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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.
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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.
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2
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den Bulcke Laure V, Annelies DB, Hans H, Sara M, Stephie S, Willem W, Jan W, Kris H, Sofie D. Comparative study of traditional and DNA-based methods for environmental impact assessment: A case study of marine aggregate extraction in the North Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174106. [PMID: 38908576 DOI: 10.1016/j.scitotenv.2024.174106] [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: 01/09/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Environmental impact assessments of marine aggregate extraction are traditionally conducted based on morphological characteristics of macrobenthos, which is time-consuming, labour-intensive and requires specific taxonomic expert knowledge. Bulk DNA metabarcoding is suggested as a promising alternative. This study compares the traditional morphological and the bulk DNA metabarcoding method to assess the impact of sand extraction activities on three sandbanks in the Belgian North Sea. Substantial differences in the detected species were observed between methods: Abundant and/or large macrobenthos species were detected by both methods, while small species or species with an exoskeleton were usually only detected by the morphological method. Taxa uniquely detected by bulk DNA metabarcoding could be explained by specimens identified at a higher taxonomic level by morphology, or by specimens with very low read numbers, probably representing species missed in the morphological sorting process, DNA traces on the specimens or false positives during PCR amplification efficiency. Despite the difference in detected species, comparable alpha and beta diversity patterns were observed by both methods, indicating that bulk DNA metabarcoding can effectively detect the overall ecological changes associated with sand extraction. We further demonstrate that bulk DNA metabarcoding reduces sample processing both in time (44 % faster) and cost (26 % cheaper) compared to the morphology-based identification. However, biomass quantification remains challenging for bulk DNA metabarcoding since of the ten most abundant genera, only two genera (Echinocardium and Ophelia) showed a significant positive correlation between biomass and read numbers. Additionally, bulk DNA metabarcoding does not provide information on life stages or size of the identified specimens. As such, our results underpin the complementary nature of both methods, wherein DNA-based analyses allow for rapid detection of community changes (as similar patterns in alpha and beta diversity and biotic index were observed), while morphology-based analyses provide additional information on e.g. secondary production (biomass) and size composition. We show how the strengths of both methods can be combined to assess the impact of sand extraction.
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Affiliation(s)
- Van den Bulcke Laure
- Flanders Research Institute for Agriculture, Fisheries and Food - Animal Science Unit, Jacobsenstraat 1, 8400 Oostende, Belgium.
| | - De Backer Annelies
- Flanders Research Institute for Agriculture, Fisheries and Food - Animal Science Unit, Jacobsenstraat 1, 8400 Oostende, Belgium
| | - Hillewaert Hans
- Flanders Research Institute for Agriculture, Fisheries and Food - Animal Science Unit, Jacobsenstraat 1, 8400 Oostende, Belgium
| | - Maes Sara
- Flanders Research Institute for Agriculture, Fisheries and Food - Animal Science Unit, Jacobsenstraat 1, 8400 Oostende, Belgium
| | - Seghers Stephie
- Flanders Research Institute for Agriculture, Fisheries and Food - Animal Science Unit, Jacobsenstraat 1, 8400 Oostende, Belgium
| | - Waegeman Willem
- University of Ghent, Department of Data Analysis and Mathematical Modelling: Knowledge-based Systems Research Group, Coupure Links 653, 9000 Gent, Belgium
| | - Wittoeck Jan
- Flanders Research Institute for Agriculture, Fisheries and Food - Animal Science Unit, Jacobsenstraat 1, 8400 Oostende, Belgium
| | - Hostens Kris
- Flanders Research Institute for Agriculture, Fisheries and Food - Animal Science Unit, Jacobsenstraat 1, 8400 Oostende, Belgium
| | - Derycke Sofie
- Flanders Research Institute for Agriculture, Fisheries and Food - Animal Science Unit, Jacobsenstraat 1, 8400 Oostende, Belgium; University of Ghent, Department of Biology: Marine Biology Research Group, Krijgslaan 281, 9000 Gent, Belgium
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3
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Chandler L, Harford AJ, Hose GC, Humphrey CL, Chariton A, Greenfield P, Davis J. Saline mine water influences eukaryote life in shallow groundwater of a tropical sandy stream. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174101. [PMID: 38906296 DOI: 10.1016/j.scitotenv.2024.174101] [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: 02/28/2024] [Revised: 05/21/2024] [Accepted: 06/16/2024] [Indexed: 06/23/2024]
Abstract
Eukaryotic communities in groundwater may be particularly sensitive to disturbance because they are adapted to stable environmental conditions and often have narrow spatial distributions. Traditional methods for characterising these communities, focussing on groundwater-inhabiting macro- and meiofauna (stygofauna), are challenging because of limited taxonomic knowledge and expertise (particularly in less-explored regions), and the time and expense of morphological identification. The primary objective of this study was to evaluate the vulnerability of eukaryote communities in shallow groundwater to mine water discharge containing elevated concentrations of magnesium (Mg) and sulfate (SO4). The study was undertaken in a shallow sand bed aquifer within a wet-dry tropical setting. The aquifer, featuring a saline mine water gradient primarily composed of elevated Mg and SO4, was sampled from piezometers in the creek channel upstream and downstream of the mine water influence during the dry season when only subsurface water flow was present. Groundwater communities were characterised using both morphological assessments of stygofauna from net samples and environmental DNA (eDNA) targeting the 18S rDNA and COI mtDNA genes. eDNA data revealed significant shifts in community composition in response to mine waters, contrasting with findings from traditional morphological composition data. Changes in communities determined using eDNA data were notably associated with concentrations of SO42-, Mg2+ and Na+, and water levels in the piezometers. This underscores the importance of incorporating molecular approaches in impact assessments, as relying solely on traditional stygofauna sampling methods in similar environments may lead to inaccurate conclusions about the responses of the assemblage to studied impacts.
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Affiliation(s)
- Lisa Chandler
- Research Institute for the Environment and Livelihoods, Faculty of Science and Technology, Charles Darwin University, Darwin, Northern Territory, Australia; Office of the Supervising Scientist, Department of Climate Change, Energy, the Environment and Water, Darwin, Northern Territory, Australia
| | - Andrew J Harford
- Research Institute for the Environment and Livelihoods, Faculty of Science and Technology, Charles Darwin University, Darwin, Northern Territory, Australia; Office of the Supervising Scientist, Department of Climate Change, Energy, the Environment and Water, Darwin, Northern Territory, Australia
| | - Grant C Hose
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia.
| | - Chris L Humphrey
- Office of the Supervising Scientist, Department of Climate Change, Energy, the Environment and Water, Darwin, Northern Territory, Australia
| | - Anthony Chariton
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Paul Greenfield
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - Jenny Davis
- Research Institute for the Environment and Livelihoods, Faculty of Science and Technology, Charles Darwin University, Darwin, Northern Territory, Australia
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Song CU, Purnaningtyas DW, Choi H, Jeon D, Kim S, Hwang H, Kim CG, Lee YH, Eyun SI. Do red tide events promote an increase in zooplankton biodiversity? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 361:124880. [PMID: 39236840 DOI: 10.1016/j.envpol.2024.124880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/30/2024] [Accepted: 09/01/2024] [Indexed: 09/07/2024]
Abstract
Red tides occurring off the southern coast of Korea impact the marine ecosystem and aquaculture industries. Zooplankton are crucial in the food web, connecting primary producers to higher predators and interact diversely with red tide organisms. This study explores dynamics of the zooplankton community over seven years including three red tide and four non-red tide years in Tongyeong using metabarcoding. In non-red tide years, zooplankton diversity showed typical seasonal patterns, increasing from June to early October. However, during red tide years, diversity remained high, with a shift in species composition-decreased Copepoda and increased Branchiopoda, Echinodermata, Malacostraca, and Annelida. Diversity indices were significantly higher in red tide years across all periods except for the richness in "after" that showed an insignificant higher value. The differences in zooplankton assemblages across periods were influenced by surface temperatures and the density of the red tide-causing alga Margalefidinium polykrikoides. Eight species emerged as indicator species and showed direct correlations with M. polykrikoides and among them, seven species were indicator species for red tide occurrence years. The ecological characteristics of M. polykrikoides blooms and their recurrent occurrences over several decades suggest that zooplankton may adapt to the toxins and use these blooms as spawning cues. Overall, this study provides comprehensive understanding on changes in zooplankton communities during red tide events, offering novel insights into their ecology.
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Affiliation(s)
- Chi-Une Song
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | | | - Hyeongwoo Choi
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Donggu Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Sung Kim
- Korea Institute of Ocean Science and Technology, Busan, 49111, South Korea
| | - Hyenjung Hwang
- Korea Institute of Ocean Science and Technology, Busan, 49111, South Korea
| | - Choong-Gon Kim
- Korea Institute of Ocean Science and Technology, Busan, 49111, South Korea
| | - Youn-Ho Lee
- KIOST School, University of Science and Technology, Busan, 49111, South Korea.
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea.
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5
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Zhang Z, Bao Y, Fang X, Ruan Y, Rong Y, Yang G. A circumpolar study of surface zooplankton biodiversity of the Southern Ocean based on eDNA metabarcoding. ENVIRONMENTAL RESEARCH 2024; 255:119183. [PMID: 38768883 DOI: 10.1016/j.envres.2024.119183] [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: 03/03/2024] [Revised: 05/02/2024] [Accepted: 05/18/2024] [Indexed: 05/22/2024]
Abstract
Under pressure from climate change and fishing, the Southern Ocean ecosystems have been changing. Zooplankton plays a vital role in the food web of the Southern Ocean and is crucial for maintaining ecosystem stability. Investigating the circumpolar-scale species composition and biodiversity of zooplankton is crucial for ensuring ecosystem-based conservation and management of the Southern Ocean in a changing climate. Here, we utilized eDNA metabarcoding to assess the biodiversity of zooplankton in the surface seawater surrounding the Antarctica based on samples collected during two expeditions spanning from 2021 to 2022. The main purpose of this paper is to provide more baseline information about circumpolar zooplankton biodiversity based on the emerging eDNA metabarcoding tool. This comprehensive approach led to the identification of over 300 distinct zooplankton species, forming a diverse community dominated by Jellyfish, Mollusca and Polychaete. Surprisingly, common dominant taxonomic groups such as krill and copepods in the Southern Ocean did not show high relative abundance (reads) in surface seawater. The results of redundancy analysis (RDA) and correlation analysis highlighted that water temperature and chlorophyll a had the most significant impact on the reads and diversity of zooplankton. Notably, the influence of water temperature on zooplankton seemed to be primarily indirect, potentially mediated by its effects on primary productivity. Increasing in primary production might lead to lower zooplankton biodiversity in the Southern Ocean in future. This research underscores the effectiveness of eDNA metabarcoding as a valuable tool for monitoring zooplankton diversity in open seas. Given the ongoing changes in temperature, sea ice extent and their impact on primary production, our findings lay a crucial foundation for using eDNA techniques to establish long-term biodiversity monitoring programs across extensive marine ecosystems in the future.
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Affiliation(s)
- Zishang Zhang
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China; Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Yongchao Bao
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Xiaoyue Fang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Yilin Ruan
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Yue Rong
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Guang Yang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
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6
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Claver C, Rodríguez-Ezpeleta N, Irigoien X, Canals O. Global distribution patterns of siphonophores across horizontal and vertical oceanic gradients. OPEN RESEARCH EUROPE 2024; 4:177. [PMID: 39279823 PMCID: PMC11399771 DOI: 10.12688/openreseurope.18226.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/30/2024] [Indexed: 09/18/2024]
Abstract
Background Siphonophores are diverse, globally distributed hydrozoans that play a central role in marine trophic webs worldwide. However, they still constitute an understudied fraction of the open ocean gelatinous taxa, mainly due to challenges related to siphonophore sampling and identification, which have led to a general knowledge gap about their diversity, distribution and abundance. Methods Here, we provide a global overview of the oceanic vertical distribution of siphonophores using DNA metabarcoding data from 77 bulk mesozooplankton samples collected at four different depth ranges (0-200, 200-500, 500-1000, 1000-3000 m depth) along the Atlantic, Pacific, and Indian Oceans during the MALASPINA-2010 circumnavigation expedition. Results We detected a total of 44 siphonophore species (which represents about one quarter of the described siphonophore species) from which 26 corresponded to Calycophores, 14 to Physonectae and 2 to Cystonectae. Our results suggest wider horizontal and vertical distributions of siphonophore species than previously described, including novel records of some species in certain oceanic basins. Also, we provide insights into the intraspecific variation of widely distributed species. Finally, we show a vertical structuring of siphonophores along the water column; Calycophores (siphonophores without pneumatophores) dominated the epipelagic (from the surface to 200 m depth) and upper mesopelagic layers (from 200 to 500 m depth), while the proportion Physonectids (siphonophores with pneumatophore) notably increased below 500 meters and were dominant at bathypelagic depths (>1000 m depth). Conclusions Our results support that the siphonophore community composition is vertically structured. Also, we provide insights into the potential existence of genetic variations within certain species that dominate some ocean basins or depth ranges. To our knowledge, this is the first time that DNA metabarcoding data is retrieved to study siphonophore distribution patterns, and the study provides evidence of the potential of molecular techniques to study the distribution of gelatinous organisms often destroyed in net sampling.
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Affiliation(s)
- Cristina Claver
- Marine Research Division, Basque Research and Technology Alliance (BRTA), AZTI Foundation Sukarrieta, Sukarrieta, Vizcaya, 48395, Spain
| | - Naiara Rodríguez-Ezpeleta
- Marine Research Division, Basque Research and Technology Alliance (BRTA), AZTI Foundation Sukarrieta, Sukarrieta, Vizcaya, 48395, Spain
| | - Xabier Irigoien
- Education Research and Innovation Foundation, NEOM Base Camp, Building Number: 4758, Ocean Science and Solutions Applied Research Institute (OSSARI), NEOM, 49643, Saudi Arabia
| | - Oriol Canals
- Marine Research Division, Basque Research and Technology Alliance (BRTA), AZTI Foundation Sukarrieta, Sukarrieta, Vizcaya, 48395, Spain
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7
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Dias HQ, Sukumaran S. Are genomic indices effective alternatives to morphology based benthic indices in biomonitoring studies? Perspectives from a major harbour and marine protected area. MARINE POLLUTION BULLETIN 2023; 187:114586. [PMID: 36652865 DOI: 10.1016/j.marpolbul.2023.114586] [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: 06/29/2022] [Revised: 12/01/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Ecological assessments are currently being conducted by traditional morpho-taxonomical identification techniques that are time-consuming and often inaccurate. Biomonitoring programs are increasingly being complemented by the more rapid and efficient DNA barcoding approach. We compared the congruency of morpho-taxonomic (AMBI - AZTI's Marine Biotic Index) and genomic (gAMBI) benthic indices in ecological quality status (EcoQS) assignation in Mumbai harbour and Malvan Marine Protected area (MPA). The study, first of its kind to adopt the gAMBI tool in the selected milieu, contributed substantial number of macrobenthic cytochrome c oxidase subunit I gene (COI) sequences that were previously unavailable in the reference library, adding sufficient genetic resources for establishing ecostatus. AMBI and gAMBI values based on presence/absence data related significantly with those derived from abundance data matrices. Taxonomic and genomic indices derived ecostatus corresponded sufficiently well despite minor discrepancies, underscoring the viability of gAMBI as a superior alternative to AMBI in monitoring studies.
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Affiliation(s)
- Heidy Q Dias
- CSIR-National Institute of Oceanography, Regional Centre Andheri (W), Mumbai 400 053, India
| | - Soniya Sukumaran
- CSIR-National Institute of Oceanography, Regional Centre Andheri (W), Mumbai 400 053, India.
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Gaonkar CC, Campbell L. Metabarcoding reveals high genetic diversity of harmful algae in the coastal waters of Texas, Gulf of Mexico. HARMFUL ALGAE 2023; 121:102368. [PMID: 36639185 DOI: 10.1016/j.hal.2022.102368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/10/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Environmental-DNA (eDNA) for metabarcoding is a rapid and effective means to investigate microplankton community composition and species diversity. The objective of this study was to examine the genetic diversity of the phytoplankton community in the Gulf of Mexico, with particular emphasis on harmful algal bloom species. Samples were collected at stations along the coast of Texas in September-October 2017 that were inundated by low salinity waters in the aftermath of Hurricane Harvey. Metabarcodes were generated from the eDNA targeting both the V4 and V8-V9 regions of the 18S rDNA gene. Evaluation of the metabarcodes revealed an unexpectedly high number of harmful algal species during this short period, including five that had not been documented in this region previously. A total of 36 harmful algal species could be differentiated based on V4 and V8-V9 metabarcode markers. Using a phylogenetic approach, the taxonomic resolution of each marker differed and not all species could be differentiated using solely one marker. The V4 region resolved species within some genera (e.g., Heterocapsa), while the V8-V9 marker was necessary to resolve species within other genera (e.g., Chattonella). In other cases, species differentiation within a genus required a combination of both markers (e.g., Prorocentrum, Karenia), or another marker will be needed to resolve all species (e.g., Alexandrium, Dinophysis). We conclude that no single marker can delineate all species, so it is recommended HAB monitoring programs use more than one marker. Overall, the observed diversity of HAB species along the Texas coast using metabarcoding exceeded reports from other parts of the world.
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Affiliation(s)
- Chetan C Gaonkar
- Department of Oceanography, Texas A&M University, College Station, TX 77843, USA
| | - Lisa Campbell
- Department of Oceanography, Texas A&M University, College Station, TX 77843, USA.
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Dornan T, Fielding S, Saunders RA, Genner MJ. Large mesopelagic fish biomass in the Southern Ocean resolved by acoustic properties. Proc Biol Sci 2022; 289:20211781. [PMID: 35078354 PMCID: PMC8790350 DOI: 10.1098/rspb.2021.1781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
The oceanic mesopelagic zone, 200-1000 m below sea level, holds abundant small fishes that play central roles in ecosystem function. Global mesopelagic fish biomass estimates are increasingly derived using active acoustics, where echosounder-generated signals are emitted, reflected by pelagic organisms and detected by transducers on vessels. Previous studies have interpreted a ubiquitous decline in acoustic reflectance towards the Antarctic continent as a reduction in mesopelagic fish biomass. Here, we use empirical data to estimate species-specific acoustic target strength for the dominant mesopelagic fish of the Scotia Sea in the Southern Ocean. We use these data, alongside estimates of fish relative abundance from net surveys, to interpret signals received in acoustic surveys and calculate mesopelagic biomass of the broader Southern Ocean. We estimate the Southern Ocean mesopelagic fish biomass to be approximately 274 million tonnes if Antarctic krill contribute to the acoustic signal, or 570 million tonnes if mesopelagic fish alone are responsible. These quantities are approximately 1.8 and 3.8 times greater than previous net-based biomass estimates. We also show a peak in fish biomass towards the seasonal ice-edge, corresponding to the preferred feeding grounds of penguins and seals, which may be at risk under future climate change scenarios. Our study provides new insights into the abundance and distributions of ecologically significant mesopelagic fish stocks across the Southern Ocean ecosystem.
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Affiliation(s)
- Tracey Dornan
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Sophie Fielding
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Ryan A. Saunders
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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Hu J, Pentinsaari M, Hebert PD. Measuring mass: variation among 3,161 species of Canadian Coleoptera and the prospects of a mass registry for all insects. PeerJ 2022; 10:e12799. [PMID: 35116199 PMCID: PMC8785658 DOI: 10.7717/peerj.12799] [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: 11/03/2021] [Accepted: 12/24/2021] [Indexed: 01/10/2023] Open
Abstract
Although biomass values are critical for diverse ecological and evolutionary analyses, they are unavailable for most insect species. Museum specimens have the potential to address this gap, but the variation introduced by sampling and preservation methods is uncertain. This study quantifies species-level variation in the body mass of Canadian Coleoptera based on the analysis of 3,744 specimens representing 3,161 Barcode Index Number (BIN) clusters. Employing the BIN system as a proxy for species allows the inclusion of groups where the taxonomic impediment prevents the assignment of specimens to a Linnaean species. By validating the reproducibility of measurements and evaluating the error introduced by operational complexities such as curatorial practice and the loss of body parts, this study demonstrates that museum specimens can speed the assembly of a mass registry. The results further indicate that congeneric species of Coleoptera generally have limited variation in mass, so a genus-level identification allows prediction of the body mass of species that have not been weighed or measured. Building on the present results, the construction of a mass registry for all insects is feasible.
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Affiliation(s)
- Jingchan Hu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
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Van den Bulcke L, De Backer A, Ampe B, Maes S, Wittoeck J, Waegeman W, Hostens K, Derycke S. Towards harmonization of DNA metabarcoding for monitoring marine macrobenthos: the effect of technical replicates and pooled DNA extractions on species detection. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.71107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
DNA-based monitoring methods are potentially faster and cheaper compared to traditional morphological benthic identification. DNA metabarcoding involves various methodological choices which can introduce bias leading to a different outcome in biodiversity patterns. Therefore, it is important to harmonize DNA metabarcoding protocols to allow comparison across studies and this requires a good understanding of the effect of methodological choices on diversity estimates. This study investigated the impact of DNA and PCR replicates on the detection of macrobenthos species in locations with high, medium and low diversity. Our results show that two to three DNA replicates were needed in locations with a high and medium diversity to detect at least 80% of the species found in the six DNA replicates, while three to four replicates were needed in the location with low diversity. In contrast to general belief, larger body size or higher abundance of the species in a sample did not increase its detection prevalence among DNA replicates. However, rare species were less consistently detected across all DNA replicates of the location with high diversity compared to locations with less diversity. Our results further show that pooling of DNA replicates did not significantly alter diversity patterns, although a small number of rare species was lost. Finally, our results confirm high variation in species detection between PCR replicates, especially for the detection of rare species. These results contribute to create reliable, time and cost efficient metabarcoding protocols for the characterization of macrobenthos.
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Zooplankton diversity monitoring strategy for the urban coastal region using metabarcoding analysis. Sci Rep 2021; 11:24339. [PMID: 34934104 PMCID: PMC8692418 DOI: 10.1038/s41598-021-03656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/29/2021] [Indexed: 11/12/2022] Open
Abstract
Marine ecosystems in urban coastal areas are exposed to many risks due to human activity. Thus, long-term and continuous monitoring of zooplankton diversity is necessary. High-throughput DNA metabarcoding has gained recognition as an efficient and highly sensitive approach to accurately describing the species diversity of marine zooplankton assemblages. In this study, we collected 30 zooplankton samples at about 2-week intervals for 1 year. Zooplankton diversity showing a typical four season pattern. Of the “total” and “common” zooplankton, we assigned 267 and 64 taxa. The cluster structure and seasonal diversity pattern were rough when only the “common” zooplankton was used. Our study examined how to maximize the benefits of metabarcoding for monitoring zooplankton diversity in urban coastal areas. The results suggest that to take full advantage of metabarcoding when monitoring a zooplankton community, it is necessary to carefully investigate potential ecosystem threats (non-indigenous species) through sufficient curation rather than disregarding low-abundance operational taxonomic units.
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Clarke LJ, Suter L, Deagle BE, Polanowski AM, Terauds A, Johnstone GJ, Stark JS. Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ 2021; 9:e12458. [PMID: 34820189 PMCID: PMC8601059 DOI: 10.7717/peerj.12458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023] Open
Abstract
Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
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Affiliation(s)
- Laurence J Clarke
- Australian Antarctic Division, Kingston, Tasmania, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Leonie Suter
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Bruce E Deagle
- Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, Australia
| | | | - Aleks Terauds
- Australian Antarctic Division, Kingston, Tasmania, Australia
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Sildever S, Laas P, Kolesova N, Lips I, Lips U, Nagai S. Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.72371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Metabarcoding in combination with high-throughput sequencing (HTS) allows simultaneous detection of multiple taxa by targeting single or several taxonomically informative gene regions from environmental DNA samples. In this study, a multiple-marker HTS approach was applied to investigate the plankton diversity and seasonal succession in the Baltic Sea from winter to autumn. Four different markers targeting the 16S, 18S, and 28S ribosomal RNA genes were employed, including a marker for more efficient dinoflagellate detection. Typical seasonal changes were observed in phyto- and bacterioplankton communities. In phytoplankton, the appearance patterns of selected common, dominant, or harmful species followed the patterns also confirmed based on 20 years of phytoplankton monitoring data. In the case of zooplankton, both macro- and microzooplankton species were detected. However, no seasonal patterns were detected in their appearance. In total, 15 and 2 new zoo- and phytoplankton species were detected from the Baltic Sea. HTS approach was especially useful for detecting microzooplankton species as well as for investigating the co-occurrence and potential interactions of different taxa. The results of this study further exemplify the efficiency of metabarcoding for biodiversity monitoring and the advantage of employing multiple markers through the detection of species not identifiable based on a single marker survey and/or by traditional morphology-based methods.
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Elbrecht V, Bourlat SJ, Hörren T, Lindner A, Mordente A, Noll NW, Schäffler L, Sorg M, Zizka VMA. Pooling size sorted Malaise trap fractions to maximize taxon recovery with metabarcoding. PeerJ 2021; 9:e12177. [PMID: 34707928 PMCID: PMC8500090 DOI: 10.7717/peerj.12177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/29/2021] [Indexed: 12/22/2022] Open
Abstract
Background Small and rare specimens can remain undetected when metabarcoding is applied on bulk samples with a high specimen size heterogeneity. This is especially critical for Malaise trap samples, where most of the biodiversity is contributed by small taxa with low biomass. The separation of samples in different size fractions for downstream analysis is one possibility to increase detection of small and rare taxa. However, experiments systematically testing different size sorting approaches and subsequent proportional pooling of fractions are lacking, but would provide important information for the optimization of metabarcoding protocols. We set out to find a size sorting strategy for Malaise trap samples that maximizes taxonomic recovery but remains scalable and time efficient. Methods Three Malaise trap samples were sorted into four size classes using dry sieving. Each fraction was homogenized and lysed. The corresponding lysates were pooled to simulate unsorted samples. Pooling was additionally conducted in equal proportions and in four different proportions enriching the small size fraction of samples. DNA from the individual size classes as well as the pooled fractions was extracted and metabarcoded using the FwhF2 and Fol-degen-rev primer set. Additionally, alternative wet sieving strategies were explored. Results The small size fractions harboured the highest diversity and were best represented when pooling in favour of small specimens. Metabarcoding of unsorted samples decreases taxon recovery compared to size sorted samples. A size separation into only two fractions (below 4 mm and above) can double taxon recovery compared to not size sorting. However, increasing the sequencing depth 3- to 4-fold can also increase taxon recovery to levels comparable with size sorting, but remains biased towards biomass rich taxa in the sample. Conclusion We demonstrate that size fractionation of Malaise trap bulk samples can increase taxon recovery. While results show distinct patterns, the lack of statistical support due to the limited number of samples processed is a limitation. Due to increased speed and lower risk of cross-contamination as well as specimen damage we recommend wet sieving and proportional pooling of the lysates in favour of the small size fraction (80–90% volume). However, for large-scale projects with time constraints, increasing sequencing depth is an alternative solution.
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Affiliation(s)
- Vasco Elbrecht
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany.,SimplexDNA AG, Winterthur, Switzerland
| | - Sarah J Bourlat
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Angie Lindner
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Adriana Mordente
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Niklas W Noll
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Livia Schäffler
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Martin Sorg
- Entomological Society Krefeld, Krefeld, Germany
| | - Vera M A Zizka
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
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17
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Kim JY, Yi M, Kim M, Lee S, Moon HS, Yong D, Yong T. Measuring the absolute abundance of the microbiome by adding yeast containing 16S rRNA gene from a hyperthermophile. Microbiologyopen 2021; 10:e1220. [PMID: 34459541 PMCID: PMC8302012 DOI: 10.1002/mbo3.1220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 11/09/2022] Open
Abstract
High-throughput sequencing (HTS) of 16S rRNA gene amplicons provides compositional information regarding the microbial community, but not the absolute abundance of the bacteria. We aimed to develop a standardized method for quantifying the absolute abundance of bacteria in microbiome studies. To demonstrate the utility of our approach, we quantified the number of bacteria from the compositional data of the fecal and cecal microbiomes. The 16S rRNA gene of a hyperthermophile, Thermus aquaticus, was cloned into Pichia pastoris (yeast) genome, and an equivalent amount of the yeast was added to the stool and cecal samples of mice before DNA extraction. 16S rRNA gene library construction and HTS were performed after DNA extraction. The absolute abundances of bacteria were calculated using T. aquaticus reads. The average relative abundances of T. aquaticus in the five stool and five cecal samples were 0.95% and 0.33%, respectively, indicating that the number of bacteria in a cecum sample is 2.9 times higher than that in a stool sample. The method proposed for quantifying the absolute abundance of the bacterial population in this study is expected to overcome the limitation of showing only compositional data in most microbiome studies.
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Affiliation(s)
- Ju Yeong Kim
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
- Brain Korea 21 PLUS Project for Medical ScienceYonsei University College of MedicineSeoulKorea
| | - Myung‐hee Yi
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| | - Myungjun Kim
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| | - Seogwon Lee
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| | - Hye Su Moon
- Department of Laboratory Medicine and Research Institute of Bacterial ResistanceYonsei University College of MedicineSeoulKorea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial ResistanceYonsei University College of MedicineSeoulKorea
| | - Tai‐Soon Yong
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
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van der Loos LM, Nijland R. Biases in bulk: DNA metabarcoding of marine communities and the methodology involved. Mol Ecol 2021; 30:3270-3288. [PMID: 32779312 PMCID: PMC8359149 DOI: 10.1111/mec.15592] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/28/2020] [Indexed: 12/22/2022]
Abstract
With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly being implemented in ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, preprocessing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of three PCR replicates, and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide-ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments and the use of whole-genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, if appropriate controls are included along the data generation process, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments.
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Affiliation(s)
- Luna M. van der Loos
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
- Present address:
Department of BiologyPhycology Research GroupGhent UniversityGhentBelgium
| | - Reindert Nijland
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
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Georges O, Fernández S, Martinez JL, Garcia-Vazquez E. DNA metabarcoding illustrates biological pollution threats of Red Sea - Dead Sea water conveyance to Dead Sea biodiversity. MARINE POLLUTION BULLETIN 2021; 168:112451. [PMID: 33971452 DOI: 10.1016/j.marpolbul.2021.112451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
The Dead Sea has a hypersaline environment where only extremophile species like Archaea, Bacteria, and fungi can survive. The Red Sea-Dead Sea Water Conveyance (RDSC) is constructing a pipeline of 180 km to import water from the Red Sea in the shrinking Dead Sea. Both seas exhibit highly different hydrographic features that determine their biodiversity. Using environmental DNA (eDNA) metabarcoding and amplifying a fragment of the cytochrome oxidase subunit I gene (COI) from water samples, we compared the communities of the Red Sea and the Dead Sea to understand the potential impact of the water conveyance project on biodiversity, following by an identification of potential biopollutants able to enter the Dead Sea for their small size. The results suggest a high likelihood of acquiring harmful algae into the Dead Sea. This study alerts about the real risk of losing the unique Dead Sea biota when the conveyance is actually undertaken.
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20
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Yang C, Bohmann K, Wang X, Cai W, Wales N, Ding Z, Gopalakrishnan S, Yu DW. Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13602] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Kristine Bohmann
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Wang Cai
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Nathan Wales
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- Department of Archaeology University of York York UK
| | - Zhaoli Ding
- Biodiversity Genomics Center Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
- School of Biological Sciences University of East AngliaNorwich Research Park Norwich UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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21
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A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes. DIVERSITY 2021. [DOI: 10.3390/d13050180] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes.
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Manning T, Thilagaraj AV, Mouradov D, Piola R, Grandison C, Gordon M, Shimeta J, Mouradov A. Diversity of dinoflagellate assemblages in coastal temperate and offshore tropical waters of Australia. BMC Ecol Evol 2021; 21:27. [PMID: 33588746 PMCID: PMC7885227 DOI: 10.1186/s12862-021-01745-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dinoflagellates are a ubiquitous and ecologically important component of marine phytoplankton communities, with particularly notable species including those associated with harmful algal blooms (HABs) and those that bioluminesce. High-throughput sequencing offers a novel approach compared to traditional microscopy for determining species assemblages and distributions of dinoflagellates, which are poorly known especially in Australian waters. RESULTS We assessed the composition of dinoflagellate assemblages in two Australian locations: coastal temperate Port Phillip Bay and offshore tropical waters of Davies Reef (Great Barrier Reef). These locations differ in certain environmental parameters reflecting latitude as well as possible anthropogenic influences. Molecular taxonomic assessment revealed more species than traditional microscopy, and it showed statistically significant differences in dinoflagellate assemblages between locations. Bioluminescent species and known associates of HABs were present at both sites. Dinoflagellates in both areas were mainly represented by the order Gymnodiniales (66%-82% of total sequence reads). In the warm waters of Davies Reef, Gymnodiniales were equally represented by the two superclades, Gymnodiniales sensu stricto (33%) and Gyrodinium (34%). In contrast, in cooler waters of Port Phillip Bay, Gymnodiniales was mainly represented by Gyrodinium (82%). In both locations, bioluminescent dinoflagellates represented up to 0.24% of the total sequence reads, with Protoperidinium the most abundant genus. HAB-related species, mainly represented by Gyrodinium, were more abundant in Port Phillip Bay (up to 47%) than at Davies Reef (28%), potentially reflecting anthropogenic influence from highly populated and industrial areas surrounding the bay. The entire assemblage of dinoflagellates, as well as the subsets of HAB and bioluminescent species, were strongly correlated with water quality parameters (R2 = 0.56-0.92). Significant predictors differed between the subsets: HAB assemblages were explained by salinity, temperature, dissolved oxygen, and total dissolved solids; whereas, bioluminescent assemblages were explained only by salinity and dissolved oxygen, and had greater variability. CONCLUSION High-throughput sequencing and genotyping revealed greater diversity of dinoflagellate assemblages than previously known in both subtropical and temperate Australian waters. Significant correlations of assemblage structure with environmental variables suggest the potential for explaining the distribution and composition of both HAB species and bioluminescent species.
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Affiliation(s)
- Tahnee Manning
- School of Science, RMIT University, Melbourne, VIC, Australia.
| | | | - Dmitri Mouradov
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Richard Piola
- Maritime Division, Defence Science & Technology Group, Fishermans Bend, Canberra, VIC, Australia
| | - Clare Grandison
- Maritime Division, Defence Science & Technology Group, Fishermans Bend, Canberra, VIC, Australia
| | - Matthew Gordon
- Maritime Division, Defence Science & Technology Group, Fishermans Bend, Canberra, VIC, Australia
| | - Jeff Shimeta
- School of Science, RMIT University, Melbourne, VIC, Australia
| | - Aidyn Mouradov
- School of Science, RMIT University, Melbourne, VIC, Australia
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Harrison JG, John Calder W, Shuman B, Alex Buerkle C. The quest for absolute abundance: The use of internal standards for DNA-based community ecology. Mol Ecol Resour 2020; 21:30-43. [PMID: 32889760 DOI: 10.1111/1755-0998.13247] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/10/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022]
Abstract
To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as 'spike-ins') into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.
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Suter L, Polanowski AM, Clarke LJ, Kitchener JA, Deagle BE. Capturing open ocean biodiversity: Comparing environmental DNA metabarcoding to the continuous plankton recorder. Mol Ecol 2020; 30:3140-3157. [PMID: 32767849 DOI: 10.1111/mec.15587] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/24/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship-based bulk plankton sampling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean zooplankton biodiversity as conventional CPR bulk sampling (~1,500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (a) conventional morphological CPR sampling and (b) bulk DNA metabarcoding of CPR collected plankton (two transects for each comparison, 40 and 44 paired samples, respectively). A metazoan-targeted cytochrome c oxidase I (COI) marker was used to characterize species-level diversity. In the 2 L seawater eDNA samples, this marker amplified large amounts of non-metazoan picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6 times more zooplankton species than morphologically analysed bulk CPR samples. COI metabarcoding of bulk DNA samples mostly avoided nonmetazoan amplifications and recovered more zooplankton species than eDNA metabarcoding. However, eDNA metabarcoding detected roughly two thirds of metazoan species and identified similar taxa contributing to community differentiation across the subtropical front separating transects. We observed a diurnal pattern in eDNA data for copepods which perform diel vertical migrations, indicating a surprisingly short temporal eDNA signal. Compared to COI, a eukaryote-targeted 18S ribosomal RNA marker detected a higher proportion, but lower diversity, of metazoans in eDNA. With refinement and standardization of methodology, eDNA metabarcoding could become an efficient tool for monitoring open ocean biodiversity.
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Affiliation(s)
- Leonie Suter
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia
| | - Andrea Maree Polanowski
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia
| | - Laurence John Clarke
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia.,Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., Australia
| | - John Andrew Kitchener
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia
| | - Bruce Emerson Deagle
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia.,Commonwealth Scientific and Industrial Research Organisation, Battery Point, Tas., Australia
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Schroeder A, Stanković D, Pallavicini A, Gionechetti F, Pansera M, Camatti E. DNA metabarcoding and morphological analysis - Assessment of zooplankton biodiversity in transitional waters. MARINE ENVIRONMENTAL RESEARCH 2020; 160:104946. [PMID: 32907716 DOI: 10.1016/j.marenvres.2020.104946] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/28/2020] [Accepted: 03/07/2020] [Indexed: 06/11/2023]
Abstract
Zooplankton biodiversity assessment is a crucial element in monitoring marine ecosystem processes and community responses to environmental alterations. In order to evaluate the suitability of metabarcoding for zooplankton biodiversity assessment and biomonitoring as a fast and more cost-effective method, seasonal zooplankton sampling was carried out in the Venice Lagoon and the nearby coastal area (Northern Adriatic Sea). The molecular analysis showed higher taxa richness compared to the classical morphological method (224 vs. 88 taxa), discriminating better the meroplanktonic component, morphologically identified only up to order level. Both methods revealed a similar spatio-temporal distribution pattern and the sequence abundances and individual counts were significantly correlated for various taxonomic groups. These results indicate that DNA metabarcoding is an efficient tool for biodiversity assessments in ecosystems with high spatial and temporal variability, where high sampling effort is required as well as fast alert systems for non-native species (NIS).
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Affiliation(s)
- Anna Schroeder
- National Research Council, Institute of Marine Sciences (CNR ISMAR) Venice, Arsenale Tesa 104, Castello 2737/F, 30122, Venice, Italy; University of Trieste, Department of Life Sciences, Via Licio Giorgieri 5, 34127, Trieste, Italy.
| | - David Stanković
- Marine Biology Station Piran, National Institute of Biology, Fornace 41, 6330, Piran, Slovenia.
| | - Alberto Pallavicini
- University of Trieste, Department of Life Sciences, Via Licio Giorgieri 5, 34127, Trieste, Italy; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy; National Interuniversity Consortium For Marine Sciences (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy.
| | - Fabrizia Gionechetti
- University of Trieste, Department of Life Sciences, Via Licio Giorgieri 5, 34127, Trieste, Italy.
| | - Marco Pansera
- National Research Council, Institute of Marine Sciences (CNR ISMAR) Venice, Arsenale Tesa 104, Castello 2737/F, 30122, Venice, Italy.
| | - Elisa Camatti
- National Research Council, Institute of Marine Sciences (CNR ISMAR) Venice, Arsenale Tesa 104, Castello 2737/F, 30122, Venice, Italy.
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DiBattista JD, Reimer JD, Stat M, Masucci GD, Biondi P, De Brauwer M, Wilkinson SP, Chariton AA, Bunce M. Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems. Sci Rep 2020; 10:8365. [PMID: 32433472 PMCID: PMC7239923 DOI: 10.1038/s41598-020-64858-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/23/2020] [Indexed: 01/29/2023] Open
Abstract
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities.
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Affiliation(s)
- Joseph D DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia. .,Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW, 2010, Australia.
| | - James D Reimer
- Molecular Invertebrate and Systematics Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia.,School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Giovanni D Masucci
- Molecular Invertebrate and Systematics Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Piera Biondi
- Molecular Invertebrate and Systematics Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Maarten De Brauwer
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia.,School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Anthony A Chariton
- Department of Biological Sciences, Macquarie University, North Ryde, 2113, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia.,Environmental Protection Authority, 215 Lambton Quay, Wellington, 6011, New Zealand
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27
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Bakker J, Wangensteen OS, Baillie C, Buddo D, Chapman DD, Gallagher AJ, Guttridge TL, Hertler H, Mariani S. Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding. Ecol Evol 2019; 9:14341-14355. [PMID: 31938523 PMCID: PMC6953649 DOI: 10.1002/ece3.5871] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/31/2019] [Accepted: 11/03/2019] [Indexed: 01/12/2023] Open
Abstract
Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic "protists," with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro-eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro-eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.
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Affiliation(s)
- Judith Bakker
- Department of Biological Sciences Florida International University Miami FL USA
- School of Engineering & Environment University of Salford Salford UK
| | - Owen S Wangensteen
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Charles Baillie
- School of Engineering & Environment University of Salford Salford UK
| | - Dayne Buddo
- Discovery Bay Marine Laboratory and Field Station University of the West Indies St. Ann Jamaica
| | - Demian D Chapman
- Department of Biological Sciences Florida International University Miami FL USA
| | | | | | - Heidi Hertler
- The School for Field Studies Centre for Marine Resource Studies South Caicos Turks and Caicos Islands
| | - Stefano Mariani
- School of Engineering & Environment University of Salford Salford UK
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Kersten O, Vetter EW, Jungbluth MJ, Smith CR, Goetze E. Larval assemblages over the abyssal plain in the Pacific are highly diverse and spatially patchy. PeerJ 2019; 7:e7691. [PMID: 31579593 PMCID: PMC6766376 DOI: 10.7717/peerj.7691] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/19/2019] [Indexed: 11/20/2022] Open
Abstract
Abyssal plains are among the most biodiverse yet least explored marine ecosystems on our planet, and they are increasingly threatened by human impacts, including future deep seafloor mining. Recovery of abyssal populations from the impacts of polymetallic nodule mining will be partially determined by the availability and dispersal of pelagic larvae leading to benthic recolonization of disturbed areas of the seafloor. Here we use a tree-of-life (TOL) metabarcoding approach to investigate the species richness, diversity, and spatial variability of the larval assemblage at mesoscales across the abyssal seafloor in two mining-claim areas in the eastern Clarion Clipperton Fracture Zone (CCZ; abyssal Pacific). Our approach revealed a previously unknown taxonomic richness within the meroplankton assemblage, detecting larvae from 12 phyla, 23 Classes, 46 Orders, and 65 Families, including a number of taxa not previously reported at abyssal depths or within the Pacific Ocean. A novel suite of parasitic copepods and worms were sampled, from families that are known to associate with other benthic invertebrates or demersal fishes as hosts. Larval assemblages were patchily distributed at the mesoscale, with little similarity in OTUs detected among deployments even within the same 30 × 30 km study area. Our results provide baseline observations on larval diversity prior to polymetallic nodule mining in this region, and emphasize our overwhelming lack of knowledge regarding larvae of the benthic boundary layer in abyssal plain ecosystems.
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Affiliation(s)
- Oliver Kersten
- Hawaii Pacific University, Kaneohe, HI, United States of America
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Eric W. Vetter
- Hawaii Pacific University, Kaneohe, HI, United States of America
| | - Michelle J. Jungbluth
- Hawaii Pacific University, Kaneohe, HI, United States of America
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Craig R. Smith
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Erica Goetze
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States of America
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29
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Ji Y, Huotari T, Roslin T, Schmidt NM, Wang J, Yu DW, Ovaskainen O. SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes. Mol Ecol Resour 2019; 20:256-267. [PMID: 31293086 DOI: 10.1111/1755-0998.13057] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/15/2019] [Accepted: 07/03/2019] [Indexed: 11/24/2022]
Abstract
The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 = .93, mitogenomes R2 = .95) and a high repeatability across environmental-sample replicates (barcodes R2 = .94, mitogenomes R2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.
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Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Tea Huotari
- Department of Agricultural Sciences, Spatial Foodweb Ecology Group, University of Helsinki, Helsinki, Finland
| | - Tomas Roslin
- Department of Agricultural Sciences, Spatial Foodweb Ecology Group, University of Helsinki, Helsinki, Finland.,Department of Ecology, Spatial Foodweb Ecology Group, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Niels Martin Schmidt
- Arctic Research Centre, Aarhus University, Aarhus, Denmark.,Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Jiaxin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,School of Biological Sciences, University of East Anglia, Norfolk, UK.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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30
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Saccò M, Blyth A, Bateman PW, Hua Q, Mazumder D, White N, Humphreys WF, Laini A, Griebler C, Grice K. New light in the dark - a proposed multidisciplinary framework for studying functional ecology of groundwater fauna. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 662:963-977. [PMID: 30795483 DOI: 10.1016/j.scitotenv.2019.01.296] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/12/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Groundwaters provide the vast majority of unfrozen freshwater resources on the planet, but our knowledge of subsurface ecosystems is surprisingly limited. Stygofauna, or stygobionts -subterranean obligate aquatic animals - provide ecosystem services such as grazing biofilms and maintaining water quality, but we know little about how their ecosystems function. The cryptic nature of groundwaters, together with the high degree of local endemism and stygofaunal site-specific adaptations, represent major obstacles for the field. To overcome these challenges, and integrate biodiversity and ecosystem function, requires a holistic design drawing on classical ecology, taxonomy, molecular ecology and geochemistry. This study presents an approach based on the integration of existing concepts in groundwater ecology with three more novel scientific techniques: compound specific stable isotope analysis (CSIA) of amino acids, radiocarbon analysis (14C) and DNA analyses of environmental samples, stygofauna and gut contents. The combination of these techniques allows elucidation of aspects of ecosystem function that are often obscured in small invertebrates and cryptic systems. Carbon (δ13C) and nitrogen (δ15N) CSIA provides a linkage between biogeochemical patterns and ecological dynamics. It allows the identification of stygofaunal food web structures and energy flows based on the metabolic pathway of specific amino groups. Concurrently, 14C provides complementary data on the carbon recycling and incorporation within the stygobiotic trophic webs. Changes in groundwater environmental conditions (e.g. aquifer recharge), and subsequent community adaptations, can be pinpointed via the measurementof the radiocarbon fingerprint of water, sediment and specimens. DNA analyses are a rapidly expanding approach in ecology. eDNA is mainly employed as a biomonitoring tool, while metabarcoding of individuals and/or gut contents provides insight into diet regimes. In all cases, the application of the approaches in combination provides more powerful data than any one alone. By combining quantitative (CSIA and 14C) and qualitative (eDNA and DNA metabarcoding) approaches via Bayesian Mixing Models (BMM), linkages can be made between community composition, energy and nutrient sources in the system, and trophic function. This suggested multidisciplinary design will contribute to a more thorough comprehension of the biogeochemical and ecological patterns within these undervalued but essential ecosystems.
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Affiliation(s)
- Mattia Saccò
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia.
| | - Alison Blyth
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia
| | - Philip W Bateman
- School of Molecular and Life Sciences, Curtin University, Perth, 6102, WA, Australia
| | - Quan Hua
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Debashish Mazumder
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Nicole White
- School of Molecular and Life Sciences, Curtin University, Perth, 6102, WA, Australia
| | - William F Humphreys
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6986, Australia; School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Alex Laini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale G.P. Usberti 33/A, 43124 Parma, Italy
| | - Christian Griebler
- Helmholtz Center Munich, Institute of Groundwater Ecology, Neuherberg, Germany; University of Vienna, Dept of Limnology and Bio-Oceanography, Vienna, Austria
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia
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31
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Frei B, Guenay Y, Bohan DA, Traugott M, Wallinger C. Molecular analysis indicates high levels of carabid weed seed consumption in cereal fields across Central Europe. JOURNAL OF PEST SCIENCE 2019; 92:935-942. [PMID: 31178674 PMCID: PMC6528783 DOI: 10.1007/s10340-019-01109-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Carabid beetles are abundant in temperate agroecosystems and can play a pivotal role as biocontrol agents. While there is good knowledge regarding their effects on invertebrate pests in some systems, comparably little is known on the rate of seed feeding under field conditions. Molecular approaches are ideally suited for investigating carabid feeding interactions; to date, however, they have only been applied to animal prey. We sampled adult carabid beetles in organic cereal fields in three regions along a Central European transect. Regurgitates from populations of the three most common species, Poecilus cupreus, Pseudoophonus rufipes and Pterostichus melanarius, were screened for plant DNA, cereal aphids, collembolans and earthworms. The frequency of carabid individuals positive for plant DNA was high (> 70%) and independent of carabid species, sex, region and the time point of sampling. Detections for non-pest and pest prey were comparably lower, with 21.6% for collembolans, 18.1% for earthworms and 4.2% for aphids, respectively. Despite the prolonged detection period of plant DNA in carabid guts, as compared to animal prey, these first results suggest that weed seeds form an important part of the adult carabid diet. It would also lend support to the hypothesis that seed-feeding carabids are biocontrol agents of weeds, with effects of regulation on the weed seedbank that depend on behavioural and contextual factors including carabid species preferences for weed seed species, their life stage and tillage practices.
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Affiliation(s)
- Britta Frei
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
- Agroecologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comte, 21000 Dijon, France
| | - Yasemin Guenay
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
- Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020 Innsbruck, Austria
| | - David A. Bohan
- Agroecologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comte, 21000 Dijon, France
| | - Michael Traugott
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Corinna Wallinger
- Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020 Innsbruck, Austria
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32
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Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events. PLoS Genet 2019; 15:e1007943. [PMID: 30735490 PMCID: PMC6368286 DOI: 10.1371/journal.pgen.1007943] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/07/2019] [Indexed: 01/08/2023] Open
Abstract
Marine ecosystems are changing rapidly as the oceans warm and become more acidic. The physical factors and the changes to ocean chemistry that they drive can all be measured with great precision. Changes in the biological composition of communities in different ocean regions are far more challenging to measure because most biological monitoring methods focus on a limited taxonomic or size range. Environmental DNA (eDNA) analysis has the potential to solve this problem in biological oceanography, as it is capable of identifying a huge phylogenetic range of organisms to species level. Here we develop and apply a novel multi-gene molecular toolkit to eDNA isolated from bulk plankton samples collected over a five-year period from a single site. This temporal scale and level of detail is unprecedented in eDNA studies. We identified consistent seasonal assemblages of zooplankton species, which demonstrates the ability of our toolkit to audit community composition. We were also able to detect clear departures from the regular seasonal patterns that occurred during an extreme marine heatwave. The integration of eDNA analyses with existing biotic and abiotic surveys delivers a powerful new long-term approach to monitoring the health of our world's oceans in the context of a rapidly changing climate.
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33
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Sawaya NA, Djurhuus A, Closek CJ, Hepner M, Olesin E, Visser L, Kelble C, Hubbard K, Breitbart M. Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding. Ecol Evol 2019; 9:1029-1040. [PMID: 30805138 PMCID: PMC6374654 DOI: 10.1002/ece3.4742] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 01/09/2023] Open
Abstract
Environmental DNA (eDNA) is the DNA suspended in the environment (e.g., water column), which includes cells, gametes, and other material derived from but not limited to shedding of tissue, scales, mucus, and fecal matter. Amplifying and sequencing marker genes (i.e., metabarcoding) from eDNA can reveal the wide range of taxa present in an ecosystem through analysis of a single water sample. Metabarcoding of eDNA provides higher resolution data than visual surveys, aiding in assessments of ecosystem health. This study conducted eDNA metabarcoding of two molecular markers (cytochrome c oxidase I (COI) and 18S ribosomal RNA (rRNA) genes) to survey eukaryotic diversity across multiple trophic levels in surface water samples collected at three sites along the coral reef tract within the Florida Keys National Marine Sanctuary (FKNMS) during four research cruises in 2015. The 18S rRNA gene sequences recovered 785 genera while the COI gene sequences recovered 115 genera, with only 33 genera shared between the two datasets, emphasizing the complementarity of these marker genes. Community composition for both genetic markers clustered by month of sample collection, suggesting that temporal variation has a larger effect on biodiversity than spatial variability in the FKNMS surface waters. Sequences from both marker genes were dominated by copepods, but each marker recovered distinct phytoplankton groups, with 18S rRNA gene sequences dominated by dinoflagellates and COI sequences dominated by coccolithophores. Although eDNA samples were collected from surface waters, many benthic species such as sponges, crustaceans, and corals were identified. These results show the utility of eDNA metabarcoding for cataloging biodiversity to establish an ecosystem baseline against which future samples can be compared in order to monitor community changes.
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Affiliation(s)
- Natalie A. Sawaya
- College of Marine ScienceUniversity of South FloridaSaint PetersburgFlorida
| | - Anni Djurhuus
- College of Marine ScienceUniversity of South FloridaSaint PetersburgFlorida
| | - Collin J. Closek
- Stanford Center for Ocean SolutionsStanford UniversityStanfordCalifornia
- Department of Civil and Environmental EngineeringStanford UniversityStanfordCalifornia
| | - Megan Hepner
- College of Marine ScienceUniversity of South FloridaSaint PetersburgFlorida
| | - Emily Olesin
- Florida Fish and Wildlife Conservation Commission‐Fish and Wildlife Research InstituteSaint PetersburgFlorida
| | - Lindsey Visser
- Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
- NOAA Atlantic Oceanographic and Meteorological LaboratoryMiamiFlorida
| | | | - Katherine Hubbard
- Florida Fish and Wildlife Conservation Commission‐Fish and Wildlife Research InstituteSaint PetersburgFlorida
| | - Mya Breitbart
- College of Marine ScienceUniversity of South FloridaSaint PetersburgFlorida
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34
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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00547] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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35
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Deiner K, Lopez J, Bourne S, Holman L, Seymour M, Grey EK, Lacoursière A, Li Y, Renshaw MA, Pfrender ME, Rius M, Bernatchez L, Lodge DM. Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.28963] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol in these environments, seawater samples were collected in a commercial port and methodologies for concentrating and purifying eDNA were tested for their effect on eukaryotic DNA yield and subsequent richness of Operational Taxonomic Units (OTUs). Different filter materials [Cellulose Nitrate (CN) and Glass Fibre (GF)], with different pore sizes (0.5 µm, 0.7 µm and 1.2 µm) and three previously published liquid phase extraction methods were tested. The number of eukaryotic OTUs detected differed by a factor of three amongst the method combinations. The combination of CN filters with phenol-chloroform-isoamyl alcohol extractions recovered a higher amount of eukaryotic DNA and OTUs compared to GF filters and the chloroform-isoamyl alcohol extraction method. Pore size was not independent of filter material but did affect the yield of eukaryotic DNA. For the OTUs assigned to a highly successful non-indigenous species, Styelaclava, the two extraction methods with phenol significantly outperformed the extraction method without phenol; other experimental treatments did not contribute significantly to detection. These results highlight that careful consideration of methods is warranted because choice of filter material and extraction method create false negative detections of marine eukaryotic OTUs and underestimate taxonomic richness from environmental samples.
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36
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Dissanayake AJ, Purahong W, Wubet T, Hyde KD, Zhang W, Xu H, Zhang G, Fu C, Liu M, Xing Q, Li X, Yan J. Direct comparison of culture-dependent and culture-independent molecular approaches reveal the diversity of fungal endophytic communities in stems of grapevine (Vitis vinifera). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0399-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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