1
|
Slaby S, Geffard A, Fisson C, Bonnevalle-Normand M, Allonier-Fernandes AS, Amara R, Bado-Nilles A, Bonnard I, Bonnard M, Burlion-Giorgi M, Cant A, Catteau A, Chaumot A, Costil K, Coulaud R, Delahaut L, Diop M, Duflot A, Geffard O, Jestin E, Le Foll F, Le Guernic A, Lopes C, Palos-Ladeiro M, Peignot Q, Poret A, Serpentini A, Tremolet G, Turiès C, Xuereb B. Advancing environmental monitoring across the water continuum combining biomarker analysis in multiple sentinel species: A case study in the Seine-Normandie Basin (France). J Environ Manage 2024; 358:120784. [PMID: 38603847 DOI: 10.1016/j.jenvman.2024.120784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/04/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Nowadays, biomarkers are recognized as valuable tools to complement chemical and ecological assessments in biomonitoring programs. They provide insights into the effects of contaminant exposures on individuals and establish connections between environmental pressure and biological response at higher levels. In the last decade, strong improvements in the design of experimental protocols and the result interpretation facilitated the use of biomarker across wide geographical areas, including aquatic continua. Notably, the statistical establishment of reference values and thresholds enabled the discrimination of contamination effects in environmental conditions, allowed interspecies comparisons, and eliminated the need of a reference site. The aim of this work was to study freshwater-estuarine-coastal water continua by applying biomarker measurements in multi-species caged organisms. During two campaigns, eight sentinel species, encompassing fish, mollusks, and crustaceans, were deployed to cover 25 sites from rivers to the sea. As much as possible, a common methodology was employed for biomarker measurements (DNA damage and phagocytosis efficiency) and data interpretation based on guidelines established using reference values and induction/inhibition thresholds (establishment of three effect levels). The methodology was successfully implemented and allowed us to assess the environmental quality. Employing multiple species per site enhances confidence in observed trends. The results highlight the feasibility of integrating biomarker-based environmental monitoring programs across a continuum scale. Biomarker results align with Water Framework Directive indicators in cases of poor site quality. Additionally, when discrepancies arise between chemical and ecological statuses, biomarker findings offer a comprehensive perspective to elucidate the disparities. Presented as a pilot project, this work contributes to gain insights into current biomonitoring needs, providing new questions and perspectives.
Collapse
Affiliation(s)
- Sylvain Slaby
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600, Le Havre, France.
| | - Alain Geffard
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, BP 1039, 51687, Reims, France.
| | - Cédric Fisson
- GIP Seine-Aval, Hangar C - Espace des Marégraphes, CS 41174, 76176, Rouen, Cedex 1, France.
| | - Matthieu Bonnevalle-Normand
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600, Le Havre, France.
| | | | - Rachid Amara
- Université Littoral Côte d'Opale, Université Lille, CNRS, IRD, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, Wimereux, France.
| | - Anne Bado-Nilles
- Institut National de l'Environnement Industriel et des Risques (INERIS), UMR-I 02 SEBIO, Parc Technologique Alata, BP 2, 60550, Verneuil-en-Halatte, France.
| | - Isabelle Bonnard
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, BP 1039, 51687, Reims, France.
| | - Marc Bonnard
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, BP 1039, 51687, Reims, France.
| | - Mayélé Burlion-Giorgi
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600, Le Havre, France.
| | - Amélie Cant
- Institut National de l'Environnement Industriel et des Risques (INERIS), UMR-I 02 SEBIO, Parc Technologique Alata, BP 2, 60550, Verneuil-en-Halatte, France.
| | - Audrey Catteau
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, BP 1039, 51687, Reims, France.
| | - Arnaud Chaumot
- INRAE, RiverLy, Ecotoxicology Laboratory, 5 Avenue de la Doua, CS20244, 69625, Villeurbanne Cedex, France.
| | - Katherine Costil
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA) Université de Caen Normandie UNICAEN, Sorbonne Université, MNHN, UPMC Univ Paris 06, UA, CNRS 8067, IRD 207, Esplanade de la paix, Caen F-14032, France.
| | - Romain Coulaud
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600, Le Havre, France.
| | - Laurence Delahaut
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, BP 1039, 51687, Reims, France.
| | - Mamadou Diop
- Université Littoral Côte d'Opale, Université Lille, CNRS, IRD, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, Wimereux, France.
| | - Aurélie Duflot
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600, Le Havre, France.
| | - Olivier Geffard
- INRAE, RiverLy, Ecotoxicology Laboratory, 5 Avenue de la Doua, CS20244, 69625, Villeurbanne Cedex, France.
| | - Emmanuel Jestin
- Agence de l'eau Seine-Normandie, 12 rue de l'Industrie CS 80148 92416 Courbevoie Cedex, France.
| | - Frank Le Foll
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600, Le Havre, France.
| | - Antoine Le Guernic
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, BP 1039, 51687, Reims, France.
| | - Christelle Lopes
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 69622, Villeurbanne, France.
| | - Mélissa Palos-Ladeiro
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, BP 1039, 51687, Reims, France.
| | - Quentin Peignot
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, BP 1039, 51687, Reims, France.
| | - Agnès Poret
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600, Le Havre, France.
| | - Antoine Serpentini
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA) Université de Caen Normandie UNICAEN, Sorbonne Université, MNHN, UPMC Univ Paris 06, UA, CNRS 8067, IRD 207, Esplanade de la paix, Caen F-14032, France.
| | - Gauthier Tremolet
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600, Le Havre, France.
| | - Cyril Turiès
- Institut National de l'Environnement Industriel et des Risques (INERIS), UMR-I 02 SEBIO, Parc Technologique Alata, BP 2, 60550, Verneuil-en-Halatte, France.
| | - Benoît Xuereb
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600, Le Havre, France.
| |
Collapse
|
2
|
Henke AN, Chilukuri S, Langan LM, Brooks BW. Reporting and reproducibility: Proteomics of fish models in environmental toxicology and ecotoxicology. Sci Total Environ 2024; 912:168455. [PMID: 37979845 DOI: 10.1016/j.scitotenv.2023.168455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Environmental toxicology and ecotoxicology research efforts are employing proteomics with fish models as New Approach Methodologies, along with in silico, in vitro and other omics techniques to elucidate hazards of toxicants and toxins. We performed a critical review of toxicology studies with fish models using proteomics and reported fundamental parameters across experimental design, sample preparation, mass spectrometry, and bioinformatics of fish, which represent alternative vertebrate models in environmental toxicology, and routinely studied animals in ecotoxicology. We observed inconsistencies in reporting and methodologies among experimental designs, sample preparations, data acquisitions and bioinformatics, which can affect reproducibility of experimental results. We identified a distinct need to develop reporting guidelines for proteomics use in environmental toxicology and ecotoxicology, increased QA/QC throughout studies, and method optimization with an emphasis on reducing inconsistencies among studies. Several recommendations are offered as logical steps to advance development and application of this emerging research area to understand chemical hazards to public health and the environment.
Collapse
Affiliation(s)
- Abigail N Henke
- Department of Biology, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA
| | | | - Laura M Langan
- Department of Environmental Science, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA.
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA.
| |
Collapse
|
3
|
Rosner A, Ballarin L, Barnay-Verdier S, Borisenko I, Drago L, Drobne D, Concetta Eliso M, Harbuzov Z, Grimaldi A, Guy-Haim T, Karahan A, Lynch I, Giulia Lionetto M, Martinez P, Mehennaoui K, Oruc Ozcan E, Pinsino A, Paz G, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. A broad-taxa approach as an important concept in ecotoxicological studies and pollution monitoring. Biol Rev Camb Philos Soc 2024; 99:131-176. [PMID: 37698089 DOI: 10.1111/brv.13015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost-effective and repeatable testing options. Additionally, their significance in the food chain and their ability to represent diverse aquatic ecosystems make them valuable subjects for (eco)toxicological studies. To ensure consistency and comparability across studies, international (eco)toxicology guidelines have been used to establish standardised methods and protocols for data collection, analysis and interpretation. However, the current standardised protocols primarily focus on a limited number of aquatic invertebrate species, mainly from Arthropoda, Mollusca and Annelida. These protocols are suitable for basic toxicity screening, effectively assessing the immediate and severe effects of toxic substances on organisms. For more comprehensive and ecologically relevant assessments, particularly those addressing long-term effects and ecosystem-wide impacts, we recommended the use of a broader diversity of species, since the present choice of taxa exacerbates the limited scope of basic ecotoxicological studies. This review provides a comprehensive overview of (eco)toxicological studies, focusing on major aquatic invertebrate taxa and how they are used to assess the impact of chemicals in diverse aquatic environments. The present work supports the use of a broad-taxa approach in basic environmental assessments, as it better represents the natural populations inhabiting various ecosystems. Advances in omics and other biochemical and computational techniques make the broad-taxa approach more feasible, enabling mechanistic studies on non-model organisms. By combining these approaches with in vitro techniques together with the broad-taxa approach, researchers can gain insights into less-explored impacts of pollution, such as changes in population diversity, the development of tolerance and transgenerational inheritance of pollution responses, the impact on organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome changes, regeneration phenomena, disease susceptibility and tissue pathologies. This review also emphasises the need for harmonised data-reporting standards and minimum annotation checklists to ensure that research results are findable, accessible, interoperable and reusable (FAIR), maximising the use and reusability of data. The ultimate goal is to encourage integrated and holistic problem-focused collaboration between diverse scientific disciplines, international standardisation organisations and decision-making bodies, with a focus on transdisciplinary knowledge co-production for the One-Health approach.
Collapse
Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, 28 avenue Valombrose, Nice, F-06107, France
| | - Ilya Borisenko
- Faculty of Biology, Department of Embryology, Saint Petersburg State University, Universitetskaya embankment 7/9, Saint Petersburg, 199034, Russia
| | - Laura Drago
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, 1111, Slovenia
| | - Maria Concetta Eliso
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Zoya Harbuzov
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Haifa, 3498838, Israel
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant, Varese, 3-21100, Italy
| | - Tamar Guy-Haim
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli-Mersin, PO 28, 33731, Turkey
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Maria Giulia Lionetto
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via prov. le Lecce -Monteroni, Lecce, I-73100, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina, 61, Palermo, I-90133, Italy
| | - Pedro Martinez
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, Barcelona, 08010, Spain
| | - Kahina Mehennaoui
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
| | - Elif Oruc Ozcan
- Faculty of Arts and Science, Department of Biology, Cukurova University, Balcali, Saricam, Adana, 01330, Turkey
| | - Annalisa Pinsino
- National Research Council, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, Milan, 20133, Italy
| | - Sébastien Cambier
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
| |
Collapse
|
4
|
Degli Esposti D, Lalouette A, Gaget K, Lepeule L, Chaabi Z, Leprêtre M, Espeyte A, Delorme N, Quéau H, Garnero L, Calevro F, Chaumot A, Geffard O. Identification and organ-specific patterns of expression of two metallothioneins in the sentinel species Gammarus fossarum. Comp Biochem Physiol B Biochem Mol Biol 2024; 269:110907. [PMID: 37827361 DOI: 10.1016/j.cbpb.2023.110907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/14/2023]
Abstract
Metal pollution is a major concern for aquatic environments. Widespread contamination by various trace metal ions has been described in freshwater streams as well as their subsequent bioaccumulation, potentially leading to toxicity and trophic transfer. Metallothioneins constitute an evolutionary conserved family of low molecular weight, cysteine-rich, metal-chelating proteins, whose known physiological functions are the maintenance of the homeostasis of essential metals, the detoxification of non-essential metals, and the protection against oxidative stress and free radicals. In this study, we identified two metallothionein-coding transcripts, mt1 and mt2, in the transcriptome of the amphipod Gammarus fossarum, a sentinel species widely used to assess the quality of watersheds. For the first time, we investigated the organ-specific patterns of expression of these two mt transcripts at the individual level in the gills and the caeca of this small crustacean. In silico analysis and experimental exposures to environmentally relevant concentrations of cadmium, zinc and silver showed that G. fossarum mt1 induction is stronger after Cd exposure compared to the other tested metals. G. fossarum mt1 was more significantly induced in the caeca than in the gills of exposed organisms for any metal exposure, while G. fossarum mt2 was, at least at the individual level, more inducible in the gills than in the caeca of G. fossarum exposed to Cd and Zn. Our results provide new genetic resources that will help to improve the understanding of metal homeostasis in this sentinel species.
Collapse
Affiliation(s)
- Davide Degli Esposti
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France.
| | - Auréline Lalouette
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Karen Gaget
- INRAE, INSA Lyon, BF2I, UMR 203, Université de Lyon, 69621 Villeurbanne, France
| | - Louveline Lepeule
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Zineb Chaabi
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Maxime Leprêtre
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Anabelle Espeyte
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Nicolas Delorme
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Hervé Quéau
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Laura Garnero
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Federica Calevro
- INRAE, INSA Lyon, BF2I, UMR 203, Université de Lyon, 69621 Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| |
Collapse
|
5
|
Binelli A, Nigro L, Sbarberi R, Della Torre C, Magni S. To be or not to be plastics? Protein modulation and biochemical effects in zebrafish embryos exposed to three water-soluble polymers. Sci Total Environ 2024; 906:167699. [PMID: 37832656 DOI: 10.1016/j.scitotenv.2023.167699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/26/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
Water-soluble polymers (WSPs) are a particular category of polymers that, due to their capability to be soluble in water, come out of the classic definition of plastic and therefore also from its regulation and control, representing a possible new environmental problem considering the number of consumer products in which they are contained. For this reason, the aim of this study was to evaluate the possible adverse effects of three of the most used WSPs (polyacrylic acid - PAA, polyethylene glycol - PEG, polyvinylpyrrolidone - PVP), administered at relevant environmental concentrations (0.001, 0.5 and 1 mg/L) to Danio rerio (zebrafish) embryos up to 120 h post fertilization. To assess the WSP toxicity at the molecular, cellular and organism level we used an integrated ecotoxicological approach of both biomarkers and high-throughput technology based on gel-free proteomics. The main results showed how all the three WSPs up-regulated many proteins (up to 74 in specimens exposed to 1 mg/L PVP) with a wide range of molecular functions and involved in numerous cellular pathways of exposed specimens. On the other hand, the measurement of biomarkers showed how PAA and PVP were able to activate the antioxidant machinery following an over-production of reactive oxygen species, while PEG produced no significant changes in the biomarkers measured. Based on the obtained results, the use and application of WSPs should be revised and regulated.
Collapse
Affiliation(s)
- Andrea Binelli
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy
| | - Lara Nigro
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy.
| | - Riccardo Sbarberi
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy
| | - Camilla Della Torre
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy
| | - Stefano Magni
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milan, Italy
| |
Collapse
|
6
|
Marghany F, Ayobahan SU, Salinas G, Schäfers C, Hollert H, Eilebrecht S. Transcriptomic and proteomic fingerprints induced by the fungicides difenoconazole and metalaxyl in zebrafish embryos. Environ Toxicol Pharmacol 2024; 105:104348. [PMID: 38135202 DOI: 10.1016/j.etap.2023.104348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
In this study, we applied OMICs analysis to identify substance-specific biomarker candidates, which may act as early indicators for specific ecotoxic modes of actions (MoA). Zebrafish embryos were exposed to two sublethal concentrations of difenoconazole and metalaxyl according to a modified protocol of the OECD test guideline No. 236. At the end of exposure, total RNA and protein were extracted, followed by transcriptomics and proteomics analysis. The analysis of significantly differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) revealed a positive exposure-response correlation in all test concentrations for both fungicides. Similarly, also a positive correlation between the obtained transcriptome and proteome data was observed, highlighting the robustness of our approach. From the detected DEGs, candidate biomarkers specific for difenoconazole (apoa1b, gatm, mylpfb and acta1b) and metalaxyl (lgals2b, abat, fabp1b.1 and myh9a) were selected, and their biological functions were discussed to assess the predictive potential.
Collapse
Affiliation(s)
- Fatma Marghany
- Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany; Department Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany; Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
| | - Steve U Ayobahan
- Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | - Gabriela Salinas
- NGS-Services for Integrative Genomics, University of Göttingen, Göttingen, Germany
| | - Christoph Schäfers
- Department Ecotoxicology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | - Henner Hollert
- Department Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany; Department Environmental Media Related Ecotoxicology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | - Sebastian Eilebrecht
- Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany.
| |
Collapse
|
7
|
Huertas-Abril PV, Jurado J, Prieto-Álamo MJ, García-Barrera T, Abril N. Proteomic analysis of the hepatic response to a pollutant mixture in mice. The protective action of selenium. Sci Total Environ 2023; 903:166558. [PMID: 37633382 DOI: 10.1016/j.scitotenv.2023.166558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Metals and pharmaceuticals contaminate water and food worldwide, forming mixtures where they can interact to enhance their individual toxicity. Here we use a shotgun proteomic approach to evaluate the toxicity of a pollutant mixture (PM) of metals (As, Cd, Hg) and pharmaceuticals (diclofenac, flumequine) on mice liver proteostasis. These pollutants are abundant in the environment, accumulate in the food chain, and are toxic to humans primarily through oxidative damage. Thus, we also evaluated the putative antagonistic effect of low-dose dietary supplementation with the antioxidant trace element selenium. A total of 275 proteins were affected by PM treatment. Functional analyses revealed an increased abundance of proteins involved in the integrated stress response that promotes translation, the inflammatory response, carbohydrate and lipid metabolism, and the sustained expression of the antioxidative response mediated by NRF2. As a consequence, a reductive stress situation arises in the cell that inhibits the RICTOR pathway, thus activating the early stage of autophagy, impairing xenobiotic metabolism, and potentiating lipid biosynthesis and steatosis. PM exposure-induced hepato-proteostatic alterations were significantly reduced in Se supplemented mice, suggesting that the use of this trace element as a dietary supplement may at least partially ameliorate liver damage caused by exposure to environmental mixtures.
Collapse
Affiliation(s)
- Paula V Huertas-Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Juan Jurado
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - María-José Prieto-Álamo
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Tamara García-Barrera
- Research Center of Natural Resources, Health, and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, Campus El Carmen, University of Huelva, Fuerzas Armadas Ave., 21007 Huelva, Spain
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain.
| |
Collapse
|
8
|
Baratange C, Baali H, Gaillet V, Bonnard I, Delahaut L, Gaillard JC, Grandjean D, Sayen S, Gallorini A, Le Bris N, Renault D, Breider F, Loizeau JL, Armengaud J, Cosio C. Bioaccumulation and molecular effects of carbamazepine and methylmercury co-exposure in males of Dreissena polymorpha. Sci Total Environ 2023; 897:165379. [PMID: 37423277 DOI: 10.1016/j.scitotenv.2023.165379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
Dreissena polymorpha is a bivalve promising for biomonitoring in freshwater ecosystems thanks to its abundance and high filtration activity allowing rapid uptake of toxicants and identification of their negative effects. Nonetheless, we still lack knowledge on its molecular responses to stress under realistic scenario, e.g. multi-contamination. Carbamazepine (CBZ) and Hg are ubiquitous pollutants sharing molecular toxicity pathways, e.g. oxidative stress. A previous study in zebra mussels showed their co-exposure to cause more alterations than single exposures, but molecular toxicity pathways remained unidentified. D. polymorpha was exposed 24 h (T24) and 72 h (T72) to CBZ (6.1 ± 0.1 μg L-1), MeHg (430 ± 10 ng L-1) and the co-exposure (6.1 ± 0.1 μg L-1CBZ and 500 ± 10 ng L-1 MeHg) at concentrations representative of polluted areas (~10× EQS). RedOx system at the gene and enzyme level, the proteome and the metabolome were compared. The co-exposure resulted in 108 differential abundant proteins (DAPs), as well as 9 and 10 modulated metabolites at T24 and T72, respectively. The co-exposure specifically modulated DAPs and metabolites involved in neurotransmission, e.g. dopaminergic synapse and GABA. CBZ specifically modulated 46 DAPs involved in calcium signaling pathways and 7 amino acids at T24. MeHg specifically modulated 55 DAPs involved in the cytoskeleton remodeling and hypoxia-induced factor 1 pathway, without altering the metabolome. Single and co-exposures commonly modulated proteins and metabolites involved in energy and amino acid metabolisms, response to stress and development. Concomitantly, lipid peroxidation and antioxidant activities were unchanged, supporting that D. polymorpha tolerated experimental conditions. The co-exposure was confirmed to cause more alterations than single exposures. This was attributed to the combined toxicity of CBZ and MeHg. Altogether, this study underlined the necessity to better characterize molecular toxicity pathways of multi-contamination that are not predictable on responses to single exposures, to better anticipate adverse effects in biota and improve risk assessment.
Collapse
Affiliation(s)
- Clément Baratange
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Hugo Baali
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Véronique Gaillet
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Isabelle Bonnard
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Laurence Delahaut
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze Cedex, France
| | - Dominique Grandjean
- Ecole Polytechnique Fédérale de Lausanne (EPFL), ENAC, IIE, Central Environmental Laboratory, Station 2, 1015 Lausanne, Switzerland
| | - Stéphanie Sayen
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), UMR CNRS 7312, BP 1039, F-51687 Reims Cedex, 2, France
| | - Andrea Gallorini
- Department F.-A. Forel for Environmental and Aquatic Sciences, Institute for Environmental Sciences, University of Geneva, Boulevard Carl-Vogt 66, 1211, Geneva 4, Switzerland
| | - Nathalie Le Bris
- Université de Rennes, CNRS, EcoBio (Ecosystèmes, biodiversité, évolution) - UMR 6553, F-35000 Rennes, France
| | - David Renault
- Université de Rennes, CNRS, EcoBio (Ecosystèmes, biodiversité, évolution) - UMR 6553, F-35000 Rennes, France; Institut Universitaire de France, 1 rue Descartes, 75231 Paris Cedex 05, France
| | - Florian Breider
- Ecole Polytechnique Fédérale de Lausanne (EPFL), ENAC, IIE, Central Environmental Laboratory, Station 2, 1015 Lausanne, Switzerland
| | - Jean-Luc Loizeau
- Department F.-A. Forel for Environmental and Aquatic Sciences, Institute for Environmental Sciences, University of Geneva, Boulevard Carl-Vogt 66, 1211, Geneva 4, Switzerland
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze Cedex, France
| | - Claudia Cosio
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), BP 1039, F-51687 Reims Cedex, France.
| |
Collapse
|
9
|
Bertile F, Matallana-Surget S, Tholey A, Cristobal S, Armengaud J. Diversifying the concept of model organisms in the age of -omics. Commun Biol 2023; 6:1062. [PMID: 37857885 PMCID: PMC10587087 DOI: 10.1038/s42003-023-05458-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023] Open
Abstract
In today's post-genomic era, it is crucial to rethink the concept of model organisms. While a few historically well-established organisms, e.g. laboratory rodents, have enabled significant scientific breakthroughs, there is now a pressing need for broader inclusion. Indeed, new organisms and models, from complex microbial communities to holobionts, are essential to fully grasp the complexity of biological principles across the breadth of biodiversity. By fostering collaboration between biology, advanced molecular science and omics communities, we can collectively adopt new models, unraveling their molecular functioning, and uncovering fundamental mechanisms. This concerted effort will undoubtedly enhance human health, environmental quality, and biodiversity conservation.
Collapse
Affiliation(s)
- Fabrice Bertile
- Université de Strasbourg, CNRS, IPHC UMR 7178, 23 rue du Loess, 67037, Strasbourg Cedex 2, France.
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping, 581 85, Sweden
- Ikerbasque, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, Leioa, 48940, Spain
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| |
Collapse
|
10
|
Chaousis S, Leusch FDL, Nouwens A, Melvin SD, van de Merwe JP. Influence of chemical dose and exposure duration on protein synthesis in green sea turtle primary cells. J Proteomics 2023; 285:104942. [PMID: 37285907 DOI: 10.1016/j.jprot.2023.104942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 05/14/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023]
Abstract
Understanding the impacts of chemical exposure in marine wildlife is challenging, due to practical and ethical constraints that preclude traditional toxicology research on these animals. This study addressed some of these limitations by presenting an ethical and high throughput cell-based approach to elucidate molecular-level effects of contaminants on sea turtles. The experimental design addressed basic questions of cell-based toxicology, including chemical dose and exposure time. Primary green turtle skin cells were exposed to polychlorinated biphenyl (PCB) 153 and perfluorononanoic acid (PFNA) for 24 and 48 h, at three sub-lethal, environmentally relevant concentrations (1, 10 and 100 μg/L). Sequential window acquisition of all theoretical mass spectra (SWATH-MS) identified over 1000 differentially abundant proteins within the 1% false discovery rate (FDR) threshold. The 24 h exposure resulted in a greater number of differentially abundant proteins, compared to 48 h exposure, for both contaminants. However, there were no statistically significant dose-response relationships for the number of differentially synthesised proteins, nor differences in the proportion of increased vs decreased proteins between or within exposure times. Known in vivo markers of contaminant exposure, superoxide dismutase and glutathione S-transferase, were differentially abundant following exposure to PCB153 and PFNA. SIGNIFICANCE: Cell-based (in vitro) proteomics provides an ethical and high throughput approach to understanding the impacts of chemical contamination on sea turtles. Through investigating effects of chemical dose and exposure duration on unique protein abundance in vitro, this study provides an optimised framework for conducting cell-based studies in wildlife proteomics, and highlights that proteins detected in vitro could act as biomarkers of chemical exposure and effect in vivo.
Collapse
Affiliation(s)
- Stephanie Chaousis
- Griffith School of Science and Environment and the Australian Rivers Institute, Griffith Univeristy, Building 51, Gold Coast Campus, QLD 4222, Australia
| | - Frederic D L Leusch
- Griffith School of Science and Environment and the Australian Rivers Institute, Griffith Univeristy, Building 51, Gold Coast Campus, QLD 4222, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biology, The University of Queensland, Building 76, QLD 4067, Australia
| | - Steven D Melvin
- Griffith School of Science and Environment and the Australian Rivers Institute, Griffith Univeristy, Building 51, Gold Coast Campus, QLD 4222, Australia
| | - Jason P van de Merwe
- Griffith School of Science and Environment and the Australian Rivers Institute, Griffith Univeristy, Building 51, Gold Coast Campus, QLD 4222, Australia.
| |
Collapse
|
11
|
Machuca-Sepúlveda J, Miranda J, Lefin N, Pedroso A, Beltrán JF, Farias JG. Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring. Biology (Basel) 2023; 12:923. [PMID: 37508354 PMCID: PMC10376755 DOI: 10.3390/biology12070923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/30/2023]
Abstract
Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.
Collapse
Affiliation(s)
- Jorge Machuca-Sepúlveda
- Doctoral Program on Natural Resources Sciences, Universidad de La Frontera, Avenida Francisco Salazar, 01145, P.O. Box 54-D, Temuco 4780000, Chile
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Javiera Miranda
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Nicolás Lefin
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Alejandro Pedroso
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Jorge F Beltrán
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Jorge G Farias
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| |
Collapse
|
12
|
Laurent J, Le Berre I, Armengaud J, Kailasam S, Couteau J, Waeles M, Le Floch S, Laroche J, Pichereau V. Integration of environmental signatures and omics-based approaches on the European flounder to assist with health assessment of estuarine ecosystems in Brittany, France. Sci Total Environ 2023; 878:163195. [PMID: 37003335 DOI: 10.1016/j.scitotenv.2023.163195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023]
Abstract
This study aimed to develop a multidisciplinary approach to assess the ecological status of six moderate-sized French estuaries. For each estuary, we gathered geographical information, hydrobiological data, chemistry of pollutants and fish biology, including integration of proteomics and transcriptomics data. This integrative study covered the entire hydrological system studied, from the watershed to the estuary, and considered all the anthropogenic factors that can impact this environment. To reach this goal, European flounder (Platichthys flesus) were collected from six estuaries in September, which ensures a minimum residence time of five months within an estuary. Geographical metrics are used to characterize land use in each watershed. The concentrations of nitrite, nitrate, organic pollutants, and trace elements were measured in water, sediments and biota. All of these environmental parameters allowed to set up a typology of estuaries. Classical fish biomarkers, coupled with molecular data from transcriptomics and shotgun proteomics, highlighted the flounder's responses to stressors in its environment. We analysed the protein abundances and gene expression levels in the liver of fish from the different estuaries. We showed clear positive deregulation of proteins associated with xenobiotic detoxification in a system characterized by a large population density and industrial activity, as well as in a predominantly agricultural catchment area (mostly cultures of vegetables and pig breeding) mainly impacted by pesticides. Fish from the latter estuary also displayed strong deregulation of the urea cycle, most probably related to high nitrogen load. Proteomic and transcriptomic data also revealed a deregulation of proteins and genes related to the response to hypoxia, and a probable endocrine disruption in some estuaries. Coupling these data allowed the precise identification of the main stressors interacting within each hydrosystem.
Collapse
Affiliation(s)
- Jennifer Laurent
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France; CEDRE, 715 rue Alain Colas, 29200 Brest, France.
| | - Iwan Le Berre
- LETG-Brest GEOMER, UMR 6554 CNRS, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAe, F-30207 Bagnols-sur-Cèze, France
| | - Senthilkumar Kailasam
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec H3A 0G1, Canada; Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Jérôme Couteau
- TOXEM, 12 rue des 4 saisons, 76290 Montivilliers, France
| | - Matthieu Waeles
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | | | - Jean Laroche
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | - Vianney Pichereau
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France.
| |
Collapse
|
13
|
Rodrigues JA, Silva M, Araújo R, Madureira L, Soares AMVM, Freitas R, Gil AM. The influence of temperature rise on the metabolic response of Ruditapes philippinarum clams to 17-α-ethinylestradiol. Sci Total Environ 2023; 877:162898. [PMID: 36934939 DOI: 10.1016/j.scitotenv.2023.162898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/09/2023] [Accepted: 03/12/2023] [Indexed: 05/06/2023]
Abstract
Untargeted Nuclear Magnetic Resonance metabolomics was employed to study the effects of warming conditions (17-21 °C) and exposure to 17-α-ethinylestradiol (EE2) on the polar metabolome of Ruditapes philippinarum clams, to identify metabolic markers for monitoring/prediction of deviant environmental conditions. Warming alone triggered changes in alanine/aspartate/glutamate, aromatic amino acids, taurine/hypotaurine and homarine/trigonelline pathways, as well as in energy metabolism, suggesting osmoregulatory adaptations and glycolytic/tricarboxylic acid (TCA) cycle activation, possibly accompanied to some extent by gluconeogenesis to preserve glycogen reserves. At 17 °C, the lowest EE2 concentration (5 ng/L) specifically engaged branched-chain and aromatic amino acids to activate the glycolysis/TCA cycle. Notably, a partial metabolic recovery was observed at 25 ng/L, whereas higher EE2 concentrations (125 and 625 ng/L) again induced significant metabolic disturbances. These included enhanced glycogen biosynthesis and increased lipid reserves, sustained by low-level glutathione-based antioxidative mechanisms that seemed active. At 21 °C, response to EE2 was notably weak at low/intermediate concentrations, becoming particularly significant at the highest EE2 concentration (625 ng/L), suggesting higher protection capacity of Ruditapes philippinarum clams under warming conditions. At 625 ng/L, disturbances in alanine/aspartate/glutamate and taurine/hypotaurine metabolisms were observed, with no evidence of enhanced carbohydrate/protein catabolism. This low energy function profile was accompanied by marked antioxidative mechanisms and choline compounds modulation for cell membrane protection/repair. These results help monitor clams´ response to temperature rise and EE2 exposure, paving the way for future effective guidance and prediction of environmental damaging effects.
Collapse
Affiliation(s)
- João A Rodrigues
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Mónica Silva
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Rita Araújo
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Leonor Madureira
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Amadeu M V M Soares
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Rosa Freitas
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana M Gil
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| |
Collapse
|
14
|
Arcanjo C, Frelon S, Armant O, Camoin L, Audebert S, Camilleri V, Cavalié I, Adam-Guillermin C, Gagnaire B. Insights into the modes of action of tritium on the early-life stages of zebrafish, Danio rerio, using transcriptomic and proteomic analyses. J Environ Radioact 2023; 261:107141. [PMID: 36878054 DOI: 10.1016/j.jenvrad.2023.107141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/29/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
In the environment, populations are exposed to different kinds of ionizing radiation. Little is known about their modes of action on non-human species, and whether or not they are similar for alpha, beta and gamma radiations, considered as the reference. In this context, tritium effects (beta emitter) under the form of tritiated water (HTO) were investigated in zebrafish, a common model in toxicology and ecotoxicology with a fully sequenced genome. Experiments were conducted on early life stages, considered to be highly sensitive to pollutants, by exposing eggs to 0.4 mGy/h of HTO until 10 days post fertilization. Tritium internalization was quantified, and effects were investigated using a combined approach of transcriptomic and proteomic analyses. Results highlighted similarities in the biological pathways affected by HTO by both techniques, such as defence response, muscle integrity and contraction, and potential visual alterations. These results correlated well with previous data obtained on earlier developmental stages (1 and 4 dpf). Interestingly, HTO effects were partly overlapping those obtained after gamma irradiation, underlying potential common modes of action. This study, therefore, brought a body of evidence on the effects of HTO observed at the molecular level on zebrafish larvae. Further studies could investigate if the effects persist in adult organisms.
Collapse
Affiliation(s)
- Caroline Arcanjo
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Sandrine Frelon
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Olivier Armant
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Luc Camoin
- Aix-Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Stéphane Audebert
- Aix-Marseille Univ., CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Virginie Camilleri
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Isabelle Cavalié
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Christelle Adam-Guillermin
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-SANTE/SDOS/LMDN, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Beatrice Gagnaire
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France.
| |
Collapse
|
15
|
Leprêtre M, Geffard O, Espeyte A, Faugere J, Ayciriex S, Salvador A, Delorme N, Chaumot A, Degli-Esposti D. Multiple reaction monitoring mass spectrometry for the discovery of environmentally modulated proteins in an aquatic invertebrate sentinel species, Gammarus fossarum. Environ Pollut 2022; 315:120393. [PMID: 36223854 DOI: 10.1016/j.envpol.2022.120393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Multiple reaction monitoring (MRM) mass spectrometry is emerging as a relevant tool for measuring customized molecular markers in freshwater sentinel species. While this technique is typically used for the validation of protein molecular markers preselected from shotgun experiments, recent gains of MRM multiplexing capacity offer new possibilities to conduct large-scale screening of animal proteomes. By combining the strength of active biomonitoring strategies and MRM technologies, this study aims to propose a new strategy for the discovery of candidate proteins that respond to environmental variability. For this purpose, 249 peptides derived from 147 proteins were monitored by MRM in 273 male gammarids caged in 56 environmental sites, representative of the diversity of French water bodies. A methodology is here proposed to identify a set of customized housekeeping peptides (HKPs) used to correct analytical batch effects and allow proper comparison of peptide levels in gammarids. A comparative analysis performed on HKPs-normalized data resulted in the identification of peptides highly modulated in the environment and derived from proteins likely involved in the environmental stress response. Overall, this study proposes a breakthrough approach to screen and identify potential proteins responding to relevant environmental conditions in sentinel species.
Collapse
Affiliation(s)
- Maxime Leprêtre
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
| | - Anabelle Espeyte
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
| | - Julien Faugere
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Sophie Ayciriex
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Arnaud Salvador
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Nicolas Delorme
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
| | | |
Collapse
|
16
|
Cao G, Zhang J, Wang W, Wu P, Ru Y, Cai Z. Mass spectrometry analysis of a ubiquitous tire rubber-derived quinone in the environment. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
17
|
Wlodkowic D, Jansen M. High-throughput screening paradigms in ecotoxicity testing: Emerging prospects and ongoing challenges. Chemosphere 2022; 307:135929. [PMID: 35944679 DOI: 10.1016/j.chemosphere.2022.135929] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/09/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
The rapidly increasing number of new production chemicals coupled with stringent implementation of global chemical management programs necessities a paradigm shift towards boarder uses of low-cost and high-throughput ecotoxicity testing strategies as well as deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity that can be used in effective risk assessment. The latter will require automated acquisition of biological data, new capabilities for big data analysis as well as computational simulations capable of translating new data into in vivo relevance. However, very few efforts have been so far devoted into the development of automated bioanalytical systems in ecotoxicology. This is in stark contrast to standardized and high-throughput chemical screening and prioritization routines found in modern drug discovery pipelines. As a result, the high-throughput and high-content data acquisition in ecotoxicology is still in its infancy with limited examples focused on cell-free and cell-based assays. In this work we outline recent developments and emerging prospects of high-throughput bioanalytical approaches in ecotoxicology that reach beyond in vitro biotests. We discuss future importance of automated quantitative data acquisition for cell-free, cell-based as well as developments in phytotoxicity and in vivo biotests utilizing small aquatic model organisms. We also discuss recent innovations such as organs-on-a-chip technologies and existing challenges for emerging high-throughput ecotoxicity testing strategies. Lastly, we provide seminal examples of the small number of successful high-throughput implementations that have been employed in prioritization of chemicals and accelerated environmental risk assessment.
Collapse
Affiliation(s)
- Donald Wlodkowic
- The Neurotox Lab, School of Science, RMIT University, Melbourne, VIC, 3083, Australia.
| | - Marcus Jansen
- LemnaTec GmbH, Nerscheider Weg 170, 52076, Aachen, Germany
| |
Collapse
|
18
|
Gajahin Gamage NT, Miyashita R, Takahashi K, Asakawa S, Senevirathna JDM. Proteomic Applications in Aquatic Environment Studies. Proteomes 2022; 10:proteomes10030032. [PMID: 36136310 PMCID: PMC9505238 DOI: 10.3390/proteomes10030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.
Collapse
Affiliation(s)
- Nadeeka Thushari Gajahin Gamage
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
| | - Rina Miyashita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Jayan Duminda Mahesh Senevirathna
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
- Correspondence:
| |
Collapse
|
19
|
Medić AB, Karadžić IM. Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation. World J Microbiol Biotechnol 2022; 38:165. [PMID: 35861883 DOI: 10.1007/s11274-022-03349-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/26/2022] [Indexed: 10/17/2022]
Abstract
Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.
Collapse
Affiliation(s)
- Ana B Medić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia.
| | - Ivanka M Karadžić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia
| |
Collapse
|
20
|
Armengaud J. Protecting our environment, a motivating outdoor game for proteomics! Proteomics 2022; 22:e2200055. [PMID: 35452157 DOI: 10.1002/pmic.202200055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 11/06/2022]
Abstract
The global Earth ecosystem faces many intertwined threats, primarily anthropogenic pollution, drastic reduction of wild spaces, faster spread of pathogens, and global climate warming. Ecotoxicology, the integration of toxicology and ecology, aims to describe the effects of toxicants on organisms, whether at the level of the population, the community, the ecosystem, or the biosphere. Sentinel species are employed to assess threats to life, giving advance warning of danger. In this issue of Proteomics, Wilde and collaborators (Proteomics 2022, 22, https://doi.org/10.1002/pmic.202100289) present a comprehensive coverage of the proteome of the crustacean Daphnia magna, a species used to evaluate aquatic pollution. This study illustrates how current shotgun proteomics technology allows straightforward quantitation of any protein for whole animals or dissected organs, making global molecular phenotyping a reality for animals. Tandem mass spectrometry operated in data-independent acquisition can be used to compare the response of sentinels to various environmental conditions. The current low number of well-annotated animal or plant genomes, the high diversity of genetic backgrounds of each species, and the paucity of knowledge about protein functions for most of the relevant sentinels pose huge challenges for data interpretation. As a result, ecology and ecotoxicology today constitute an exceptional field for proteomics.
Collapse
Affiliation(s)
- Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, SPI, Département Médicaments et Technologies pour la Santé (DMTS), Bagnols-sur-Cèze, France
| |
Collapse
|
21
|
González-Penagos CE, Zamora-Briseño JA, Améndola-Pimenta M, Elizalde-Contreras JM, Árcega-Cabrera F, Cruz-Quintana Y, Santana-Piñeros AM, Cañizárez-Martínez MA, Pérez-Vega JA, Ruiz-May E, Rodríguez-Canul R. Integrative description of changes occurring on zebrafish embryos exposed to water-soluble crude oil components and its mixture with a chemical surfactant. Toxicol Appl Pharmacol 2022; 445:116033. [PMID: 35452689 DOI: 10.1016/j.taap.2022.116033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022]
Abstract
The effects of crude oil spills are an ongoing problem for wildlife and human health in both marine and freshwater aquatic environments. Bioassays of model organisms are a convenient way to assess the potential risks of the substances involved in oil spills. Zebrafish embryos (ZFE) are a useful to reach a fast and detailed description of the toxicity of the pollutants, including both the components of the crude oil itself and substances that are commonly used for crude oil spill mitigation (e.g. surfactants). Here, we evaluated the survival rate, as well as histological, morphological, and proteomic changes in ZFE exposed to Water Accumulated Fraction (WAF) of light crude oil and in mixture with dioctyl sulfosuccinate sodium (DOSS, e.g. CEWAF: Chemically Enhanced WAF), a surfactant that is frequently used in chemical dispersant formulations. Furthermore, we compared de hydrocarbon concentration of WAF and CEWAF of the sublethal dilution. In histological, morphological, and gene expression variables, the ZFE exposed to WAF showed less changes than those exposed to CEWAF. Proteomic changes were more dramatic in ZFE exposed to WAF, with important alterations in spliceosomal and ribosomal proteins, as well as proteins related to eye and retinal photoreceptor development and heart function. We also found that the concentration of high molecular weight hydrocarbons in water was slighly higher in presence of DOSS, but the low molecular weight hydrocarbons concentration was higher in WAF. These results provide an important starting point for identifying useful crude-oil exposure biomarkers in fish species.
Collapse
Affiliation(s)
- Carlos Eduardo González-Penagos
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico
| | - Jesús Alejandro Zamora-Briseño
- Laboratorio de Entomología Molecular, Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, El Instituto de Ecología, Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz, CP 91070, Mexico
| | - Monica Améndola-Pimenta
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico
| | - José Miguel Elizalde-Contreras
- Laboratorio de Entomología Molecular, Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, El Instituto de Ecología, Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz, CP 91070, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de Abrigo S/N, Sisal, Yucatán 97356, Mexico
| | - Yanis Cruz-Quintana
- Grupo de Investigación en Sanidad Acuícola, Inocuidad y Salud Ambiental, Facultad de Ciencias Veterinarias, Departamento de Acuicultura y Pesca, Universidad Técnica de Manabí, Ciudadela Universitaria, Bahía de Caráquez, Manabí 130104, Ecuador
| | - Ana María Santana-Piñeros
- Grupo de Investigación en Sanidad Acuícola, Inocuidad y Salud Ambiental, Facultad de Ciencias Veterinarias, Departamento de Acuicultura y Pesca, Universidad Técnica de Manabí, Ciudadela Universitaria, Bahía de Caráquez, Manabí 130104, Ecuador
| | - Mayra Alejandra Cañizárez-Martínez
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico
| | - Juan Antonio Pérez-Vega
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico
| | - Eliel Ruiz-May
- Laboratorio de Entomología Molecular, Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, El Instituto de Ecología, Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz, CP 91070, Mexico.
| | - Rossanna Rodríguez-Canul
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico.
| |
Collapse
|
22
|
Beale DJ, Jones OAH, Bose U, Broadbent JA, Walsh TK, van de Kamp J, Bissett A. Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience. Emerg Top Life Sci 2022:ETLS20210261. [PMID: 35403668 DOI: 10.1042/ETLS20210261] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022]
Abstract
Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of ‘ecosurveillance’, especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.
Collapse
|
23
|
Scalese G, Kostenkova K, Crans DC, Gambino D. Metallomics and other omics approaches in antiparasitic metal-based drug research. Curr Opin Chem Biol 2022; 67:102127. [DOI: 10.1016/j.cbpa.2022.102127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/17/2021] [Accepted: 01/24/2022] [Indexed: 01/08/2023]
|
24
|
Medić A, Hüttmann N, Lješević M, Risha Y, Berezovski MV, Minić Z, Karadžić I. A study of the flexibility of the carbon catabolic pathways of extremophilic P. aeruginosa san ai exposed to benzoate versus glucose as sole carbon sources by multi omics analytical platform. Microbiol Res 2022; 259:126998. [PMID: 35276454 DOI: 10.1016/j.micres.2022.126998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/17/2022] [Accepted: 02/26/2022] [Indexed: 10/19/2022]
Abstract
Polyextremophilic, hydrocarbonoclastic Pseudomonas aeruginosa san ai can survive under extreme environmental challenges in the presence of a variety of pollutants such as organic solvents and hydrocarbons, particularly aromatics, heavy metals, and high pH. To date, the metabolic plasticity of the extremophilic P. aeruginosa, has not been sufficiently studied in regard to the effect of changing carbon sources. Therefore, the present study explores the carbon metabolic pathways of polyextremophilic P. aeruginosa san ai grown on sodium benzoate versus glucose and its potential for aromatic degradation. P. aeruginosa san ai removed/metabolised nearly 430 mg/L of benzoate for 48 h, demonstrating a high capacity for aromatic degradation. Comparative functional proteomics, targeted metabolomics and genomics analytical approaches were employed to study the carbon metabolism of the P. aeruginosa san ai. Functional proteomic study of selected enzymes participating in the β-ketoadipate and the Entner-Doudoroff pathways revealed a metabolic reconfiguration induced by benzoate compared to glucose. Metabolome analysis implied the existence of both catechol and protocatechuate branches of the β-ketoadipate pathway. Enzymatic study of benzoate grown cultures confirmed the activity of the ortho- catechol branch of the β-ketoadipate pathway. Even high concentrations of benzoate did not show increased stress protein synthesis, testifying to its extremophilic nature capable of surviving in harsh conditions. This ability of Pseudomonas aeruginosa san ai to efficiently degrade benzoate can provide a wide range of use of this strain in environmental and agricultural application.
Collapse
Affiliation(s)
- Ana Medić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia
| | - Nico Hüttmann
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Marija Lješević
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, Njegoševa 12, 11000 Belgrade, Serbia
| | - Yousef Risha
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Maxim V Berezovski
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Zoran Minić
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Ivanka Karadžić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia.
| |
Collapse
|
25
|
Wilde MV, Brehm J, Schwarzer M, Stöckl JB, Laforsch C, Fröhlich T. Improving the proteome coverage of Daphnia magna - implications for future ecotoxicoproteomics studies. Proteomics 2022; 22:e2100289. [PMID: 35143708 DOI: 10.1002/pmic.202100289] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/02/2022] [Accepted: 02/02/2022] [Indexed: 11/09/2022]
Abstract
Aquatic pollution is an increasing problem and requires extensive research efforts to understand associated consequences and to find suitable solutions. The crustacean Daphnia is a keystone species in lacustrine ecosystems by connecting primary producers with higher trophic levels. Therefore, Daphnia is perfectly suitable to investigate biological effects of freshwater pollution and is frequently used as an important model organism in ecotoxicology. The field of ecotoxicoproteomics has become increasingly prevalent, as proteins are important for an organism's physiology and respond rapidly to changing environmental conditions. However, one obstacle in proteome analysis of Daphnia is highly abundant proteins like vitellogenin, decreasing the analytical depth of proteome analysis. To improve proteome coverage in Daphnia, we established an easy-to-use procedure based on the LC-MS/MS of whole daphnids and the dissected Daphnia gut, which is the main tissue getting in contact with soluble and particulate pollutants, separately. Using a comprehensive spectral library, generated by gas-phase fractionation and a data-independent acquisition method, we identified 4621 and 5233 protein groups at high confidence (false discovery rate < 0.01) in Daphnia and Daphnia gut samples, respectively. By combining both datasets, a proteome coverage of 6027 proteins was achieved, demonstrating the effectiveness of our approach. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Magdalena V Wilde
- Gene Center Munich, Laboratory for Functional Genome Analysis (LAFUGA), LMU München, Feodor-Lynen-Straße 25, Munich, 81377, Germany
| | - Julian Brehm
- University of Bayreuth, Animal Ecology 1, Universitätsstraße 30, Bayreuth, 95447, Germany
| | - Michael Schwarzer
- University of Bayreuth, Animal Ecology 1, Universitätsstraße 30, Bayreuth, 95447, Germany
| | - Jan B Stöckl
- Gene Center Munich, Laboratory for Functional Genome Analysis (LAFUGA), LMU München, Feodor-Lynen-Straße 25, Munich, 81377, Germany
| | - Christian Laforsch
- University of Bayreuth, Animal Ecology 1, Universitätsstraße 30, Bayreuth, 95447, Germany
| | - Thomas Fröhlich
- Gene Center Munich, Laboratory for Functional Genome Analysis (LAFUGA), LMU München, Feodor-Lynen-Straße 25, Munich, 81377, Germany
| |
Collapse
|
26
|
Agwunobi DO, Li M, Wang N, Chang G, Zhang X, Xue X, Yu Z, Wang H, Liu J. Proteomic analysis suggests that monoterpenes in lemongrass disrupt Ca 2+ homeostasis in Haemaphysalis longicornis leading to mitochondrial depolarization and cytotoxicity. Proteomics 2022; 22:e2100156. [PMID: 34997954 DOI: 10.1002/pmic.202100156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 12/18/2022]
Abstract
Complex mixtures of bioactive ingredients in plant essential oils present complex chemistries which involve different modes of action. An increasing body of scientific reports has recently focused on the acaricidal activities of plant essential oils attributed to their monoterpene components, but information about their underlying molecular mechanism of action is scarce. Here, after the chemical analysis of lemongrass oil, a proteomic analysis of the ovary, salivary gland, and midgut of Haemaphysalis longicornis exposed to Cymbopogon citratus (lemongrass) essential oil was performed via data-independent acquisition mass spectrometry (DIA-MS) technology to further elucidate the molecular mechanisms involved. Pathway analysis reveals the activation of metabolic pathways mediated by oxidoreductases and transferases. Furthermore, the upregulation of various calcium-associated proteins and the upregulation of cytochrome c1, cytochrome c oxidase polypeptide IV, and programmed cell death protein 6-like isoform X1 suggest a cytotoxic mode of action via the formation of reactive oxygen species (ROS), mitochondrial Ca2+ overload, mitochondrial uncoupling, and depolarization, and ATP depletion leading to either apoptotic or necrotic death. Morphological alterations observed after the RNAi of a major detoxification enzyme (glutathione S-transferase) merit further investigation. Hence, the cytotoxic mode of action exhibited by C. citratus oil could be vital for the development of eco-friendly acaricide.
Collapse
Affiliation(s)
- Desmond O Agwunobi
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Mengxue Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ningmei Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Guomin Chang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiaojing Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiaomin Xue
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhijun Yu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hui Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| |
Collapse
|
27
|
Medvecky M, Mandalakis M. PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems. Front Chem 2021; 9:722087. [PMID: 34490209 PMCID: PMC8416534 DOI: 10.3389/fchem.2021.722087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest.
Collapse
Affiliation(s)
- Matej Medvecky
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom.,Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic.,Veterinary Research Institute, Brno, Czech Republic
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| |
Collapse
|
28
|
Lionetto MG, Caricato R, Giordano ME. Pollution Biomarkers in the Framework of Marine Biodiversity Conservation: State of Art and Perspectives. Water 2021; 13:1847. [DOI: 10.3390/w13131847] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Marine biodiversity is threatened by several anthropogenic pressures. Pollution deriving from the discharge of chemical contaminants in the sea represents one of the main threats to the marine environment, influencing the health of organisms, their ability to recover their homeostatic status, and in turn endangering biodiversity. Molecular and cellular responses to chemical pollutants, known as biomarkers, are effect-based methodologies useful for detecting exposure and for assessing the effects of pollutants on biota in environmental monitoring. The present review analyzes and discusses the recent literature on the use of biomarkers in the framework of biodiversity conservation. The study shows that pollution biomarkers can be useful tools for monitoring and assessment of pollution threat to marine biodiversity, both in the environmental quality monitoring of protected areas and the assessment of the health status of species at risk. Moreover, key areas of the research that need further development are suggested, such as the development of omics-based biomarkers specifically addressed to conservation purposes and their validation in the field, the extension of the biomarker study to a wider number of endangered species, and the development of organic guidelines for the application of the biomarker approach in support to conservation policies and management.
Collapse
|
29
|
Koenig N, Almunia C, Bonnal-Conduzorgues A, Armengaud J, Chaumot A, Geffard O, Esposti DD. Co-expression network analysis identifies novel molecular pathways associated with cadmium and pyriproxyfen testicular toxicity in Gammarus fossarum. Aquat Toxicol 2021; 235:105816. [PMID: 33838495 DOI: 10.1016/j.aquatox.2021.105816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/12/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Omics approaches are continuously providing new clues on the mechanisms of action of contaminants in species of environmental relevance, contributing to the emergence of molecular ecotoxicology. Co-expression network approaches represent a suitable methodological framework for studying the rich content of omics datasets. This study aimed to find evidence of key pathways and proteins related to the testicular toxicity in the sentinel crustacean species Gammarus fossarum exposed to endocrine disruptors using a weighted protein co-expression network analysis. From a shotgun proteomics dataset of male gonads of G. fossarum organisms exposed to cadmium (Cd), pyriproxyfen (Pyr) and methoxyfenozide (Met) in laboratory conditions, four distinct modules were identified as significantly correlated to contaminants' exposure. Protein set enrichment analysis identified modules involved in cytoskeleton organization and oxidative stress response associated with the Cd exposure. The module associated with Pyr exposure was associated with endoplasmic reticulum stress (ER) response, and the module correlated with Met exposure was characterized by a significant proportion of amphipod-restricted proteins whose functions are still not characterized. Our results show that co-expression networks are efficient and adapted tools to identify new potential mode of actions from environmental sentinel species, such as G. fossarum, using a proteogenomic approach, even without an annotated genome.
Collapse
Affiliation(s)
- Natacha Koenig
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Christine Almunia
- Université Paris-Saclay, Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI-Li2D, F-30207 Bagnols-sur-Cèze, France
| | - Aurore Bonnal-Conduzorgues
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Jean Armengaud
- Université Paris-Saclay, Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI-Li2D, F-30207 Bagnols-sur-Cèze, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Davide Degli Esposti
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France.
| |
Collapse
|
30
|
Tlili S, Mouneyrac C. New challenges of marine ecotoxicology in a global change context. Mar Pollut Bull 2021; 166:112242. [PMID: 33706213 DOI: 10.1016/j.marpolbul.2021.112242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 02/23/2021] [Accepted: 02/28/2021] [Indexed: 05/27/2023]
Abstract
Currently, research agenda in marine ecotoxicology is facing new challenges with the emergence of newly and complex synthetized chemicals. The study of the fate and adverse effects of toxicants remains increasingly complicated with global change events. Ecotoxicology had provided for a decades, precious scientific data and knowledge but also technical and management tools for the environmental community. Regarding those, it is necessary to update methodologies dealing with these issues such as combined effect of conventional and emergent stressors and global changes. In this point of view article, we discuss one hand the new challenges of ecotoxicology in this context, and in the other hand, the need of updating agenda and methodologies currently used in monitoring programs and finally recommendations and future research needs. Among recommendations, it could be cited the necessity to perform long-term experiments, the standardization of sentinel species and taking benefit from baseline studies and omics technologies.
Collapse
Affiliation(s)
- Sofiene Tlili
- Laboratoire Mer, Molécules, Santé (MMS, EA 2160), Université Catholique, de l'Ouest, 49000 Angers, France.
| | - Catherine Mouneyrac
- Laboratoire Mer, Molécules, Santé (MMS, EA 2160), Université Catholique, de l'Ouest, 49000 Angers, France
| |
Collapse
|
31
|
Abstract
Proteins are the ultimate product of gene expression. As they hinge between gene transcription and phenotype, they offer a more realistic perspective of toxicopathic effects, responses and even susceptibility to insult than targeting genes and mRNAs while dodging some inter-individual variability that hinders measuring downstream endpoints like metabolites or enzyme activity. Toxicologists have long focused on proteins as biomarkers but the advent of proteomics shifted risk assessment from narrow single-endpoint analyses to whole-proteome screening, enabling deriving protein-centric adverse outcome pathways (AOPs), which are pivotal for the derivation of Systems Biology informally named Systems Toxicology. Especially if coupled pathology, the identification of molecular initiating events (MIEs) and AOPs allow predictive modeling of toxicological pathways, which now stands as the frontier for the next generation of toxicologists. Advances in mass spectrometry, bioinformatics, protein databases and top-down proteomics create new opportunities for mechanistic and effects-oriented research in all fields, from ecotoxicology to pharmacotoxicology.
Collapse
Affiliation(s)
- Carolina Madeira
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal
| | - Pedro M Costa
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal.
| |
Collapse
|
32
|
Ankley GT, Cureton P, Hoke RA, Houde M, Kumar A, Kurias J, Lanno R, McCarthy C, Newsted J, Salice CJ, Sample BE, Sepúlveda MS, Steevens J, Valsecchi S. Assessing the Ecological Risks of Per- and Polyfluoroalkyl Substances: Current State-of-the Science and a Proposed Path Forward. Environ Toxicol Chem 2021; 40:564-605. [PMID: 32897586 PMCID: PMC7984443 DOI: 10.1002/etc.4869] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 05/19/2023]
Abstract
Per- and poly-fluoroalkyl substances (PFAS) encompass a large, heterogenous group of chemicals of potential concern to human health and the environment. Based on information for a few relatively well-understood PFAS such as perfluorooctane sulfonate and perfluorooctanoate, there is ample basis to suspect that at least a subset can be considered persistent, bioaccumulative, and/or toxic. However, data suitable for determining risks in either prospective or retrospective assessments are lacking for the majority of PFAS. In August 2019, the Society of Environmental Toxicology and Chemistry sponsored a workshop that focused on the state-of-the-science supporting risk assessment of PFAS. The present review summarizes discussions concerning the ecotoxicology and ecological risks of PFAS. First, we summarize currently available information relevant to problem formulation/prioritization, exposure, and hazard/effects of PFAS in the context of regulatory and ecological risk assessment activities from around the world. We then describe critical gaps and uncertainties relative to ecological risk assessments for PFAS and propose approaches to address these needs. Recommendations include the development of more comprehensive monitoring programs to support exposure assessment, an emphasis on research to support the formulation of predictive models for bioaccumulation, and the development of in silico, in vitro, and in vivo methods to efficiently assess biological effects for potentially sensitive species/endpoints. Addressing needs associated with assessing the ecological risk of PFAS will require cross-disciplinary approaches that employ both conventional and new methods in an integrated, resource-effective manner. Environ Toxicol Chem 2021;40:564-605. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
Collapse
Affiliation(s)
- Gerald T. Ankley
- Great Lakes Toxicology and Ecology Division, US Environmental Protection AgencyDuluthMinnesotaUSA
| | - Philippa Cureton
- Science and Risk Assessment Division, Environment and Climate Change Canada, GatineauQuebecCanada
| | | | - Magali Houde
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, MontrealQuebecCanada
| | - Anupama Kumar
- Land and Water, Commonwealth Scientific and Industrial Research Organisation UrrbraeSouth AustraliaAustralia
| | - Jessy Kurias
- Science and Risk Assessment Division, Environment and Climate Change Canada, GatineauQuebecCanada
| | | | | | | | | | | | - Maria S. Sepúlveda
- Department of Forestry and Natural Resources, Purdue UniversityWest LayetteIndianaUSA
| | - Jeffery Steevens
- US Geological Survey, Columbia Environmental Research CenterColumbiaMissouriUSA
| | - Sara Valsecchi
- Water Research Institute, National Research CouncilBrugherioMonza and BrianzaItaly
| |
Collapse
|
33
|
Balbi T, Auguste M, Ciacci C, Canesi L. Immunological Responses of Marine Bivalves to Contaminant Exposure: Contribution of the -Omics Approach. Front Immunol 2021; 12:618726. [PMID: 33679759 PMCID: PMC7930816 DOI: 10.3389/fimmu.2021.618726] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 01/22/2021] [Indexed: 12/27/2022] Open
Abstract
The increasing number of data studies on the biological impact of anthropogenic chemicals in the marine environment, together with the great development of invertebrate immunology, has identified marine bivalves as a key invertebrate group for studies on immunological responses to pollutant exposure. Available data on the effects of contaminants on bivalve immunity, evaluated with different functional and molecular endpoints, underline that individual functional parameters (cellular or humoral) and the expression of selected immune-related genes can distinctly react to different chemicals depending on the conditions of exposure. Therefore, the measurement of a suite of immune biomarkers in hemocytes and hemolymph is needed for the correct evaluation of the overall impact of contaminant exposure on the organism's immunocompetence. Recent advances in -omics technologies are revealing the complexity of the molecular players in the immune response of different bivalve species. Although different -omics represent extremely powerful tools in understanding the impact of pollutants on a key physiological function such as immune defense, the -omics approach has only been utilized in this area of investigation in the last few years. In this work, available information obtained from the application of -omics to evaluate the effects of pollutants on bivalve immunity is summarized. The data shows that the overall knowledge on this subject is still quite limited and that to understand the environmental relevance of any change in immune homeostasis induced by exposure to contaminants, a combination of both functional assays and cutting-edge technology (transcriptomics, proteomics, and metabolomics) is required. In addition, the utilization of metagenomics may explain how the complex interplay between the immune system of bivalves and its associated bacterial communities can be modulated by pollutants, and how this may in turn affect homeostatic processes of the host, host–pathogen interactions, and the increased susceptibility to disease. Integrating different approaches will contribute to knowledge on the mechanism responsible for immune dysfunction induced by pollutants in ecologically and economically relevant bivalve species and further explain their sensitivity to multiple stressors, thus resulting in health or disease.
Collapse
Affiliation(s)
- Teresa Balbi
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Manon Auguste
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Caterina Ciacci
- Department of Biomolecular Sciences (DIBS), University of Urbino, Urbino, Italy
| | - Laura Canesi
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| |
Collapse
|
34
|
Vieira L, Hissa DC, Souza T, Gonçalves ÍFS, Evaristo JAM, Nogueira FCS, Carvalho AFU, Farias D. Assessing the effects of an acute exposure to worst-case concentration of Cry proteins on zebrafish using the embryotoxicity test and proteomics analysis. Chemosphere 2021; 264:128538. [PMID: 33038734 DOI: 10.1016/j.chemosphere.2020.128538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
Cry1C, Cry1F and Cry1Ab are insecticidal proteins from Bacillus thuringiensis (Bt) which are expressed in transgenic crops. Given the entry of these proteins into aquatic environments, it is relevant to evaluate their impacts on aquatic organisms. In this work, we sought to evaluate the effects of Cry1C, Cry1F and Cry1Ab on zebrafish embryos and larvae of a predicted worst-case scenario concentration of these proteins (set to 1.1 mg/L). For that, we coupled a traditional toxicity approach (the zebrafish embryotoxicity test and dosage of enzymatic biomarkers) to gel free proteomics analysis. At the concentration tested, these proteins did not cause adverse effects in the zebrafish early life stages, either by verifying phenotypic endpoints of toxicity or alterations in representative enzymatic biomarkers (catalase, glutathione-S-tranferase and lactate-dehydrogenase). At the molecular level, the Cry proteins tested lead to very small changes in the proteome of zebrafish larvae. In a global way, these proteins upregulated the expression of vitellogenins. Besides that, Cry1C e Cry1F deregulated heterogeneous nuclear ribonucleoproteins (Hnrnpa0l and Hnrnpaba, respectively), implicated in mRNA processing and gene regulation. Overall, these data lead to the conclusion that Cry1C, Cry1F and Cry1Ab proteins, even at a very high concentration, have limited effects in the early stages of zebrafish life.
Collapse
Affiliation(s)
- Leonardo Vieira
- Post-Graduation Program in Biochemistry, Department of Biochemistry and Molecular Biology, Building 907, Campus Pici, Federal University of Ceara, 60455-970, Fortaleza, Brazil
| | - Denise Cavalcante Hissa
- Department of Biology, Building 909, Campus Pici, Federal University of Ceara, 60455-970, Fortaleza, Brazil
| | - Terezinha Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Oncology, Maastricht University, Maastricht, the Netherlands
| | - Íris Flávia Sousa Gonçalves
- Post-Graduation Program in Biochemistry, Department of Biochemistry and Molecular Biology, Building 907, Campus Pici, Federal University of Ceara, 60455-970, Fortaleza, Brazil; Laboratory for Risk Assessment of Novel Technologies, Department of Molecular Biology, Federal University of Paraiba, 58051-900, João Pessoa, Brazil
| | - Joseph Alberto Medeiros Evaristo
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Fábio César Sousa Nogueira
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil; Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Ana Fontenele Urano Carvalho
- Post-Graduation Program in Biochemistry, Department of Biochemistry and Molecular Biology, Building 907, Campus Pici, Federal University of Ceara, 60455-970, Fortaleza, Brazil; Department of Biology, Building 909, Campus Pici, Federal University of Ceara, 60455-970, Fortaleza, Brazil
| | - Davi Farias
- Post-Graduation Program in Biochemistry, Department of Biochemistry and Molecular Biology, Building 907, Campus Pici, Federal University of Ceara, 60455-970, Fortaleza, Brazil; Laboratory for Risk Assessment of Novel Technologies, Department of Molecular Biology, Federal University of Paraiba, 58051-900, João Pessoa, Brazil.
| |
Collapse
|
35
|
Abstract
Since its inception, liquid chromatography-mass spectrometry (LC-MS) has been continuously improved upon in many aspects, including instrument capabilities, sensitivity, and resolution. Moreover, the costs to purchase and operate mass spectrometers and liquid chromatography systems have decreased, thus increasing affordability and availability in sectors outside of academic and industrial research. Processing power has also grown immensely, cutting the time required to analyze samples, allowing more data to be feasibly processed, and allowing for standardized processing pipelines. As a result, proteomics via LC-MS has become popular in many areas of biological sciences, forging an important seat for itself in targeted and untargeted assays, pure and applied science, the laboratory, and the clinic. In this chapter, many of these applications of LC-MS-based proteomics and an outline of how they can be executed will be covered. Since the field of personalized medicine has matured alongside proteomics, it has also come to rely on various mass spectrometry methods and will be elaborated upon as well. As time goes on and mass spectrometry evolves, there is no doubt that its presence in these areas, and others, will only continue to grow.
Collapse
|
36
|
Sánchez-Marín P, Vidal-Liñán L, Fernández-González LE, Montes R, Rodil R, Quintana JB, Carrera M, Mateos J, Diz AP, Beiras R. Proteomic analysis and biochemical alterations in marine mussel gills after exposure to the organophosphate flame retardant TDCPP. Aquat Toxicol 2021; 230:105688. [PMID: 33316748 DOI: 10.1016/j.aquatox.2020.105688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/27/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
Organophosphate flame retardants (OPFRs) are (re-)emergent environmental pollutants increasingly being used because of the restriction of other flame retardants. The chlorinated OPFR, tris(1,3-dichloro-2-propyl) phosphate (TDCPP) is among those of highest environmental concern, but its potential effects in the marine environment have rarely been investigated. We exposed a widely used sentinel marine mussel species, Mytilus galloprovincialis, to 10 μg L-1 of TDCPP during 28 days and studied: (i) the kinetics of bioaccumulation and elimination of the compound, (ii) the effect on two molecular biomarkers, glutathione S-transferase (GST) and acetylcholinesterase (AChE) activities, and (iii) proteomic alterations in the gills, following an isobaric labeling quantitative shotgun proteomic approach, at two exposure times (7 and 28 days). Uptake and elimination of TDCPP by mussels were very fast, and the bioconcentration factor of this compound in mussels was 147 L kgww-1, confirming that this compound is not very bioaccumulative, as predicted by its chemical properties. GST activity was not affected by TDCPP exposure, but AChE activity was inhibited by TDCPP at both 7 and 28 days of exposure. Proteomic analysis revealed subtle effects of TDCPP in mussel gills, since few proteins (less than 2 % of the analysed proteome) were significantly affected by TDCPP, and effect sizes were low. The most relevant effects detected were the up-regulation of epimerase family protein SDR39U1, an enzyme that could be involved in detoxification processes, at both exposure times, and the down-regulation of receptor-type tyrosine-protein phosphatase N2-like (PTPRN2) after 7 days of exposure, which is involved in neurotransmitter secretion and might be related to the neurotoxicity described for this compound. Exposure time rather than TDCPP exposure was the most important driver of protein abundance changes, with 33 % of the proteome being affected by this factor, suggesting that stress caused by laboratory conditions could be an important confounding factor that needs to be controlled in similar ecotoxicology studies. Proteomic data are available via ProteomeXchange with identifier PXD019720.
Collapse
Affiliation(s)
- Paula Sánchez-Marín
- Department of Ecology and Animal Biology, University of Vigo, 36310 Vigo, Galicia, Spain; Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, 36390 Vigo, Spain.
| | - Leticia Vidal-Liñán
- Department of Ecology and Animal Biology, University of Vigo, 36310 Vigo, Galicia, Spain; Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, 36390 Vigo, Spain
| | - Laura Emilia Fernández-González
- Department of Ecology and Animal Biology, University of Vigo, 36310 Vigo, Galicia, Spain; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| | - Rosa Montes
- Department of Analytical Chemistry, Nutrition and Food Sciences, Institute of Research in Chemical and Biological Analysis (IAQBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rosario Rodil
- Department of Analytical Chemistry, Nutrition and Food Sciences, Institute of Research in Chemical and Biological Analysis (IAQBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José Benito Quintana
- Department of Analytical Chemistry, Nutrition and Food Sciences, Institute of Research in Chemical and Biological Analysis (IAQBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Mónica Carrera
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), 36208 Vigo, Spain
| | - Jesús Mateos
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), 36208 Vigo, Spain
| | - Angel P Diz
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| | - Ricardo Beiras
- Department of Ecology and Animal Biology, University of Vigo, 36310 Vigo, Galicia, Spain; Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| |
Collapse
|
37
|
De Felice B, Parolini M. Can Proteomics Be Considered as a Valuable Tool to Assess the Toxicity of Nanoparticles in Marine Bivalves? JMSE 2020; 8:1033. [DOI: 10.3390/jmse8121033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Exposure to nanoparticles (NPs) has been identified as a major concern for marine ecosystems. Because of their peculiar physico-chemical features, NPs are accumulated in marine organisms, which suffer a variety of adverse effects. In particular, bivalve mollusks represent a unique target for NPs, mainly because they are suspension-feeders with highly developed processes for cellular internalization of nano- and micrometric particles. Several studies have demonstrated that the uptake and the accumulation of NPs can induce sub-lethal effects towards marine bivalves. However, to understand the real risk of NP exposures the application of the so-called “omics” techniques (e.g., proteomics, genomics, metabolomics, lipidomics) has been suggested. In particular, proteomics has been used to study the effects of NPs and their mechanism(s) of action in marine bivalves, but to date its application is still limited. The present review aims at summarizing the state of the art concerning the application of proteomics as a tool to investigate the effects of nanoparticles on the proteome of marine bivalves, and to critically discuss the advantages and limitations of proteomics in this field of research. Relying on results obtained by studies that applied proteomics on bivalve tissues, proteomics application needs to be considered cautiously as a promising and valuable tool to shed light on toxicity and mechanism(s) of action of NPs. Although on one hand, the analysis of the current literature demonstrated undeniable strengths, potentiality and reliability of proteomics, on the other hand a number of limitations suggest that some gaps of knowledge need to be bridged, and methodological and technical improvements are necessary before proteomics can be readily and routinely applied to nanotoxicology studies.
Collapse
|
38
|
López-Pedrouso M, Varela Z, Franco D, Fernández JA, Aboal JR. Can proteomics contribute to biomonitoring of aquatic pollution? A critical review. Environ Pollut 2020; 267:115473. [PMID: 32882465 DOI: 10.1016/j.envpol.2020.115473] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Aquatic pollution is one of the greatest environmental problems, and therefore its control represents one of the major challenges in this century. In recent years, proteomics has emerged as a powerful tool for searching protein biomarkers in the field of pollution biomonitoring. For biomonitoring marine contamination, there is a consensus that bivalves are preferred organisms to assess organic and inorganic pollutants. Thus, the bivalve proteome was intensively studied, particularly the mussel. It is well documented that heavy metal pollution and organic chemicals altered the structural proteins causing degradation of tissues of molluscs. Also, it is well known that proteins involved in stress oxidative such as glutathione and enzymes as catalase, superoxide dismutase or peroxisomes are overexpressed in response to contaminants. Additionally, using bivalves, other groups of proteins proposed as pollution biomarkers are the metabolic proteins. Even though other marine species are used to monitor the pollution, the presence of proteomic tools in these studies is scarce. Concerning freshwater pollution field, a great variety of animal species (fish and crustaceans) are used as biomonitors in proteomics studies compared to plants that are scarcely analysed. In fish species, proteins involved in stress oxidative such as heat shock family or proteins from lipid and carbohydrate metabolism were proposed as candidate biomarkers. On the contrary, for crustaceans there is a lack of proteomic studies individually assessing the contaminants. Novel scenarios, including emerging contaminants and new threats, will require proteomic technology for a systematic search of protein biomarkers and a greater knowledge at molecular level of those cellular pathways induced by contamination.
Collapse
Affiliation(s)
- M López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, 15872, A Coruña, Spain.
| | - Z Varela
- CRETUS Institute, Department of Functional Biology, Ecology Unit, University of Santiago de Compostela, Santiago de Compostela, 15872, A Coruña, Spain
| | - D Franco
- Centro Tecnológico de La Carne de Galicia, Rúa Galicia Nº 4, Parque Tecnológico de Galicia, San Cibrao Das Viñas, 32900, Ourense, Spain
| | - J A Fernández
- CRETUS Institute, Department of Functional Biology, Ecology Unit, University of Santiago de Compostela, Santiago de Compostela, 15872, A Coruña, Spain
| | - J R Aboal
- CRETUS Institute, Department of Functional Biology, Ecology Unit, University of Santiago de Compostela, Santiago de Compostela, 15872, A Coruña, Spain
| |
Collapse
|
39
|
Abstract
Natural habitats are rapidly declining due to urbanisation, with a concomitant decline in biodiversity in highly urbanised areas. Yet thousands of different species have colonised urban environments. These organisms are exposed to novel urban conditions, which are sometimes beneficial, but most often challenging, such as increased ambient temperature, chemicals, noise and light pollution, dietary alterations and disturbance by humans. Given the fundamental role of physiological responses in coping with such conditions, certain physiological systems such as the redox system, metabolism and hormones are thought to specifically influence organisms' ability to persist and cope with urbanisation. However, these physiological systems often show mixed responses to urbanisation. Does this mean that some individuals, populations or species are resilient to the urban environmental challenges? Or is something missing from our analyses, leading us to erroneous conclusions regarding the impact of urbanisation? To understand the impact of urbanisation, I argue that a more integrated mechanistic and ecological approach is needed, along with experiments, in order to fully understand the physiological responses; without knowledge of their ecological and evolutionary context, physiological measures alone can be misinterpreted. Furthermore, we need to further investigate the causes of and capacity for individual plasticity in order to understand not only the impact of urbanisation, but also species resilience. I argue that abiotic and biotic urban factors can interact (e.g. pollution with micro- and macronutrients) to either constrain or relax individual physiological responses - and, thereby, plasticity - on a temporal and/or spatial scale, which can lead to erroneous conclusions regarding the impact of urbanisation.
Collapse
|
40
|
Liang X, Martyniuk CJ, Simmons DBD. Are we forgetting the "proteomics" in multi-omics ecotoxicology? Comp Biochem Physiol Part D Genomics Proteomics 2020; 36:100751. [PMID: 33142247 DOI: 10.1016/j.cbd.2020.100751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 07/19/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Proteomics plays a significant role in discerning the effects of chemical exposures in animal taxa. Multi-omics applications have become more pervasive in toxicology, however questions remain about whether proteomics is being utilized by the community to its full potential - are we placing too much stock in transcriptomics and other omics approaches for developing adverse outcome pathways? Proteins are more relevant than transcripts because they are direct mediators of the resulting phenotype. There is also rarely perfect stoichiometry between transcript and protein abundance and transcript abundance may not accurately predict physiologic response. Proteins direct all levels of phenotype: structural proteins dictate physical form, enzymes catalyze biochemical reactions, and proteins act as signaling proteins, antibodies, transporters, ion pumps, and transcription factors to control gene expression. Molecular initiating events (MIEs) of AOPs predominantly occur at the level of the protein (e.g. ligand-receptor binding) and proteomics can elucidate novel MIEs and mapping KEs in AOPs. This critical review highlights the need for proteomics in multi-omics studies in environmental toxicology and outlines steps required for inclusion and wider acceptance in chemical risk assessment. We also present case studies of multi-omics approaches that utilize proteomics and discuss some of the challenges and opportunities for proteomics in comparative ecotoxicology. Our intention is not to minimize the importance of other omics technologies, as each has strengths and limitations, but rather to encourage researchers to consider proteomics-based methods in multi-omics studies and AOP development.
Collapse
Affiliation(s)
- Xuefang Liang
- Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Christopher J Martyniuk
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, UF Genetics Institute, University of Florida, Gainesville, FL, USA
| | | |
Collapse
|
41
|
Faugere J, Gouveia D, Ayciriex S, Chaumot A, Almunia C, François A, Armengaud J, Lemoine J, Geffard O, Degli-Esposti D, Salvador A. High-multiplexed monitoring of protein biomarkers in the sentinel Gammarus fossarum by targeted scout-MRM assay, a new vision for ecotoxicoproteomics. J Proteomics 2020; 226:103901. [PMID: 32668291 DOI: 10.1016/j.jprot.2020.103901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/02/2020] [Accepted: 07/08/2020] [Indexed: 11/23/2022]
Abstract
Ecotoxicoproteomics employs mass spectrometry-based approaches centered on proteins of sentinel organisms to assess for instance, chemical toxicity in fresh water. In this study, we combined proteogenomics experiments and a novel targeted proteomics approach free from retention time scheduling called Scout-MRM. This methodology will enable the measurement of simultaneously changes in the relative abundance of multiple proteins involved in key physiological processes and potentially impacted by contaminants in the freshwater sentinel Gammarus fossarum. The development and validation of the assay were performed to target 157 protein biomarkers of this non-model organism. We carefully chose and validated the transitions to monitor using conventional parameters (linearity, repeatability, LOD, LOQ). Finally, the potential of the methodology is illustrated by measuring 277-peptide-plex assay (831 transitions) in sentinel animals exposed in natura to different agricultural sites potentially exposed to pesticide contamination. Multivariate data analyses highlighted the modulation of several key proteins involved in feeding and molting. This multiplex-targeted proteomics assay paves the way for the discovery and the use of a large panel of novel protein biomarkers in emergent ecotoxicological models for environmental monitoring in the future. BIOLOGICAL SIGNIFICANCE: The study contributed to the development of Scout-MRM for the high-throughput quantitation of a large panel of proteins in the Gammarus fossarum freshwater sentinel. Increasing the number of markers in ecotoxicoproteomics is of most interest to assess the impact of pollutants in freshwater organisms. The development and validation of the assay enabled the monitoring of a large panel of reporter peptides of exposed gammarids. To illustrate the applicability of the methodology, animals from different agricultural sites were analysed. The application of the assay highlighted the modulation of some biomarker proteins involved in key physiological pathways, such as molting, feeding and general stress response. Increasing multiplexing capabilities and field test will provide the development of diagnostic protein biomarkers for emergent ecotoxicological models in future environmental biomonitoring programs.
Collapse
|
42
|
Leprêtre M, Palos-Ladeiro M, Faugere J, Almunia C, Lemoine J, Armengaud J, Geffard A, Salvador A. From shotgun to targeted proteomics: rapid Scout-MRM assay development for monitoring potential immunomarkers in Dreissena polymorpha. Anal Bioanal Chem 2020; 412:7333-7347. [DOI: 10.1007/s00216-020-02868-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
|
43
|
Cogne Y, Gouveia D, Chaumot A, Degli-Esposti D, Geffard O, Pible O, Almunia C, Armengaud J. Proteogenomics-Guided Evaluation of RNA-Seq Assembly and Protein Database Construction for Emergent Model Organisms. Proteomics 2020; 20:e1900261. [PMID: 32249536 DOI: 10.1002/pmic.201900261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/24/2020] [Indexed: 11/10/2022]
Abstract
Proteogenomics is gaining momentum as, today, genomics, transcriptomics, and proteomics can be readily performed on any new species. This approach allows key alterations to molecular pathways to be identified when comparing conditions. For animals and plants, RNA-seq-informed proteomics is the most popular means of interpreting tandem mass spectrometry spectra acquired for species for which the genome has not yet been sequenced. It relies on high-performance de novo RNA-seq assembly and optimized translation strategies. Here, several pre-treatments for Illumina RNA-seq reads before assembly are explored to translate the resulting contigs into useful polypeptide sequences. Experimental transcriptomics and proteomics datasets acquired for individual Gammarus fossarum freshwater crustaceans are used, the most relevant procedure is defined by the ratio of MS/MS spectra assigned to peptide sequences. Removing reads with a mean quality score of less than 17-which represents a single probable nucleotide error on 150-bp reads-prior to assembly, increases the proteomics outcome. The best translation using Transdecoder is achieved with a minimal open reading frame length of 50 amino acids and systematic selection of ORFs longer than 900 nucleotides. Using these parameters, transcriptome assembly and translation informed by proteomics pave the way to further improvements in proteogenomics.
Collapse
Affiliation(s)
- Yannick Cogne
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Duarte Gouveia
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Arnaud Chaumot
- INRAE, UR RiverLY Laboratoire d'écotoxicologie, Centre de Lyon-Villeurbanne, Villeurbanne, F-69625, France
| | - Davide Degli-Esposti
- INRAE, UR RiverLY Laboratoire d'écotoxicologie, Centre de Lyon-Villeurbanne, Villeurbanne, F-69625, France
| | - Olivier Geffard
- INRAE, UR RiverLY Laboratoire d'écotoxicologie, Centre de Lyon-Villeurbanne, Villeurbanne, F-69625, France
| | - Olivier Pible
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Christine Almunia
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| |
Collapse
|
44
|
Leprêtre M, Almunia C, Armengaud J, Le Guernic A, Salvador A, Geffard A, Palos-Ladeiro M. Identification of immune-related proteins of Dreissena polymorpha hemocytes and plasma involved in host-microbe interactions by differential proteomics. Sci Rep 2020; 10:6226. [PMID: 32277127 PMCID: PMC7148315 DOI: 10.1038/s41598-020-63321-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/27/2020] [Indexed: 12/04/2022] Open
Abstract
Biological responses of zebra mussel Dreissena polymorpha are investigated to assess the impact of contaminants on aquatic organisms and ecosystems. In addition to concentrate chemical contaminants in their tissues, zebra mussels accumulate several microorganisms such as viruses, protozoa and bacteria. In order to understand the molecular mechanisms involved in the defence against microorganisms this study aims at identifying immune proteins from D. polymorpha hemolymph involved in defence against protozoa and viruses. For this purpose, hemolymph were exposed ex vivo to Cryptosporidium parvum and RNA poly I:C. Differential proteomics on both hemocytes and plasma revealed immune proteins modulated under exposures. Different patterns of response were observed after C. parvum and RNA poly I:C exposures. The number of modulated proteins per hemolymphatic compartments suggest that C. parvum is managed in cells while RNA poly I:C is managed in plasma after 4 h exposure. BLAST annotation and GO terms enrichment analysis revealed further characteristics of immune mechanisms. Results showed that many proteins involved in the recognition and destruction of microorganisms were modulated in both exposure conditions, while proteins related to phagocytosis and apoptosis were exclusively modulated by C. parvum. This differential proteomic analysis highlights in zebra mussels modulated proteins involved in the response to microorganisms, which reflect a broad range of immune mechanisms such as recognition, internalization and destruction of microorganisms. This study paves the way for the identification of new markers of immune processes that can be used to assess the impact of both chemical and biological contaminations on the health status of aquatic organisms.
Collapse
Affiliation(s)
- Maxime Leprêtre
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, BP 1039, 51687, Reims, CEDEX, France
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, F-69100, Villeurbanne, France
| | - Christine Almunia
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Antoine Le Guernic
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, BP 1039, 51687, Reims, CEDEX, France
| | - Arnaud Salvador
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, F-69100, Villeurbanne, France
| | - Alain Geffard
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, BP 1039, 51687, Reims, CEDEX, France
| | - Mélissa Palos-Ladeiro
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, BP 1039, 51687, Reims, CEDEX, France.
| |
Collapse
|
45
|
Cuvillier-Hot V, Lenoir A. Invertebrates facing environmental contamination by endocrine disruptors: Novel evidences and recent insights. Mol Cell Endocrinol 2020; 504:110712. [PMID: 31962147 DOI: 10.1016/j.mce.2020.110712] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 02/08/2023]
Abstract
The crisis of biodiversity we currently experience raises the question of the impact of anthropogenic chemicals on wild life health. Endocrine disruptors are notably incriminated because of their possible effects on development and reproduction, including at very low doses. As commonly recorded in the field, the burden they impose on wild species also concerns invertebrates, with possible specificities linked with the specific physiology of these animals. A better understanding of chemically-mediated endocrine disruption in these species has clearly gained from knowledge accumulated on vertebrate models. But the molecular pathways specific to invertebrates also need to be reckoned, which implies dedicated research efforts to decipher their basic functioning in order to be able to assess its possible disruption. The recent rising of omics technologies opens the way to an intensification of these efforts on both aspects, even in species almost uninvestigated so far.
Collapse
Affiliation(s)
| | - Alain Lenoir
- IRBI, Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS, Faculté des Sciences, Parc de Grandmont, Université de Tours, Tours, France
| |
Collapse
|
46
|
Breitwieser M, Barbarin M, Plumejeaud-Perreau C, Dubillot E, Guyot T, Huet V, Churlaud C, Coulombier T, Brenon I, Fichet D, Imbert N, Thomas H. Biomonitoring of Mimachlamys varia transplanted to areas impacted by human activities (La Rochelle Marina, France). Chemosphere 2020; 243:125199. [PMID: 31734599 DOI: 10.1016/j.chemosphere.2019.125199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
The development of human activities on French Atlantic coastlines (La Rochelle) lead to chronic pollution of the environment by organic (pesticides, hydrocarbons, agrochemicals) and inorganic (heavy metals) contaminants. These past years, several regulations have been implemented to preserve coastal environments. The purpose of this study was to perform biomonitoring of bivalve species using an outdoor caging technique. The goal of our work was to assess the impact of harbour's trace elements on the state of health of the marine bivalve Mimachlamys varia. First, various molecular defence biomarkers were measured: SOD (oxidative stress), GST (detoxification process), MDA (lipid peroxidation), and Laccase (immune reaction). Thus, in April 2016, scallops were collected at three caging sites, which differ by their levels of pollution, after transplantation into port areas (fairing, rainwater) and a control site (marsh). Bivalve samples were taken at three sampling dates (D0, D07, D21). Biomarker assays were performed in the digestive glands due to their bioaccumulation properties. The second aim was to explore the impacts of inorganic pollutants placed in environmental harbour's sites. After 21 days, the biomarker response of transplanted bivalves revealed a SOD decrease, Laccase and GST stimulations, higher concentrations in Cu, Fe, As, Co, Mn, Zn, Sn and no significant variation of MDA concentration. Our ecological relevance of biomarker approaches opens interesting perspectives to identify M. varia such as a pertinent marine sentinel species. The several selected biomarkers determined could confirm their ability to appraise the water quality of hydro-systems located in French coastlines, such as port areas.
Collapse
Affiliation(s)
- Marine Breitwieser
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Marine Barbarin
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Christine Plumejeaud-Perreau
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Emmanuel Dubillot
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Thierry Guyot
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Valérie Huet
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Carine Churlaud
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France
| | - Thibaut Coulombier
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Isabelle Brenon
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Denis Fichet
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Nathalie Imbert
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| | - Hélène Thomas
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 rue Olympe de Gouges, F-17042, La Rochelle Cedex 01, France.
| |
Collapse
|
47
|
Borcier E, Artigaud S, Gaillard JC, Armengaud J, Charrier G, Couteau J, Receveur J, Ouddane B, Diop M, Amara R, Laroche J, Pichereau V. Coupling caging and proteomics on the European flounder (Platichthys flesus) to assess the estuarine water quality at micro scale. Sci Total Environ 2019; 695:133760. [PMID: 31421344 DOI: 10.1016/j.scitotenv.2019.133760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/09/2019] [Accepted: 08/02/2019] [Indexed: 06/10/2023]
Abstract
Estuaries are important areas highly vulnerable to anthropogenic pollutions. Therefore, the assessment of estuarine water quality is a major ecological issue. In this study, we sampled juveniles of the European flounder in the "pristine" Canche estuary, and caged them in Canche and in two polluted sites of the Seine estuary, Rouen and Fosse Nord. After one month, the metal and organic pollutants in these sites were assessed, and we evaluated several phenotypic indicators (condition index, RNA/DNA ratios and genotoxicity), and extracted the proteins in fish livers for analysis using a shotgun proteomics approach. The results showed strong modifications in the fish caged in both sites of the Seine estuary, as compared to those caged in Canche. In particular, many proteins involved in phase I and phase II detoxification reactions were accumulated in the liver of fish caged in the site showing the highest pollution, Rouen. In addition, we observed a general disruption of metabolism, in particular an increase in lipid synthesis and carbohydrate degradation in Rouen, and a decrease in the abundance of proteins associated to translational activity in Fosse Nord. At both sites, several stress proteins were decreased. The proteomic impact of the encagement by itself was also evaluated, by comparing the liver proteome of fish caged in Canche to that of fish stayed in natura during the same time. The results showed proteomic signatures of exposure to stressful conditions (particularly heat stress), most probably related to the micro-habitat in which the cages were placed. In conclusion, the caging technique is of great interest for ecotoxicological assessment of estuarine waters, but should consider that the results are representative of the micro-habitat around the cages, which does not necessarily represent the overall heterogeneity of the estuarine environment.
Collapse
Affiliation(s)
- Elodie Borcier
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | | | - Jean-Charles Gaillard
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France
| | | | | | | | | | | | | | - Jean Laroche
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | | |
Collapse
|
48
|
Kwan YH, Zhang D, Mestre NC, Wong WC, Wang X, Lu B, Wang C, Qian PY, Sun J. Comparative Proteomics on Deep-Sea Amphipods after in Situ Copper Exposure. Environ Sci Technol 2019; 53:13981-13991. [PMID: 31638389 DOI: 10.1021/acs.est.9b04503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interest in deep-sea mining increased along with the environmental concerns of these activities to the deep-sea fauna. The discovery of optimal biomarkers of deep-sea mining activities in deep-sea species is a crucial step toward the supply of important ecological information for environmental impact assessment. In this study, an in situ copper exposure experiment was performed on deep-sea scavenging amphipods. Abyssorchomene distinctus individuals were selected among all the exposed amphipods for molecular characterization. Copper concentration within the gut was assessed, followed by a tandem mass tag-based coupled with two-dimensional liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) applied to identify and quantify the protein expression changes after 48 h of exposure. 2937 proteins were identified and annotated, and 1918 proteins among all identified proteins were assigned by at least two nonambiguous peptides. The screening process was performed based on the differences in protein abundance and the specific correlation between the proteins and copper in previous studies. These differentially produced proteins include Na+/K+ ATPase, cuticle, chitinase, and proteins with unknown function. Their abundances showed correlation with copper and had high sensitivity to indicate the copper level, being here proposed as biomarker candidates for deep-sea mining activities in the future. This is a key step in the development of environmental impact assessment of deep-sea mining activities integrating ecotoxicological data.
Collapse
Affiliation(s)
- Yick Hang Kwan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| | - Dongsheng Zhang
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Nélia C Mestre
- CIMA - Centro de Investigação Marinha e Ambiental , Universidade do Algarve , Campus de Gambelas, 8005-139 Faro , Portugal
| | - Wai Chuen Wong
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| | - Xiaogu Wang
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Bo Lu
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Chunsheng Wang
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| | - Jin Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| |
Collapse
|
49
|
Gouveia D, Cogne Y, Gaillard JC, Almunia C, Pible O, François A, Degli-Esposti D, Geffard O, Chaumot A, Armengaud J. Shotgun proteomics datasets acquired on Gammarus pulex animals sampled from the wild. Data Brief 2019; 27:104650. [PMID: 31687451 PMCID: PMC6820120 DOI: 10.1016/j.dib.2019.104650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/27/2019] [Accepted: 10/03/2019] [Indexed: 11/10/2022] Open
Abstract
This data article associated with the manuscript “Comparative proteomics in the wild: accounting for intrapopulation variability improves describing proteome response in a Gammarus pulex field population exposed to cadmium” refers to the shotgun proteomics analysis performed on 40 Gammarus pulex animals sampled from the wild. Proteins were extracted, digested with trypsin, and the resulting peptides were identified by tandem mass spectrometry. Here, we present the list of proteins from males and the list of proteins from females that are differentially detected between the Brameloup and the Pollon populations. Data are available via ProteomeXchange with identifiers PXD013656 and PXD013712, respectively.
Collapse
Affiliation(s)
- Duarte Gouveia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France
| | - Yannick Cogne
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France
| | - Christine Almunia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France
| | - Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France
| | - Adeline François
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625 Villeurbanne, France
| | - Davide Degli-Esposti
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625 Villeurbanne, France
| | - Olivier Geffard
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625 Villeurbanne, France
| | - Arnaud Chaumot
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625 Villeurbanne, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France
| |
Collapse
|
50
|
Cogne Y, Degli-Esposti D, Pible O, Gouveia D, François A, Bouchez O, Eché C, Ford A, Geffard O, Armengaud J, Chaumot A, Almunia C. De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups. Sci Data 2019; 6:184. [PMID: 31562330 PMCID: PMC6764967 DOI: 10.1038/s41597-019-0192-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/13/2019] [Indexed: 11/17/2022] Open
Abstract
Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species. Measurement(s) | transcription profiling assay | Technology Type(s) | RNA sequencing | Factor Type(s) | sex • species | Sample Characteristic - Organism | Gammarus • Echinogammarus | Sample Characteristic - Environment | habitat |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9777905
Collapse
Affiliation(s)
- Yannick Cogne
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Davide Degli-Esposti
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Duarte Gouveia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Adeline François
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, F-31320, Castanet-Tolosan, France
| | - Camille Eché
- GeT-PlaGe, Genotoul, INRA Auzeville, F-31320, Castanet-Tolosan, France
| | - Alex Ford
- School of Biological Sciences, Institute of Marine Sciences Laboratories, P04 9LY, Portsmouth, United Kingdom
| | - Olivier Geffard
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France.
| | - Arnaud Chaumot
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Christine Almunia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| |
Collapse
|