1
|
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.
Collapse
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
| |
Collapse
|
2
|
Coppo GC, Pereira AP, Netto SA, Bernardino AF. Meiofauna at a tropical sandy beach in the SW Atlantic: the influence of seasonality on diversity. PeerJ 2024; 12:e17727. [PMID: 39011380 PMCID: PMC11249015 DOI: 10.7717/peerj.17727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 06/20/2024] [Indexed: 07/17/2024] Open
Abstract
Background Sandy beaches are dynamic environments housing a large diversity of organisms and providing important environmental services. Meiofaunal metazoan are small organisms that play a key role in the sediment. Their diversity, distribution and composition are driven by sedimentary and oceanographic parameters. Understanding the diversity patterns of marine meiofauna is critical in a changing world. Methods In this study, we investigate if there is seasonal difference in meiofaunal assemblage composition and diversity along 1 year and if the marine seascapes dynamics (water masses with particular biogeochemical features, characterized by temperature, salinity, absolute dynamic topography, chromophoric dissolved organic material, chlorophyll-a, and normalized fluorescent line height), rainfall, and sediment parameters (total organic matter, carbonate, carbohydrate, protein, lipids, protein-to-carbohydrate, carbohydrate-to-lipids, and biopolymeric carbon) affect significatively meiofaunal diversity at a tropical sandy beach. We tested two hypotheses here: (i) meiofaunal diversity is higher during warmer months and its composition changes significatively among seasons along a year at a tropical sandy beach, and (ii) meiofaunal diversity metrics are significantly explained by marine seascapes characteristics and sediment parameters. We used metabarcoding (V9 hypervariable region from 18S gene) from sediment samples to assess the meiofaunal assemblage composition and diversity (phylogenetic diversity and Shannon's diversity) over a period of 1 year. Results Meiofauna was dominated by Crustacea (46% of sequence reads), Annelida (28% of sequence reads) and Nematoda (12% of sequence reads) in periods of the year with high temperatures (>25 °C), high salinity (>31.5 ppt), and calm waters. Our data support our initial hypotheses revealing a higher meiofaunal diversity (phylogenetic and Shannon's Diversity) and different composition during warmer periods of the year. Meiofaunal diversity was driven by a set of multiple variables, including biological variables (biopolymeric carbon) and organic matter quality (protein content, lipid content, and carbohydrate-to-lipid ratio).
Collapse
Affiliation(s)
- Gabriel C Coppo
- Grupo de Ecologia Bentônica, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Araiene P Pereira
- Grupo de Ecologia Bentônica, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Sergio A Netto
- Marítima Estudos Bênticos, Laguna, Santa Catarina, Brazil
| | - Angelo F Bernardino
- Grupo de Ecologia Bentônica, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| |
Collapse
|
3
|
Coppo G, Pais FS, Ferreira TO, Halanych KM, Donnelly K, Mazzuco AC, Bernardino AF. Transition of an estuarine benthic meiofauna assemblage 1.7 and 2.8 years after a mining disaster. PeerJ 2023; 11:e14992. [PMID: 36935931 PMCID: PMC10022502 DOI: 10.7717/peerj.14992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/12/2023] [Indexed: 03/15/2023] Open
Abstract
Background Estuaries are transitional coastal ecosystems that are threatened by multiple sources of human pollution. In 2015, mining tailings from an upstream dam failure caused massive metal contamination that impacted benthic assemblages on the Brazilian Rio Doce estuary. Methods In this study, we investigate and compare meiofaunal assemblages with eDNA metabarcoding 1.7 years (2017) and 2.8 years (2018) after the initial contamination by mine tailings in order to evaluate the continued impact of sediment mine tailing contaminants on the structure of benthic assemblages after the disaster. Results The community was dominated by Arthropoda and Nematoda 1.7 yr after the impacts (42 and 29% of meiofaunal sequence reads, respectively) but after 2.8 years Arthropoda (64.8% of meiofaunal sequence reads) and Rotifera (11.8%) were the most common taxa. This continued impact on meiofaunal assemblage revealed a lower phylogenetic diversity (7.8-fold) in 2018, despite overall decrease in metal concentration (Al, Ba, Cr, As, Fe, Zn, Mn, Pb, Cd, Co) in sediments. Our data suggests that differences in benthic assemblages and loss of diversity may be influenced by contaminants in sediments of this estuary, and indicate that broad eDNA assessments are greatly useful to understand the full range of biodiversity changes in dynamic estuarine ecosystems.
Collapse
Affiliation(s)
- Gabriel Coppo
- Grupo de Ecologia Bentônica, Department of Oceanography, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Fabiano S. Pais
- Plataforma de Bioinformática, Instituto René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Tiago O. Ferreira
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Ken M. Halanych
- Center for Marine Science, University of North Carolina at Wilmington, Wilmington, NC, United States of America
| | - Kyle Donnelly
- Center for Marine Science, University of North Carolina at Wilmington, Wilmington, NC, United States of America
| | - Ana Carolina Mazzuco
- Grupo de Ecologia Bentônica, Department of Oceanography, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Angelo F. Bernardino
- Grupo de Ecologia Bentônica, Department of Oceanography, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| |
Collapse
|
4
|
Bailey SA, Brydges T, Casas-Monroy O, Kydd J, Linley RD, Rozon RM, Darling JA. First evaluation of ballast water management systems on operational ships for minimizing introductions of nonindigenous zooplankton. MARINE POLLUTION BULLETIN 2022; 182:113947. [PMID: 35926436 PMCID: PMC10949186 DOI: 10.1016/j.marpolbul.2022.113947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/05/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Ballast water is a leading pathway for the global introduction of aquatic nonindigenous species. Most international ships are expected to install ballast water management systems (BWMS) by 2024 to treat ballast water before release. This study examines if ballast water discharges managed by BWMS are meeting standards for organisms ≥50 μm in minimum dimension (i.e., <10 organisms per m3; typically zooplankton). Representative samples of ballast water were collected from 29 ships (using 14 different BWMS) arriving to Canada during 2017-2018. Fourteen samples (48 %) had zooplankton concentrations clearly exceeding the standard (ranging from 18 to 3822 organisms per m3). Nonetheless, compared to earlier management strategies, BWMS appear to reduce the frequency of high-risk introduction events. BWMS filter mesh size was an important predictor of zooplankton concentration following treatment. Greater rates of compliance may be achieved as ship crews gain experience with operation and maintenance of BWMS.
Collapse
Affiliation(s)
- Sarah A Bailey
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada.
| | - Torben Brydges
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - Oscar Casas-Monroy
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - Jocelyn Kydd
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - R Dallas Linley
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - Robin M Rozon
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - John A Darling
- Center for Environmental Measurement & Modeling, United States Environmental Protection Agency, Research Triangle Park, NC, USA
| |
Collapse
|
5
|
Dully V, Rech G, Wilding TA, Lanzén A, MacKichan K, Berrill I, Stoeck T. Comparing sediment preservation methods for genomic biomonitoring of coastal marine ecosystems. MARINE POLLUTION BULLETIN 2021; 173:113129. [PMID: 34784523 DOI: 10.1016/j.marpolbul.2021.113129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
To avoid loss of genetic information in environmental DNA (eDNA) field samples, the preservation of nucleic acids during field sampling is a critical step. In the development of standard operating procedures (SOPs) for eDNA-based compliance monitoring, the effect of different routinely used sediment preservations on biological community structures serving as bioindicators has gone untested. We compared eDNA metabarcoding results of marine bacterial communities from sample aliquots that were treated with a nucleic acid preservation solution (treated samples) and aliquots that were frozen without further treatment (non-treated samples). Sediment samples were obtained from coastal locations subjected to different stressors (aquaculture, urbanization, industry). DNA extraction efficiency, bacterial community profiles, and measures of alpha- and beta-diversity were highly congruent between treated and non-treated samples. As both preservation methods provide the same relevant information to environmental managers and regulators, we recommend the inclusion of both methods into SOPs for biomonitoring in marine coastal environments.
Collapse
Affiliation(s)
- Verena Dully
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
| | - Giulia Rech
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Scotland, United Kingdom
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Iain Berrill
- Scottish Salmon Producers Organization, Edinburgh, Scotland, United Kingdom
| | - Thorsten Stoeck
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany.
| |
Collapse
|
6
|
Vieira PE, Lavrador AS, Parente MI, Parretti P, Costa AC, Costa FO, Duarte S. Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13305] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Pedro E. Vieira
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Ana S. Lavrador
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Manuela I. Parente
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
| | - Paola Parretti
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
- MARE – Marine and Environmental Sciences Centre Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI) Edifício Madeira Tecnopolo Funchal Portugal
| | - Ana C. Costa
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| |
Collapse
|
7
|
Antich A, Palacin C, Wangensteen OS, Turon X. To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics 2021; 22:177. [PMID: 33820526 PMCID: PMC8020537 DOI: 10.1186/s12859-021-04115-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. RESULTS Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in different orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little influence on the final outcome. CONCLUSIONS We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.
Collapse
Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain
| | - Creu Palacin
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona and Research Institute of Biodiversity (IRBIO), Barcelona, Catalonia, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsö, Norway.
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain.
| |
Collapse
|
8
|
Garcia-Vazquez E, Georges O, Fernandez S, Ardura A. eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters. Sci Rep 2021; 11:7224. [PMID: 33790382 PMCID: PMC8012656 DOI: 10.1038/s41598-021-86731-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the "missing biomass") is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.
Collapse
Affiliation(s)
- Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria S/N, 33006, Oviedo, Spain
| | - Oriane Georges
- Department of Functional Biology, University of Oviedo, C/Julian Claveria S/N, 33006, Oviedo, Spain
| | - Sara Fernandez
- Department of Natural Sciences, School of Science and Computing, Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, H91 T8NW, Ireland
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, C/Julian Claveria S/N, 33006, Oviedo, Spain.
| |
Collapse
|
9
|
Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates. WATER 2021. [DOI: 10.3390/w13030331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.
Collapse
|