.0112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Abstract
Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.
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Affiliation(s)
- Emilie Boulanger
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Nicolas Loiseau
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | - Véronique Arnal
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Pierre Boissery
- Agence de l'Eau Rhône-Méditerranée-Corse, Délégation de Marseille, Marseille, France
| | | | | | - Nacim Guellati
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
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19
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Progress on Research Regarding Ecology and Biodiversity of Coastal Fisheries and Nektonic Species and Their Habitats within Coastal Landscapes. DIVERSITY 2021. [DOI: 10.3390/d13040168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This paper aims to highlight the new research and significant advances in our understanding of links between coastal habitat quality/quantity/diversity and the diversity of fisheries species and other mobile aquatic species (hereafter nekton) that use them within coastal landscapes. This topic is quite diverse owing to the myriad of habitat types found in coastal marine waters and the variety of life history strategies fisheries species and nekton use in these environments. Thus, we focus our review on five selective but relevant topics, habitat templates, essential fish habitat, habitat mosaics/habitat connectivity, transitory/ephemeral habitat, and the emerging/maturing approaches to the study of fish-habitat systems as a roadmap to its development. We have highlighted selected important contributions in the progress made on each topic to better identify and quantify landscape scale interactions between living biota and structured habitats set within a dynamic landscape.
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20
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Antich A, Palacin C, Wangensteen OS, Turon X. To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics 2021; 22:177. [PMID: 33820526 PMCID: PMC8020537 DOI: 10.1186/s12859-021-04115-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. RESULTS Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in different orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little influence on the final outcome. CONCLUSIONS We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain
| | - Creu Palacin
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona and Research Institute of Biodiversity (IRBIO), Barcelona, Catalonia, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsö, Norway.
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain.
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21
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de Jonge DSW, Merten V, Bayer T, Puebla O, Reusch TBH, Hoving HJT. A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201388. [PMID: 33972853 PMCID: PMC8074623 DOI: 10.1098/rsos.201388] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/04/2021] [Indexed: 05/19/2023]
Abstract
Cephalopods are pivotal components of marine food webs, but biodiversity studies are hampered by challenges to sample these agile marine molluscs. Metabarcoding of environmental DNA (eDNA) is a potentially powerful technique to study oceanic cephalopod biodiversity and distribution but has not been applied thus far. We present a novel universal primer pair for metabarcoding cephalopods from eDNA, Ceph18S (Forward: 5'-CGC GGC GCT ACA TAT TAG AC-3', Reverse: 5'-GCA CTT AAC CGA CCG TCG AC-3'). The primer pair targets the hypervariable region V2 of the nuclear 18S rRNA gene and amplifies a relatively short target sequence of approximately 200 bp in order to allow the amplification of degraded DNA. In silico tests on a reference database and empirical tests on DNA extracts from cephalopod tissue estimate that 44-66% of cephalopod species, corresponding to about 310-460 species, can be amplified and identified with this primer pair. A multi-marker approach with the novel Ceph18S and two previously published cephalopod mitochondrial 16S rRNA primer sets targeting the same region (Jarman et al. 2006 Mol. Ecol. Notes. 6, 268-271; Peters et al. 2015 Mar. Ecol. 36, 1428-1439) is estimated to amplify and identify 89% of all cephalopod species, of which an estimated 19% can only be identified by Ceph18S. All sequences obtained with Ceph18S were submitted to GenBank, resulting in new 18S rRNA sequences for 13 cephalopod taxa.
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Affiliation(s)
- Daniëlle S. W. de Jonge
- Faculty of Mathematics and Natural Sciences, University of Groningen, Groningen, The Netherlands
| | - Véronique Merten
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Till Bayer
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Oscar Puebla
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Ecology Department, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Thorsten B. H. Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Henk-Jan T. Hoving
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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22
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Ladin ZS, Ferrell B, Dums JT, Moore RM, Levia DF, Shriver WG, D'Amico V, Trammell TLE, Setubal JC, Wommack KE. Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems. Sci Rep 2021; 11:1629. [PMID: 33452291 PMCID: PMC7811025 DOI: 10.1038/s41598-020-80602-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.
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Affiliation(s)
- Zachary S Ladin
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA.
| | - Barbra Ferrell
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
| | - Jacob T Dums
- Biotechnology Program, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ryan M Moore
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
| | - Delphis F Levia
- Department of Entomology and Wildlife Ecology, University of Delaware, 250 Townsend Hall, Newark, DE, 19716, USA
| | - W Gregory Shriver
- Departments of Geography and Spatial Sciences and Plant and Soil Sciences, University of Delaware, 216C Pearson Hall, Newark, DE, 19716, USA
| | - Vincent D'Amico
- US Forest Service, Northern Research Station, Newark, DE, USA
| | - Tara L E Trammell
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA
| | - João Carlos Setubal
- Instituto de Química, University of Sao Paulo, São Paulo, SP, 05508-000, Brazil
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA
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23
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Leray M, Machida RJ. Seabed mining could come at a high price for a unique fauna. Mol Ecol 2020; 29:4506-4509. [PMID: 33030747 DOI: 10.1111/mec.15678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 11/29/2022]
Abstract
The deep seafloor is teeming with life, most of which remains poorly known to science. It also constitutes an important reserve of natural resources, particularly minerals, that mining companies will start harvesting in the next few years (Nat Rev Earth Environ, 1, 2020, 158). In this context, broad biodiversity assessments of deep-sea ecosystems are urgently needed to establish a baseline prior to mining. However, significant gaps in our taxonomic knowledge and the high cost of sampling in the deep sea limit the effectiveness of conventional morphology-based surveys. In this issue of Molecular Ecology, Laroche et al. (Mol Ecol, 2020) capitalize on high throughput molecular methods to conduct one of the most detailed and rigorous surveys of the composition and biogeography of deep-seafloor metazoan communities to date. The authors show that deep seamounts in the Clarion Clipperton Zone are inhabited by rich metazoan communities that are distinct from those of the surrounding abyssal plains. These results have important conservation implications: if communities on deep seamounts were to persist after large-scale industrial mining operations on the surrounding plains, the seamounts would not serve as appropriate reservoirs to repopulate impacted areas.
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Affiliation(s)
- Matthieu Leray
- Smithsonian Tropical Research Institute, Ancon, Republic of Panama
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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