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Redouane EM, Núñez A, Achouak W, Barakat M, Alex A, Martins JC, Tazart Z, Mugani R, Zerrifi SEA, Haida M, García AM, Campos A, Lahrouni M, Oufdou K, Vasconcelos V, Oudra B. Microcystin influence on soil-plant microbiota: Unraveling microbiota modulations and assembly processes in the rhizosphere of Vicia faba. Sci Total Environ 2024; 918:170634. [PMID: 38325456 DOI: 10.1016/j.scitotenv.2024.170634] [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: 12/27/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Microcystins (MCs) are frequently detected in cyanobacterial bloom-impacted waterbodies and introduced into agroecosystems via irrigation water. They are widely known as phytotoxic cyanotoxins, which impair the growth and physiological functions of crop plants. However, their impact on the plant-associated microbiota is scarcely tackled and poorly understood. Therefore, we aimed to investigate the effect of MCs on microbiota-inhabiting bulk soil (BS), root adhering soil (RAS), and root tissue (RT) of Vicia faba when exposed to 100 μg L-1 MCs in a greenhouse pot experiment. Under MC exposure, the structure, co-occurrence network, and assembly processes of the bacterial microbiota were modulated with the greatest impact on RT-inhabiting bacteria, followed by BS and, to a lesser extent, RAS. The analyses revealed a significant decrease in the abundances of several Actinobacteriota-related taxa within the RT microbiota, including the most abundant and known genus of Streptomyces. Furthermore, MCs significantly increased the abundance of methylotrophic bacteria (Methylobacillus, Methylotenera) and other Proteobacteria-affiliated genera (e.g., Paucibacter), which are supposed to degrade MCs. The co-occurrence network of the bacterial community in the presence of MCs was less complex than the control network. In MC-exposed RT, the turnover in community composition was more strongly driven by deterministic processes, as proven by the beta-nearest taxon index. Whereas in MC-treated BS and RAS, both deterministic and stochastic processes can influence community assembly to some extent, with a relative dominance of deterministic processes. Altogether, these results suggest that MCs may reshape the structure of the microbiota in the soil-plant system by reducing bacterial taxa with potential phytobeneficial traits and increasing other taxa with the potential capacity to degrade MCs.
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Affiliation(s)
- El Mahdi Redouane
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech 40000, Morocco; CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos 4450-208, Portugal
| | - Andrés Núñez
- Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid (ETSII-UPM), Madrid 28006, Spain; Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, Murcia 30100, Spain
| | - Wafa Achouak
- Aix Marseille University, CEA, CNRS, BIAM, Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), Saint Paul Lez Durance 13115, France.
| | - Mohamed Barakat
- Aix Marseille University, CEA, CNRS, BIAM, Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), Saint Paul Lez Durance 13115, France
| | - Anoop Alex
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos 4450-208, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Porto 4169-007, Portugal
| | - José Carlos Martins
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos 4450-208, Portugal
| | - Zakaria Tazart
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech 40000, Morocco; AgroBioSciences, Plant Stress Physiology Laboratory, Mohammed VI Polytechnic University, Benguerir 43150, Morocco
| | - Richard Mugani
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech 40000, Morocco
| | - Soukaina El Amrani Zerrifi
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech 40000, Morocco; Higher Institute of Nurses Professions and Health Techniques of Guelmim, Guelmim 81000, Morocco
| | - Mohammed Haida
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech 40000, Morocco
| | - Ana M García
- Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid (ETSII-UPM), Madrid 28006, Spain
| | - Alexandre Campos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos 4450-208, Portugal
| | - Majida Lahrouni
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech 40000, Morocco
| | - Khalid Oufdou
- Laboratory of Microbial Biotechnologies, Agrosciences, and Environment (BioMAgE), Labeled Research Unit-CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech 40000, Morocco
| | - Vitor Vasconcelos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos 4450-208, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Porto 4169-007, Portugal
| | - Brahim Oudra
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech 40000, Morocco
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Alahmad A, Harir M, Fochesato S, Tulumello J, Walker A, Barakat M, Ndour PMS, Schmitt-Kopplin P, Cournac L, Laplaze L, Heulin T, Achouak W. Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet. Microbiome 2024; 12:1. [PMID: 38167150 PMCID: PMC10763007 DOI: 10.1186/s40168-023-01727-3] [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] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/19/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities. RESULTS Utilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The ß-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines. CONCLUSIONS This research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil-plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant-microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies. Video Abstract.
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Affiliation(s)
- Abdelrahman Alahmad
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
- UniLaSalle, SFR NORVEGE FED 4277, AGHYLE Rouen UP 2018.C101, 3 Rue du Tronquet, 76130, Mont-Saint- Aignan, France
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Chair Analytl Food Chem, Technical University of Munich, 85354, Freising, Weihenstephan, Germany
| | - Sylvain Fochesato
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Joris Tulumello
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Mohamed Barakat
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Papa Mamadou Sitor Ndour
- CIRAD, INRAE, Eco&Sols, Université de Montpellier, Institut Agro, IRD FR, Montpellier, France
- UCEIV-ULCO, 50 Rue Ferdinand Buisson, 62228, Calais, France
- LMI IESOL, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Chair Analytl Food Chem, Technical University of Munich, 85354, Freising, Weihenstephan, Germany
| | - Laurent Cournac
- CIRAD, INRAE, Eco&Sols, Université de Montpellier, Institut Agro, IRD FR, Montpellier, France
- LMI IESOL, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Laurent Laplaze
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LMI LAPSE, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Thierry Heulin
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France.
| | - Wafa Achouak
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France.
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Blache A, Achouak W. Extraction and Purification of Outer Membrane Vesicles and Their Associated RNAs. Methods Mol Biol 2024; 2741:11-24. [PMID: 38217646 DOI: 10.1007/978-1-0716-3565-0_2] [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] [Indexed: 01/15/2024]
Abstract
Outer membrane vesicles (OMVs), produced by Gram negative-bacteria and sRNAs, are key players in cell-to-cell communication and interactions of bacteria with the environment. OMVs act as information carriers and encapsulate various molecules such as proteins, lipids, metabolites, and RNAs. OMVs and sRNAs play a broad range of functions from pathogenesis to stress resistance, to biofilm formation and both mediate interkingdom signaling. Various studies indicate that there is a mechanism of intercellular communication mediated by OMV-derived bacterial RNAs that is conserved among certain bacterial species. Here we describe methods for the extraction and purification of vesicles produced by Gram-negative bacteria, such as Pseudomonas brassicacearum and Escherichia coli, and address methods for the extraction of OMVs-derived sRNA and techniques for the analysis of sRNAs.
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Affiliation(s)
- Anaïs Blache
- CEA, CNRS, Aix Marseille University Lab of Microbial Ecology of the Rhizosphere (LEMiRE), UMR7265 BIAM, Saint-Paul-lez-Durance, France
| | - Wafa Achouak
- CEA, CNRS, Aix Marseille University Lab of Microbial Ecology of the Rhizosphere (LEMiRE), UMR7265 BIAM, Saint-Paul-lez-Durance, France.
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4
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Turbant F, Waeytens J, Blache A, Esnouf E, Raussens V, Węgrzyn G, Achouak W, Wien F, Arluison V. Interactions and Insertion of Escherichia coli Hfq into Outer Membrane Vesicles as Revealed by Infrared and Orientated Circular Dichroism Spectroscopies. Int J Mol Sci 2023; 24:11424. [PMID: 37511182 PMCID: PMC10379585 DOI: 10.3390/ijms241411424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The possible carrier role of Outer Membrane Vesicles (OMVs) for small regulatory noncoding RNAs (sRNAs) has recently been demonstrated. Nevertheless, to perform their function, these sRNAs usually need a protein cofactor called Hfq. In this work we show, by using a combination of infrared and circular dichroism spectroscopies, that Hfq, after interacting with the inner membrane, can be translocated into the periplasm, and then be exported in OMVs, with the possibility to be bound to sRNAs. Moreover, we provide evidence that Hfq interacts with and is inserted into OMV membranes, suggesting a role for this protein in the release of sRNA outside the vesicle. These findings provide clues to the mechanism of host-bacteria interactions which may not be defined solely by protein-protein and protein-outer membrane contacts, but also by the exchange of RNAs, and in particular sRNAs.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Anaïs Blache
- Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), BIAM, CEA, CNRS, Aix Marseille University, 13115 Saint Paul Lez Durance, France
| | - Emeline Esnouf
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Vincent Raussens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Wafa Achouak
- Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), BIAM, CEA, CNRS, Aix Marseille University, 13115 Saint Paul Lez Durance, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, 75006 Paris, France
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5
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Martinez Ostormujof L, Teychené S, Achouak W, Fochesato S, Bakarat M, Rodriguez‐Ruiz I, Bergel A, Erable B. Systemic Analysis of the Spatiotemporal Changes in Multi‐Species Electroactive Biofilms to Clarify the Gradual Decline of Current Generation in Microbial Anodes. ChemElectroChem 2023. [DOI: 10.1002/celc.202201135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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6
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Jabeur R, Guyon V, Toth S, Pereira AE, Huynh MP, Selmani Z, Boland E, Bosio M, Beuf L, Clark P, Vallenet D, Achouak W, Audiffrin C, Torney F, Paul W, Heulin T, Hibbard BE, Toepfer S, Sallaud C. A novel binary pesticidal protein from Chryseobacterium arthrosphaerae controls western corn rootworm by a different mode of action to existing commercial pesticidal proteins. PLoS One 2023; 18:e0267220. [PMID: 36800363 PMCID: PMC9937505 DOI: 10.1371/journal.pone.0267220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/04/2022] [Indexed: 02/18/2023] Open
Abstract
The western corn rootworm (WCR) Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) remains one of the economically most important pests of maize (Zea mays) due to its adaptive capabilities to pest management options. This includes the ability to develop resistance to some of the commercial pesticidal proteins originating from different strains of Bacillus thuringiensis. Although urgently needed, the discovery of new, environmentally safe agents with new modes of action is a challenge. In this study we report the discovery of a new family of binary pesticidal proteins isolated from several Chryseobacterium species. These novel binary proteins, referred to as GDI0005A and GDI0006A, produced as recombinant proteins, prevent growth and increase mortality of WCR larvae, as does the bacteria. These effects were found both in susceptible and resistant WCR colonies to Cry3Bb1 and Cry34Ab1/Cry35Ab1 (reassigned Gpp34Ab1/Tpp35Ab1). This suggests GDI0005A and GDI0006A may not share the same binding sites as those commercially deployed proteins and thereby possess a new mode of action. This paves the way towards the development of novel biological or biotechnological management solutions urgently needed against rootworms.
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Affiliation(s)
- Rania Jabeur
- Limagrain Europe, Centre de recherche, Chappes, France
| | | | - Szabolcs Toth
- Integrated Pest Management Department, Hungarian University of Agriculture and Life Sciences—MATE, Godollo, Hungary
- CABI Switzerland, c/o Plant Protection and Soil Conservation Directorate, Hodmezovasarhely, Hungary
| | - Adriano E. Pereira
- Division of Plant Science & Technology, University of Missouri, Columbia, MO, United States of America
| | - Man P. Huynh
- Division of Plant Science & Technology, University of Missouri, Columbia, MO, United States of America
| | - Zakia Selmani
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediène, USTHB, Alger, Algérie
| | - Erin Boland
- Genective USA Corp, Champaign, IL, United States of America
| | - Mickael Bosio
- Limagrain Europe, Centre de recherche, Chappes, France
| | - Laurent Beuf
- Limagrain Europe, Centre de recherche, Chappes, France
| | - Pete Clark
- Genective USA Corp, Champaign, IL, United States of America
| | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Evry, Université Paris-Saclay, CNRS, Evry, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Saint Paul-Lez-Durance, France
| | | | | | - Wyatt Paul
- Limagrain Europe, Centre de recherche, Chappes, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Saint Paul-Lez-Durance, France
| | - Bruce E. Hibbard
- USDA-ARS, Plant Genetics Research Unit, Univ. Missouri, Columbia, MO, United States of America
| | - Stefan Toepfer
- CABI Switzerland, c/o Plant Protection and Soil Conservation Directorate, Hodmezovasarhely, Hungary
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7
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Selmani Z, Attard E, Lauga B, Barakat M, Ortet P, Tulumello J, Achouak W, Kaci Y, Heulin T. Culturing the desert microbiota. Front Microbiol 2023; 14:1098150. [PMID: 37113232 PMCID: PMC10126307 DOI: 10.3389/fmicb.2023.1098150] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved an original method for isolating strains consisting of "culturing" grains of sand directly on Petri dishes (grain-by-grain method). This method allowed to cultivate up to 10% of the bacteria counted on the surface of grains of the three sites studied in the Great Western Erg in Algeria (Timoudi, Béni Abbès, and Taghit), knowing that on average about 10 bacterial cells colonize each grain. The diversity of culturable bacteria (collection of 290 strains) predicted by 16S rRNA gene sequencing revealed that Arthrobacter subterraneus, Arthrobacter tecti, Pseudarthrobacter phenanthrenivorans, Pseudarthrobacter psychrotolerans, and Massilia agri are the dominant species. The comparison of the culture-dependent and -independent (16S rRNA gene metabarcoding) approaches at the Timoudi site revealed 18 bacterial genera common to both approaches with a relative overestimation of the genera Arthrobacter/Pseudarthrobacter and Kocuria, and a relative underestimation of the genera Blastococcus and Domibacillus by the bacterial culturing approach. The bacterial isolates will allow further study on the mechanisms of tolerance to desiccation, especially in Pseudomonadota (Proteobacteria).
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Affiliation(s)
- Zakia Selmani
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Eleonore Attard
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Béatrice Lauga
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Mohamed Barakat
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Philippe Ortet
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Joris Tulumello
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Wafa Achouak
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Yahia Kaci
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
| | - Thierry Heulin
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
- *Correspondence: Thierry Heulin,
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8
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de la Fuente Cantó C, Diouf MN, Ndour PMS, Debieu M, Grondin A, Passot S, Champion A, Barrachina C, Pratlong M, Gantet P, Assigbetsé K, Kane N, Cubry P, Diedhiou AG, Heulin T, Achouak W, Vigouroux Y, Cournac L, Laplaze L. Genetic control of rhizosheath formation in pearl millet. Sci Rep 2022; 12:9205. [PMID: 35655088 PMCID: PMC9163325 DOI: 10.1038/s41598-022-13234-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 12/17/2021] [Accepted: 05/13/2022] [Indexed: 11/09/2022] Open
Abstract
The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub-Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.
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Affiliation(s)
| | - M N Diouf
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.,Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L'Ouest (IESOL), Dakar, Senegal.,Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, Dakar, Sénégal
| | - P M S Ndour
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.,Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L'Ouest (IESOL), Dakar, Senegal
| | - M Debieu
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - A Grondin
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France.,Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Senegal.,CERAAS, Thiès, Senegal
| | - S Passot
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - A Champion
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | | | - M Pratlong
- Montpellier GenomiX, Montpellier, France
| | - P Gantet
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - K Assigbetsé
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.,Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L'Ouest (IESOL), Dakar, Senegal
| | - N Kane
- Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Senegal
| | - P Cubry
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - A G Diedhiou
- Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Senegal.,Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, Dakar, Sénégal
| | - T Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France
| | - W Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France
| | - Y Vigouroux
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - L Cournac
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Laplaze
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France. .,Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Senegal.
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9
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Behairi S, Baha N, Barakat M, Ortet P, Achouak W, Heulin T, Kaci Y. Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil. Extremophiles 2022; 26:18. [PMID: 35652980 DOI: 10.1007/s00792-022-01268-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/05/2022] [Indexed: 11/04/2022]
Abstract
Hypersaline ecosystems host a particular microbiota, which can be specifically recruited by halophytes. In order to broaden our knowledge of hypersaline ecosystems, an in natura study was conducted on the microbiota associated with the halophyte Halocnemum strobilaceum from alkaline-saline arid soil in Algeria. We collected and identified a total of 414 strains isolated from root tissues (RT), root-adhering soil (RAS), non-adhering rhizospheric soil (NARS) and bulk soil (BS) using different NaCl concentrations. Our data showed that halophilic and halotolerant bacterial isolates in BS and the rhizosphere belonged to 32 genera distributed in Proteobacteria (49%), Firmicutes (36%), Actinobacteria (14%) and Bacteroidetes (1%). Bacterial population size and species diversity were greatly increased in the rhizosphere (factor 100). The reservoir of diversity in BS was dominated by the genera Bacillus and Halomonas. Bacillus/Halomonas ratio decreased with the proximity to the roots from 2.2 in BS to 0.3 at the root surface. Salt screening of the strains showed that species belonging to nine genera were able to grow up to 5.1 M NaCl. Thus, we found that H. strobilaceum exerted a strong effect on the diversity of the recruited microbiota with an affinity strongly attributed to the genus Halomonas.
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Affiliation(s)
- Sabrina Behairi
- Team of Soil Biology, Laboratory of Organisms Biology and Physiology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria
| | - Nassima Baha
- Team of Soil Biology, Laboratory of Organisms Biology and Physiology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria
| | - Mohamed Barakat
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Philippe Ortet
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Wafa Achouak
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Thierry Heulin
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Yahia Kaci
- Team of Soil Biology, Laboratory of Organisms Biology and Physiology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria.
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10
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Laveilhé A, Fochesato S, Lalaouna D, Heulin T, Achouak W. Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues. Microb Biotechnol 2022; 15:2083-2096. [PMID: 35502577 PMCID: PMC9249325 DOI: 10.1111/1751-7915.14023] [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: 10/21/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudomonads play crucial roles in plant growth promotion and control of plant diseases. However, under natural conditions, other microorganisms competing for the same nutrient resources in the rhizosphere may exert negative control over their phytobeneficial characteristics. We assessed the expression of phytobeneficial genes involved in biocontrol, biostimulation and iron regulation such as, phlD, hcnA, acdS, and iron‐small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co‐cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. We found that the antifungal activity of P. brassicacearum depends mostly on the production of DAPG and not on HCN whose production is suppressed by fungi. We have also shown that the two‐competing bacterial strains modulate the plant growth promotion activity of P. brassicacearum by modifying the expression of phlD, hcnA and acdS according to iron availability. Overall, it allows us to better understand the complexity of the multiple molecular dialogues that take place underground between microorganisms and between plants and its rhizosphere microbiota and to show that synergy in favour of phytobeneficial gene expression may exist between different bacterial species. We assessed the expression of phytobeneficial genes, phlD, hcnA and acdS, and iron‐small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co‐cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. Our study illustrates that interkingdom and interspecies interactions in addition to external factors may affect the success of introduced beneficial microorganisms by modulating the expression of phytobeneficial genes.
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Affiliation(s)
- Arnaud Laveilhé
- Lab Microbial Ecology of the Rhizosphere (LEMiRE), CEA, CNRS, BIAM, Aix Marseille Univ, Saint-Paul-Lez-Durance, F-13108, France
| | - Sylvain Fochesato
- Lab Microbial Ecology of the Rhizosphere (LEMiRE), CEA, CNRS, BIAM, Aix Marseille Univ, Saint-Paul-Lez-Durance, F-13108, France
| | - David Lalaouna
- ARN UPR 9002, Université de Strasbourg, CNRS, Strasbourg, F-67000, France
| | - Thierry Heulin
- Lab Microbial Ecology of the Rhizosphere (LEMiRE), CEA, CNRS, BIAM, Aix Marseille Univ, Saint-Paul-Lez-Durance, F-13108, France
| | - Wafa Achouak
- Lab Microbial Ecology of the Rhizosphere (LEMiRE), CEA, CNRS, BIAM, Aix Marseille Univ, Saint-Paul-Lez-Durance, F-13108, France
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11
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Franzino T, Boubakri H, Cernava T, Abrouk D, Achouak W, Reverchon S, Nasser W, Haichar FEZ. Implications of carbon catabolite repression for plant-microbe interactions. Plant Commun 2022; 3:100272. [PMID: 35529946 PMCID: PMC9073323 DOI: 10.1016/j.xplc.2021.100272] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
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Affiliation(s)
- Theophile Franzino
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), 13108 Saint-Paul-Lez-Durance, France
| | - Sylvie Reverchon
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - William Nasser
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
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12
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Macías-Pérez LA, Levard C, Barakat M, Angeletti B, Borschneck D, Poizat L, Achouak W, Auffan M. Contrasted microbial community colonization of a bauxite residue deposit marked by a complex geochemical context. J Hazard Mater 2022; 424:127470. [PMID: 34687997 DOI: 10.1016/j.jhazmat.2021.127470] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 08/04/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Bauxite residue is the alkaline byproduct generated during alumina extraction and is commonly landfilled in open-air deposits. The growth in global alumina production have raised environmental concerns about these deposits since no large-scale reuses exist to date. Microbial-driven techniques including bioremediation and critical metal bio-recovery are now considered sustainable and cost-effective methods to revalorize bauxite residues. However, the establishment of microbial communities and their active role in these strategies are still poorly understood. We thus determined the geochemical composition of different bauxite residues produced in southern France and explored the development of bacterial and fungal communities using Illumina high-throughput sequencing. Physicochemical parameters were influenced differently by the deposit age and the bauxite origin. Taxonomical analysis revealed an early-stage microbial community dominated by haloalkaliphilic microorganisms and strongly influenced by chemical gradients. Microbial richness, diversity and network complexity increased significantly with the deposit age, reaching an equilibrium community composition similar to typical soils after decades of natural weathering. Our results suggested that salinity, pH, and toxic metals affected the bacterial community structure, while fungal community composition showed no clear correlations with chemical variations.
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Affiliation(s)
- Luis Alberto Macías-Pérez
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France; Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France.
| | - Clément Levard
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France.
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France.
| | - Bernard Angeletti
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France.
| | - Daniel Borschneck
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France.
| | | | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France.
| | - Mélanie Auffan
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France; Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA.
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13
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Tulumello J, Chabert N, Rodriguez J, Long J, Nalin R, Achouak W, Heulin T. Rhizobium alamii improves water stress tolerance in a non-legume. Sci Total Environ 2021; 797:148895. [PMID: 34346368 DOI: 10.1016/j.scitotenv.2021.148895] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 04/27/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
With the increasing demand for alternative solutions to replace or optimize the use of synthetic fertilizers and pesticides, the inoculation of bacteria that can contribute to the growth and health of plants (PGPR) is essential. The properties classically sought in PGPR are the production of phytohormones and other growth-promoting molecules, and more rarely the production of exopolysaccharides. We compared the effect of two strains of exopolysaccharide-producing Rhizobium alamii on rapeseed grown in a calcareous silty-clay soil under water stress conditions or not. The effect of factors 'water stress' and 'inoculation' were evaluated on plant growth parameters and the diversity of microbiota associated to root and root-adhering soil compartments. Water stress resulted in a significant decrease in leaf area, shoot biomass and RAS/RT ratio (root-adhering soil/root tissues), as well as overall beta-diversity. Inoculation with R. alamii YAS34 and GBV030 under water-stress conditions produced the same shoot dry biomass compared to uninoculated treatment in absence of water stress, and both strains increased shoot biomass under water-stressed conditions (+7% and +15%, respectively). Only R. alamii GBV030 significantly increased shoot biomass under unstressed or water-stressed conditions compared to the non-inoculated control (+39% and +15%, respectively). Alpha-diversity of the root-associated microbiota after inoculation with R. alamii YAS34 was significantly reduced. Beta-diversity was significantly modified after inoculation with R. alamii GBV030 under unstressed conditions. LEfSe analysis identified characteristic bacterial families, Flavobacteriaceae and Comamonadaceae, in the RT and RAS compartments for the treatment inoculated by R. alamii GBV030 under unstressed conditions, as well as Halomonadaceae (RT) and several species belonging to Actinomycetales (RAS). We showed that R. alamii GBV030 had a PGPR effect on rapeseed growth, increasing its tolerance to water stress, probably involving its capacity to produce exopolysaccharides, and other plant growth-promoting (PGP) traits.
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Affiliation(s)
- Joris Tulumello
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, Saint Paul-Lez-Durance F-13108, France; BioIntrant 139, Rue Philippe de Girard, Pertuis F-84120, France.
| | - Nicolas Chabert
- BioIntrant 139, Rue Philippe de Girard, Pertuis F-84120, France.
| | - Julie Rodriguez
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, Saint Paul-Lez-Durance F-13108, France; BioIntrant 139, Rue Philippe de Girard, Pertuis F-84120, France.
| | - Justine Long
- BioIntrant 139, Rue Philippe de Girard, Pertuis F-84120, France.
| | - Renaud Nalin
- BioIntrant 139, Rue Philippe de Girard, Pertuis F-84120, France.
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, Saint Paul-Lez-Durance F-13108, France.
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, Saint Paul-Lez-Durance F-13108, France.
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14
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Rimboud M, Etcheverry L, Barakat M, Achouak W, Bergel A, Délia ML. Hypersaline microbial fuel cell equipped with an oxygen-reducing microbial cathode. Bioresour Technol 2021; 337:125448. [PMID: 34320736 DOI: 10.1016/j.biortech.2021.125448] [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: 05/10/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
Microbial anodes and oxygen reducing microbial cathodes were designed separately under constant polarization at + 0.1 V/SCE in a hypersaline medium (NaCl 45 g/L). They were then associated to design two-compartment microbial fuel cells (MFCs). These MFCs produced up to 209 ± 24 mW m-2 during a week. This was the first demonstration that hypersaline MFCs equipped with microbial cathodes can produce power density at this level. Desulfuromonas sp. were confirmed to be key species of the anodes. The efficiency of the cathodes was linked to the development of a redox system centred at + 0.2 V/SCE and to the presence of Gammaproteobacteria (Alteromonadales and Oceanospirillales), especially an unclassified order phylogenetically linked to the genus Thioalobacter. Comparing the different performance of the four MFCs with the population analyses suggested that polarization at + 0.1 V/SCE should be maintained longer to promote the growth of Thioalobacter on the cathode and thus increase the MFC performance.
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Affiliation(s)
- Mickaël Rimboud
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 4 Allée Emile Monso, 31432 Toulouse, France
| | - Luc Etcheverry
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 4 Allée Emile Monso, 31432 Toulouse, France
| | - Mohamed Barakat
- Lab of Microbial Ecology of the Rhizosphere (LEMIRE), BIAM, UMR 7265, CEA-CNRS-Aix Marseille University, CEA Cadarache, 13108 Saint Paul Lez Durance, France
| | - Wafa Achouak
- Lab of Microbial Ecology of the Rhizosphere (LEMIRE), BIAM, UMR 7265, CEA-CNRS-Aix Marseille University, CEA Cadarache, 13108 Saint Paul Lez Durance, France
| | - Alain Bergel
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 4 Allée Emile Monso, 31432 Toulouse, France
| | - Marie-Line Délia
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 4 Allée Emile Monso, 31432 Toulouse, France.
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15
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Hugoni M, Galland W, Lecomte S, Bruto M, Barakat M, Piola F, Achouak W, Haichar FEZ. Effects of the Denitrification Inhibitor "Procyanidins" on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome. Microorganisms 2021; 9:1406. [PMID: 34209897 PMCID: PMC8306639 DOI: 10.3390/microorganisms9071406] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 12/04/2022] Open
Abstract
Some plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca2+ in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil.
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Affiliation(s)
- Mylène Hugoni
- VetAgro Sup, UMR Ecologie Microbienne, Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69622 Villeurbanne, France; (M.H.); (W.G.); (S.L.)
- Institut Universitaire de France (IUF), CEDEX 05, F-75231 Paris, France
| | - William Galland
- VetAgro Sup, UMR Ecologie Microbienne, Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69622 Villeurbanne, France; (M.H.); (W.G.); (S.L.)
| | - Solène Lecomte
- VetAgro Sup, UMR Ecologie Microbienne, Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69622 Villeurbanne, France; (M.H.); (W.G.); (S.L.)
| | - Maxime Bruto
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon, Université Lyon 1, CNRS, UMR5558, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France;
| | - Mohamed Barakat
- Laboratory of Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille University, CEA, CNRS, BIAM, F-13108 Saint-Paul-Lez-Durance, France; (M.B.); (W.A.)
| | - Florence Piola
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France;
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille University, CEA, CNRS, BIAM, F-13108 Saint-Paul-Lez-Durance, France; (M.B.); (W.A.)
| | - Feth el Zahar Haichar
- Microbiologie, Adaptation, Pathogénie, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, 10 rue Raphaël Dubois, F-69622 Villeurbanne, France
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16
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Ortet P, Fochesato S, Bitbol AF, Whitworth DE, Lalaouna D, Santaella C, Heulin T, Achouak W, Barakat M. Evolutionary history expands the range of signaling interactions in hybrid multikinase networks. Sci Rep 2021; 11:11763. [PMID: 34083699 PMCID: PMC8175716 DOI: 10.1038/s41598-021-91260-w] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein communicating via intramolecular phosphotransfer. Here, we report how evolutionary relationships between hybrid HKs can be used as predictors of potential intermolecular and intramolecular interactions (‘phylogenetic promiscuity’). We used domain-swap genes chimeras to investigate the specificity of phosphotransfer within hybrid HKs of the GacS–GacA multikinase network of Pseudomonas brassicacearum. The receiver domain of GacS was replaced with those from nine donor hybrid HKs. Three chimeras with receivers from other hybrid HKs demonstrated correct functioning through complementation of a gacS mutant, which was dependent on strains having a functional gacA. Formation of functional chimeras was predictable on the basis of evolutionary heritage, and raises the possibility that HKs sharing a common ancestor with GacS might remain components of the contemporary GacS network. The results also demonstrate that understanding the evolutionary heritage of signaling domains in sophisticated networks allows their rational rewiring by simple domain transplantation, with implications for the creation of designer networks and inference of functional interactions.
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Affiliation(s)
- Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Sylvain Fochesato
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Anne-Florence Bitbol
- CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR8237), Sorbonne Université, 75005, Paris, France.,Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK
| | - David Lalaouna
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.,CNRS, ARN UPR 9002, Université de Strasbourg, 67000, Strasbourg, France
| | - Catherine Santaella
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.
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El Alaoui A, Raklami A, Bechtaoui N, El Gharmali A, Ouhammou A, Imziln B, Achouak W, Pajuelo E, Oufdou K. Use of native plants and their associated bacteria rhizobiomes to remediate-restore Draa Sfar and Kettara mining sites, Morocco. Environ Monit Assess 2021; 193:232. [PMID: 33772660 DOI: 10.1007/s10661-021-08977-4] [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: 11/05/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Soil and mine tailings are unreceptive to plant growth representing an imminent threat to the environment and resource sustainability. Using indigenous plants and their associated rhizobacteria to restore mining sites would be an eco-friendly solution to mitigate soil-metal toxicity. Soil prospection from Draa Sfar and Kettara mining sites in Morocco was carried out during different seasons for native plant sampling and rhizobacteria screening. The sites have been colonized by fifteen tolerant plant species having different capacities to accumulate Cu, Zn, and P in their shoots/root systems. In Draa Sfar mine, Suaeda vera J.F. Gmel., Sarcocornia fruticosa (L.) A.J. Scott., and Frankenia corymbosa Desf. accumulated mainly Cu (more than 90 mg kg-1), Atriplex halimus L. accumulated Zn (mg kg-1), and Frankenia corymbosa Desf. accumulated Pb (14 mg kg-1). As for Kettara mine, Aizoon canariense L. mainly accumulated Zn (270 mg kg-1), whereas Forsskalea tenacissima L. was the best shoot Cu accumulator with up to 50 mg kg-1, whereas Cu accumulation in roots was 21 mg kg-1. The bacterial screening revealed the strains' abilities to tolerate heavy metals up to 50 mg kg-1 Cu, 250 mg kg-1 Pb, and 150 mg kg-1 Zn. Isolated strains belonged mainly to Bacillaceae (73.33%) and Pseudomonadaceae (10%) and expressed different plant growth-promoting traits, alongside their antifungal activity. Results from this study will provide an insight into the ability of native plants and their associated rhizobacteria to serve as a basis for remediation-restoration strategies.
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Affiliation(s)
- Abdelkhalek El Alaoui
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
- LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, Aix-Marseille University, CEA, CNRS, UMR7265, F-13108, Saint Paul Lez Durance, France
| | - Anas Raklami
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco.
| | - Noura Bechtaoui
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Abdelhay El Gharmali
- Laboratory of Water, Biodiversity and Global Change, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Ahmed Ouhammou
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Boujamaa Imziln
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Wafa Achouak
- LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, Aix-Marseille University, CEA, CNRS, UMR7265, F-13108, Saint Paul Lez Durance, France
| | - Eloisa Pajuelo
- Department of Microbiology and Parasitology, University of Seville, PO Box 1095, 41080, Seville, Spain
| | - Khalid Oufdou
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
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18
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Rimboud M, Barakat M, Achouak W, Bergel A, Délia ML. Oxygen-reducing microbial cathodes in hypersaline electrolyte. Bioresour Technol 2021; 319:124165. [PMID: 33039843 DOI: 10.1016/j.biortech.2020.124165] [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: 07/29/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Hypersaline electrolytes offer a way to boost the development of microbial fuel cells by overcoming the issue due to the low conductivity of the usual media. Efficient halotolerant bioanodes have already been designed but O2-reducing cathodes remain a strong bottleneck. Here, O2-reducing biocathodes were designed by using salt marsh sediment as the inoculum and a hypersaline media (45 g/L NaCl) of high conductivity (10.4 S m-1). Current density up to 2.2 A m-2 was reached from potential of +0.2 V/SCE. The efficiency of the biocathodes was correlated to the presence of Gammaproteobacteria strain(s) related to Thiohalobacter thiocyanaticus, which were considerably enriched in the best performing biocathodes. This work opens up new perspectives to overcome the O2 reduction issue in hypersaline MFCs by designing efficient halotolerant microbial cathodes and pointing out the strains that should now be focused to improve them.
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Affiliation(s)
- Mickaël Rimboud
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Allée Emile Monso, 31432 Toulouse, France
| | - Mohamed Barakat
- Laboratoire d'Ecologie Microbienne de la Rhizosphère et des Environnements Extrêmes (LEMIRE), BIAM, UMR 7265, CEA-CNRS-Aix Marseille Université, CEA Cadarache, 13108 Saint Paul Lez Durance, France
| | - Wafa Achouak
- Laboratoire d'Ecologie Microbienne de la Rhizosphère et des Environnements Extrêmes (LEMIRE), BIAM, UMR 7265, CEA-CNRS-Aix Marseille Université, CEA Cadarache, 13108 Saint Paul Lez Durance, France
| | - Alain Bergel
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Allée Emile Monso, 31432 Toulouse, France
| | - Marie-Line Délia
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Allée Emile Monso, 31432 Toulouse, France.
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Benidire L, El Khalloufi F, Oufdou K, Barakat M, Tulumello J, Ortet P, Heulin T, Achouak W. Phytobeneficial bacteria improve saline stress tolerance in Vicia faba and modulate microbial interaction network. Sci Total Environ 2020; 729:139020. [PMID: 32498175 DOI: 10.1016/j.scitotenv.2020.139020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 02/21/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 05/25/2023]
Abstract
Increased global warming, caused by climate change and human activities, will seriously hinder plant development, such as increasing salt concentrations in soils, which will limit water availability for plants. To ensure optimal plant growth under such changing conditions, microorganisms that improve plant growth and health must be integrated into agricultural practices. In the present work, we examined the fate of Vicia faba microbiota structure and interaction network upon inoculation with plant-nodulating rhizobia (Rhizobium leguminosarum RhOF125) and non-nodulating strains (Paenibacillus mucilaginosus BLA7 and Ensifer meliloti RhOL1) in the presence (or absence) of saline stress. Inoculated strains significantly improved plant tolerance to saline stress, suggesting either a direct or indirect effect on the plant response to such stress. To determine the structure of microbiota associated with V. faba, samples of the root-adhering soil (RAS), and the root tissues (RT) of seedlings inoculated (or not) with equal population size of RhOF125, BLA7 and RhOL1 strains and grown in the presence (or absence) of salt, were used to profile the microbial composition by 16S rRNA gene sequencing. The inoculation did not show a significant impact on the composition of the RT microbiota or RAS microbiota. The saline stress shifted the RAS microbiota composition, which correlated with a decrease in Enterobacteriaceae and an increase in Sphingobacterium, Chryseobacterium, Stenotrophomonas, Agrobacterium and Sinorhizobium. When the microbiota of roots and RAS are considered together, the interaction networks for each treatment are quite different and display different key populations involved in community assembly. These findings indicate that upon seed inoculation, community interaction networks rather than their composition may contribute to helping plants to better tolerate environmental stresses. The way microbial populations interfere with each other can have an impact on their functions and thus on their ability to express the genes required to help plants tolerate stresses.
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Affiliation(s)
- Loubna Benidire
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France; Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco; High School of Technology Laayoune, Ibn Zohr University, Morocco
| | - Fatima El Khalloufi
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France; Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco; Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty of Khouribga, Sultan Moulay Slimane University, Beni Mellal, B.P.: 145, 25000, Khouribga, Morocco
| | - Khalid Oufdou
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Mohamed Barakat
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Joris Tulumello
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France; Biointrant, SAS BioIntrant, 84120 Pertuis, France
| | - Philippe Ortet
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Thierry Heulin
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Wafa Achouak
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France.
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De Luca G, Fochesato S, Lavergne J, Forest KT, Barakat M, Ortet P, Achouak W, Heulin T, Verméglio A. Light on the cell cycle of the non-photosynthetic bacterium Ramlibacter tataouinensis. Sci Rep 2019; 9:16505. [PMID: 31712689 PMCID: PMC6848086 DOI: 10.1038/s41598-019-52927-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/22/2019] [Indexed: 12/27/2022] Open
Abstract
Ramlibacter tataouinensis TTB310, a non-photosynthetic betaproteobacterium isolated from a semi-arid region of southern Tunisia, forms both rods and cysts. Cysts are resistant to desiccation and divide when water and nutrients are available. Rods are motile and capable of dissemination. Due to the strong correlation between sunlight and desiccation, light is probably an important external signal for anticipating desiccating conditions. Six genes encoding potential light sensors were identified in strain TTB310. Two genes encode for bacteriophytochromes, while the four remaining genes encode for putative blue light receptors. We determined the spectral and photochemical properties of the two recombinant bacteriophytochromes RtBphP1 and RtBphP2. In both cases, they act as sensitive red light detectors. Cyst divisions and a complete cyst-rod-cyst cycle are the main processes in darkness, whereas rod divisions predominate in red or far-red light. Mutant phenotypes caused by the inactivation of genes encoding bacteriophytochromes or heme oxygenase clearly show that both bacteriophytochromes are involved in regulating the rod-rod division. This process could favor rapid rod divisions at sunrise, after dew formation but before the progressive onset of desiccation. Our study provides the first evidence of a light-based strategy evolved in a non-photosynthetic bacterium to exploit scarse water in a desert environment.
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Affiliation(s)
- Gilles De Luca
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Sylvain Fochesato
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Jérôme Lavergne
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France.
| | - André Verméglio
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
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Rimboud M, Achouak W. Electroautotrophy of Thioalkalivibrio nitratireducens. Bioelectrochemistry 2019; 126:48-55. [DOI: 10.1016/j.bioelechem.2018.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/05/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
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Achouak W, Abrouk D, Guyonnet J, Barakat M, Ortet P, Simon L, Lerondelle C, Heulin T, Haichar FEZ. Plant hosts control microbial denitrification activity. FEMS Microbiol Ecol 2019; 95:5307930. [DOI: 10.1093/femsec/fiz021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Danis Abrouk
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Julien Guyonnet
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Laurent Simon
- Université de Lyon, Université Lyon 1, UMR5023 LEHNA, CNRS, ENTPE, F‐69622 Villeurbanne Cedex, France
| | - Catherine Lerondelle
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Feth el Zahar Haichar
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
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Guyonnet JP, Guillemet M, Dubost A, Simon L, Ortet P, Barakat M, Heulin T, Achouak W, Haichar FEZ. Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation. Front Plant Sci 2018; 9:1662. [PMID: 30559748 PMCID: PMC6265440 DOI: 10.3389/fpls.2018.01662] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/26/2018] [Indexed: 05/20/2023]
Abstract
Plant strategies for soil nutrient uptake have the potential to strongly influence plant-microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation via root exudation.
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Affiliation(s)
- Julien P. Guyonnet
- Laboratoire d’Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA 1418, Villeurbanne, France
| | - Martin Guillemet
- Laboratoire d’Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA 1418, Villeurbanne, France
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Audrey Dubost
- Laboratoire d’Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA 1418, Villeurbanne, France
| | - Laurent Simon
- CNRS, UMR 5023 LEHNA, Univ Lyon, Université Claude Bernard Lyon 1, Université Lyon 1, ENTPE, Villeurbanne, France
| | - Philippe Ortet
- CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment, UMR 7265 BIAM, CEA, Aix Marseille Univ, Saint-Paul-lès-Durance, France
- CNRS, FR3098 ECCOREV, Aix Marseille Univ, Aix-en-Provence, France
| | - Mohamed Barakat
- CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment, UMR 7265 BIAM, CEA, Aix Marseille Univ, Saint-Paul-lès-Durance, France
- CNRS, FR3098 ECCOREV, Aix Marseille Univ, Aix-en-Provence, France
| | - Thierry Heulin
- CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment, UMR 7265 BIAM, CEA, Aix Marseille Univ, Saint-Paul-lès-Durance, France
- CNRS, FR3098 ECCOREV, Aix Marseille Univ, Aix-en-Provence, France
| | - Wafa Achouak
- CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment, UMR 7265 BIAM, CEA, Aix Marseille Univ, Saint-Paul-lès-Durance, France
| | - Feth el Zahar Haichar
- Laboratoire d’Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA 1418, Villeurbanne, France
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Chabert N, Bonnefoy V, Achouak W. Quorum sensing improves current output with Acidithiobacillus ferrooxidans. Microb Biotechnol 2017; 11:136-140. [PMID: 28925584 PMCID: PMC5743822 DOI: 10.1111/1751-7915.12797] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 06/27/2017] [Accepted: 07/07/2017] [Indexed: 12/13/2022] Open
Abstract
Acidithiobacillus ferrooxidans is a strict acidophilic chemolithoautotrophic bacterium that obtains its energy from reduced inorganic sulfur species or ferrous iron oxidation under aerobic conditions. Carbon felt electrodes were pre‐colonized by A. ferrooxidansATCC 23270T using ferrous iron or sulfur as electron donors, via the addition (or not) of a mixture of C14 acyl‐homoserine lactones (C14‐AHLs). Electrode coverage during pre‐colonization was sparse regardless of the electron donor source, whereas activation of quorum sensing significantly enhanced it. Microbial fuel cells (MFCs) inoculated with pre‐colonized electrodes (which behaved as biocathodes) were more efficient in terms of current production when iron was used as an electron donor. Biocathode coverage and current output were remarkably increased to −0.56 A m−2 by concomitantly using iron‐based metabolism and C14‐AHLs. Cyclic voltammetry displayed different electrochemical reactions in relation to the nature of the electron donor, underlying the implication of different electron transfer mechanisms.
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Affiliation(s)
- Nicolas Chabert
- CEA, CNRS, UMR7265, ECCOREV FR 3098, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement Extrêmes, Aix Marseille Univ, F-13108, St Paul Les Durance, France
| | - Violaine Bonnefoy
- CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, Marseille, France
| | - Wafa Achouak
- CEA, CNRS, UMR7265, ECCOREV FR 3098, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement Extrêmes, Aix Marseille Univ, F-13108, St Paul Les Durance, France
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Ndour PMS, Gueye M, Barakat M, Ortet P, Bertrand-Huleux M, Pablo AL, Dezette D, Chapuis-Lardy L, Assigbetsé K, Kane NA, Vigouroux Y, Achouak W, Ndoye I, Heulin T, Cournac L. Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation. Front Plant Sci 2017; 8:1288. [PMID: 28798755 PMCID: PMC5529415 DOI: 10.3389/fpls.2017.01288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/07/2017] [Indexed: 05/25/2023]
Abstract
Root exudation contributes to soil carbon allocation and also to microbial C and energy supply, which subsequently impacts soil aggregation around roots. Biologically-driven soil structural formation is an important driver of soil fertility. Plant genetic determinants of exudation and more generally of factors promoting rhizosphere soil aggregation are largely unknown. Here, we characterized rhizosphere aggregation in a panel of 86 pearl millet inbred lines using a ratio of root-adhering soil dry mass per root tissue dry mass (RAS/RT). This ratio showed significant variations between lines, with a roughly 2-fold amplitude between lowest and highest average values. For 9 lines with contrasting aggregation properties, we then compared the bacterial diversity and composition in root-adhering soil. Bacterial α-diversity metrics increased with the "RAS/RT ratio." Regarding taxonomic composition, the Rhizobiales were stimulated in lines showing high aggregation level whereas Bacillales were more abundant in lines with low ratio. 184 strains of cultivable exopolysaccharides-producing bacteria have been isolated from the rhizosphere of some lines, including members from Rhizobiales and Bacillales. However, at this stage, we could not find a correlation between abundance of EPS-producing species in bacterial communities and the ratio RAS/RT. These results illustrated the impact of cereals genetic trait variation on soil physical properties and microbial diversity. This opens the possibility of considering plant breeding to help management of soil carbon content and physical characteristics through carbon rhizodeposition in soil.
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Affiliation(s)
- Papa M. S. Ndour
- IRD, UMR Eco&Sols, LMI IESOL, Centre de recherche ISRA-IRDDakar, Sénégal
- Département de Biologie Végétale, Université Cheikh Anta DiopDakar, Sénégal
| | - Mariama Gueye
- IRD, UMR Eco&Sols, LMI IESOL, Centre de recherche ISRA-IRDDakar, Sénégal
| | - Mohamed Barakat
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Philippe Ortet
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Marie Bertrand-Huleux
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Anne-Laure Pablo
- Eco&Sols, Cirad, INRA, IRD, Montpellier SupAgro, Université de MontpellierMontpellier, France
| | - Damien Dezette
- Eco&Sols, Cirad, INRA, IRD, Montpellier SupAgro, Université de MontpellierMontpellier, France
| | - Lydie Chapuis-Lardy
- Eco&Sols, Cirad, INRA, IRD, Montpellier SupAgro, Université de MontpellierMontpellier, France
| | - Komi Assigbetsé
- IRD, UMR Eco&Sols, LMI IESOL, Centre de recherche ISRA-IRDDakar, Sénégal
| | - Ndjido Ardo Kane
- Laboratoire National de Recherches sur les Productions Végétales, Institut Sénégalais de Recherches Agricoles, Centre de Recherche de Bel AirDakar, Senegal
| | | | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Ibrahima Ndoye
- Département de Biologie Végétale, Université Cheikh Anta DiopDakar, Sénégal
| | - Thierry Heulin
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Laurent Cournac
- IRD, UMR Eco&Sols, LMI IESOL, Centre de recherche ISRA-IRDDakar, Sénégal
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Avellan A, Auffan M, Masion A, Levard C, Bertrand M, Rose J, Santaella C, Achouak W. Remote Biodegradation of Ge-Imogolite Nanotubes Controlled by the Iron Homeostasis of Pseudomonas brassicacearum. Environ Sci Technol 2016; 50:7791-7798. [PMID: 27347687 DOI: 10.1021/acs.est.6b01455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The toxicity of high-aspect-ratio nanomaterials (HARNs) is often associated with oxidative stress. The essential nutrient Fe may also be responsible of oxidative stress through the production of reactive oxygen species. In the present study, it has been examined to what extent adding Fenton reaction promoting Fe impacted the toxicity of an alumino-germanate model HARN. Structural addition of only 0.95% wt Fe to Ge-imogolite not only alleviated the toxicity observed in the case of Fe-free nanotubes but also stimulated bacterial growth. This was attributed to the metabolization of siderophore-mobilized Fe from the nanotube structure. This was evidenced by the regulation of the homeostasis-monitoring intracellular Fe levels. This was accompanied by a biodegradation of the nanotubes approaching 40%, whereas the Fe-free nanomaterial remained nearly untouched.
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Affiliation(s)
- Astrid Avellan
- Aix-Marseille Université, CNRS, IRD, CEREGE UM34 , 13545 Aix en Provence, France
- iCEINT, International Consortium for the Environmental Implications of NanoTechology, CNRS, Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache , 13108 St-Paul-lez-Durance, France
| | - Melanie Auffan
- Aix-Marseille Université, CNRS, IRD, CEREGE UM34 , 13545 Aix en Provence, France
- iCEINT, International Consortium for the Environmental Implications of NanoTechology, CNRS, Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
| | - Armand Masion
- Aix-Marseille Université, CNRS, IRD, CEREGE UM34 , 13545 Aix en Provence, France
- iCEINT, International Consortium for the Environmental Implications of NanoTechology, CNRS, Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
| | - Clément Levard
- Aix-Marseille Université, CNRS, IRD, CEREGE UM34 , 13545 Aix en Provence, France
- iCEINT, International Consortium for the Environmental Implications of NanoTechology, CNRS, Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
| | - Marie Bertrand
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache , 13108 St-Paul-lez-Durance, France
| | - Jérôme Rose
- Aix-Marseille Université, CNRS, IRD, CEREGE UM34 , 13545 Aix en Provence, France
- iCEINT, International Consortium for the Environmental Implications of NanoTechology, CNRS, Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
| | - Catherine Santaella
- iCEINT, International Consortium for the Environmental Implications of NanoTechology, CNRS, Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache , 13108 St-Paul-lez-Durance, France
| | - Wafa Achouak
- iCEINT, International Consortium for the Environmental Implications of NanoTechology, CNRS, Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache , 13108 St-Paul-lez-Durance, France
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Hamidat M, Barakat M, Ortet P, Chanéac C, Rose J, Bottero JY, Heulin T, Achouak W, Santaella C. Design Defines the Effects of Nanoceria at a Low Dose on Soil Microbiota and the Potentiation of Impacts by the Canola Plant. Environ Sci Technol 2016; 50:6892-6901. [PMID: 27243334 DOI: 10.1021/acs.est.6b01056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Soils act as nanoceria sinks via agricultural spreading and surface waters. Canola plants were grown for one month in soil spiked with nanoceria (1 mg·kg(-1)). To define the role of nanomaterials design on environmental impacts, we studied nanoceria with different sizes (3.5 or 31 nm) and coating (citrate). We measured microbial activities involved in C, N, and P cycling in the rhizosphere and unplanted soil. Bacterial community structure was analyzed in unplanted soil, rhizosphere, and plant roots by 454-pyrosequencing of the 16S rRNA gene. This revealed an impact gradient dependent on nanomaterials design, ranging from decreased microbial enzymatic activities in planted soil to alterations in bacterial community structure in roots. Particle size/aggregation was a key parameter in modulating nanoceria effects on root communities. Citrate coating lowered the impact on microbial enzymatic activities but triggered variability in the bacterial community structure near the plant root. Some nanoceria favored taxa whose closest relatives are hydrocarbon-degrading bacteria and disadvantaged taxa frequently associated in consortia with disease-suppressive activity toward plant pathogens. This work provides a basis to determine outcomes of nanoceria in soil, at a dose close to predicted environmental concentrations, and to design them to minimize these impacts.
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Affiliation(s)
- Mohamed Hamidat
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Mohamed Barakat
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Philippe Ortet
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Corinne Chanéac
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- Chimie de la Matière Condensée, UMR7574, Collège de France, Université de Jussieu , Paris F-75231, France
| | - Jérome Rose
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- CNRS, Aix-Marseille Université, IRD, CEREGE UM34, F-13545 Aix en Provence, France
| | - Jean-Yves Bottero
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- CNRS, Aix-Marseille Université, IRD, CEREGE UM34, F-13545 Aix en Provence, France
| | - Thierry Heulin
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Catherine Santaella
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
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28
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Haichar FEZ, Heulin T, Guyonnet JP, Achouak W. Stable isotope probing of carbon flow in the plant holobiont. Curr Opin Biotechnol 2016; 41:9-13. [PMID: 27019410 DOI: 10.1016/j.copbio.2016.02.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/27/2023]
Abstract
Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with 13C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.
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Affiliation(s)
- Feth El Zahar Haichar
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France.
| | - Thierry Heulin
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
| | - Julien P Guyonnet
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
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29
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Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LFW, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P. Back to the Future of Soil Metagenomics. Front Microbiol 2016; 7:73. [PMID: 26903960 PMCID: PMC4748112 DOI: 10.3389/fmicb.2016.00073] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Joseph Nesme
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de LyonEcully, France; Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)Neuherberg, Germany
| | - Wafa Achouak
- Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France
| | - Spiros N Agathos
- Earth and Life Institute, Catholic University of LouvainLouvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech UniversityUrcuquí, Ecuador
| | - Mark Bailey
- Natural Environment Research Council, Centre for Ecology and Hydrology Oxford, UK
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences Praha, Czech Republic
| | - Dominique Brunel
- Institut National de la Recherche Agronomique, US1279, Etude du Polymorphisme des Génomes Végétaux, CEA, Institut de Génomique, Centre National de Génotypage Evry, France
| | - Åsa Frostegård
- NMBU Nitrogen Group, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences Aas, Norway
| | - Thierry Heulin
- Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, The Faculty of Agriculture, Food and Environment, The Otto Warburg-Minerva Center in Agricultural Biotechnology, The Hebrew University of Jerusalem Rehovot, Israel
| | - Kristiina L Kruus
- Enzymology of Renewable Biomass, VTT, Technical Research Centre of Finland Espoo, Finland
| | - George A Kowalchuk
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
| | - Antonio Lagares
- Departamento de Ciencia Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Centro Científico Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de La Plata La Plata, Argentina
| | | | - Philippe Lemanceau
- Institut National de la Recherche Agronomique, UMR 1347, Agroécologie, Université de Bourgogne Dijon, France
| | - Denis Le Paslier
- CEA/Direction des sciences du vivant/Institut de Génomique. Genoscope, Centre National de la Recherche Scientifiue UMR 8030, Université d'Evry Val d'Essonne Evry, France
| | - Ines Mandic-Mulec
- Department of Food Science and Technology, Biotechnical Faculty- University of Ljubljana Ljubljana, Slovenia
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia Norwich, UK
| | - David D Myrold
- Department of Crop and Soil Science, Oregon State University Corvallis, OR, USA
| | | | - Paolo Nannipieri
- Department of Agrifood and Environmental Science, University of Florence Florence, Italy
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, National University of IrelandCork, Ireland; School of Biomedical Science, Curtin UniversityPerth, WA, Australia
| | - John J Parnell
- National Ecological Observatory Network Boulder, CO, USA
| | - Alfred Pühler
- Center for Biotechnology, Institute for Genome Research and Systems Biology, Genome Research of Industrial Microorganisms, Bielefeld University Bielefeld, Germany
| | - Victor Pylro
- Genomics and Computational Biology Group, René Rachou Research Centre - CPqRR/FIOCRUZ Belo Horizonte, Brazil
| | - Juan L Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | | | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Neuherberg, Germany
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Alexander Sczyrba
- Center for Biotechnology and Faculty of Technology, Computational Metagenomics, Bielefeld University Bielefeld, Germany
| | - Angela Sessitsch
- Health and Environment Department, Bioresources, AIT Austrian Institute of Technology GmbH Tulln, Austria
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University Huddinge, Sweden
| | - Jan Sørensen
- Section of Genetics and Microbiology, Department of Plant and Environmental Microbiology, University of Copenhagen Frederiksberg, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | | | - Edward Topp
- Agriculture and Agri-Food Canada, Department of Biology, University of Western Ontario London, ON, Canada
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras Agrinio, Greece
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Geertje van Keulen
- Institute of Life Science, Medical School, Swansea University Swansea, UK
| | - Franco Widmer
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope Zürich, Switzerland
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna Vienna, Austria
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong Hong Kong, China
| | - Xiaojun Zhang
- Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Liping Zhao
- Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Yong-Guan Zhu
- Institute of Urban Environment, Chinese Academy of Sciences Xiamen, China
| | - Timothy M Vogel
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon Ecully, France
| | - Pascal Simonet
- Institute of Life Science, Medical School, Swansea University Swansea, UK
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El Khalloufi F, Oufdou K, Bertrand M, Lahrouni M, Oudra B, Ortet P, Barakat M, Heulin T, Achouak W. Microbiote shift in the Medicago sativa rhizosphere in response to cyanotoxins extract exposure. Sci Total Environ 2016; 539:135-142. [PMID: 26356186 DOI: 10.1016/j.scitotenv.2015.08.127] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 03/10/2015] [Revised: 07/06/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
The bloom-containing water bodies may have an impact due to cyanotoxins production on other microorganisms and aquatic plants. Where such water is being used for crops irrigation, the presence of cyanotoxins may also have a toxic impact on terrestrial plants and their rhizosphere microbiota. For that purpose, PCR-based 454 pyrosequencing was applied to phylogenetically characterize the bacterial community of Medicago sativa rhizosphere in response to cyanotoxins extract. This analysis revealed a wide diversity at species level, which decreased from unplanted soil to root tissues indicating that only some populations were able to compete for nutrients and niches in this selective habitat. Gemmatimonas, Actinobacteria, Deltaproteobacteria and Opitutae mainly inhabited the bulk soil, whereas, the root-adhering soil and the root tissues were inhabited by Gammaproteobacteria and Alphaproteobacteria. The proportion of these populations fluctuated in response to cyanotoxins extract exposure. Betaproteobacteria proportion increased in the three studied compartments, whereas Gammaproteobacteria proportion decreased except in the bulk soil. This study revealed the potential toxicity of cyanotoxins extract towards Actinobacteria, Gemmatimonas, Deltaproteobacteria, and Gammaproteobacteria, however Clostridia, Opitutae and bacteria related with Betaproteobacteria, were stimulated denoting their tolerance. Altogether, these data indicate that crop irrigation using cyanotoxins containing water might alter the rhizosphere functioning.
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Affiliation(s)
- Fatima El Khalloufi
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France; Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco; University Hassan 1st. Polydisciplinary Faculty of Khouribga, BP. 145, 25000 Khouribga, Morocco
| | - Khalid Oufdou
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Marie Bertrand
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Majida Lahrouni
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Brahim Oudra
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Philippe Ortet
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Mohamed Barakat
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Thierry Heulin
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Wafa Achouak
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France.
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Chabert N, Amin Ali O, Achouak W. All ecosystems potentially host electrogenic bacteria. Bioelectrochemistry 2015; 106:88-96. [PMID: 26298511 DOI: 10.1016/j.bioelechem.2015.07.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [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: 01/29/2015] [Revised: 07/09/2015] [Accepted: 07/09/2015] [Indexed: 01/30/2023]
Abstract
Instead of requiring metal catalysts, MFCs utilize bacteria that oxidize organic matter and either transfer electrons to the anode or take electrons from the cathode. These devices are thus based on a wide microbial diversity that can convert a large array of organic matter components into sustainable and renewable energy. A wide variety of explored environments were found to host electrogenic bacteria, including extreme environments. In the present review, we describe how different ecosystems host electrogenic bacteria, as well as the physicochemical, electrochemical and biological parameters that control the currents from MFCs. We also report how using new molecular techniques allowed characterization of electrochemical biofilms and identification of potentially new electrogenic species. Finally we discuss these findings in the context of future research directions.
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Affiliation(s)
- Nicolas Chabert
- CEA, DSV, IBEB, Lab of Microbial Ecology of the Rhizosphere & Extreme Environment (LEMiRE), 13108 Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108 Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Oulfat Amin Ali
- CEA, DSV, IBEB, Lab of Microbial Ecology of the Rhizosphere & Extreme Environment (LEMiRE), 13108 Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108 Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Wafa Achouak
- CEA, DSV, IBEB, Lab of Microbial Ecology of the Rhizosphere & Extreme Environment (LEMiRE), 13108 Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108 Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France.
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Abstract
Small regulatory RNAs (sRNAs) play a key role in many physiological and adaptive responses in bacteria. Faced with rapidly changing environments, it is more advantageous for bacteria to use sRNA-mediated responses than regulation by protein transcriptional factors, as sRNAs act at the post-transcriptional level and require less energy and time for their synthesis and turnover. The use of RNA deep sequencing has provided hundreds of sRNA candidates in different bacterial species that interact with plants. Here, we review the most recent results for the involvement of bacterial sRNAs in beneficial as well as deleterious plant–bacteria interactions. We describe the current view for the role of sRNAs, which are suggested to improve competition for both niches and resources in plant-interacting bacteria. These sRNAs also help plant-associated bacteria individually adapt to the rapidly changing conditions to which they are exposed, during different stages of this interaction.
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Abstract
The P2CS database (http://www.p2cs.org/) is a comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs). TCSs are comprised of a receptor histidine kinase (HK) and a partner response regulator (RR) and control important prokaryotic behaviors. The latest incarnation of P2CS includes 164 651 TCS proteins, from 2758 sequenced prokaryotic genomes. Several important new features have been added to P2CS since it was last described. Users can search P2CS via BLAST, adding hits to their cart, and homologous proteins can be aligned using MUSCLE and viewed using Jalview within P2CS. P2CS also provides phylogenetic trees based on the conserved signaling domains of the RRs and HKs from entire genomes. HK and RR trees are annotated with gene organization and domain architecture, providing insights into the evolutionary origin of the contemporary gene set. The majority of TCSs are encoded by adjacent HK and RR genes, however, ‘orphan’ unpaired TCS genes are also abundant and identifying their partner proteins is challenging. P2CS now provides paired HK and RR trees with proteins from the same genetic locus indicated. This allows the appraisal of evolutionary relationships across entire TCSs and in some cases the identification of candidate partners for orphan TCS proteins.
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Affiliation(s)
- Philippe Ortet
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK
| | - Catherine Santaella
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - Wafa Achouak
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - Mohamed Barakat
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
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Haichar FEZ, Santaella C, Heulin T, Achouak W. Root exudates mediated interactions belowground. Soil Biology and Biochemistry 2014; 77:69-80. [PMID: 0 DOI: 10.1016/j.soilbio.2014.06.017] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Rousseau R, Santaella C, Achouak W, Godon JJ, Bonnafous A, Bergel A, Délia ML. Correlation of the Electrochemical Kinetics of High-Salinity-Tolerant Bioanodes with the Structure and Microbial Composition of the Biofilm. ChemElectroChem 2014. [DOI: 10.1002/celc.201402153] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Auffan M, Tella M, Santaella C, Brousset L, Paillès C, Barakat M, Espinasse B, Artells E, Issartel J, Masion A, Rose J, Wiesner MR, Achouak W, Thiéry A, Bottero JY. An adaptable mesocosm platform for performing integrated assessments of nanomaterial risk in complex environmental systems. Sci Rep 2014; 4:5608. [PMID: 25001877 PMCID: PMC4085617 DOI: 10.1038/srep05608] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [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: 02/20/2014] [Accepted: 06/12/2014] [Indexed: 11/23/2022] Open
Abstract
Physical-chemists, (micro)biologists, and ecologists need to conduct meaningful experiments to study the environmental risk of engineered nanomaterials with access to relevant mechanistic data across several spatial and temporal scales. Indoor aquatic mesocosms (60L) that can be tailored to virtually mimic any ecosystem appear as a particularly well-suited device. Here, this concept is illustrated by a pilot study aimed at assessing the distribution of a CeO2-based nanomaterial within our system at low concentration (1.5 mg/L). Physico-chemical as well as microbiological parameters took two weeks to equilibrate. These parameters were found to be reproducible across the 9-mesocosm setup over a 45-day period of time. Recovery mass balances of 115 ± 18% and 60 ± 30% of the Ce were obtained for the pulse dosing and the chronic dosing, respectively. This demonstrated the relevance of our experimental approach that allows for adequately monitoring the fate and impact of a given nanomaterial.
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Affiliation(s)
- Mélanie Auffan
- 1] CNRS, Aix-Marseille Université, CEREGE UM34, UMR 7330, 13545 Aix en Provence, France [2] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [3] Center for the Environmental Implications of NanoTechnology CEINT, Duke University, Durham, North Carolina 27707, USA
| | - Marie Tella
- 1] CNRS, Aix-Marseille Université, CEREGE UM34, UMR 7330, 13545 Aix en Provence, France [2] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France
| | - Catherine Santaella
- 1] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [2] CNRS, Aix-Marseille Université, CEA Cadarache DSV/IBEB/SBVME, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), UMR 7265, Saint Paul lez Durance, France
| | - Lenka Brousset
- 1] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [2] CNRS, Aix-Marseille Université, CNRS, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), UMR 7263, Marseille, France
| | - Christine Paillès
- 1] CNRS, Aix-Marseille Université, CEREGE UM34, UMR 7330, 13545 Aix en Provence, France [2] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France
| | - Mohamed Barakat
- 1] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [2] CNRS, Aix-Marseille Université, CEA Cadarache DSV/IBEB/SBVME, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), UMR 7265, Saint Paul lez Durance, France
| | - Benjamin Espinasse
- 1] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [2] Center for the Environmental Implications of NanoTechnology CEINT, Duke University, Durham, North Carolina 27707, USA
| | - Ester Artells
- 1] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [2] CNRS, Aix-Marseille Université, CNRS, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), UMR 7263, Marseille, France
| | - Julien Issartel
- 1] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [2] CNRS, Aix-Marseille Université, CNRS, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), UMR 7263, Marseille, France
| | - Armand Masion
- 1] CNRS, Aix-Marseille Université, CEREGE UM34, UMR 7330, 13545 Aix en Provence, France [2] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France
| | - Jérôme Rose
- 1] CNRS, Aix-Marseille Université, CEREGE UM34, UMR 7330, 13545 Aix en Provence, France [2] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [3] Center for the Environmental Implications of NanoTechnology CEINT, Duke University, Durham, North Carolina 27707, USA
| | - Mark R Wiesner
- 1] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [2] Center for the Environmental Implications of NanoTechnology CEINT, Duke University, Durham, North Carolina 27707, USA
| | - Wafa Achouak
- 1] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [2] CNRS, Aix-Marseille Université, CEA Cadarache DSV/IBEB/SBVME, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), UMR 7265, Saint Paul lez Durance, France
| | - Alain Thiéry
- 1] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [2] CNRS, Aix-Marseille Université, CNRS, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), UMR 7263, Marseille, France
| | - Jean-Yves Bottero
- 1] CNRS, Aix-Marseille Université, CEREGE UM34, UMR 7330, 13545 Aix en Provence, France [2] International Consortium for the Environmental Implications of Nanotechnology iCEINT, CNRS-Duke University, Aix en Provence, France [3] Center for the Environmental Implications of NanoTechnology CEINT, Duke University, Durham, North Carolina 27707, USA
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Ketep SF, Bergel A, Bertrand M, Barakat M, Achouak W, Fourest E. Forming microbial anodes with acetate addition decreases their capability to treat raw paper mill effluent. Bioresour Technol 2014; 164:285-291. [PMID: 24862005 DOI: 10.1016/j.biortech.2014.04.088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 02/25/2014] [Revised: 04/22/2014] [Accepted: 04/26/2014] [Indexed: 06/03/2023]
Abstract
Microbial anodes were formed under polarization at -0.3 V/SCE on graphite plates in effluents from a pulp and paper mill. The bioanodes formed with the addition of acetate led to the highest current densities (up to 6A/m(2)) but were then unable to oxidize the raw effluent efficiently (0.5A/m(2)). In contrast, the bioanodes formed without acetate addition were fully able to oxidize the organic matter contained in the effluent, giving up to 4.5A/m(2) in continuous mode. Bacterial communities showed less bacterial diversity for the acetate-fed bioanodes compared to those formed in raw effluents. Deltaproteobacteria were the most abundant taxonomic group, with a high diversity for bioanodes formed without acetate addition but with almost 100% Desulfuromonas for the acetate-fed bioanodes. The addition of acetate to form the microbial anodes induced microbial selection, which was detrimental to the treatment of the raw effluent.
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Affiliation(s)
- Stéphanie F Ketep
- Centre Technique du Papier, BP 251, 38044 Grenoble Cedex 9, France; Laboratoire de Génie Chimique, CNRS-Université de Toulouse, 31432 Toulouse, France
| | - Alain Bergel
- Laboratoire de Génie Chimique, CNRS-Université de Toulouse, 31432 Toulouse, France.
| | - Marie Bertrand
- CEA, DSV, IBEB, SBVME, Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMiRE), Saint-Paul-lez-Durance, France; CNRS, UMR 7265, FR CNRS 3098 ECCOREV, Saint-Paul-lez-Durance, France; Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Mohamed Barakat
- CEA, DSV, IBEB, SBVME, Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMiRE), Saint-Paul-lez-Durance, France; CNRS, UMR 7265, FR CNRS 3098 ECCOREV, Saint-Paul-lez-Durance, France; Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Wafa Achouak
- CEA, DSV, IBEB, SBVME, Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMiRE), Saint-Paul-lez-Durance, France; CNRS, UMR 7265, FR CNRS 3098 ECCOREV, Saint-Paul-lez-Durance, France; Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Eric Fourest
- Centre Technique du Papier, BP 251, 38044 Grenoble Cedex 9, France
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Santaella C, Allainmat B, Simonet F, Chanéac C, Labille J, Auffan M, Rose J, Achouak W. Aged TiO2-based nanocomposite used in sunscreens produces singlet oxygen under long-wave UV and sensitizes Escherichia coli to cadmium. Environ Sci Technol 2014; 48:5245-5253. [PMID: 24697310 DOI: 10.1021/es500216t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
TiO2-based nanocomposite (NC) are widely used as invisible UV protectant in cosmetics. These nanomaterials (NMs) end in the environment as altered materials. We have investigated the properties of T-Lite SF, a TiO2-NC used as sunscreen, after weathering in water and under light. We have examined the formation of ROS and their consequences on cell physiology of Escherichia coli. Our results show that aged-T-Lite SF produced singlet oxygen under low intensity long wave UV and formed hydroxyl radicals at high intensity. Despite the production of these ROS, T-Lite SF had neither effect on the viability of E. coli nor on mutant impaired in oxidative stress, did not induce mutagenesis and did not impair the integrity of membrane lipids, thus seemed safe to bacteria. However, when pre-exposed to T-Lite SF under low intensity UV, cells turned out to be more sensitive to cadmium, a priority pollutant widely disseminated in soil and surface waters. This effect was not a Trojan horse: sensitization of cells was dependent on the formation of singlet oxygen. These results provide a basis for caution, especially on NMs that have no straight environmental toxicity. It is crucial to anticipate indirect and combined effects of environmental pollutants and NMs.
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Affiliation(s)
- Catherine Santaella
- CEA, IBEB , Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments, Saint-Paul-lez-Durance, F-13108, France
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Cercado B, Byrne N, Bertrand M, Pocaznoi D, Rimboud M, Achouak W, Bergel A. Garden compost inoculum leads to microbial bioanodes with potential-independent characteristics. Bioresour Technol 2013; 134:276-284. [PMID: 23500585 DOI: 10.1016/j.biortech.2013.01.123] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 06/01/2023]
Abstract
Garden compost leachate was used to form microbial bioanodes under polarization at -0.4, -0.2 and +0.1 V/SCE. Current densities were 6.3 and 8.9 A m(-2) on average at -0.4 and +0.1 V/SCE respectively, with acetate 10 mM. The catalytic cyclic voltammetry (CV) showed similar electrochemical characteristics for all bioanodes and indicated that the lower currents recorded at -0.4V/SCE were due to the slower interfacial electron transfer rate at this potential, consistently with conventional electrochemical kinetics. RNA- and DNA-based DGGE evidenced that the three dominant bacterial groups Geobacter, Anaerophaga and Pelobacter were identical for all bioanodes and did not depend on the polarization potential. Only non-turnover CVs showed differences in the redox equipment of the biofilms, the highest potential promoting multiple electron transfer pathways. This first description of a potential-independent electroactive microbial community opens up promising prospects for the design of stable bioanodes for microbial fuel cells.
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Affiliation(s)
- Bibiana Cercado
- Laboratoire de Génie Chimique (LGC), CNRS, Université de Toulouse (INPT), 4 allée Emile Monso, BP 84234, 31432 Toulouse, France
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Ketep SF, Bergel A, Bertrand M, Achouak W, Fourest E. Lowering the applied potential during successive scratching/re-inoculation improves the performance of microbial anodes for microbial fuel cells. Bioresour Technol 2013; 127:448-455. [PMID: 23138069 DOI: 10.1016/j.biortech.2012.09.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 06/01/2023]
Abstract
Microbial anodes were formed under polarisation at -0.2V/SCE on smooth graphite plate electrodes with paper mill effluents. Primary, secondary and tertiary biofilms were formed by a successive scratching and re-inoculation procedure. The secondary and tertiary biofilms formed while decreasing the polarisation potential allowed the anodes to provide current density of 6A/m(2) at -0.4V/SCE. In contrast, applying -0.4V/SCE initially to form the primary biofilms did not lead to the production of current. Consequently, the scratching/re-inoculation procedure combined with progressive lowering of the applied potential revealed an efficient new procedure that gave efficient microbial anodes able to work at low potential. The observed progressive pH drift to alkaline values above 9 explained the open circuit potentials as low as -0.6 V/SCE. The remarkable performance of the electrode at alkaline pH was attributed to the presence of Desulfuromonas acetexigens as the single dominant species in the tertiary microbial anodes.
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Affiliation(s)
- Stephanie F Ketep
- Centre Technique du Papier, 341 Rue de la Papeterie, 38400 Saint Martin d'Hères, France.
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Roumagnac P, Richaud P, Barakat M, Ortet P, Roncato MA, Heulin T, Peltier G, Achouak W, Cournac L. Reversible oxygen-tolerant hydrogenase carried by free-living N2-fixing bacteria isolated from the rhizospheres of rice, maize, and wheat. Microbiologyopen 2012; 1:349-61. [PMID: 23233392 PMCID: PMC3535381 DOI: 10.1002/mbo3.37] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 04/27/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 12/03/2022] Open
Abstract
Hydrogen production by microorganisms is often described as a promising sustainable and clean energy source, but still faces several obstacles, which prevent practical application. Among them, oxygen sensitivity of hydrogenases represents one of the major limitations hampering the biotechnological implementation of photobiological production processes. Here, we describe a hierarchical biodiversity-based approach, including a chemochromic screening of hydrogenase activity of hundreds of bacterial strains collected from several ecosystems, followed by mass spectrometry measurements of hydrogenase activity of a selection of the H2-oxidizing bacterial strains identified during the screen. In all, 131 of 1266 strains, isolated from cereal rhizospheres and basins containing irradiating waste, were scored as H2-oxidizing bacteria, including Pseudomonas sp., Serratia sp., Stenotrophomonas sp., Enterobacter sp., Rahnella sp., Burkholderia sp., and Ralstonia sp. isolates. Four free-living N2-fixing bacteria harbored a high and oxygen-tolerant hydrogenase activity, which was not fully inhibited within entire cells up to 150–250 μmol/L O2 concentration or within soluble protein extracts up to 25–30 μmol/L. The only hydrogenase-related genes that we could reveal in these strains were of the hyc type (subunits of formate hydrogenlyase complex). The four free-living N2-fixing bacteria were closely related to Enterobacter radicincitans based on the sequences of four genes (16S rRNA, rpoB, hsp60, and hycE genes). These results should bring interesting prospects for microbial biohydrogen production and might have ecophysiological significance for bacterial adaptation to the oxic–anoxic interfaces in the rhizosphere.
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Affiliation(s)
- Philippe Roumagnac
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, F-34398, Montpellier Cedex-5, France
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Nercessian O, Parot S, Délia ML, Bergel A, Achouak W. Harvesting electricity with Geobacter bremensis isolated from compost. PLoS One 2012; 7:e34216. [PMID: 22470538 PMCID: PMC3314594 DOI: 10.1371/journal.pone.0034216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 02/25/2012] [Indexed: 11/18/2022] Open
Abstract
Electrochemically active (EA) biofilms were formed on metallic dimensionally stable anode-type electrode (DSA), embedded in garden compost and polarized at +0.50 V/SCE. Analysis of 16S rRNA gene libraries revealed that biofilms were heavily enriched in Deltaproteobacteria in comparison to control biofilms formed on non-polarized electrodes, which were preferentially composed of Gammaproteobacteria and Firmicutes. Among Deltaproteobacteria, sequences affiliated with Pelobacter and Geobacter genera were identified. A bacterial consortium was cultivated, in which 25 isolates were identified as Geobacter bremensis. Pure cultures of 4 different G. bremensis isolates gave higher current densities (1400 mA/m2 on DSA, 2490 mA/m2 on graphite) than the original multi-species biofilms (in average 300 mA/m2 on DSA) and the G. bremensis DSM type strain (100–300 A/m2 on DSA; 2485 mA/m2 on graphite). FISH analysis confirmed that G. bremensis represented a minor fraction in the original EA biofilm, in which species related to Pelobacter genus were predominant. The Pelobacter type strain did not show EA capacity, which can explain the lower performance of the multi-species biofilms. These results stressed the great interest of extracting and culturing pure EA strains from wild EA biofilms to improve the current density provided by microbial anodes.
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Affiliation(s)
- Olivier Nercessian
- CEA, DSV, IBEB, SBVME, Lab Ecol Microb Rhizosphere and Environ Extrem (LEMiRE), Saint-Paul-lez-Durance, France
- CNRS UMR 7265 and FR CNRS 3098 ECCOREV, Saint-Paul-lez-Durance, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Sandrine Parot
- Laboratoire de Génie Chimique, Centre National de la Recherche Scientifique, Université de Toulouse (INPT), Toulouse, France
| | - Marie-Line Délia
- Laboratoire de Génie Chimique, Centre National de la Recherche Scientifique, Université de Toulouse (INPT), Toulouse, France
| | - Alain Bergel
- Laboratoire de Génie Chimique, Centre National de la Recherche Scientifique, Université de Toulouse (INPT), Toulouse, France
| | - Wafa Achouak
- CEA, DSV, IBEB, SBVME, Lab Ecol Microb Rhizosphere and Environ Extrem (LEMiRE), Saint-Paul-lez-Durance, France
- CNRS UMR 7265 and FR CNRS 3098 ECCOREV, Saint-Paul-lez-Durance, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, France
- * E-mail:
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Haichar FEZ, Roncato MA, Achouak W. Stable isotope probing of bacterial community structure and gene expression in the rhizosphere of Arabidopsis thaliana. FEMS Microbiol Ecol 2012; 81:291-302. [PMID: 22385286 DOI: 10.1111/j.1574-6941.2012.01345.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 02/20/2012] [Accepted: 02/20/2012] [Indexed: 11/27/2022] Open
Abstract
The rhizosphere is an active compartment where plant and microorganisms establish a molecular dialogue. In this study, we analysed the impact of Arabidopsis thaliana on bacterial community structure and the expression of certain beneficial genes using DNA- and mRNA-SIP in the rhizosphere of plantlets grown under (13)CO(2) for 13, 21 and 27 days. DNA- and rRNA-SIP revealed changes in bacterial communities inhabiting the rhizosphere soil that were probably related to modification of root exudates, while root-colonizing populations were maintained over time suggesting their metabolic versatility and adaptation. The impact of the plant via root exudates on the expression of the noncoding RNAs rsmZ, acdS gene encoding 1-aminocyclopropane-1-carboxylate deaminase and nosZ gene encoding nitrous oxide reductase, in the root-adhering soil and on the roots of A. thaliana was determined using mRNA-SIP. Results showed that these genes were present and expressed by bacteria inhabiting roots and by those that derive nutrients from the breakdown of organic matter in soils or from root exudates. The expression of rsmZ under natural conditions indicates the importance of noncoding RNAs in bacterial adaptation to their ecological niches.
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Affiliation(s)
- Feth el Zahar Haichar
- CEA, DSV, IBEB, SBVME, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance, France
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Schue M, Fekete A, Ortet P, Brutesco C, Heulin T, Schmitt-Kopplin P, Achouak W, Santaella C. Modulation of metabolism and switching to biofilm prevail over exopolysaccharide production in the response of Rhizobium alamii to cadmium. PLoS One 2011; 6:e26771. [PMID: 22096497 PMCID: PMC3212527 DOI: 10.1371/journal.pone.0026771] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 10/03/2011] [Indexed: 11/19/2022] Open
Abstract
Heavy metals such as cadmium (Cd(2+)) affect microbial metabolic processes. Consequently, bacteria adapt by adjusting their cellular machinery. We have investigated the dose-dependent growth effects of Cd(2+) on Rhizobium alamii, an exopolysaccharide (EPS)-producing bacterium that forms a biofilm on plant roots. Adsorption isotherms show that the EPS of R. alamii binds cadmium in competition with calcium. A metabonomics approach based on ion cyclotron resonance Fourier transform mass spectrometry has showed that cadmium alters mainly the bacterial metabolism in pathways implying sugars, purine, phosphate, calcium signalling and cell respiration. We determined the influence of EPS on the bacterium response to cadmium, using a mutant of R. alamii impaired in EPS production (MSΔGT). Cadmium dose-dependent effects on the bacterial growth were not significantly different between the R. alamii wild type (wt) and MSΔGT strains. Although cadmium did not modify the quantity of EPS isolated from R. alamii, it triggered the formation of biofilm vs planktonic cells, both by R. alamii wt and by MSΔGT. Thus, it appears that cadmium toxicity could be managed by switching to a biofilm way of life, rather than producing EPS. We conclude that modulations of the bacterial metabolism and switching to biofilms prevails in the adaptation of R. alamii to cadmium. These results are original with regard to the conventional role attributed to EPS in a biofilm matrix, and the bacterial response to cadmium.
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Affiliation(s)
- Mathieu Schue
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Agnes Fekete
- Helmholtz-Zentrum Muenchen-German Research Center for Environmental Health, Institute for Ecological Chemistry, Department of BioGeochemistry and Analysis, Neuherberg, Germany
| | - Philippe Ortet
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Catherine Brutesco
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Thierry Heulin
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Philippe Schmitt-Kopplin
- Helmholtz-Zentrum Muenchen-German Research Center for Environmental Health, Institute for Ecological Chemistry, Department of BioGeochemistry and Analysis, Neuherberg, Germany
- Department for Chemical-Technical Analysis Research Center Weihenstephan for Brewing and Food Quality, Technische Universität München, Freising-Weihenstephan, Germany
| | - Wafa Achouak
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Catherine Santaella
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
- * E-mail:
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Mondani L, Benzerara K, Carrière M, Christen R, Mamindy-Pajany Y, Février L, Marmier N, Achouak W, Nardoux P, Berthomieu C, Chapon V. Influence of uranium on bacterial communities: a comparison of natural uranium-rich soils with controls. PLoS One 2011; 6:e25771. [PMID: 21998695 PMCID: PMC3187815 DOI: 10.1371/journal.pone.0025771] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [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: 06/10/2011] [Accepted: 09/11/2011] [Indexed: 11/30/2022] Open
Abstract
This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE) revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil.
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Affiliation(s)
- Laure Mondani
- CEA, DSV, IBEB, Laboratoire Interactions Protéine Métal, Saint-Paul-lez-Durance, France
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De Luca G, Barakat M, Ortet P, Fochesato S, Jourlin-Castelli C, Ansaldi M, Py B, Fichant G, Coutinho PM, Voulhoux R, Bastien O, Maréchal E, Henrissat B, Quentin Y, Noirot P, Filloux A, Méjean V, DuBow MS, Barras F, Barbe V, Weissenbach J, Mihalcescu I, Verméglio A, Achouak W, Heulin T. The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment. PLoS One 2011; 6:e23784. [PMID: 21912644 PMCID: PMC3164672 DOI: 10.1371/journal.pone.0023784] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 07/25/2011] [Indexed: 11/22/2022] Open
Abstract
Ramlibacter tataouinensis TTB310(T) (strain TTB310), a betaproteobacterium isolated from a semi-arid region of South Tunisia (Tataouine), is characterized by the presence of both spherical and rod-shaped cells in pure culture. Cell division of strain TTB310 occurs by the binary fission of spherical "cyst-like" cells ("cyst-cyst" division). The rod-shaped cells formed at the periphery of a colony (consisting mainly of cysts) are highly motile and colonize a new environment, where they form a new colony by reversion to cyst-like cells. This unique cell cycle of strain TTB310, with desiccation tolerant cyst-like cells capable of division and desiccation sensitive motile rods capable of dissemination, appears to be a novel adaptation for life in a hot and dry desert environment. In order to gain insights into strain TTB310's underlying genetic repertoire and possible mechanisms responsible for its unusual lifestyle, the genome of strain TTB310 was completely sequenced and subsequently annotated. The complete genome consists of a single circular chromosome of 4,070,194 bp with an average G+C content of 70.0%, the highest among the Betaproteobacteria sequenced to date, with total of 3,899 predicted coding sequences covering 92% of the genome. We found that strain TTB310 has developed a highly complex network of two-component systems, which may utilize responses to light and perhaps a rudimentary circadian hourglass to anticipate water availability at the dew time in the middle/end of the desert winter nights and thus direct the growth window to cyclic water availability times. Other interesting features of the strain TTB310 genome that appear to be important for desiccation tolerance, including intermediary metabolism compounds such as trehalose or polyhydroxyalkanoate, and signal transduction pathways, are presented and discussed.
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Affiliation(s)
- Gilles De Luca
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France.
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Vandecandelaere I, Nercessian O, Faimali M, Segaert E, Mollica A, Achouak W, De Vos P, Vandamme P. Bacterial diversity of the cultivable fraction of a marine electroactive biofilm. Bioelectrochemistry 2010; 78:62-6. [DOI: 10.1016/j.bioelechem.2009.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 06/29/2009] [Accepted: 07/08/2009] [Indexed: 10/20/2022]
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Bressan M, Roncato MA, Bellvert F, Comte G, Haichar FZ, Achouak W, Berge O. Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots. ISME J 2009; 3:1243-57. [PMID: 19554039 DOI: 10.1038/ismej.2009.68] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched (13)CO(2) atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities.
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Affiliation(s)
- Mélanie Bressan
- Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), Saint-Paul-lez-Durance, France
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Vandecandelaere I, Nercessian O, Segaert E, Achouak W, Mollica A, Faimali M, Vandamme P. Nautella italica gen. nov., sp. nov., isolated from a marine electroactive biofilm. Int J Syst Evol Microbiol 2009; 59:811-7. [PMID: 19329612 DOI: 10.1099/ijs.0.002683-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five isolates obtained from a marine electroactive biofilm grown on a stainless steel cathode were investigated by using a polyphasic taxonomic approach. Analyses of whole-cell fatty acid methyl esters and 16S rRNA gene sequences showed that the isolates belonged to the Roseobacter lineage of the class Alphaproteobacteria. Both phenotypic and genotypic analyses demonstrated that the five new isolates constituted a single species that did not represent a recognized member of the Roseobacter lineage. Therefore the five isolates represent a novel genus and species, for which the name Nautella italica gen. nov., sp. nov. is proposed. The type strain is LMG 24365(T) (=CCUG 55857(T)). The DNA G+C content of the type strain is 61 mol%.
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Affiliation(s)
- Ilse Vandecandelaere
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium.
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Erable B, Roncato MA, Achouak W, Bergel A. Sampling natural biofilms: a new route to build efficient microbial anodes. Environ Sci Technol 2009; 43:3194-3199. [PMID: 19534134 DOI: 10.1021/es803549v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Electrochemically active biofilms were constructed on graphite anodes under constant polarization at -0.1V vs saturated calomel reference (SCE) with 10 mM acetate as substrate. The reactors were inoculated with three different microbial samples that were drawn from exactly the same place in a French Atlantic coastal port (i) by scraping the biofilm that had formed naturally on the surface of a floating bridge, (ii) by taking marine sediments just under the floating bridge, and (iii) by taking nearby beach sand. Current densities of 2.0 A/m2 were reached using the biofilm sample as inoculum while only 0.4 A/m2 and 0.8 A/m2 were obtained using the underlying sediments and the beach sand, respectively. The structure of bacterial communities forming biofilms was characterized by denaturing gradient gel electrophoresis (DGGE) analysis, and revealed differences between samples with the increase in relative intensities of some bands and the appearance of others. Bacteria close related to Bacteroidetes, Halomonas, and Marinobacterium were retrieved only from the efficient EA-biofilms formed from natural biofilms, whereas, bacteria close related to Mesoflavibacter were predominant on biofilm formed from sediments. The marine biofilm was selected as the inoculum to further optimize the microbial anode. Epifluorescence microscopy and SEM confirmed that maintaining the electrode under constant polarization promoted rapid settlement of the electrode surface by a bacterial monolayer film. The microbial anode was progressively adapted to the consumption of acetate by three serial additions of substrate, thus improving the Coulombic efficiency of acetate consumption from 31 to 89%. The possible oxidation of sulfide played only a very small part in the current production and the biofilm was not able to oxidize hydrogen. Graphite proved to be more efficient than dimensionally stable anode (DSA) or stainless steel butthis result might be due to differences in the surface roughness rather than the intrinsic features of the materials. Finally, a maximal current density of 7.9 A/m2 was reached with 10 mM acetate after only 8 days of biofilm formation at -0.1 V/SCE. These results are among the best performance values reported in the literature. Using natural biofilms as inoculum should, consequently, be a new, very promising wayto rapidly build more efficient microbial electrodes than those produced when the inoculum is drawn from bulk environments.
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Affiliation(s)
- Benjamin Erable
- Laboratoire de Génie Chimique CNRS, Université de Toulouse, 5 rue Paulin Talabot BP1301, 31106 Toulouse, France.
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