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Beale DJ, Nguyen TV, Bose U, Shah R, Nelis JLD, Stockwell S, Broadbent JA, Nilsson S, Rane R, Court L, Lettoof DC, Pandey G, Walsh TK, Shaw S, Llinas J, Limpus D, Limpus C, Braun C, Baddiley B, Vardy S. Metabolic disruptions and impaired reproductive fitness in wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated per- and polyfluoroalkyl substances (PFAS). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171743. [PMID: 38494020 DOI: 10.1016/j.scitotenv.2024.171743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Per- and poly-fluoroalkyl substances (PFAS) pose a threat to organisms and ecosystems due to their persistent nature. Ecotoxicology endpoints used in regulatory guidelines may not reflect multiple, low-level but persistent stressors. This study examines the biological effects of PFAS on Eastern short-necked turtles in Queensland, Australia. In this study, blood samples were collected and analysed for PFAS, hormone levels, and functional omics endpoints. High levels of PFAS were found in turtles at the impacted site, with PFOS being the dominant constituent. The PFAS profiles of males and females differed, with males having higher PFAS concentrations. Hormone concentrations differed between impacted and reference sites in male turtles, with elevated testosterone and corticosterone indicative of stress. Further, energy utilisation, nucleotide synthesis, nitrogen metabolism, and amino acid synthesis were altered in both male and female turtles from PFAS-impacted sites. Both sexes show similar metabolic responses to environmental stressors from the PFAS-contaminated site, which may adversely affect their reproductive fitness. Purine metabolism, caffeine metabolism, and ferroptosis pathway changes in turtles can cause gout, cell death, and overall health problems. Further, the study showed that prolonged exposure to elevated PFAS levels in the wild could compromise turtle reproductive fitness by disrupting reproductive steroids and metabolic pathways.
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Affiliation(s)
- David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Qld 4102, Australia.
| | - Thao V Nguyen
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Qld 4102, Australia
| | - Utpal Bose
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Qld 4067, Australia
| | - Rohan Shah
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Qld 4102, Australia; School of Health and Biomedical Sciences, STEM College, RMIT University, Bundoora West, Vic 3083, Australia; Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn Vic 3122, Australia
| | - Joost Laurus Dinant Nelis
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Qld 4067, Australia
| | - Sally Stockwell
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Qld 4067, Australia
| | - James A Broadbent
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Qld 4067, Australia
| | - Sandra Nilsson
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, Qld 4102, Australia
| | - Rahul Rane
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Parkville, Vic 3052, Australia
| | - Leon Court
- Environment, Commonwealth Scientific and Industrial Research Organisation, CSIRO Black Mountain Laboratories, Acton, ACT 2602, Australia
| | - Damian C Lettoof
- Environment, Commonwealth Scientific and Industrial Research Organisation, CSIRO Centre for Environment and Life Sciences, Floreat, WA 6014, Australia
| | - Gunjan Pandey
- Environment, Commonwealth Scientific and Industrial Research Organisation, CSIRO Black Mountain Laboratories, Acton, ACT 2602, Australia
| | - Thomas K Walsh
- Environment, Commonwealth Scientific and Industrial Research Organisation, CSIRO Black Mountain Laboratories, Acton, ACT 2602, Australia
| | - Stephanie Shaw
- Wildlife and Threatened Species Operations, Department of Environment and Science, Queensland Government, Moggill, Qld 4070, Australia
| | - Josh Llinas
- The Unusual Pet Vets Jindalee, Veterinarian, Jindalee, Qld 4074, Australia
| | - Duncan Limpus
- Aquatic Threatened Species, Wildlife and Threatened Species Operations, Department of Environment and Science, Queensland Government, Dutton Park, Qld 4102, Australia
| | - Colin Limpus
- Aquatic Threatened Species, Wildlife and Threatened Species Operations, Department of Environment and Science, Queensland Government, Dutton Park, Qld 4102, Australia
| | - Christoph Braun
- Water Quality and Investigations, Science and Technology Division, Department of Environment and Science, Queensland Government, Dutton Park, Qld 4102, Australia
| | - Brenda Baddiley
- Water Quality and Investigations, Science and Technology Division, Department of Environment and Science, Queensland Government, Dutton Park, Qld 4102, Australia
| | - Suzanne Vardy
- Water Quality and Investigations, Science and Technology Division, Department of Environment and Science, Queensland Government, Dutton Park, Qld 4102, Australia
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2
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de Souza HM, de Almeida RF, Lopes AP, Hauser-Davis RA. Review: Fish bile, a highly versatile biomarker for different environmental pollutants. Comp Biochem Physiol C Toxicol Pharmacol 2024; 278:109845. [PMID: 38280442 DOI: 10.1016/j.cbpc.2024.109845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/05/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
Ecotoxicological assessments encompass a broad spectrum of biochemical endpoints and ecological factors, allowing for comprehensive assessments concerning pollutant exposure levels and their effects on both fish populations and surrounding ecosystems. While these evaluations offer invaluable insights into the overall health and dynamics of aquatic environments, they often provide an integrated perspective, making it challenging to pinpoint the precise sources and individual-level responses to environmental contaminants. In contrast, biliary pollutant excretion assessments represent a focused approach aimed at understanding how fish at the individual level respond to environmental stressors. In this sense, the analysis of pollutant profiles in fish bile not only serves as a valuable exposure indicator, but also provides critical information concerning the uptake, metabolism, and elimination of specific contaminants. Therefore, by investigating unique and dynamic fish responses to various pollutants, biliary assessments can contribute significantly to the refinement of ecotoxicological studies. This review aims to discuss the multifaceted utility of bile as a potent biomarker for various environmental pollutants in fish in targeted monitoring strategies, such as polycyclic aromatic hydrocarbons, metals, pesticides, pharmaceuticals, estrogenic compounds, resin acids, hepatotoxins and per- and polyfluorinated substances. The main caveats of this type of assessment are also discussed, as well as future directions of fish bile studies.
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Affiliation(s)
- Heloise Martins de Souza
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil; Programa de Pós-Graduação em Biodiversidade e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Regina Fonsêca de Almeida
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ CEP 22453-900, Brazil
| | - Amanda Pontes Lopes
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil; Programa de Pós-Graduação em Biodiversidade e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Rachel Ann Hauser-Davis
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil.
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3
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Henke AN, Chilukuri S, Langan LM, Brooks BW. Reporting and reproducibility: Proteomics of fish models in environmental toxicology and ecotoxicology. THE SCIENCE OF THE TOTAL ENVIRONMENT 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] [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.
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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.
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4
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Li Y, Lyu J, Wang Y, Ye M, Wang H. Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions. Chem Res Toxicol 2024; 37:1-15. [PMID: 38146056 DOI: 10.1021/acs.chemrestox.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinity-driven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, Beijing, 102206, China
| | - Hailin Wang
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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5
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Srivastava N, Shiburaj S, Khare SK. Pan-genomic comparison of a potential solvent-tolerant alkaline protease-producing Exiguobacterium sp. TBG-PICH-001 isolated from a marine habitat. 3 Biotech 2023; 13:371. [PMID: 37854939 PMCID: PMC10579205 DOI: 10.1007/s13205-023-03796-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023] Open
Abstract
The identification and applicability of bacteria are inconclusive until comprehended with genomic repositories. Our isolate, Exiguobacterium sp. TBG-PICH-001 exhibited excellent halo- and organic solvent tolerance with simultaneous production of alkaline protease/s (0.512 IU/mL). The crude protease (1 IU) showed a 43.57% degradation of whey protein. The bulk proteins in the whey were hydrolyzed to smaller peptides which were evident in the SDS-PAGE profile. With such characteristics, the isolate became interesting for its genomic studies. The TBG-PICH-001 genome was found to be 3.14 Mb in size with 17 contigs and 47.33% GC content. The genome showed 3176 coding genes, and 2699 genes were characterized for their functionality. The Next-Generation-Sequencing of the genome identified only the isolate's genus; hence we attempted to delineate its species position. The genomes of the isolate and other representative Exiguobacterium spp. were compared based on orthologous genes (Orthovenn2 server). A pan-genomic analysis revealed the match of TBG-PICH-001 with 15 uncharacterized Exiguobacterium genomes at the species level. All these collectively matched with Exiguobacterium indicum, and the results were reconfirmed through phylogenetic studies. Further, the Exiguobacterium indicum genomes were engaged for homology studies rendering 11 classes of protease genes. Two putative proteases (Zinc metalloprotease and Serine protease) obtained from homology were checked for PCR amplification using genomic DNA of TBG-PICH-001 and other Exiguobacterium genomes. The results showed amplification only in the Exiguobacterium indicum genome. These protease genes, after sequencing, were matched with the TBG-PICH-001 genome. Their presence in its whole genome experimentally validated the study. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03796-5.
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Affiliation(s)
- Nitin Srivastava
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016 India
| | - Sugathan Shiburaj
- Department of Botany, University of Kerala, Palayam, Thiruvananthapuram, Kerala 695034 India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016 India
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6
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Kanerva M, Tue NM, Kunisue T, Vuori KA, Iwata H. Multi-level assessment of the origin, feeding area and organohalogen contamination on salmon from the Baltic Sea. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115424. [PMID: 37672939 DOI: 10.1016/j.ecoenv.2023.115424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/04/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023]
Abstract
The Atlantic salmon (Salmo salar) population in the Baltic Sea consists of wild and hatchery-reared fish that have been released into the sea to support salmon stocks. During feeding migration, salmon migrate to different parts of the Baltic Sea and are exposed to various biotic and abiotic stressors, such as organohalogen compounds (OHCs). The effects of salmon origin (wild or hatchery-reared), feeding area (Baltic Main Basin, Bothnian Sea, and Gulf of Finland), and OHC concentration on the differences in hepatic proteome of salmon were investigated. Multi-level analysis of the OHC concentration, transcriptome, proteome, and oxidative stress biomarkers measured from the same salmon individuals were performed to find the key variables (origin, feeding area, OHC concentrations, and oxidative stress) that best account for the differences in the transcriptome and proteome between the salmon groups. When comparing wild and hatchery-reared salmon, differences were found in xenobiotic and amino acid metabolism-related pathways. When comparing salmon from different feeding areas, the amino acid and carbohydrate metabolic pathways were notably different. Several proteins found in these pathways are correlated with the concentrations of polychlorinated biphenyls (PCBs). The multi-level analysis also revealed amino acid metabolic pathways in connection with PCBs and oxidative stress variables related to glutathione metabolism. Other pathways found in the multi-level analysis included genetic information processes related to ribosomes, signaling and cellular processes related to the cytoskeleton, and the immune system, which were connected mainly to the concentrations of Polychlorinated biphenyls and Dichlorodiphenyltrichloroethane and their metabolites. These results suggest that the hepatic proteome of salmon in the Baltic Sea, together with the transcriptome, is more affected by the OHC concentrations and oxidative stress of the feeding area than the origin of the salmon.
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Affiliation(s)
- Mirella Kanerva
- CMES, Lab. of Environmental Toxicology, Ehime University, Bunkyo-cho 2-5, 790-8577, Matsuyama, Japan.
| | - Nguyen Minh Tue
- CMES, Lab. of Environmental Chemistry, Ehime University, Bunkyo-cho 2-5, 790-8577, Matsuyama, Japan
| | - Tatsuya Kunisue
- CMES, Lab. of Environmental Chemistry, Ehime University, Bunkyo-cho 2-5, 790-8577, Matsuyama, Japan
| | - Kristiina Am Vuori
- Department of Equine and Small Animal Medicine, University of Helsinki, P.O. Box 57, Koetilantie 2, FI-00014, Helsinki, Finland
| | - Hisato Iwata
- CMES, Lab. of Environmental Toxicology, Ehime University, Bunkyo-cho 2-5, 790-8577, Matsuyama, Japan.
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7
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Leprêtre M, Degli Esposti D, Sugier K, Espeyte A, Gaillard JC, Delorme N, Duflot A, Bonnard I, Coulaud R, Boulangé-Lecomte C, Xuereb B, Palos Ladeiro M, Geffard A, Geffard O, Armengaud J, Chaumot A. Organ-oriented proteogenomics functional atlas of three aquatic invertebrate sentinel species. Sci Data 2023; 10:643. [PMID: 37735452 PMCID: PMC10514328 DOI: 10.1038/s41597-023-02545-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
Proteogenomic methodologies have enabled the identification of protein sequences in wild species without annotated genomes, shedding light on molecular mechanisms affected by pollution. However, proteomic resources for sentinel species are limited, and organ-level investigations are necessary to expand our understanding of their molecular biology. This study presents proteomic resources obtained from proteogenomic analyses of key organs (hepatopancreas, gills, hemolymph) from three established aquatic sentinel invertebrate species of interest in ecotoxicological/ecological research and environmental monitoring: Gammarus fossarum, Dreissena polymorpha, and Palaemon serratus. Proteogenomic analyses identified thousands of proteins for each species, with over 90% of them being annotated to putative function. Functional analysis validated the relevance of the proteomic atlases by revealing similarities in functional annotation of catalogues of proteins across analogous organs in the three species, while deep contrasts between functional profiles are delimited across different organs in the same organism. These organ-level proteomic atlases are crucial for future research on these sentinel animals, aiding in the evaluation of aquatic environmental risks and providing a valuable resource for ecotoxicological studies.
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Affiliation(s)
- Maxime Leprêtre
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, 5 rue de la Doua, F-69625, Villeurbanne, France.
| | - Davide Degli Esposti
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, 5 rue de la Doua, F-69625, Villeurbanne, France
| | - Kevin Sugier
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, 5 rue de la Doua, F-69625, Villeurbanne, France
| | - Anabelle Espeyte
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, 5 rue de la Doua, F-69625, Villeurbanne, France
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
| | - Nicolas Delorme
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, 5 rue de la Doua, F-69625, Villeurbanne, France
| | - Aurélie Duflot
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600, Le Havre, 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
| | - Romain Coulaud
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600, Le Havre, France
| | - Céline Boulangé-Lecomte
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600, Le Havre, France
| | - Benoît Xuereb
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600, Le Havre, 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
| | - 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
| | - Olivier Geffard
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, 5 rue de la Doua, F-69625, Villeurbanne, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, 5 rue de la Doua, F-69625, Villeurbanne, France.
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8
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Morin S, Artigas J. Twenty Years of Research in Ecosystem Functions in Aquatic Microbial Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1867-1888. [PMID: 37401851 DOI: 10.1002/etc.5708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/20/2022] [Accepted: 06/27/2023] [Indexed: 07/05/2023]
Abstract
One of the major threats to freshwater biodiversity is water pollution including excessive loads of nutrients, pesticides, industrial chemicals, and/or emerging contaminants. The widespread use of organic pesticides for agricultural and nonagricultural (industry, gardening, etc.) purposes has resulted in the presence of their residues in various environments, including surface waters. However, the contribution of pesticides to the deterioration of freshwater ecosystems (i.e., biodiversity decline and ecosystem functions impairment) remains uncertain. Once in the aquatic environment, pesticides and their metabolites can interact with microbial communities, causing undesirable effects. The existing legislation on ecological quality assessment of water bodies in Europe is based on water chemical quality and biological indicator species (Water Framework Directive, Pesticides Directive), while biological functions are not yet included in monitoring programs. In the present literature review, we analyze 20 years (2000-2020) of research on ecological functions provided by microorganisms in aquatic ecosystems. We describe the set of ecosystem functions investigated in these studies and the range of endpoints used to establish causal relationships between pesticide exposure and microbial responses. We focus on studies addressing the effects of pesticides at environmentally realistic concentrations and at the microbial community level to inform the ecological relevance of the ecotoxicological assessment. Our literature review highlights that most studies were performed using benthic freshwater organisms and that autotrophic and heterotrophic communities are most often studied separately, usually testing the pesticides that target the main microbial component (i.e., herbicides for autotrophs and fungicides for heterotrophs). Overall, most studies demonstrate deleterious impacts on the functions studied, but our review points to the following shortcomings: (1) the nonsystematic analysis of microbial functions supporting aquatic ecosystems functioning, (2) the study of ecosystem functions (i.e., nutrient cycling) via proxies (i.e., potential extracellular enzymatic activity measurements) which are sometimes disconnected from the current ecosystem functions, and (3) the lack of consideration of chronic exposures to assess the impact of, adaptations to, or recovery of aquatic microbial communities from pesticides. Environ Toxicol Chem 2023;42:1867-1888. © 2023 SETAC.
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Affiliation(s)
| | - Joan Artigas
- Laboratoire Microorganismes: Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
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9
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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 2023; 12:923. [PMID: 37508354 PMCID: PMC10376755 DOI: 10.3390/biology12070923] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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.
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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
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Bertucci A. Symbiotoxicity: The Ability of Environmental Stressors to Damage Healthy Microbiome Structure and Interactions with the Host. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:979-981. [PMID: 36825733 DOI: 10.1002/etc.5592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/13/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Anthony Bertucci
- Ifremer, CCEM Contamination Chimique des Écosystèmes Marins, Nantes, France
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11
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Gouin N, Notte AM, Kolok AS, Bertin A. Pesticide exposure affects DNA methylation patterns in natural populations of a mayfly. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161096. [PMID: 36572299 DOI: 10.1016/j.scitotenv.2022.161096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Chemical pollutants derived from agricultural activities represent a major threat to freshwater biota. Despite growing evidence involving epigenetic processes, such as DNA methylation, in response to pesticide contamination in agroecosystems, research on wild populations of non-model species remains scarce, particularly for endemic freshwater arthropods. Using the MethylRAD method, this study investigates whether exposure to pesticide contamination in natural populations of the endemic mayfly A. torrens produces genome wide changes in levels of DNA methylation. From a total of 1,377,147 MethylRAD markers produced from 285 specimens collected at 30 different study sites along the Limarí watershed of north-central Chile, six showed significant differential methylation between populations exposed and unexposed to pesticides. In all cases the effect of pesticides was positive, independent and stronger than the effects detected for other spatial and environmental factors. Only one candidate marker appeared correlated significantly with additional variables, nitrate and calcium levels, which also reflects the impact of agrichemicals and could additionally suggest, to a lower extent, antagonistic effects of mineral salts concentration for this specific marker. These results suggest that the effect of pesticide exposure on methylation levels is apparent at these six MethylRAD markers in A. torrens populations. Such data is challenging to obtain in natural populations and is, for the most part, lacking in ecotoxicological studies. Our study shows that DNA methylation processes are involved in the response to pesticide contamination in populations of the mayfly A. torrens in their natural habitat, and provides new evidence regarding the impact of pesticide contamination and agricultural activities on the endemic fauna of lotic ecosystems.
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Affiliation(s)
- Nicolas Gouin
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, Raúl Bitrán 1305, La Serena, Chile; Departamento de Biología, Universidad de La Serena, Raúl Bitrán 1305, La Serena, Chile; Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Raúl Bitrán 1305, La Serena, Chile.
| | - Ana-Maria Notte
- Programa de doctorado en Biología y Ecología Aplicada, Departamento de Biología, Universidad de La Serena, Raúl Bitrán 1305, La Serena, Chile
| | - Alan S Kolok
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844-3002, United States
| | - Angéline Bertin
- Departamento de Biología, Universidad de La Serena, Raúl Bitrán 1305, La Serena, Chile
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12
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Faugere J, Brunet TA, Clément Y, Espeyte A, Geffard O, Lemoine J, Chaumot A, Degli-Esposti D, Ayciriex S, Salvador A. Development of a multi-omics extraction method for ecotoxicology: investigation of the reproductive cycle of Gammarus fossarum. Talanta 2023; 253:123806. [PMID: 36113334 DOI: 10.1016/j.talanta.2022.123806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/24/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Omics study exemplified by proteomics, lipidomics or metabolomics, provides the opportunity to get insight of the molecular modifications occurring in living organisms in response to contaminants or in different physiological conditions. However, individual omics discloses only a single layer of information leading to a partial image of the biological complexity. Multiplication of samples preparation and processing can generate analytical variations resulting from several extractions and instrumental runs. To get all the -omics information at the proteins, metabolites and lipids level coming from a unique sample, a specific sample preparation must be optimized. In this study, we streamlined a biphasic extraction procedure based on a MTBE/Methanol mixture to provide the simultaneous extraction of polar (proteins, metabolites) and apolar compounds (lipids) for multi-omics analyses from a unique biological sample by a liquid chromatography (LC)/mass spectrometry (MS)/MS-based targeted approach. We applied the methodology for the study of female amphipod Gammarus fossarum during the reproductive cycle. Multivariate data analyses including Partial Least Squares Discriminant Analysis and multiple factor analysis were applied for the integration of the multi-omics data sets and highlighted molecular signatures, specific to the different stages.
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Affiliation(s)
- 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
| | - Thomas Alexandre Brunet
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Yohann Clément
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Anabelle Espeyte
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | - Jérôme Lemoine
- 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 Chaumot
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, 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.
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13
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Qiao R, Mortimer M, Richter J, Rani-Borges B, Yu Z, Heinlaan M, Lin S, Ivask A. Hazard of polystyrene micro-and nanospheres to selected aquatic and terrestrial organisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158560. [PMID: 36087672 DOI: 10.1016/j.scitotenv.2022.158560] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Plastics contamination in the environment is a major concern. Risk assessment of micro- and nanoplastics (MPL and NPL) poses significant challenges due to MPL and NPL heterogeneity regarding compositional polymers, particle sizes and morphologies in the environment. Yet, there exists considerable toxicological literature on commercial polystyrene (PS) micro- and nanospheres. Although such particles do not directly represent the environmental MPL and NPL, their toxicity data should be used to advance the hazard assessment of plastics. Here, toxicity data of PS micro- and nanospheres for microorganisms, aquatic and terrestrial invertebrates, fish, and higher plants was collected and analyzed. The evaluation of 294 papers revealed that aquatic invertebrates were the most studied organisms, nanosized PS was studied more often than microsized PS, acute exposures prevailed over chronic exposures, the toxicity of PS suspension additives was rarely addressed, and ∼40 % of data indicated no organismal effects of PS. Toxicity mechanisms were mainly studied in fish and nematode Caenorhabditis elegans, providing guidance for relevant studies in higher organisms. Future studies should focus on environmentally relevant plastics concentrations, wide range of organisms, co-exposures with other pollutants, and method development for plastics identification and quantification to fill the gap of bioaccumulation assessment of plastics.
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Affiliation(s)
- Ruxia Qiao
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Monika Mortimer
- Institute of Environmental and Health Sciences, College of Quality and Safety Engineering, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Jelizaveta Richter
- National Institute of Chemical Physics and Biophysics, Laboratory of Environmental Toxicology, Tallinn 12618, Estonia
| | - Bárbara Rani-Borges
- Institute of Science and Technology, São Paulo State University, UNESP, Alto da Boa Vista, Sorocaba, São Paulo 18087-180, Brazil; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Zhenyang Yu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Margit Heinlaan
- National Institute of Chemical Physics and Biophysics, Laboratory of Environmental Toxicology, Tallinn 12618, Estonia.
| | - Sijie Lin
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Angela Ivask
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia.
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Gruszecka-Kosowska A, Ampatzoglou A, Aguilera M. Integration of Omics Approaches Enhances the Impact of Scientific Research in Environmental Applications. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19148758. [PMID: 35886610 PMCID: PMC9317225 DOI: 10.3390/ijerph19148758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022]
Abstract
In the original article [...]
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Affiliation(s)
- Agnieszka Gruszecka-Kosowska
- Department of Environmental Protection, Faculty of Geology, Geophysics, and Environmental Protection, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Krakow, Poland
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada (UGR), 18071 Granada, Spain;
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada (UGR-INYTA), 18016 Granada, Spain
- Correspondence: (A.G.-K.); (M.A.)
| | - Antonis Ampatzoglou
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada (UGR), 18071 Granada, Spain;
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada (UGR-INYTA), 18016 Granada, Spain
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada (UGR), 18071 Granada, Spain;
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada (UGR-INYTA), 18016 Granada, Spain
- IBS—Instituto de Investigación Biosanitaria, 18012 Granada, Spain
- Correspondence: (A.G.-K.); (M.A.)
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15
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Khosrovyan A, Doria HB, Kahru A, Pfenninger M. Polyamide microplastic exposure elicits rapid, strong and genome-wide evolutionary response in the freshwater non-biting midge Chironomus riparius. CHEMOSPHERE 2022; 299:134452. [PMID: 35367228 DOI: 10.1016/j.chemosphere.2022.134452] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Susceptibility to hazardous materials and contamination is largely determined by genetic make-up and evolutionary history of affected organisms. Yet evolutionary adaptation and microevolutionary processes triggered by contaminants are rarely considered in ecotoxicology. Using an evolve and resequencing approach, we investigated genome-wide responses of the midge C. riparius exposed to virgin polyamide microplastics (0-180 μm size range, at concentration 1 g kg-1) during seven consecutive generations. The results were integrated to a parallel life-cycle experiment ran under the same exposure conditions. Emergence, life-cycle trait, showed first a substantial reduction in larval survival, followed by a rapid recovery within three generations. On the genomic level, we observed substantial selectively driven allele frequency changes (mean 0.566 ± 0.0879) within seven generations, associated with a mean selection coefficient of 0.322, indicating very strong selection pressure. Putative selection targets were mainly connected to oxidative stress in the microplastics exposed C. riparius population. This is the first multigenerational study on chironomids to provide evidence that upon exposure to polyamide microplastic there are changes on the genomic level, providing basis to rapid adaptation of aquatic organisms to microplastics.
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Affiliation(s)
- Alla Khosrovyan
- National Institute of Chemical Physics and Biophysics, Laboratory of Environmental Toxicology, 23 Akadeemia Tee, 12618, Tallinn, Estonia.
| | - Halina Binde Doria
- Dept. Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| | - Anne Kahru
- National Institute of Chemical Physics and Biophysics, Laboratory of Environmental Toxicology, 23 Akadeemia Tee, 12618, Tallinn, Estonia; Estonian Academy of Sciences, 6 Kohtu, 10130, Tallinn, Estonia
| | - Markus Pfenninger
- Dept. Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany; Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
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16
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Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience. Emerg Top Life Sci 2022; 6:185-199. [PMID: 35403668 PMCID: PMC9023019 DOI: 10.1042/etls20210261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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.
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