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3 results on '"Emna Zeghal"'

1. The Potential Role of Marine Fungi in Plastic Degradation – A Review

Author

Emna Zeghal, Annika Vaksmaa, Hortense Vielfaure, Teun Boekhout, Helge Niemann, and Evolutionary and Population Biology (IBED, FNWI)

Subjects
Science, Microorganism, marine plastic debris, Ocean Engineering, QH1-199.5, Aquatic Science, Oceanography, biodegradation, Marine pollution, 03 medical and health sciences, Organic matter, 14. Life underwater, Microbial biodegradation, Marine fungi, VDP::Mathematics and natural science: 400, 030304 developmental biology, Water Science and Technology, Pollutant, chemistry.chemical_classification, 0303 health sciences, Global and Planetary Change, 030306 microbiology, Ecology, fungi, Fungi, Marine habitats, General. Including nature conservation, geographical distribution, VDP::Matematikk og Naturvitenskap: 400, Biodegradation, marine pollution, chemistry, 13. Climate action, plastic degradation, Environmental science
Abstract

Plastic debris has been accumulating in the marine realm since the start of plastic mass production in the 1950s. Due to the adverse effects on ocean life, the fate of plastics in the marine environment is an increasingly important environmental issue. Microbial degradation, in addition to weathering, has been identified as a potentially relevant breakdown route for marine plastic debris. Although many studies have focused on microbial colonization and the potential role of microorganisms in breaking down marine plastic debris, little is known about fungi-plastic interactions. Marine fungi are a generally understudied group of microorganisms but the ability of terrestrial and lacustrine fungal taxa to metabolize recalcitrant compounds, pollutants, and some plastic types (e.g., lignin, solvents, pesticides, polyaromatic hydrocarbons, polyurethane, and polyethylene) indicates that marine fungi could be important degraders of complex organic matter in the marine realm, too. Indeed, recent studies demonstrated that some fungal strains from the ocean, such as Zalerion maritimum have the ability to degrade polyethylene. This mini-review summarizes the available information on plastic-fungi interactions in marine environments. We address (i) the currently known diversity of fungi colonizing marine plastic debris and provide (ii) an overview of methods applied to investigate the role of fungi in plastic degradation, highlighting their advantages and drawbacks. We also highlight (iii) the underestimated role of fungi as plastic degraders in marine habitats.

Published
2021
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2. BactoTraits – A functional trait database to evaluate how natural and man-induced changes influence the assembly of bacterial communities

Author

Florian Lemmel, Philippe Usseglio-Polatera, Albin Meyer, Emna Zeghal, Florence Maunoury-Danger, Pascale Bauda, Aurélie Cébron, Corinne Leyval, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes aquatiques et changements globaux (UR EABX), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, Ecological diagnostic, Range (biology), General Decision Sciences, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, Database, 03 medical and health sciences, Microbial ecology, Ecosystem, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, QH540-549.5, 030304 developmental biology, Trophic level, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 2. Zero hunger, Abiotic component, 0303 health sciences, Facultative, Bacteria, Ecology, Aquatic ecosystem, PAH, 15. Life on land, 13. Climate action, Metals, Trait, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, Functional traits
Abstract

In the environment, abiotic (climatic conditions, physico-chemical parameters), biotic (interactions between microorganisms, vegetation and fauna), and anthropogenic (stress, pollution) filters are driving the microbial diversity observed locally. A key question in microbial ecology is to understand the impact of these filters on bacterial diversity and ecosystem functioning. To highlight the responses of bacterial assemblages to these ecological filters, a new approach based on bacterial functional traits has been developed. This approach provides a functional picture of bacterial assemblages using morphological, physiological, and genomic traits as proxies of functions, and leads to a generalizable approach over a larger range of ecosystems with different bacterial diversities. We have created a user-friendly database of bacterial functional traits, thanks to the properties of 19,455 bacterial strains. This database has been called BactoTraits. For example, oxygen preference, size and shape of bacteria, motility, optimum and range of pH and temperature, genome GC percent and trophic type are among the 19 traits included in BactoTraits. Based on the best-informed strains in the database, we identified five functional groups (i.e. mesophiles, competitors, colonizers, stress-sensitives and stress-tolerants) exhibiting a wide strain taxonomic diversity but with quite similar trait profile combinations. As an example of application, BactoTraits was used to characterize the traits and functional diversity of bacterial assemblages in soil samples from 10 sites with different physico-chemical properties and various levels of metal and polycyclic aromatic hydrocarbon (PAH) contaminations. Inference of functional traits was based on taxonomic diversity information obtained by high-throughput sequencing of 16S rDNA. This trait-based approach has allowed to discriminate soils according to their physico-chemical properties and levels of contamination and to go further into the description of the bacterial assemblages. Several bacterial traits were identified as indicators of specific contaminants such as metals (e.g. filament shape, microaerophile and temperature optimum/range higher than 40 °C) or PAHs (e.g. spherical shape, facultative anaerobe/aerobe, no spore production, pH optimum ≥ 8, low temperature optimum but high temperature variation tolerance). Inferring trait values from a taxonomy-based approach can be extended readily to other microbial systems and contexts such as (i) studies on soils and aquatic ecosystems, (ii) microbial ecology along various environmental gradients, (iii) human, plant and animal microbiotes, as well as (iv) trophic interactions between bacterial communities and their predators.

Published
2021
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3. Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov

Author

Bénédicte Ménez, Marianne Quéméneur, Céline Vandecasteele, Emna Zeghal, Anne Postec, Eléonore Frouin, Marc Garel, Gaël Erauso, Bernard Ollivier, Christian Tamburini, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), MEB, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut méditerranéen d'océanologie (MIO), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
Microbiology (medical), Firmicutes, Microorganism, Hydrostatic pressure, lcsh:QR1-502, oceanic crust, serpentinization, Atlantis Massif, 7. Clean energy, Microbiology, anaerobic culture, lcsh:Microbiology, 03 medical and health sciences, Botany, Primary nutritional groups, 14. Life underwater, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Chemistry, 16S ribosomal RNA, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 13. Climate action, Halotolerance, hydrostatic pressure, Fermentation, Proteobacteria, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, subseafloor
Abstract

International audience; Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10–25°C and pH 8.5 showed that Firmicutes and Proteobacteria were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the in situ pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-AT was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named Petrocella atlantisensis is a novel species of a new genus within the newly described family Vallitaleaceae (order Clostridiales, phylum Firmicutes). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric [FeFe] hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-AT. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.

Published
2019
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