Metabolomics: A Promising Tool for Environmental Sciences?

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Environmental Metabolomics".

Deadline for manuscript submissions: closed (15 June 2024) | Viewed by 3360

Special Issue Editors


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Guest Editor
LBBM-BAE USR 3579 UPMC-CNRS, Bâtiment S, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, CEDEX, 66860 Perpignan, France
Interests: environmental chemistry; environmental microbiology; analytical techniques; microbial ecology

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Guest Editor
UAR 32778 CRIOBE EPHE-CNRS-UPVD, Bâtiment T, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, CEDEX, 66860 Perpignan, France
Interests: environmental chemistry; analytical techniques (LC-MS, GC-MS, NMR); metabolomics; molecular biology

Special Issue Information

Dear Colleagues,

Metabolomics is a recent science that appeared about 20 years ago and allows for the study of all the small organic molecules (<1500 Da), called metabolites, present within a biological system (endogenous) or coming from the environment (exogenous). It is now widely used in fields such as basic biology, medicine, clinical pharmacology, toxicology, and nutrition, but its use in environmental science is still limited. Thus, significant challenges still remain in this field, and in particular, many methodological developments regarding analytical data acquisition procedures (suitable sampling, sample preparation, and extract analysis) need to be largely pursued. In addition, appropriate statistical tools for the analysis of large metabolomic datasets must also be strengthened. Thus, the correct interpretation of environmental metabolomics data requires constant methodological development. In order to provide complementary information, this approach can be coupled with other omics methods such as metabarcoding or metatranscriptomics in order to propose new methods of investigation in environmental sciences.

The objective of this Special Issue is to highlight the latest applied research in environmental metabolomics and to provide an update on possible coupling between metabolomics and other omics data.

Dr. Christophe Calvayrac
Dr. Marie-Virginie Salvia
Guest Editors

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Keywords

  • metabolomics
  • environmental sciences
  • data processing
  • metabarcoding
  • metatranscriptomics

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Published Papers (2 papers)

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23 pages, 2408 KiB  
Article
Validation of the Chemical and Biological Steps Required Implementing an Advanced Multi-Omics Approach for Assessing the Fate and Impact of Contaminants in Lagoon Sediments
by Anouar Mejait, Aurélie Fildier, Barbara Giroud, Gaëlle Daniele, Laure Wiest, Delphine Raviglione, Jules Kotarba, Eve Toulza, Triana Ramirez, Alexia Lanseman, Camille Clerissi, Emmanuelle Vulliet, Christophe Calvayrac and Marie-Virginie Salvia
Metabolites 2024, 14(8), 454; https://doi.org/10.3390/metabo14080454 - 17 Aug 2024
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Abstract
The increasing use of chemicals requires a better understanding of their presence and dynamics in the environment, as well as their impact on ecosystems. The aim of this study was to validate the first steps of an innovative multi-omics approach based on metabolomics [...] Read more.
The increasing use of chemicals requires a better understanding of their presence and dynamics in the environment, as well as their impact on ecosystems. The aim of this study was to validate the first steps of an innovative multi-omics approach based on metabolomics and 16S metabarcoding data for analyses of the fate and impact of contaminants in Mediterranean lagoons. Semi-targeted analytical procedures for water and sediment matrices were implemented to assess chemical contamination of the lagoon: forty-six compounds were detected, 28 of which could be quantified in water (between 0.09 and 47.4 ng/L) and sediment (between 0.008 and 26.3 ng/g) samples using the UHPLC-MS/MS instrument. In addition, a non-targeted approach (UHPLC-HRMS) using four different sample preparation protocols based on solid/liquid extractions or an automated pressurized fluid extraction system (EDGE®) was carried out to determine the protocol with the best metabolome coverage, efficiency and reproducibility. Solid/liquid extraction using the solvent mixture acetonitrile/methanol (50/50) was evaluated as the best protocol. Microbial diversity in lagoon sediment was also measured after DNA extraction using five commercial extraction kits. Our study showed that the DNeasy PowerSoil Pro Qiagen kit (Promega, USA) was the most suitable for assessing microbial diversity in fresh sediment. Full article
(This article belongs to the Special Issue Metabolomics: A Promising Tool for Environmental Sciences?)
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Review

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21 pages, 8955 KiB  
Review
A Review of Transcriptomics and Metabolomics in Plant Quality and Environmental Response: From Bibliometric Analysis to Science Mapping and Future Trends
by Qi Yan, Guoshuai Zhang, Xinke Zhang and Linfang Huang
Metabolites 2024, 14(5), 272; https://doi.org/10.3390/metabo14050272 - 8 May 2024
Cited by 1 | Viewed by 1793
Abstract
Transcriptomics and metabolomics offer distinct advantages in investigating the differentially expressed genes and cellular entities that have the greatest influence on end-phenotype, making them crucial techniques for studying plant quality and environmental responses. While numerous relevant articles have been published, a comprehensive summary [...] Read more.
Transcriptomics and metabolomics offer distinct advantages in investigating the differentially expressed genes and cellular entities that have the greatest influence on end-phenotype, making them crucial techniques for studying plant quality and environmental responses. While numerous relevant articles have been published, a comprehensive summary is currently lacking. This review aimed to understand the global and longitudinal research trends of transcriptomics and metabolomics in plant quality and environmental response (TMPQE). Utilizing bibliometric methods, we presented a comprehensive science mapping of the social structure, conceptual framework, and intellectual foundation of TMPQE. We uncovered that TMPQE research has been categorized into three distinct stages since 2020. A citation analysis of the 29 most cited articles, coupled with a content analysis of recent works (2020–2023), highlight five potential research streams in plant quality and environmental responses: (1) biosynthetic pathways, (2) abiotic stress, (3) biotic stress, (4) development and ripening, and (5) methodologies and tools. Current trends and future directions are shaped by technological advancements, species diversity, evolving research themes, and an environmental ecology focus. Overall, this review provides a novel and comprehensive perspective to understand the longitudinal trend on TMPQE. Full article
(This article belongs to the Special Issue Metabolomics: A Promising Tool for Environmental Sciences?)
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