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Carvalho J, Garrido-Maestu A, Azinheiro S, Fuciños P, Barros-Velázquez J, De Miguel RJ, Gros V, Prado M. Faster monitoring of the invasive alien species (IAS) Dreissena polymorpha in river basins through isothermal amplification. Sci Rep 2021; 11:10175. [PMID: 33986380 PMCID: PMC8119715 DOI: 10.1038/s41598-021-89574-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/28/2021] [Indexed: 11/25/2022] Open
Abstract
Zebra mussel (Dreissena polymorpha) is considered as one of the 100 most harmful IAS in the world. Traditional detection methods have limitations, and PCR based environmental DNA detection has provided interesting results for early warning. However, in the last years, the development of isothermal amplification methods has received increasing attention. Among them, loop-mediated isothermal amplification (LAMP) has several advantages, including its higher tolerance to the presence of inhibitors and the possibility of naked-eye detection, which enables and simplifies its potential use in decentralized settings. In the current study, a real-time LAMP (qLAMP) method for the detection of Dreissena polymorpha was developed and tested with samples from the Guadalquivir River basin, together with two real-time PCR (qPCR) methods using different detection chemistries, targeting a specific region of the mitochondrial gene cytochrome C oxidase subunit I. All three developed approaches were evaluated regarding specificity, sensitivity and time required for detection. Regarding sensitivity, both qPCR approaches were more sensitive than qLAMP by one order of magnitude, however the qLAMP method proved to be as specific and much faster being performed in just 9 min versus 23 and 29 min for the qPCR methods based on hydrolysis probe and intercalating dye respectively.
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Affiliation(s)
- Joana Carvalho
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.,Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Sarah Azinheiro
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.,Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pablo Fuciños
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Ramón J De Miguel
- Department of Zoology, University of Cordoba, Córdoba, Spain.,Guadalictio S.L., Córdoba, Spain
| | - Verónica Gros
- Confederación Hidrográfica del Guadalquivir, Ministerio para la Transición Ecológica y el Reto Demográfico, Sevilla, Spain
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.
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Wegner B, Kronsbein AL, Gillefalk M, van de Weyer K, Köhler J, Funke E, Monaghan MT, Hilt S. Mutual Facilitation Among Invading Nuttall's Waterweed and Quagga Mussels. FRONTIERS IN PLANT SCIENCE 2019; 10:789. [PMID: 31316530 PMCID: PMC6611401 DOI: 10.3389/fpls.2019.00789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/29/2019] [Indexed: 06/02/2023]
Abstract
Nuttall's waterweed (Elodea nuttallii) is the most abundant invasive aquatic plant species in several European countries. Elodea populations often follow a boom-bust cycle, but the causes and consequences of this dynamics are yet unknown. We hypothesize that both boom and bust periods can be affected by dreissenid mussel invasions. While mutual facilitations between these invaders could explain their rapid parallel expansion, subsequent competition for space might occur. To test this hypothesis, we use data on temporal changes in the water quality and the abundance of E. nuttallii and the quagga mussel Dreissena rostriformis bugensis in a temperate shallow lake. Lake Müggelsee (Germany) was turbid and devoid of submerged macrophytes for 20 years (1970-1989), but re-colonization with macrophytes started in 1990 upon reductions in nutrient loading. We mapped macrophyte abundance from 1999 and mussel abundance from 2011 onwards. E. nuttallii was first detected in 2011, spread rapidly, and was the most abundant macrophyte species by 2017. Native macrophyte species were not replaced, but spread more slowly, resulting in an overall increase in macrophyte coverage to 25% of the lake surface. The increased abundance of E. nuttallii was paralleled by increasing water clarity and decreasing total phosphorus concentrations in the water. These changes were attributed to a rapid invasion by quagga mussels in 2012. In 2017, they covered about one-third of the lake area, with mean abundances of 3,600 mussels m-2, filtering up to twice the lake's volume every day. The increasing light availability in deeper littoral areas supported the rapid spread of waterweed, while in turn waterweed provided surface for mussel colonization. Quantities of dreissenid mussels and E. nuttallii measured at 24 locations were significantly correlated in 2016, and yearly means of E. nuttallii quantities increased with increasing mean dreissenid mussel quantities between 2011 and 2018. In 2018, both E. nuttallii and dreissenid abundances declined. These data imply that invasive waterweed and quagga mussels initially facilitated their establishment, supporting the invasional meltdown hypothesis, while subsequently competition for space may have occurred. Such temporal changes in invasive species interaction might contribute to the boom-bust dynamics that have been observed in Elodea populations.
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Affiliation(s)
- Benjamin Wegner
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Faculty VI: Planning, Building and Environment, Institute for Ecology, Technical University Berlin, Berlin, Germany
| | - Anna Lena Kronsbein
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Mikael Gillefalk
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Faculty VI: Planning, Building and Environment, Institute for Ecology, Technical University Berlin, Berlin, Germany
| | | | - Jan Köhler
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Elisabeth Funke
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michael T. Monaghan
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Sabine Hilt
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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Kerambrun E, Delahaut L, Geffard A, David E. Differentiation of sympatric zebra and quagga mussels in ecotoxicological studies: A comparison of morphometric data, gene expression, and body metal concentrations. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 154:321-328. [PMID: 29482127 DOI: 10.1016/j.ecoenv.2018.02.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/13/2018] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
The zebra mussel is among the best studied freshwater molluscs in ecotoxicology, but information on the quagga mussel is lacking. Considering its potential spread, we selected a river in France in which zebra and quagga mussels coexisted, and then we used genetic markers to differentiate the two species and compared morphological parameters. cDNA sequencing assays of ten genes already used in zebra mussels were performed on quagga mussels to obtain functional specific primers. Then we analyzed the expression of genes involved in cellular metabolic activities (Cytochrome-c-oxidase - cox, and ATP synthase - atp), detoxification processes (Glutathione-S-Transferase - gst), oxidative stress (Catalase - cat), and digestive functions (Amylase - amy) on the two species. Whereas morphometric analysis underlined similarities in shape between the two species, relative gene expression profiles and metal concentrations evidenced strong differences. Quagga mussels notably presented half as high concentrations in Cd and Pb, two particularly toxic elements, as zebra mussels. These results imply that i) particular attention should be paid to properly distinguish the two species considering their similar external appearance, and ii) zebra mussels cannot be replaced by quagga mussels in ecotoxicological studies without preliminary investigations on biomarker response patterns. To our knowledge, this study is the first to have undertaken such an approach in gene expression analysis in quagga mussels, and more generally to have compared such biomarker responses of zebra and quagga mussels in the field.
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Affiliation(s)
- E Kerambrun
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France.
| | - L Delahaut
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France
| | - A Geffard
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France
| | - E David
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France
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Liu J, Jiang J, Song S, Tornabene L, Chabarria R, Naylor GJP, Li C. Multilocus DNA barcoding - Species Identification with Multilocus Data. Sci Rep 2017; 7:16601. [PMID: 29192249 PMCID: PMC5709489 DOI: 10.1038/s41598-017-16920-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Species identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of barcoding method does not always work when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus barcoding framework that is based on gene capture and "next-generation" sequencing. We selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA barcoding. We applied our method on two exemplar datasets each containing a pair of sister fish species: Siniperca chuatsi vs. Sini. kneri and Sicydium altum vs. Sicy. adelum, where the COI barcoding approach failed. Both of our empirical and simulated results demonstrated that under limited gene flow and enough separation time, we could correctly identify species using multilocus barcoding method. We anticipate that, as the cost of DNA sequencing continues to fall that our multilocus barcoding approach will eclipse existing single-locus DNA barcoding methods as a means to better understand the diversity of the living world.
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Affiliation(s)
- Junning Liu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China
| | - Shuli Song
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China
| | - Luke Tornabene
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Ryan Chabarria
- College of Science & Engineering, Texas A&M University - Corpus Christi, Corpus Christi, TX, 78412-5806, USA
| | | | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China.
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.
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Kerambrun E, Rioult D, Delahaut L, Evariste L, Pain-Devin S, Auffret M, Geffard A, David E. Variations in gene expression levels in four European zebra mussel, Dreissena polymorpha, populations in relation to metal bioaccumulation: A field study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 134P1:53-63. [PMID: 27588554 DOI: 10.1016/j.ecoenv.2016.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
The present study was performed to validate the suitability of using gene expression in zebra mussels, Dreissena polymorpha, for biomonitoring of freshwater environment. Mussels were collected in four French rivers (Meuse, Moselle, Oise and Vilaine) in spring and autumn. Relative gene expression of 9 candidate genes involved in cellular metabolic activities (Cytochrome-c-oxidase - cox, and ATP synthase - atp), detoxification process (Metallothionein - mt and Glutathion-S-Transferase - gst), oxidative stress (Catalase - cat, Superoxyde Dismutase - sod and Glutathion peroxidase - gpx) and digestive functions (Amylase - amy and Cellulase - ghf) were measured in digestive gland. Metal bioaccumulation in tissues and morphometric parameters were also analyzed to interpret molecular responses. All our results are consistent with different physiological reactions to environmental condition between zebra mussel populations. In spring, the levels of mt, sod, gpx, cat, atp, amy and ghf relative expression were significantly higher in mussels with the lowest metal bioaccumulation (the Meuse) compared to at least one of the other sites. In autumn, this higher expression levels in Meuse River were still observed for gpx, cat, atp and amy. This study has also pointed out different sources of variability in gene expression (individual size, season, trophic resources and origin of mussels) which are inevitable in natural fluctuant environment. This underlines the importance to take them into account in field study to propose a correct interpretation of biomarker responses.
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Affiliation(s)
- E Kerambrun
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France.
| | - D Rioult
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France; Université de Reims Champagne-Ardenne/INERIS, Plateau Technique mobile de cytométrie environnementale MOBICYTE, France
| | - L Delahaut
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France
| | - L Evariste
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France; Institut National de la Recherche Scientifique, INRS, Institut Armand Frappier, 531 Boulevard des Prairies, Laval, Quebec, Canada H7V 1B7
| | - S Pain-Devin
- Université de Lorraine, UMR 7360 LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), CNRS, France
| | - M Auffret
- Université de Bretagne Occidentale, UMR 6539-LEMAR (Laboratoire des Sciences de l'Environnement Marin), IUEM, UBO-CNRS-IRD-Ifremer, F-29280 Plouzane, France
| | - A Geffard
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France
| | - E David
- Université de Reims Champagne-Ardenne, UMR-I 02 SEBIO (Stress Environnementaux et BIOsurveillance des milieux aquatiques), INERIS-URCA-ULH, France
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Interbreeding among deeply divergent mitochondrial lineages in the American cockroach (Periplaneta americana). Sci Rep 2015; 5:8297. [PMID: 25656854 PMCID: PMC4650827 DOI: 10.1038/srep08297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/14/2015] [Indexed: 01/25/2023] Open
Abstract
DNA barcoding promises to be a useful tool to identify pest species assuming adequate representation of genetic variants in a reference library. Here we examined mitochondrial DNA barcodes in a global urban pest, the American cockroach (Periplaneta americana). Our sampling effort generated 284 cockroach specimens, most from New York City, plus 15 additional U.S. states and six other countries, enabling the first large-scale survey of P. americana barcode variation. Periplaneta americana barcode sequences (n = 247, including 24 GenBank records) formed a monophyletic lineage separate from other Periplaneta species. We found three distinct P. americana haplogroups with relatively small differences within (≤0.6%) and larger differences among groups (2.4%-4.7%). This could be interpreted as indicative of multiple cryptic species. However, nuclear DNA sequences (n = 77 specimens) revealed extensive gene flow among mitochondrial haplogroups, confirming a single species. This unusual genetic pattern likely reflects multiple introductions from genetically divergent source populations, followed by interbreeding in the invasive range. Our findings highlight the need for comprehensive reference databases in DNA barcoding studies, especially when dealing with invasive populations that might be derived from multiple genetically distinct source populations.
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