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Hellal J, Barthelmebs L, Bérard A, Cébron A, Cheloni G, Colas S, Cravo-Laureau C, De Clerck C, Gallois N, Hery M, Martin-Laurent F, Martins J, Morin S, Palacios C, Pesce S, Richaume A, Vuilleumier S. Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges. FEMS Microbiol Ecol 2023; 99:fiad102. [PMID: 37669892 PMCID: PMC10516372 DOI: 10.1093/femsec/fiad102] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023] Open
Abstract
Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.
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Affiliation(s)
| | - Lise Barthelmebs
- Université de Perpignan Via Domitia, Biocapteurs – Analyse-Environnement, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Annette Bérard
- UMR EMMAH INRAE/AU – équipe SWIFT, 228, route de l'Aérodrome, 84914 Avignon Cedex 9, France
| | | | - Giulia Cheloni
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Simon Colas
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro-Bio Tech (Liege University), Passage des Déportés 2, 5030 Gembloux, Belgium
| | | | - Marina Hery
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Fabrice Martin-Laurent
- Institut Agro Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie, 21065 Dijon, France
| | - Jean Martins
- IGE, UMR 5001, Université Grenoble Alpes, CNRS, G-INP, INRAE, IRD Grenoble, France
| | | | - Carmen Palacios
- Université de Perpignan Via Domitia, CEFREM, F-66860 Perpignan, France
- CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | | | - Agnès Richaume
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France
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Belliardo C, Koutsovoulos GD, Rancurel C, Clément M, Lipuma J, Bailly-Bechet M, Danchin EGJ. Improvement of eukaryotic protein predictions from soil metagenomes. Sci Data 2022; 9:311. [PMID: 35710557 PMCID: PMC9203802 DOI: 10.1038/s41597-022-01420-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI's IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.
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Affiliation(s)
- Carole Belliardo
- Institut Sophia Agrobiotech, Université Côte d'Azur, INRAE, CNRS, Sophia Antipolis, France.
- MYCOPHYTO, 540 Avenue de la Plaine, 06250, Mougins, France.
| | | | - Corinne Rancurel
- Institut Sophia Agrobiotech, Université Côte d'Azur, INRAE, CNRS, Sophia Antipolis, France
| | | | - Justine Lipuma
- MYCOPHYTO, 540 Avenue de la Plaine, 06250, Mougins, France
| | - Marc Bailly-Bechet
- Institut Sophia Agrobiotech, Université Côte d'Azur, INRAE, CNRS, Sophia Antipolis, France
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, Université Côte d'Azur, INRAE, CNRS, Sophia Antipolis, France.
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Saco PM, McDonough KR, Rodriguez JF, Rivera-Zayas J, Sandi SG. The role of soils in the regulation of hazards and extreme events. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200178. [PMID: 34365831 PMCID: PMC8349632 DOI: 10.1098/rstb.2020.0178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
The frequency and intensity of natural hazards and extreme events has increased throughout the last century, resulting in adverse socioeconomic and ecological impacts worldwide. Key factors driving this increase include climate change, the growing world population, anthropogenic activities and ecosystem degradation. One ecologically focused approach that has shown potential towards the mitigation of these hazard events is the concept of nature's contributions to people (or NCP), which focuses on enhancing the material and non-material benefits of an ecosystem to reduce hazard vulnerability and enhance overall human well-being. Soils, in particular, have been identified as a key ecosystem component that may offer critical hazard regulating functionality. Thus, this review investigates the modulating role of soils in the regulation of natural hazards and extreme events, with a focus on floods, droughts, landslides and sand/dust storms, within the context of NCP. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.
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Affiliation(s)
- P. M. Saco
- Centre for Water Security and Environmental Sustainability (CWSES) and School of Engineering, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - K. R. McDonough
- Centre for Water Security and Environmental Sustainability (CWSES) and School of Engineering, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - J. F. Rodriguez
- Centre for Water Security and Environmental Sustainability (CWSES) and School of Engineering, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - J. Rivera-Zayas
- Department of Natural Resources and Environmental Management, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - S. G. Sandi
- Centre for Water Security and Environmental Sustainability (CWSES) and School of Engineering, The University of Newcastle, Callaghan, New South Wales 2308, Australia
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Smith P, Keesstra SD, Silver WL, Adhya TK. The role of soils in delivering Nature's Contributions to People. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200169. [PMID: 34365820 DOI: 10.1098/rstb.2020.0169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This theme issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). The papers in this issue show that soils can contribute positively to the delivery of all NCP. These contributions can be maximized through careful soil management to provide healthy soils, but poorly managed, degraded or polluted soils may contribute negatively to the delivery of NCP. Soils are also shown to contribute positively to the UN Sustainable Development Goals. Papers in the theme issue emphasize the need for careful soil management. Priorities for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation, (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health, productivity and sustainability and to prevent degradation, and (iii) for degraded soils, restore to full soil health. Our knowledge of what constitutes sustainable soil management is mature enough to implement best management practices, in order to maintain and improve soil health. The papers in this issue show the vast potential of soils to contribute to NCP. This is not only desirable, but essential to sustain a healthy planet and if we are to deliver sustainable development in the decades to come. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.
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Affiliation(s)
- Pete Smith
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
| | - Saskia D Keesstra
- Team Soil, Water and Land Use, Wageningen Environmental Research, Wageningen, The Netherlands.,Civil, Surveying and Environmental Engineering and Centre for Water Security and Environmental Sustainability, The University of Newcastle, Callaghan, Australia
| | - Whendee L Silver
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Tapan K Adhya
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
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Smith P, Keesstra SD, Silver WL, Adhya TK, De Deyn GB, Carvalheiro LG, Giltrap DL, Renforth P, Cheng K, Sarkar B, Saco PM, Scow K, Smith J, Morel JC, Thiele-Bruhn S, Lal R, McElwee P. Soil-derived Nature's Contributions to People and their contribution to the UN Sustainable Development Goals. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200185. [PMID: 34365826 DOI: 10.1098/rstb.2020.0185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
This special issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). Here, we combine this assessment and previously published relationships between NCP and delivery on the UN Sustainable Development Goals (SDGs) to infer contributions of soils to the SDGs. We show that in addition to contributing positively to the delivery of all NCP, soils also have a role in underpinning all SDGs. While highlighting the great potential of soils to contribute to sustainable development, it is recognized that poorly managed, degraded or polluted soils may contribute negatively to both NCP and SDGs. The positive contribution, however, cannot be taken for granted, and soils must be managed carefully to keep them healthy and capable of playing this vital role. A priority for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation; (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health and sustainability and to prevent degradation; and (iii) for degraded soils, restore to full soil health. We have enough knowledge now to move forward with the implementation of best management practices to maintain and improve soil health. This analysis shows that this is not just desirable, it is essential if we are to meet the SDG targets by 2030 and achieve sustainable development more broadly in the decades to come. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.
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Affiliation(s)
- Pete Smith
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Saskia D Keesstra
- Soil, Water and Land Use Team, Wageningen University and Research, Wageningen, The Netherlands.,Civil, Surveying and Environmental Engineering and Centre for Water Security and Environmental Sustainability, University of Newcastle, Callaghan, Australia
| | - Whendee L Silver
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | | | - Gerlinde B De Deyn
- Soil, Water and Land Use Team, Wageningen University and Research, Wageningen, The Netherlands
| | - Luísa G Carvalheiro
- Departamento de Ecologia, Universidade Federal de Goiás, 74001-970, Goiânia, Brazil.,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Donna L Giltrap
- Manaaki Whenua Landcare Research, Palmerston North, New Zealand
| | - Phil Renforth
- Research Centre for Carbon Solutions, Heriot Watt University, Edinburgh, UK
| | - Kun Cheng
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Binoy Sarkar
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Patricia M Saco
- Civil, Surveying and Environmental Engineering and Centre for Water Security and Environmental Sustainability, University of Newcastle, Callaghan, Australia
| | - Kate Scow
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Jo Smith
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Jean-Claude Morel
- Tribology and Systems Dynamics Laboratory (LTDS-UMR CNRS 5513), National School of Civil Engineering (ENTPE), University of Lyon, Lyon, France
| | | | - Rattan Lal
- Carbon Management and Sequestration Center, Ohio State University, Columbus, OH, USA
| | - Pam McElwee
- Department of Human Ecology, Rutgers University, New Brunswick, NJ, USA
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