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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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Pawlowski J, Cermakova K, Cordier T, Frontalini F, Apothéloz-Perret-Gentil L, Merzi T. Assessing the potential of nematode metabarcoding for benthic monitoring of offshore oil platforms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173092. [PMID: 38729369 DOI: 10.1016/j.scitotenv.2024.173092] [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: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Environmental DNA metabarcoding is gaining momentum as a time and cost-effective tool for biomonitoring and environmental impact assessment. Yet, its use as a replacement for the conventional marine benthic monitoring based on morphological analysis of macrofauna is still challenging. Here we propose to study the meiofauna, which is much better represented in sediment DNA samples. We focus on nematodes, which are the most numerous and diverse group of meiofauna. Our aim is to assess the potential of nematode metabarcoding to monitor impacts associated with offshore oil platform activities. To achieve this goal, we used nematode-optimized marker (18S V1V2-Nema) and universal eukaryotic marker (18S V9) region to analyse 252 sediment DNA samples collected near three offshore oil platforms in the North Sea. For both markers, we analysed changes in alpha and beta diversity in relation to distance from the platforms and environmental variables. We also defined three impact classes based on selected environmental variables that are associated with oil extraction activities and used random forest classifiers to compare the predictive performance of both datasets. Our results show that alpha- and beta-diversity of nematodes varies with the increasing distance from the platforms. The variables directly related to platform activity, such as Ba and THC, strongly influence the nematode community. The nematode metabarcoding data provide more robust predictive models than eukaryotic data. Furthermore, the nematode community appears more stable in time and space, as illustrated by the overlap of nematode datasets obtained from the same platform three years apart. A significative negative correlation between distance and Shannon diversity also advocates for higher performance of the V1V2-Nema over the V9. Overall, these results suggest that the sensitivity of nematodes is higher compared to the eukaryotic community. Hence, nematode metabarcoding has the potential to become an effective tool for benthic monitoring in marine environment.
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Affiliation(s)
- J Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland; ID-Gene ecodiagnostics, Plan-les-Ouates, Switzerland.
| | - K Cermakova
- ID-Gene ecodiagnostics, Plan-les-Ouates, Switzerland
| | - T Cordier
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Norway
| | - F Frontalini
- Department of Pure and Applied Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | | | - T Merzi
- TotalEnergies OneTech, Centre Scientifique et Technique Jean Feger, Pau, France
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Kravtsova LS, Peretolchina TE, Triboy TI, Nebesnykh IA, Tupikin AE, Kabilov MR. A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding. Vavilovskii Zhurnal Genet Selektsii 2023; 27:694-702. [PMID: 38213463 PMCID: PMC10782034 DOI: 10.18699/vjgb-23-80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 01/13/2024] Open
Abstract
The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinvertebrate metabarcoding. A total of 118009 reads of the COI gene fragment (at least 313 bp in length) were obtained. The correlation of the Spearman coefficient (S = 0.6, p<0.05) with the abundance of macroinvertebrates in the samples before DNA extraction showed that the number of reads can serve as an indirect characteristic of the abundance of a species (operational taxonomic unit, OTU). 115 OTUs belonging to the higher taxa of macroinvertebrates were identified: Porifera, 1; Platyhelminthes, 3; Annelida, 38; Arthropoda, 55; Mollusca, 18. At a high level of resolution (with homology with GenBank reference sequences ≥ 95 %, coverage ≥ 90 %), 46 taxa of macroinvertebrates comprising three communities were registered: one dominated by molluscs (Choanomphalus conf. maacki) and two dominated by chironomids (Orthocladius gregarius Linev., Sergentia baicalensis Tshern.). Communities are characterized by low species diversity according to Shannon (from 0.7 to 1.2 bits), high concentration of dominance according to Simpson (from 0.5 to 0.7) and low evenness according to Pielou (from 0.3 to 0.4). Dominants and subdominants in the communities account for 91 to 96 % of COI gene fragment reads. The spatial distribution of the dominant species identified in the communities is influenced by the geomorphological features of the bottom and the composition of sediments in the area studied. The approach proposed for studying the structure of macroinvertebrate communities based on DNA metabarcoding and next generation sequencing can be recommended for express assessment of the state of aquatic ecosystems in the monitoring.
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Affiliation(s)
- L S Kravtsova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T E Peretolchina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T I Triboy
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - I A Nebesnykh
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - A E Tupikin
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Chua PYS, Bourlat SJ, Ferguson C, Korlevic P, Zhao L, Ekrem T, Meier R, Lawniczak MKN. Future of DNA-based insect monitoring. Trends Genet 2023:S0168-9525(23)00038-0. [PMID: 36907721 DOI: 10.1016/j.tig.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).
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Affiliation(s)
- Physilia Y S Chua
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sarah J Bourlat
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Adenauerallee 127, 53113 Bonn, Germany
| | - Cameron Ferguson
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Petra Korlevic
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leia Zhao
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Bourret A, Nozères C, Parent E, Parent GJ. Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository. METABARCODING AND METAGENOMICS 2023. [DOI: 10.3897/mbmg.7.98539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Biodiversity assessments relying on DNA have increased rapidly over the last decade. However, the reliability of taxonomic assignments in metabarcoding studies is variable and affected by the reference databases and the assignment methods used. Species level assignments are usually considered as reliable using regional libraries but unreliable using public repositories. In this study, we aimed to test this assumption for metazoan species detected in the Gulf of St. Lawrence in the Northwest Atlantic. We first created a regional library (GSL-rl) by data mining COI barcode sequences from BOLD, and included a reliability ranking system for species assignments. We then estimated 1) the accuracy and precision of the public repository NCBI-nt for species assignments using sequences from the regional library and 2) compared the detection and reliability of species assignments of a metabarcoding dataset using either NCBI-nt or the regional library and popular assignment methods. With NCBI-nt and sequences from the regional library, the BLAST-LCA (least common ancestor) method was the most precise method for species assignments, but the accuracy was higher with the BLAST-TopHit method (>80% over all taxa, between 70% and 90% amongst taxonomic groups). With the metabarcoding dataset, the reliability of species assignments was greater using GSL-rl compared to NCBI-nt. However, we also observed that the total number of reliable species assignments could be maximized using both GSL-rl and NCBI-nt with different optimized assignment methods. The use of a two-step approach for species assignments, i.e., using a regional library and a public repository, could improve the reliability and the number of detected species in metabarcoding studies.
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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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Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. DIVERSITY 2023. [DOI: 10.3390/d15020174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The introduction of non-indigenous species (NIS) is one of the major threats to the integrity of European coastal ecosystems. DNA-based assessments have been increasingly adopted for monitoring NIS. However, the accuracy of DNA-based taxonomic assignments is largely dependent on the completion and reliability of DNA barcode reference libraries. As such, we aimed to compile and audit a DNA barcode reference library for marine invertebrate NIS occurring in Europe. To do so, we compiled a list of NIS using three databases: the European Alien Species Information Network (EASIN), the Information System on Aquatic Non-indigenous and Cryptogenic Species (AquaNIS), and the World Register of Introduced Marine Species (WRiMS). For each species, we retrieved the available cytochrome c oxidase subunit I (COI) mitochondrial gene sequences from the Barcode of Life Data System (BOLD) and used the Barcode, Audit & Grade System (BAGS) to check congruence between morphospecies names and Barcode Index Numbers (BINs). From the 1249 species compiled, approximately 42% had records on BOLD, among which 56% were discordant. We further analyzed these cases to determine the causes of the discordances and attributed additional annotation tags. Of the 622 discordant BINs, after revision, 35% were successfully solved, which increased the number of NIS detected in metabarcoding datasets from 12 to 16. However, a fair number of BINs remained discordant. Reliability of reference barcode records is particularly critical in the case of NIS, where erroneous identification may trigger action or inaction when not required.
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Willassen E, Westgaard JI, Kongsrud JA, Hanebrekke T, Buhl-Mortensen P, Holte B. Benthic invertebrates in Svalbard fjords-when metabarcoding does not outperform traditional biodiversity assessment. PeerJ 2022; 10:e14321. [PMID: 36415859 PMCID: PMC9676020 DOI: 10.7717/peerj.14321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
To protect and restore ecosystems and biodiversity is one of the 10 challenges identified by the United Nations's Decade of the Ocean Science. In this study we used eDNA from sediments collected in two fjords of the Svalbard archipelago and compared the taxonomic composition with traditional methods through metabarcoding, targeting mitochondrial CO1, to survey benthos. Clustering of 21.6 mill sequence reads with a d value of 13 in swarm, returned about 25 K OTU reads. An identification search with the BOLD database returned 12,000 taxonomy annotated sequences spanning a similarity range of 50% to 100%. Using an acceptance filter of minimum 90% similarity to the CO1 reference sequence, we found that 74% of the ca 100 taxon identified sequence reads were Polychaeta and 22% Nematoda. Relatively few other benthic invertebrate species were detected. Many of the identified sequence reads were extra-organismal DNA from terrestrial, planktonic, and photic zone sources. For the species rich Polychaeta, we found that, on average, only 20.6% of the species identified from morphology were also detected with DNA. This discrepancy was not due to missing reference sequences in the search database, because 90-100% (mean 96.7%) of the visually identified species at each station were represented with barcodes in Boldsystems. The volume of DNA samples is small compared with the volume searched in visual sorting, and the replicate DNA-samples in sum covered only about 2% of the surface area of a grab. This may considerably reduce the detection rate of species that are not uniformly distributed in the sediments. Along with PCR amplification bias and primer mismatch, this may be an important reason for the limited congruence of species identified with the two approaches. However, metabarcoding also identified 69 additional species that are usually overlooked in visual sample sorting, demonstrating how metabarcoding can complement traditional methodology by detecting additional, less conspicuous groups of organisms.
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Affiliation(s)
- Endre Willassen
- Department of Natural History, University of Bergen, Bergen, Norway
| | - Jon-Ivar Westgaard
- Department of Population Genetics, Institute of Marine Research, Tromsø, Troms, Norway
| | | | - Tanja Hanebrekke
- Department of Population Genetics, Institute of Marine Research, Tromsø, Troms, Norway
| | - Pål Buhl-Mortensen
- Department of Bentic Communities, Institute of Marine Research, Bergen, Norway
| | - Børge Holte
- Department of Bentic Communities, Institute of Marine Research, Tromsø, Troms, Norway
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Gold Z, Wall AR, Schweizer TM, Pentcheff ND, Curd EE, Barber PH, Meyer RS, Wayne R, Stolzenbach K, Prickett K, Luedy J, Wetzer R. A manager's guide to using eDNA metabarcoding in marine ecosystems. PeerJ 2022; 10:e14071. [PMID: 36405018 PMCID: PMC9673773 DOI: 10.7717/peerj.14071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Adam R. Wall
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Teia M. Schweizer
- Department of Fish and Wildlife Conservation Biology, Colorado State University, Fort Collins, CO, United States of America
| | - N. Dean Pentcheff
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Emily E. Curd
- Department of Natural Sciences, Landmark College, Putney, VT, United States of America
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Kevin Stolzenbach
- Wood Environment and Infrastructure, Inc., San Diego, CA, United States of America
| | - Kat Prickett
- Port of Los Angeles, Los Angeles, CA, United States of America
| | - Justin Luedy
- Port of Long Beach, Long Beach, CA, United States of America
| | - Regina Wetzer
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
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Turon M, Nygaard M, Guri G, Wangensteen OS, Præbel K. Fine-scale differences in eukaryotic communities inside and outside salmon aquaculture cages revealed by eDNA metabarcoding. Front Genet 2022; 13:957251. [PMID: 36092881 PMCID: PMC9458982 DOI: 10.3389/fgene.2022.957251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
Aquaculture impacts on marine benthic ecosystems are widely recognized and monitored. However, little is known about the community changes occurring in the water masses surrounding aquaculture sites. In the present study, we studied the eukaryotic communities inside and outside salmonid aquaculture cages through time to assess the community changes in the neighbouring waters of the farm. Water samples were taken biweekly over five months during the production phase from inside the cages and from nearby points located North and South of the salmon farm. Eukaryotic communities were analyzed by eDNA metabarcoding of the partial COI Leray-XT fragment. The results showed that eukaryotic communities inside the cages were significantly different from those in the outside environment, with communities inside the cages having higher diversity values and more indicator species associated with them. This is likely explained by the appearance of fouling species that colonize the artificial structures, but also by other species that are attracted to the cages by other means. Moreover, these effects were highly localized inside the cages, as the communities identified outside the cages, both North and South, had very similar eukaryotic composition at each point in time. Overall, the eukaryotic communities, both inside and outside the cages, showed similar temporal fluctuations through the summer months, with diversity peaks occurring at the end of July, beginning of September, and in the beginning of November, with the latter showing the highest Shannon diversity and richness values. Hence, our study suggests that seasonality, together with salmonid aquaculture, are the main drivers of eukaryotic community structure in surface waters surrounding the farm.
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Affiliation(s)
- Marta Turon
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Magnus Nygaard
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Gledis Guri
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian Institute of Marine Research, Tromsø, Norway
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Kim Præbel,
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Harbuzov Z, Farberova V, Tom M, Pallavicini A, Stanković D, Lotan T, Lubinevsky H. Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition. Mar Genomics 2022; 65:100980. [PMID: 35963148 DOI: 10.1016/j.margen.2022.100980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022]
Abstract
The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470-490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342-3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.
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Affiliation(s)
- Zoya Harbuzov
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel; Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel.
| | - Valeria Farberova
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel; Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel
| | - Moshe Tom
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - David Stanković
- National institute of Biology, Department of Organisms and Ecosystems Research, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Tamar Lotan
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel
| | - Hadas Lubinevsky
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel
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12
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Evaluating eDNA for Use within Marine Environmental Impact Assessments. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this review, the use of environmental DNA (eDNA) within Environmental Impact Assessment (EIA) is evaluated. EIA documents provide information required by regulators to evaluate the potential impact of a development project. Currently eDNA is being incorporated into biodiversity assessments as a complementary method for detecting rare, endangered or invasive species. However, questions have been raised regarding the maturity of the field and the suitability of eDNA information as evidence for EIA. Several key issues are identified for eDNA information within a generic EIA framework for marine environments. First, it is challenging to define the sampling unit and optimal sampling strategy for eDNA with respect to the project area and potential impact receptor. Second, eDNA assay validation protocols are preliminary at this time. Third, there are statistical issues around the probability of obtaining both false positives (identification of taxa that are not present) and false negatives (non-detection of taxa that are present) in results. At a minimum, an EIA must quantify the uncertainty in presence/absence estimates by combining series of Bernoulli trials with ad hoc occupancy models. Finally, the fate and transport of DNA fragments is largely unknown in environmental systems. Shedding dynamics, biogeochemical and physical processes that influence DNA fragments must be better understood to be able to link an eDNA signal with the receptor’s state. The biggest challenge is that eDNA is a proxy for the receptor and not a direct measure of presence. Nonetheless, as more actors enter the field, technological solutions are likely to emerge for these issues. Environmental DNA already shows great promise for baseline descriptions of the presence of species surrounding a project and can aid in the identification of potential receptors for EIA monitoring using other methods.
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13
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Abstract
Lumbrineridae is a family of marine annelids with simple external morphology but complex and diverse jaw apparatuses consisting of paired maxillae and mandibles. Here we present the first phylogeny of lumbrinerids based on combination of nuclear (18S rDNA) and mitochondrial (COI, 16S rDNA) markers utilizing Bayesian inference and Maximum Likelihood approaches. Despite limited taxon sampling, our results support monophyly of the genera Abyssoninoe, Augeneria, Gallardoneris, Lumbrineriopsis, and Ninoe and indicate polyphyly of the genera Lumbrineris (the type genus of the family) and Scoletoma. None of the morphological characters traditionally used in lumbrinerid systematics, such as the presence of connecting plates, four pairs of maxillae, bidentate simple hooded hooks, colorless maxillae IV, and multidentate maxillae IV were found to be exclusive homologies for a well-supported clade and have probably evolved several times independently within Lumbrineridae.
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15
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Govender A, Singh S, Groeneveld J, Pillay S, Willows-Munro S. Experimental validation of taxon-specific mini-barcode primers for metabarcoding of zooplankton. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e02469. [PMID: 34626511 DOI: 10.1002/eap.2469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 04/23/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
Metabarcoding to determine the species composition and diversity of marine zooplankton communities is a fast-developing field in which the standardization of methods is yet to be fully achieved. The selection of genetic markers and primer choice are particularly important because they substantially influence species detection rates and accuracy. Validation is therefore an important step in the design of metabarcoding protocols. We developed taxon-specific mini-barcode primers for the cytochrome c oxidase subunit I (COI) gene region and used an experimental approach to test species detection rates and primer accuracy of the newly designed primers for prawns, shrimps and crabs and published primers for marine lobsters and fish. Artificially assembled mock communities (with known species ratios) and unsorted coastal tow-net zooplankton samples were sequenced and the detected species were compared with those seeded in mock communities to test detection rates. Taxon-specific primers increased detection rates of target taxa compared with a universal primer set. Primer cocktails (multiple primer sets) significantly increased species detection rates compared with single primer pairs and could detect up to 100% of underrepresented target taxa in mock communities. Taxon-specific primers recovered fewer false-positive or false-negative results than the universal primer. The methods used to design taxon-specific mini-barcodes and the experimental mock community validation protocols shown here can easily be applied to studies on other groups and will allow for a level of standardization among studies undertaken in different ecosystems or geographic locations.
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Affiliation(s)
- Ashrenee Govender
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg, KwaZulu-Natal, 3201, South Africa
- Oceanographic Research Institute, King Shaka Avenue, Point, Durban, KwaZulu-Natal, 4001, South Africa
| | - Sohana Singh
- Oceanographic Research Institute, King Shaka Avenue, Point, Durban, KwaZulu-Natal, 4001, South Africa
| | - Johan Groeneveld
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg, KwaZulu-Natal, 3201, South Africa
- Oceanographic Research Institute, King Shaka Avenue, Point, Durban, KwaZulu-Natal, 4001, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Umbilo Rd, Durban, KwaZulu-Natal, 4001, South Africa
| | - Sandi Willows-Munro
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg, KwaZulu-Natal, 3201, South Africa
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16
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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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17
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Fayram AH, Wood JS, Swigle B. A comparison of genetically and morphometrically identified macroinvertebrate community index scores with implications for aquatic life use attainment. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 194:18. [PMID: 34888736 DOI: 10.1007/s10661-021-09525-w] [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: 06/15/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Measures of aquatic macroinvertebrate communities are often used to characterize water quality and indicate whether waterbodies are meeting management expectations. The accuracy of these measures depends on the skill and experience of the person identifying the macroinvertebrates, and obtaining these measures can be relatively expensive due to the time necessary for identification. Utilizing genetic identification of macroinvertebrate taxa has the potential to reduce the time of sample processing, identify a greater number of taxa, and increase the resolution of identification. We compared Colorado multi-metric index (MMI) scores from seven locations in the Big Thompson River, CO, based on genetic and morphometric identification and estimated the ability of MMI scores based on genetic identification to characterize aquatic life use attainment management thresholds. We found a significant linear relationship (p = 0.002, R2 = 0.87) between MMI scores generated by genetic and morphological identification. MMIs support the following aquatic life use designations as defined by the Colorado Water Quality Control Commission: Impaired < 40, Attaining > 48, and Ambiguous 40-48. These values correspond to MMIs based on genetic identification as Impaired < 20, Attaining > 64, and Ambiguous = 21-63 based on the prediction interval of the regression equation. Our results suggest that using genetically identified macroinvertebrates to estimate MMI scores can provide some degree of certainty regarding aquatic life use designations, and while it may be inappropriate at the current time to entirely replace morphologically based biotic integrity measures with those based on molecular identification, there are opportunities in their use.
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Affiliation(s)
- Andrew H Fayram
- Loveland Water and Power, 902 S. Boise Ave, Loveland, CO, 80537, USA.
| | - John S Wood
- Pisces Molecular, 1600 Range Street, Suite 201, Boulder, CO, 80301, USA
| | - Benjamin Swigle
- Colorado Parks and Wildlife, 317 W Prospect Rd, Fort Collins, CO, 80526, USA
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18
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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.
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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.
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19
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Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters. BIOLOGY 2021; 10:biology10111092. [PMID: 34827084 PMCID: PMC8614736 DOI: 10.3390/biology10111092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022]
Abstract
Simple Summary The biodiversity and ecological status assessment of transitional water ecosystems by benthic macroinvertebrates investigation could use DNA barcode tools for more rapid and efficient outputs. The principal limits of this application are the incompleteness of DNA barcode databases, the identification of optimal primers set, and the gap in the species sequences. The influence of the incompleteness of DNA barcode libraries on species diversity indices, ecological indicators, and ecological status assessment in transitional waters of the southeast Mediterranean were analysed, underlying the importance to implement DNA barcode libraries and to put an effort toward specific species at a local level. Abstract The ecological assessment of European aquatic ecosystems is regulated under the framework directives on strategy for water and marine environments. Benthic macroinvertebrates are the most used biological quality element for ecological assessment of rivers, coastal-marines, and transitional waters. The morphological identification of benthic macroinvertebrates is the current tool for their assessment. Recently, DNA-based tools have been proposed as effective alternatives. The main current limits of DNA-based applications include the incompleteness of species recorded in the DNA barcode reference libraries and the primers bias. Here, we analysed the influence of the incompleteness of DNA barcode databases on species diversity indices, ecological indicators, and ecological assessment in transitional waters of the southeast Mediterranean, taking into account the availability of commonly sequenced and deposited genomic regions for listed species. The ecological quality status assigned through the potential application of both approaches to the analysed transitional water ecosystems was different in 27% of sites. We also analysed the inter-specific genetic distances to evaluate the potential application of the DNA metabarcoding method. Overall, this work highlights the importance to expand the barcode databases and to analyse, at the regional level, the gaps in the DNA barcodes.
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20
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Cavaliere M, Barrenechea Angeles I, Montresor M, Bucci C, Brocani L, Balassi E, Margiotta F, Francescangeli F, Bouchet VMP, Pawlowski J, Frontalini F. Assessing the ecological quality status of the highly polluted Bagnoli area (Tyrrhenian Sea, Italy) using foraminiferal eDNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:147871. [PMID: 34098278 DOI: 10.1016/j.scitotenv.2021.147871] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Morphology-based benthic foraminifera indices are increasingly used worldwide for biomonitoring the ecological quality of marine sediments. The recent development of foraminiferal eDNA metabarcoding offers a reliable, time-, and cost-effective alternative to morphology-based foraminiferal biomonitoring. However, the practical applications of these new tools are still highly limited. In the present study, we evaluate the response of benthic foraminifera and define the ecological quality status (EcoQS) in the Bagnoli area (Tyrrhenian Sea, Italy) based on a traditional morphology-based approach and eDNA metabarcoding. The geochemical data show that several sites in front of the former industrial plant contain higher concentrations of potentially toxic elements than the effect range median and are characterized by the highest total organic carbon (TOC) content, whereas the distantly located sites can be considered relatively low- to unpolluted. Significant differences (i.e., diversity and assemblage composition) in both morphological and molecular datasets were found between the relatively low- to unpolluted and the most polluted areas. Similarly, the selected ecological indices of both morphological and molecular datasets strikingly and congruently resulted in a clear separation following the environmental stress gradient. The molecular indices (i.e., g-exp(H'bc), g-Foram AMBI, and g-Foram AMBI-MOTUs) reliably identified poor-to-bad EcoQS in the polluted area in front of the former industrial plant. On the other hand, the Foram-AMBI based on morphology well identified an overall trend but seemed to overestimate the EcoQS if the traditional class boundaries were considered. The congruent and complementary trends between morphological and metabarcoding data observed in the case of the Bagnoli site further support the application of foraminiferal metabarcoding in routine biomonitoring to assess the environmental impacts of heavily polluted marine areas.
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Affiliation(s)
- M Cavaliere
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy.
| | - I Barrenechea Angeles
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland; Department of Earth Sciences, University of Geneva, 1205 Geneva, Switzerland
| | - M Montresor
- Stazione Zoologica Anton Dohrn, 80122 Naples, Italy
| | - C Bucci
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - L Brocani
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - E Balassi
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - F Margiotta
- Stazione Zoologica Anton Dohrn, 80122 Naples, Italy
| | - F Francescangeli
- University of Hamburg, Institute for Geology, Centre for Earth System Research and Sustainability, 20146 Hamburg, Germany
| | - V M P Bouchet
- University of Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, Station Marine de Wimereux, F 59000 Lille, France
| | - J Pawlowski
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - F Frontalini
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
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21
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Zaiko A, Greenfield P, Abbott C, von Ammon U, Bilewitch J, Bunce M, Cristescu ME, Chariton A, Dowle E, Geller J, Ardura Gutierrez A, Hajibabaei M, Haggard E, Inglis GJ, Lavery SD, Samuiloviene A, Simpson T, Stat M, Stephenson S, Sutherland J, Thakur V, Westfall K, Wood SA, Wright M, Zhang G, Pochon X. Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment. Mol Ecol Resour 2021; 22:519-538. [PMID: 34398515 DOI: 10.1111/1755-0998.13485] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/21/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022]
Abstract
Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical samples and primer sets using varying laboratory procedures. Homogenized biofouling samples collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories (amplification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the samples grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality samples gave the best improvement in sample classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, sample defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future biodiversity studies using metabarcoding.
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Affiliation(s)
- Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Paul Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia.,Environmental (e)DNA and Biomonitoring Lab, Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Cathryn Abbott
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ulla von Ammon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Jaret Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA), Hataitai, Wellington, New Zealand
| | - Michael Bunce
- Environmental Protection Authority, Wellington, New Zealand
| | | | - Anthony Chariton
- Environmental (e)DNA and Biomonitoring Lab, Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Eddy Dowle
- School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jonathan Geller
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | | | | | - Emmet Haggard
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | - Graeme J Inglis
- National Institute of Water & Atmospheric Research Ltd (NIWA), Christchurch, New Zealand
| | - Shane D Lavery
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Tiffany Simpson
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Michael Stat
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Sarah Stephenson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Judy Sutherland
- National Institute of Water & Atmospheric Research Ltd (NIWA), Hataitai, Wellington, New Zealand
| | - Vibha Thakur
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kristen Westfall
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
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22
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Ibabe A, Miralles L, Carleos CE, Soto-López V, Menéndez-Teleña D, Bartolomé M, Montes HJ, González M, Dopico E, Garcia-Vazquez E, Borrell YJ. Building on gAMBI in ports for a challenging biological invasions scenario: Blue-gNIS as a proof of concept. MARINE ENVIRONMENTAL RESEARCH 2021; 169:105340. [PMID: 33930798 DOI: 10.1016/j.marenvres.2021.105340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/05/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
The status of aquatic ecosystems has historically been monitored by the use of biotic indices. However, few biotic measures consider the presence of non-indigenous species as a sign of anthropogenic pollution and habitat disturbance even when this may seriously affect the metric scores and ecological status classifications of an environment. Today, biological invasions are currently one of the greatest threats to biodiversity and sustainable blue economies around the world. In this work, environmental assessments were conducted in the Port of Gijon, Northern Spain, using eDNA metabarcoding, and the gAMBI (genetics based AZTI Marine Biotic Index) was estimated. Results indicate a high/good ecological status within the port. However, nine non-indigenous species and five invasive species were found, and a modification of the gAMBI that includes species invasiveness was proposed: Blue-gNIS. The index was preliminary tested against existing validated indices such as gAMBI, BENTIX (based on the ecology of macroinvertebrates) and ALEX (based on the invasiveness of the species). Blue-gNIS classified the port in a good ecological status and showed its potential usefulness to achieve more complete water quality assessments of ports.
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Affiliation(s)
- A Ibabe
- Genetics, Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain
| | - L Miralles
- Genetics, Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain; Ecohydros S.L., Polígono Industrial de Cros, Edif. 5-Nave 8, 39600, Maliaño, Cantabria, Spain
| | - C E Carleos
- Department of Statistics and Operations Research and Mathematics Didactics, University of Oviedo, Facultad de Ciencias, C/ Federico García Lorca, s/n, 33007, Oviedo, Spain
| | - V Soto-López
- Department of Marine Science and Technology, University of Oviedo, Escuela Superior de Marina Civil, Campus de Gijón C/Blasco de Garay s/n, 33203, Gijón, Asturias, Spain
| | - D Menéndez-Teleña
- Department of Marine Science and Technology, University of Oviedo, Escuela Superior de Marina Civil, Campus de Gijón C/Blasco de Garay s/n, 33203, Gijón, Asturias, Spain
| | - M Bartolomé
- Department of Marine Science and Technology, University of Oviedo, Escuela Superior de Marina Civil, Campus de Gijón C/Blasco de Garay s/n, 33203, Gijón, Asturias, Spain
| | - H J Montes
- Department of Marine Science and Technology, University of Oviedo, Escuela Superior de Marina Civil, Campus de Gijón C/Blasco de Garay s/n, 33203, Gijón, Asturias, Spain
| | - M González
- CEO of Environmental Sustainability, Port Authority of Gijon, Spain
| | - E Dopico
- Department of Educational Sciences, C/ Aniceto Sela s/n, 33005, Oviedo, Spain
| | - E Garcia-Vazquez
- Genetics, Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain
| | - Y J Borrell
- Genetics, Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain.
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23
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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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24
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Buchner D, Beermann AJ, Leese F, Weiss M. Cooking small and large portions of “biodiversity‐soup”: Miniaturized DNA metabarcoding PCRs perform as good as large‐volume PCRs. Ecol Evol 2021. [DOI: 10.1002/ece3.7753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Dominik Buchner
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
| | - Arne J. Beermann
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
| | - Florian Leese
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
| | - Martina Weiss
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
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25
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Rodríguez-Ezpeleta N, Zinger L, Kinziger A, Bik HM, Bonin A, Coissac E, Emerson BC, Lopes CM, Pelletier TA, Taberlet P, Narum S. Biodiversity monitoring using environmental DNA. Mol Ecol Resour 2021; 21:1405-1409. [PMID: 34032015 DOI: 10.1111/1755-0998.13399] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022]
Affiliation(s)
| | - Lucie Zinger
- Département de biologie, Institut de Biologie de l'ENS (IBENS, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Andrew Kinziger
- Department of Fisheries Biology, Humboldt State University, Arcata, CA, USA
| | - Holly M Bik
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Aurélie Bonin
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Eric Coissac
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC, La Laguna, Spain
| | - Carla Martins Lopes
- Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP, Rio Claro, SP, Brazil
| | | | - Pierre Taberlet
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France.,The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway
| | - Shawn Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, University of Idaho, Hagerman, ID, USA
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26
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Kravtsova LS, Peretolchina TE, Triboy TI, Nebesnykh IA, Kupchinskiy AB, Tupikin AE, Kabilov MR. The Study of the Diversity of Hydrobionts from Listvennichny Bay of Lake Baikal by DNA Metabarcoding. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421040050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Rimet F, Aylagas E, Borja Á, Bouchez A, Canino A, Chauvin C, Chonova T, Ciampor Jr F, Costa FO, Ferrari BJD, Gastineau R, Goulon C, Gugger M, Holzmann M, Jahn R, Kahlert M, Kusber WH, Laplace-Treyture C, Leese F, Leliaert F, Mann DG, Marchand F, Méléder V, Pawlowski J, Rasconi S, Rivera S, Rougerie R, Schweizer M, Trobajo R, Vasselon V, Vivien R, Weigand A, Witkowski A, Zimmermann J, Ekrem T. Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.58056] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.
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28
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He X, Gilmore SR, Sutherland TF, Hajibabaei M, Miller KM, Westfall KM, Pawlowski J, Abbott CL. Biotic signals associated with benthic impacts of salmon farms from eDNA metabarcoding of sediments. Mol Ecol 2021; 30:3158-3174. [PMID: 33481325 DOI: 10.1111/mec.15814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 12/06/2020] [Accepted: 01/15/2021] [Indexed: 01/04/2023]
Abstract
Environmental DNA (eDNA) metabarcoding can rapidly characterize the composition and diversity of benthic communities, thus it has high potential utility for routine assessments of benthic impacts of marine finfish farming. In this study, 126 sediment grab samples from 42 stations were collected at six salmon farms in British Columbia, Canada. Benthic community changes were assessed by both eDNA metabarcoding of metazoans and macrofaunal polychaete surveys. The latter was done by analysing 11,466 individuals using a combination of morphology-based taxonomy and DNA barcoding. Study objectives were to: (i) compare biotic signals associated with benthic impacts of salmon farming in the two data sources, and (ii) identify potential eDNA indicators to facilitate monitoring in Canada. Alpha diversity parameters were consistently reduced near fish cage edge and negatively correlated with pore-water sulphide concentration, with coefficients ranging from -0.62 to -0.48. Although Polychaeta are a common indicator group, the negative correlation with pore-water sulphide concentration was much stronger for Nematoda OTU richness (correlation coefficient: -0.86) than for Polychaeta (correlation coefficient: -0.38). Presence/absence of Capitella generally agreed well between the two methods despite that they differed in the volume of sediments sampled and the molecular marker used. Multiple approaches were used to identify OTUs related to organic enrichment statuses. We demonstrate that eDNA metabarcoding generates biotic signals that could be leveraged for environmental assessment of benthic impacts of fish farms in multiple ways: both alpha diversity and Nematoda OTU richness could be used to assess the spatial extent of impact, and OTUs related to organic enrichment could be used to develop local biotic indices.
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Affiliation(s)
- Xiaoping He
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Scott R Gilmore
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Terri F Sutherland
- Pacific Science Enterprise Centre, Fisheries and Oceans Canada, West Vancouver, BC, Canada
| | - Mehrdad Hajibabaei
- Department of Integrative Biology & Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Kristen M Westfall
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland.,ID-Gene Ecodiagnostics, Geneva, Switzerland
| | - Cathryn L Abbott
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
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29
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Attia El Hili R, Achouri MS, Verneau O. Cytochrome c oxydase I phylogenetic analysis of Haemogregarina parasites (Apicomplexa, Coccidia, Eucoccidiorida, Haemogregarinidae) confirms the presence of three distinct species within the freshwater turtles of Tunisia. Parasitol Int 2021; 82:102306. [PMID: 33610828 DOI: 10.1016/j.parint.2021.102306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 11/18/2022]
Abstract
Species of Haemogregarina are apicomplexan blood parasites that use vertebrates as intermediate hosts. Due to limited interspecific morphological characters within the genus during the last decade, 18S rRNA gene sequences were widely used for species identification. As coinfection patterns were recently reported from nuclear molecular data for two sympatric freshwater turtles Mauremys leprosa and Emys orbicularis from Tunisia, our objectives were to design COI specific primers to confirm the presence of three distinct species in both host species. Blood samples were collected from 22 turtles, from which DNAs were extracted and used as templates for amplification. Following different rounds of PCR and nested PCR, we designed specific Haemogregarina COI primers that allowed the sequencing of nine distinct haplotypes. Phylogenetic Bayesian analysis revealed the occurrence of three well-differentiated sublineages that clustered together into a single clade. Based on pairwise genetic distances (p-distance), we confirmed the occurrence of three distinct but phylogenetically closely related species coinfecting M. leprosa and E. orbicularis in the same aquatic environments. Our results demonstrate that the use of fast evolving genes within Haemogregarina will help to investigate the parasite diversity within both intermediate vertebrate and definitive invertebrate hosts, and to assess the evolution, historical biogeography and specificity of haemogregarines.
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Affiliation(s)
- Rahma Attia El Hili
- University of Tunis El Manar, Faculty of Sciences of Tunis, Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06 Tunis, Tunisia; Université Perpignan Via Domitia, Centre de Formation et de Recherche sur les Environnements Méditerranéens, Perpignan, France; CNRS, Centre de Formation et de Recherche sur les Environnements Méditerranéens, Perpignan, France
| | - Mohamed Sghaier Achouri
- University of Tunis El Manar, Faculty of Sciences of Tunis, Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06 Tunis, Tunisia
| | - Olivier Verneau
- Université Perpignan Via Domitia, Centre de Formation et de Recherche sur les Environnements Méditerranéens, Perpignan, France; CNRS, Centre de Formation et de Recherche sur les Environnements Méditerranéens, Perpignan, France; Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa.
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30
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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.
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31
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Meyer A, Boyer F, Valentini A, Bonin A, Ficetola GF, Beisel JN, Bouquerel J, Wagner P, Gaboriaud C, Leese F, Dejean T, Taberlet P, Usseglio-Polatera P. Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering. Mol Ecol 2020; 30:3203-3220. [PMID: 33150613 DOI: 10.1111/mec.15723] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/15/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022]
Abstract
Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time-consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular-based alternative to the morphology-based monitoring of streams using macroinvertebrates. We compared results achieved with the standard morphological identification of organisms sampled in 18 sites located on 15 French wadeable streams to results obtained with the DNA metabarcoding identification of sorted bulk material of the same macroinvertebrate samples, using read numbers (expressed as relative frequencies) as a proxy for abundances. In particular, we evaluated how combining and filtering metabarcoding data obtained from three different markers (COI: BF1-BR2, 18S: Euka02 and 16S: Inse01) could improve the efficiency of bioassessment. In total, 140 taxa were identified based on morphological criteria, and 127 were identified based on DNA metabarcoding using the three markers, with an overlap of 99 taxa. The threshold values used for sequence filtering based on the "best identity" criterion and the number of reads had an effect on the assessment efficiency of data obtained with each marker. Compared to single marker results, combining data from different markers allowed us to improve the match between biotic index values obtained with the bulk DNA versus morphology-based approaches. Both approaches assigned the same ecological quality class to a majority (86%) of the site sampling events, highlighting both the efficiency of metabarcoding as a biomonitoring tool but also the need for further research to improve this efficiency.
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Affiliation(s)
- Albin Meyer
- Université de Lorraine, CNRS, LIEC, Metz, France
| | - Frédéric Boyer
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
| | | | - Aurélie Bonin
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France.,SPYGEN, Le Bourget du Lac, France.,Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Gentile Francesco Ficetola
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France.,Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | | | | | | | | | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
| | | | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France.,UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
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32
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Aylagas E, Borja A, Pochon X, Zaiko A, Keeley N, Bruce K, Hong P, Ruiz GM, Stein ED, Theroux S, Geraldi N, Ortega A, Gajdzik L, Coker DJ, Katan Y, Hikmawan T, Saleem A, Alamer S, Jones BH, Duarte CM, Pearman J, Carvalho S. Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140780. [PMID: 32693276 DOI: 10.1016/j.scitotenv.2020.140780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Molecular-based approaches can provide timely biodiversity assessments, showing an immense potential to facilitate decision-making in marine environmental management. However, the uptake of molecular data into environmental policy remains minimal. Here, we showcase a selection of local to global scale studies applying molecular-based methodologies for environmental management at various stages of implementation. Drawing upon lessons learned from these case-studies, we provide a roadmap to facilitate applications of DNA-based methods to marine policies and to overcome the existing challenges. The main impediment identified is the need for standardized protocols to guarantee data comparison across spatial and temporal scales. Adoption of Translational Molecular Ecology - the sustained collaboration between molecular ecologists and stakeholders, will enhance consensus with regards to the objectives, methods, and outcomes of environmental management projects. Establishing a sustained dialogue among stakeholders is key to accelerating the adoption of molecular-based approaches for marine monitoring and assessment.
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Affiliation(s)
- Eva Aylagas
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Angel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Nigel Keeley
- Benthic Resources and Processors Group, Institute of Marine Research, Postboks 6606 Langnes, 9296 Tromsø, Norway
| | - Kat Bruce
- Nature Metrics Ltd, CABI site, Bakeham Lane, Egham TW20 9TY, United Kingdom
| | - Peiying Hong
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD 21037, USA; Aquatic Bioinvasion Research and Policy Institute, Environmental Science and Management, Portland State University, Portland, OR 97201, USA
| | - Eric D Stein
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Susanna Theroux
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Nathan Geraldi
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alejandra Ortega
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Laura Gajdzik
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Darren J Coker
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yasser Katan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Tyas Hikmawan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Ammar Saleem
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Sultan Alamer
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Burton H Jones
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - John Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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33
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Apothéloz-Perret-Gentil L, Bouchez A, Cordier T, Cordonier A, Guéguen J, Rimet F, Vasselon V, Pawlowski J. Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index. Mol Ecol 2020; 30:2959-2968. [PMID: 32979002 PMCID: PMC8358953 DOI: 10.1111/mec.15646] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/24/2020] [Accepted: 09/02/2020] [Indexed: 01/04/2023]
Abstract
Recently, several studies demonstrated the usefulness of diatom eDNA metabarcoding as an alternative to assess the ecological quality of rivers and streams. However, the choice of the taxonomic marker as well as the methodology for data analysis differ between these studies, hampering the comparison of their results and effectiveness. The aim of this study was to compare two taxonomic markers commonly used in diatom metabarcoding and three distinct analytical approaches to infer a molecular diatom index. We used the values of classical morphological diatom index as a benchmark for this comparison. We amplified and sequenced both a fragment of the rbcL gene and the V4 region of the 18S rRNA gene for 112 epilithic samples from Swiss and French rivers. We inferred index values using three analytical approaches: by computing it directly from taxonomically assigned sequences, by calibrating de novo the ecovalues of all metabarcodes, and by using a supervised machine learning algorithm to train predictive models. In general, the values of index obtained using the two "taxonomy-free" approaches, encompassing molecular assignment and machine learning, were closer correlated to the values of the morphological index than the values based on taxonomically assigned sequences. The correlations of the three analytical approaches were higher in the case of rbcL compared to the 18S marker, highlighting the importance of the reference database which is more complete for the rbcL marker. Our study confirms the effectiveness of diatom metabarcoding as an operational tool for rivers ecological quality assessment and shows that the analytical approaches by-passing the taxonomic assignments are particularly efficient when reference databases are incomplete.
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Affiliation(s)
- Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene ecodiagnostics, Geneva, Switzerland
| | - Agnès Bouchez
- UMR CARRTEL, INRAE, Université Savoie Mont-Blanc, Thonon, France
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene ecodiagnostics, Geneva, Switzerland
| | - Arielle Cordonier
- Department of Territorial Management, Water Ecology Service, Geneva, Switzerland
| | - Julie Guéguen
- UMR CARRTEL, INRAE, Université Savoie Mont-Blanc, Thonon, France
| | - Frederic Rimet
- UMR CARRTEL, INRAE, Université Savoie Mont-Blanc, Thonon, France
| | - Valentin Vasselon
- Pôle R&D "ECLA", Thonon-les-Bains, France.,OFB, Site INRA UMR CARRTEL, Thonon-les-Bains, France
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene ecodiagnostics, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
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34
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Mauffrey F, Cordier T, Apothéloz-Perret-Gentil L, Cermakova K, Merzi T, Delefosse M, Blanc P, Pawlowski J. Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding. Mol Ecol 2020; 30:3007-3022. [PMID: 33070453 DOI: 10.1111/mec.15698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/15/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
Since 2010, considerable efforts have been undertaken to monitor the environmental status of European marine waters and ensuring the development of methodological standards for the evaluation of this status. However, the current routine biomonitoring implicates time-consuming and costly manual sorting and morphological identification of benthic macrofauna. Environmental DNA (eDNA) metabarcoding represents an alternative to the traditional monitoring method with very promising results. Here, we tested it further by performing eDNA metabarcoding of benthic eukaryotic communities in the vicinity of two offshore oil and gas platforms in the North Sea. Three different genetic markers (18S V1V2, 18S V9 and COI) were used to assess the environmental pressures induced by the platforms. All markers showed patterns of alpha and beta diversity consistent with morphology-based macrofauna analyses. In particular, the communities' structure inferred from metabarcoding and morphological data significantly changed along distance gradients from the platforms. The impact of the operational discharges was also detected by the variation of biotic index values, AMBI index showing the best correlation between morphological and eDNA data sets. Finally, the sediment physicochemical parameters were used to build a local de novo pressure index that served as benchmark to test the potential of a taxonomy-free approach. Our study demonstrates that metabarcoding approach outperforms morphology-based approach and can be used as a cost and time-saving alternative solution to the traditional morphology-based monitoring in order to monitor more efficiently the impact of industrial activities on marine biodiversity.
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Affiliation(s)
- Florian Mauffrey
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Kristina Cermakova
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Thomas Merzi
- Total SA, Centre Scientifique et Technique Jean Feger, Pau, France
| | | | - Philippe Blanc
- Total SA, Centre Scientifique et Technique Jean Feger, Pau, France
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
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35
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Schenk J, Höss S, Brinke M, Kleinbölting N, Brüchner-Hüttemann H, Traunspurger W. Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy. ENVIRONMENT INTERNATIONAL 2020; 143:105922. [PMID: 32663713 DOI: 10.1016/j.envint.2020.105922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/04/2020] [Accepted: 06/20/2020] [Indexed: 05/19/2023]
Abstract
The use of bioindicator species is a widely applied approach to evaluate ecological conditions, and several indices have been designed for this purpose. To assess the impact of pollution, especially in sediments, a pollution-sensitive index based on nematodes, one of the most abundant and species-rich groups of metazoa, was developed. The NemaSPEAR[%] index in its original form relies on the morphological inspection of nematode species. The application of a morphologically based NemaSPEAR[%] at the genus-level was previously validated. The present study evaluated a NemaSPEAR[%] index based on metabarcoding of nematode communities and tested the potential of fragments from the 28S rDNA, 18S rDNA and cytochrome c oxidase subunit I (COI) genes. In general, molecular-based results tended to show a poorer condition than morphology-based results for the investigated sites. At the genus level, NemaSPEAR[%] values based on morphological data strongly correlated with those based on molecular data for both the 28S rDNA and the 18S rDNA gene fragments (R2 = 0.86 and R2 = 0.74, respectively). Within the dominant genera (>3%) identified by morphology, 68% were detected by at least one of the two ribosomal markers. At the species level, however, concordance was less pronounced, as there were several deviations of the molecular from the morphological data. These differences could mostly be attributed to shortcomings in the reference database used in the molecular-based assignments. Our pilot study shows that a molecularly based, genus-level NemaSPEAR[%] can be successfully applied to evaluate polluted sediment. Future studies need to validate this approach further, e.g. with bulk extractions of whole meiofaunal communities in order to circumvent time-consuming nematode isolation. Further database curation with abundant NemaSPEAR[%] species will also increase the applicability of this approach.
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Affiliation(s)
- Janina Schenk
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany.
| | - Sebastian Höss
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany; Ecossa, Giselastrasse 6, 82319 Starnberg, Germany.
| | - Marvin Brinke
- Federal Institute of Hydrology (BfG), Mainzer Tor 1, 56068 Koblenz, Germany.
| | - Nils Kleinbölting
- Center for Biotechnology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.
| | | | - Walter Traunspurger
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany.
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36
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Hardulak LA, Morinière J, Hausmann A, Hendrich L, Schmidt S, Doczkal D, Müller J, Hebert PDN, Haszprunar G. DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species. Mol Ecol Resour 2020; 20:1542-1557. [PMID: 32559020 DOI: 10.1111/1755-0998.13212] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 01/09/2023]
Abstract
DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.
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Affiliation(s)
- Laura A Hardulak
- SNSB-Zoologische Staatssammlung München, Munich, Germany.,Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Axel Hausmann
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Lars Hendrich
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Dieter Doczkal
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Jörg Müller
- National Park Bavarian Forest, Grafenau, Germany.,Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, University of Würzburg, Biocenter, Rauhenebrach, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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37
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Frühe L, Cordier T, Dully V, Breiner HW, Lentendu G, Pawlowski J, Martins C, Wilding TA, Stoeck T. Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes. Mol Ecol 2020; 30:2988-3006. [PMID: 32285497 DOI: 10.1111/mec.15434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/02/2023]
Abstract
Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental classification based on standard macroinvertebrate surveys. The most promising approaches to infer EQ from biotic indices (BI) are supervised machine learning (SML) and the calculation of indicator values (IndVal). In this study we compared the performance of both approaches using DNA metabarcodes of bacteria and ciliates as bioindicators obtained from 152 samples collected from seven Norwegian salmon farms. Results from standard macroinvertebrate-monitoring of the same samples were used as reference to compare the accuracy of both approaches. First, SML outperformed the IndVal approach to infer EQ from eDNA metabarcodes. The Random Forest (RF) algorithm appeared to be less sensitive to noisy data (a typical feature of massive environmental sequence data sets) and uneven data coverage across EQ classes (a typical feature of environmental compliance monitoring scheme) compared to a widely used method to infer IndVals for the calculation of a BI. Second, bacteria allowed for a more accurate EQ assessment than ciliate eDNA metabarcodes. For the implementation of DNA metabarcoding into routine monitoring programmes to assess EQ around salmon aquaculture cages, we therefore recommend bacterial DNA metabarcodes in combination with SML to classify EQ categories based on molecular signatures.
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Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Hans-Werner Breiner
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Guillaume Lentendu
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics Ltd, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | | | - Thomas A Wilding
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, Scotland
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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38
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Martínez A, Eckert EM, Artois T, Careddu G, Casu M, Curini-Galletti M, Gazale V, Gobert S, Ivanenko VN, Jondelius U, Marzano M, Pesole G, Zanello A, Todaro MA, Fontaneto D. Human access impacts biodiversity of microscopic animals in sandy beaches. Commun Biol 2020; 3:175. [PMID: 32313088 PMCID: PMC7170908 DOI: 10.1038/s42003-020-0912-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/23/2020] [Indexed: 01/25/2023] Open
Abstract
Whereas most work to understand impacts of humans on biodiversity on coastal areas has focused on large, conspicuous organisms, we highlight effects of tourist access on the diversity of microscopic marine animals (meiofauna). We used a DNA metabarcoding approach with an iterative and phylogeny-based approach for the taxonomic assignment of meiofauna and relate diversity patterns to the numbers of tourists accessing sandy beaches on an otherwise un-impacted island National Park. Tourist frequentation, independently of differences in sediment granulometry, beach length, and other potential confounding factors, affected meiofaunal diversity in the shallow “swash” zone right at the mean water mark; the impacts declined with water depth (up to 2 m). The indicated negative effect on meiofauna may have a consequence on all the biota including the higher trophic levels. Thus, we claim that it is important to consider restricting access to beaches in touristic areas, in order to preserve biodiversity. Martínez et al. use DNA metabarcoding and a phylogeny-based approach to demonstrate the effects of tourist access on meiofauna diversity of beaches in Asinara National Park. Their results show that tourist frequentation decreases meiofaunal diversity at the shallow “swash” zone, and can be used to inform tourist access and management of beaches.
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Affiliation(s)
- Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania, Italy
| | - Ester M Eckert
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania, Italy
| | - Tom Artois
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Giovanni Careddu
- Parco Nazionale dell'Asinara, Area Marina Protetta, Porto Torres, Italy
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | | | - Vittorio Gazale
- Parco Nazionale dell'Asinara, Area Marina Protetta, Porto Torres, Italy
| | - Stefan Gobert
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Viatcheslav N Ivanenko
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Marinella Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), Bari, Italy.,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari "A. Moro", Bari, Italy
| | - Aldo Zanello
- Parco Nazionale dell'Asinara, Area Marina Protetta, Porto Torres, Italy
| | - M Antonio Todaro
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania, Italy.
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39
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Sigamani S, Perumal M, Thivakaran GA, Thangavel B, Kandasamy K. DNA barcoding of macrofauna act as a tool for assessing marine ecosystem. MARINE POLLUTION BULLETIN 2020; 152:107891. [PMID: 27423443 DOI: 10.1016/j.marpolbul.2016.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/09/2016] [Accepted: 07/11/2016] [Indexed: 06/06/2023]
Abstract
Nowadays, marine ecosystem monitoring and assessment are increasingly depending on variety of molecular tools. With these background, DNA barcoding play a key role in species identification with increasing speed and accuracy, and although the suitability for developing genetic tools like genomic AMBI (gAMBI). Presently we have submitted 13 benthic polychaete species using mtCOI to GenBank. Of these, nine species were newly submitted, and hence they act as a benchmark and reference organism for identifying respective polychaete species worldwide in the near future. Based on that, our study results tend to be helpful for motivating among the researcher in order to implementing the genomic AMBI (gAMBI).
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Affiliation(s)
- Sivaraj Sigamani
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India.
| | - Murugesan Perumal
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India
| | | | - Balasubramanian Thangavel
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India
| | - Kathiresan Kandasamy
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India
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40
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Buchner D, Beermann AJ, Laini A, Rolauffs P, Vitecek S, Hering D, Leese F. Analysis of 13,312 benthic invertebrate samples from German streams reveals minor deviations in ecological status class between abundance and presence/absence data. PLoS One 2019; 14:e0226547. [PMID: 31869356 PMCID: PMC6927632 DOI: 10.1371/journal.pone.0226547] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/28/2019] [Indexed: 11/18/2022] Open
Abstract
Benthic invertebrates are the most commonly used organisms used to assess ecological status as required by the EU Water Framework Directive (WFD). For WFD-compliant assessments, benthic invertebrate communities are sampled, identified and counted. Taxa × abundance matrices are used to calculate indices and the resulting scores are compared to reference values to determine the ecological status class. DNA-based tools, such as DNA metabarcoding, provide a new and precise method for species identification but cannot deliver robust abundance data. To evaluate the applicability of DNA-based tools to ecological status assessment, we evaluated whether the results derived from presence/absence data are comparable to those derived from abundance data. We analysed benthic invertebrate community data obtained from 13,312 WFD assessments of German streams. Broken down to 30 official stream types, we compared assessment results based on abundance and presence/absence data for the assessment modules “organic pollution” (i.e., the saprobic index) and “general degradation” (a multimetric index) as well as their underlying metrics. In 76.6% of cases, the ecological status class did not change after transforming abundance data to presence/absence data. In 12% of cases, the status class was reduced by one (e.g., from good to moderate), and in 11.2% of cases, the class increased by one. In only 0.2% of cases, the status shifted by two classes. Systematic stream type-specific deviations were found and differences between abundance and presence/absence data were most prominent for stream types where abundance information contributed directly to one or several metrics of the general degradation module. For a single stream type, these deviations led to a systematic shift in status from ‘good’ to ‘moderate’ (n = 201; with only n = 3 increasing). The systematic decrease in scores was observed, even when considering simulated confidence intervals for abundance data. Our analysis suggests that presence/absence data can yield similar assessment results to those for abundance-based data, despite type-specific deviations. For most metrics, it should be possible to intercalibrate the two data types without substantial efforts. Thus, benthic invertebrate taxon lists generated by standardised DNA-based methods should be further considered as a complementary approach.
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Affiliation(s)
- Dominik Buchner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
| | - Arne J. Beermann
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
- Centre for Water and Environmental Research (ZWU), Essen, Germany
| | - Alex Laini
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parma, Italy
| | - Peter Rolauffs
- University of Duisburg-Essen, Aquatic Ecology, Essen, Germany
| | - Simon Vitecek
- WasserCluster Lunz, Lunz am See, Austria
- University of Natural Resources Vienna, Wien, Austria
| | - Daniel Hering
- Centre for Water and Environmental Research (ZWU), Essen, Germany
- University of Duisburg-Essen, Aquatic Ecology, Essen, Germany
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
- Centre for Water and Environmental Research (ZWU), Essen, Germany
- * E-mail:
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41
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Weigand H, Beermann AJ, Čiampor F, Costa FO, Csabai Z, Duarte S, Geiger MF, Grabowski M, Rimet F, Rulik B, Strand M, Szucsich N, Weigand AM, Willassen E, Wyler SA, Bouchez A, Borja A, Čiamporová-Zaťovičová Z, Ferreira S, Dijkstra KDB, Eisendle U, Freyhof J, Gadawski P, Graf W, Haegerbaeumer A, van der Hoorn BB, Japoshvili B, Keresztes L, Keskin E, Leese F, Macher JN, Mamos T, Paz G, Pešić V, Pfannkuchen DM, Pfannkuchen MA, Price BW, Rinkevich B, Teixeira MAL, Várbíró G, Ekrem T. DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 678:499-524. [PMID: 31077928 DOI: 10.1016/j.scitotenv.2019.04.247] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 05/21/2023]
Abstract
Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.
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Affiliation(s)
- Hannah Weigand
- Musée National d'Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg.
| | - Arne J Beermann
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Universitaetsstr. 5, 45141 Essen, Germany.
| | - Fedor Čiampor
- Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Zoology Lab, Dúbravská cesta 9, 84523 Bratislava, Slovakia.
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710--057 Braga, Portugal.
| | - Zoltán Csabai
- University of Pécs, Faculty of Sciences, Department of Hydrobiology, Ifjúság útja 6, H7624 Pécs, Hungary.
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710--057 Braga, Portugal.
| | - Matthias F Geiger
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany.
| | - Michał Grabowski
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237 Łódź, Poland.
| | - Frédéric Rimet
- INRA, Université Savoie Mont Blanc, UMR Carrtel, FR-74200 Thonon-les-Bains, France.
| | - Björn Rulik
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany.
| | - Malin Strand
- Swedish University of Agricultural Sciences, Swedish Species Information Centre, Uppsala, Sweden.
| | | | - Alexander M Weigand
- Musée National d'Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg; University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Universitaetsstr. 5, 45141 Essen, Germany.
| | - Endre Willassen
- University of Bergen, University Museum of Bergen, NO-5007 Bergen, Norway.
| | - Sofia A Wyler
- info fauna - Centre Suisse de Cartographie de la Faune (CSCF), Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland.
| | - Agnès Bouchez
- INRA, Université Savoie Mont Blanc, UMR Carrtel, FR-74200 Thonon-les-Bains, France.
| | - Angel Borja
- AZTI - Marine Research Division, Herrera Kaia, Portualdea z/g, 20110 Pasaia, Gipuzkoa, Spain.
| | - Zuzana Čiamporová-Zaťovičová
- Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Zoology Lab, Dúbravská cesta 9, 84523 Bratislava, Slovakia.
| | - Sónia Ferreira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | | | - Ursula Eisendle
- University of Salzburg, Department of Biosciences, Hellbrunnerstraße 34, 5020 Salzburg, Austria.
| | - Jörg Freyhof
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany.
| | - Piotr Gadawski
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237 Łódź, Poland.
| | - Wolfram Graf
- University of Natural Resources and Life Sciences, Vienna, Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), Gregor-Mendel-Straße 33/DG, 1180 Vienna, Austria.
| | - Arne Haegerbaeumer
- Bielefeld University, Department of Animal Ecology, Konsequenz 45, 33615 Bielefeld, Germany.
| | | | - Bella Japoshvili
- Ilia State University, Institute of Zoology, ⅗ Cholokashvili ave, 0179 Tbilisi, Georgia.
| | - Lujza Keresztes
- Babeș-Bolyai University, Faculty of Biology and Geology, Center of Systems Biology, Biodiversity and Bioresources, Cliniclor 5-7, 400006 Cluj Napoca, Romania
| | - Emre Keskin
- Ankara University, Agricultural Faculty, Department of Fisheries and Aquaculture, Evolutionary Genetics Laboratory (eGL), Ankara, Turkey.
| | - Florian Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Universitaetsstr. 5, 45141 Essen, Germany.
| | - Jan N Macher
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands.
| | - Tomasz Mamos
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237 Łódź, Poland.
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel.
| | - Vladimir Pešić
- University of Montenegro, Department of Biology, Cetinjski put bb., 20000 Podgorica, Montenegro
| | | | | | | | - Buki Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel.
| | - Marcos A L Teixeira
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710--057 Braga, Portugal
| | - Gábor Várbíró
- MTA Centre for Ecological Research, Danube Research Institute, Department of Tisza River Research, Bem square 18/C, H4026 Debrecen, Hungary.
| | - Torbjørn Ekrem
- Norwegian University of Science and Technology, NTNU University Museum, Department of Natural History, NO-7491 Trondheim, Norway.
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42
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Blackman R, Mächler E, Altermatt F, Arnold A, Beja P, Boets P, Egeter B, Elbrecht V, Filipe AF, Jones J, Macher J, Majaneva M, Martins F, Múrria C, Meissner K, Pawlowski J, Schmidt Yáñez P, Zizka V, Leese F, Price B, Deiner K. Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments. METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.34735] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised samples (bulk DNA), 2) DNA extracted from sample preservative (fixative DNA), and 3) environmental DNA (eDNA) from water or sediment. We provide a brief overview of metabarcoding macroinvertebrate communities from each DNA source and identify challenges for their application to routine monitoring. To advance the utilisation of DNA-based monitoring for macroinvertebrates, we propose an experimental design template for a series of methodological calibration tests. The template compares sources of DNA with the goal of identifying the effects of molecular processing steps on precision and accuracy. Furthermore, the same samples will be morphologically analysed, which will enable the benchmarking of molecular to traditional processing approaches. In doing so we hope to highlight pathways for the development of DNA-based methods for the monitoring of freshwater macroinvertebrates.
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Borja A, Chust G, Muxika I. Forever young: The successful story of a marine biotic index. ADVANCES IN MARINE BIOLOGY 2019; 82:93-127. [PMID: 31229151 DOI: 10.1016/bs.amb.2019.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In 2000, the AZTI's Marine Biotic Index (AMBI) was published and was one of a number of marine benthic indices development to assess the ecological status of soft-bottom macroinvertebrates. This index, and its derivatives, has been very successful in its application to different geographical areas, across the world, as well as to different environments, from the intertidal to the abyssal, or from tidal freshwater to offshore habitats. In this review, we explain the story behind the AMBI development, and look for an explanation of the index's success. For doing that, we comment on the current practicalities of the index, we present the new AMBI species list, with 9251 taxa, we dismantle six myths around this index, and examine the past and the future of the index. We show that the solid ecological roots of the index make it a robust tool to assess the status of marine benthic communities, at any time and environment. Hence, we think that it will be 'forever young' helping managers in taking informed decisions to improve benthic marine systems.
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Affiliation(s)
- Angel Borja
- AZTI, Marine Research Division, Pasaia, Spain.
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Cordier T, Lanzén A, Apothéloz-Perret-Gentil L, Stoeck T, Pawlowski J. Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring. Trends Microbiol 2019; 27:387-397. [DOI: 10.1016/j.tim.2018.10.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/17/2018] [Accepted: 10/30/2018] [Indexed: 01/28/2023]
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Singer GAC, Fahner NA, Barnes JG, McCarthy A, Hajibabaei M. Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater. Sci Rep 2019; 9:5991. [PMID: 30979963 PMCID: PMC6461652 DOI: 10.1038/s41598-019-42455-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/01/2019] [Indexed: 11/09/2022] Open
Abstract
The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.
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Affiliation(s)
- G A C Singer
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - N A Fahner
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - J G Barnes
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - A McCarthy
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - M Hajibabaei
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada.
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
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Stoeck T, Pan H, Dully V, Forster D, Jung T. Towards an eDNA metabarcode-based performance indicator for full-scale municipal wastewater treatment plants. WATER RESEARCH 2018; 144:322-331. [PMID: 30053623 DOI: 10.1016/j.watres.2018.07.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/15/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
Knowledge-driven management for wastewater treatment plant (WWTP) performance becomes increasingly important considering the globally growing production of wastewater and the rising demand of clean water supply. Even though the potential of microbial organisms (bacteria and protists) as bioindicators for WWTP performance is well known, it is far from being fully exploited for routine monitoring programs. Therefore, we here used massive sequencing of environmental (e)DNA metabarcodes from bacterial (V3-V4 region of the SSU rRNA gene) and eukaryote (V9 region of the SSU rRNA gene) communities in 21 activated sludge samples obtained from full-scale municipal WWTPs in Germany. Microbial community patterns were compared to standard WWTP operating parameters and two traditionally used WWTP performance indicators (Sludge Biotic Index and Sludge Index). Both indices showed low concordance and hardly correlated with chemical WWTP performance parameters nor did they correlate with microbial community structures. In contrast, microbial community profiles significantly correlated with WWTP performance parameters and operating conditions of the plants under study. Therefore, eDNA metabarcode profiles of whole microbial communities indicate the performance of WWTP and can provide useful information for management strategies. We here suggest a strategy for the development of an eDNA metabarcode based bioindicator system, which can be implemented in future standard monitoring programs for WWTP performance and effluent quality.
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Affiliation(s)
- Thorsten Stoeck
- University of Kaiserslautern, Ecology Group, D-67663, Kaiserslautern, Germany.
| | - Hongbo Pan
- University of Kaiserslautern, Ecology Group, D-67663, Kaiserslautern, Germany; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Verena Dully
- University of Kaiserslautern, Ecology Group, D-67663, Kaiserslautern, Germany
| | - Dominik Forster
- University of Kaiserslautern, Ecology Group, D-67663, Kaiserslautern, Germany
| | - Thorsten Jung
- Stadtentwässerung Kaiserslautern, D-67659, Kaiserslautern, Germany
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Beentjes KK, Speksnijder AGCL, Schilthuizen M, Schaub BE, van der Hoorn BB. The influence of macroinvertebrate abundance on the assessment of freshwater quality in The Netherlands. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.26744] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The use of molecular tools for the detection and identification of invertebrate species enables the development of more easily standardisable inventories of biological elements for water quality assessments, as it circumvents human-based bias and errors in species identifications. Current Ecological Quality Ratio (EQR) assessments methods, however, often rely on abundance data. Translating metabarcoding sequence data into biomass or specimen abundances has proven difficult, as PCR amplification bias due to primer mismatching often provides skewed proportions of read abundances. While some potential solutions have been proposed in previous research, we instead looked at the necessity of abundance data in EQR assessments. In this study, we used historical monitoring data from natural (lakes, rivers and streams) and artificial (ditches and canals) water bodies to assess the impact of species abundances on the EQR scores for macroinvertebrates in the Water Framework Directive (WFD) monitoring programme of The Netherlands. By removing all the abundance data from the taxon observations, we simulated presence/absence-based monitoring, for which EQRs were calculated according to traditional methods. Our results showed a strong correlation between abundance-based and presence/absence-based EQRs. EQR scores were generally higher without abundances (75.8% of all samples), which resulted in 9.1% of samples being assigned to a higher quality class. The majority of the samples (89.7%) were assigned to the same quality class in both cases. These results are valuable for the incorporation of presence/absence metabarcoding data into water quality assessment methodology, potentially eliminating the need to translate metabarcoding data into biomass or absolute specimen counts for EQR assessments.
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Pawlowski J, Kelly-Quinn M, Altermatt F, Apothéloz-Perret-Gentil L, Beja P, Boggero A, Borja A, Bouchez A, Cordier T, Domaizon I, Feio MJ, Filipe AF, Fornaroli R, Graf W, Herder J, van der Hoorn B, Iwan Jones J, Sagova-Mareckova M, Moritz C, Barquín J, Piggott JJ, Pinna M, Rimet F, Rinkevich B, Sousa-Santos C, Specchia V, Trobajo R, Vasselon V, Vitecek S, Zimmerman J, Weigand A, Leese F, Kahlert M. The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1295-1310. [PMID: 29801222 DOI: 10.1016/j.scitotenv.2018.05.002] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/11/2018] [Accepted: 05/01/2018] [Indexed: 05/05/2023]
Abstract
The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.
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Affiliation(s)
- Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland.
| | - Mary Kelly-Quinn
- School of Biology & Environmental Science, University College Dublin, Ireland
| | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland(;) Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | | | - Pedro Beja
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Angela Boggero
- LifeWatch, Italy and CNR-Institute of Ecosystem Study (CNR-ISE), Largo Tonolli 50, 28922 Verbania Pallanza, Italy
| | - Angel Borja
- AZTI, Marine Research Division, Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | - Agnès Bouchez
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Isabelle Domaizon
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Maria Joao Feio
- Marine and Environmental Sciences Centre, Faculty of Sciences and Technology, Department of Life Sciences, University of Coimbra, Portugal
| | - Ana Filipa Filipe
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Riccardo Fornaroli
- University of Milano Bicocca, Department of Earth and Environmental Sciences(DISAT), Piazza della Scienza 1,20126 Milano, Italy
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), 1180 Vienna, Austria
| | - Jelger Herder
- RAVON, Postbus 1413, Nijmegen 6501 BK, The Netherlands
| | | | - J Iwan Jones
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Marketa Sagova-Mareckova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovska 507, 16106 Praha 6, Czechia
| | - Christian Moritz
- ARGE Limnologie GesmbH, Hunoldstraße 14, 6020 Innsbruck, Austria
| | - Jose Barquín
- Environmental Hydraulics Institute "IHCantabria", Universidad de Cantabria, C/ Isabel Torres n°15, Parque Científico y Tecnológico de Cantabria, 39011 Santander, Spain
| | - Jeremy J Piggott
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, the University of Dublin, College Green, Dublin 2, Ireland; Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand
| | - Maurizio Pinna
- Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy
| | - Frederic Rimet
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Buki Rinkevich
- Israel Oceanographic and Limnological Research, Tel- Shikmona, Haifa 31080, Israel
| | - Carla Sousa-Santos
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Valeria Specchia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy
| | - Rosa Trobajo
- IRTA, Institute of Agriculture and Food Research and Technology, Marine and Continental Waters Program, Carretera Poble Nou Km 5.5, E-43540 St. Carles de la Ràpita, Catalonia, Spain
| | - Valentin Vasselon
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Simon Vitecek
- Department of Limnology and Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Jonas Zimmerman
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany
| | - Alexander Weigand
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany; Musée National d'Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Maria Kahlert
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE - 750 07 Uppsala, Sweden
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Forster D, Filker S, Kochems R, Breiner HW, Cordier T, Pawlowski J, Stoeck T. A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture. J Eukaryot Microbiol 2018; 66:294-308. [DOI: 10.1111/jeu.12670] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/22/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Dominik Forster
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Sabine Filker
- Molecular Ecology; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Rebecca Kochems
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Hans-Werner Breiner
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Tristan Cordier
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
| | - Jan Pawlowski
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
- ID-Gene ecodiagnostics Ltd.; Campus Biotech Innovation Park 1202 Geneva Switzerland
| | - Thorsten Stoeck
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
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Fernández S, Rodríguez S, Martínez JL, Borrell YJ, Ardura A, García-Vázquez E. Evaluating freshwater macroinvertebrates from eDNA metabarcoding: A river Nalón case study. PLoS One 2018; 13:e0201741. [PMID: 30089147 PMCID: PMC6082553 DOI: 10.1371/journal.pone.0201741] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/20/2018] [Indexed: 11/19/2022] Open
Abstract
Rivers are a vital resource for human wellbeing. To reduce human impact on water bodies, the European Union has established an essential regulatory framework for protection and sustainable management (WFD; 2000/60/EC). In this strategy, reliable and economic bioindicators are a fundamental component. Benthic macroinvertebrates are the group most commonly used as bioindicators through all European countries. However, their conventional assessment currently entails serious cost-efficiency limitations. In this study, we have tested the reliability of metabarcoding as a tool to record river macroinvertebrates using samples from a mock community (in vitro validation) and eDNA extracted for field validation from water from six sites within a north Iberian river (River Nalón, Asturias, Spain). Two markers (V4 region within the nuclear 18S rDNA and a fragment of the mitochondrial COI gene) were amplified and sequenced using an Illumina platform. The molecular technique has proven to be more sensitive than the visual one. A cost-benefit analysis shows that the metabarcoding approach is more expensive than conventional techniques for determining macroinvertebrate communities but requires fewer sampling and identification efforts. Our results suggest metabarcoding is a useful tool for alternative assessment of freshwater quality.
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Affiliation(s)
- Sara Fernández
- Department of Functional Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Saúl Rodríguez
- Department of Functional Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Jose L. Martínez
- Unit of DNA Analysis, Scientific-Technical Services, University of Oviedo, Oviedo, Asturias, Spain
| | - Yaisel J. Borrell
- Department of Functional Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Eva García-Vázquez
- Department of Functional Biology, University of Oviedo, Oviedo, Asturias, Spain
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