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Baumel A, Nieto Feliner G, Médail F, La Malfa S, Di Guardo M, Bou Dagher Kharrat M, Lakhal-Mirleau F, Frelon V, Ouahmane L, Diadema K, Sanguin H, Viruel J. Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of a fruit tree in the Mediterranean. Mol Ecol 2022; 31:4095-4111. [PMID: 35691023 PMCID: PMC9541536 DOI: 10.1111/mec.16563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/13/2022] [Accepted: 06/08/2022] [Indexed: 12/22/2022]
Abstract
Intense research efforts over the last two decades have renewed our understanding of plant phylogeography and domestication in the Mediterranean basin. Here we aim to investigate the evolutionary history and the origin of domestication of the carob tree (Ceratonia siliqua), which has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to delimit seven carob evolutionary units (CEUs). We investigated genome‐wide diversity and evolutionary patterns of the CEUs with 3557 single nucleotide polymorphisms generated by restriction‐site associated DNA sequencing (RADseq). To address the complex wild vs. cultivated status of sampled trees, we classified 56 sampled populations across the Mediterranean basin as wild, seminatural or cultivated. Nuclear and cytoplasmic loci were identified from RADseq data and separated for analyses. Phylogenetic analyses of these genomic‐wide data allowed us to resolve west‐to‐east expansions from a single long‐term refugium probably located in the foothills of the High Atlas Mountains near the Atlantic coast. Our findings support multiple origins of domestication with a low impact on the genetic diversity at range‐wide level. The carob was mostly domesticated from locally selected wild genotypes and scattered long‐distance westward dispersals of domesticated varieties by humans, concomitant with major historical migrations by Romans, Greeks and Arabs. Ex situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in southwest Morocco, south Spain and eastern Mediterranean. Our study highlights the relevance of wild and seminatural habitats in the conservation of genetic resources for cultivated trees.
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Affiliation(s)
- Alex Baumel
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | | | - Frédéric Médail
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Magda Bou Dagher Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Beirut, Lebanon
| | - Fatma Lakhal-Mirleau
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Valentine Frelon
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Lahcen Ouahmane
- Faculté des Sciences Semlalia, Laboratoire de Biotechnologies Microbiennes Agrosciences et Environnement, Université Cadi Ayyad Marrakech, Marrakech, Morocco
| | - Katia Diadema
- Conservatoire Botanique National Méditerranéen de Porquerolles (CBNMed), Hyères, France
| | - Hervé Sanguin
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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2
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Fall F, Sanguin H, Fall D, Tournier E, Bakhoum N, Ndiaye C, Diouf D, Bâ AM. Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant-Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient. Microb Ecol 2022; 83:886-898. [PMID: 34245330 DOI: 10.1007/s00248-021-01779-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/02/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. robustus and P. juliflora, but the AM fungal community determinants are largely unknown. The current field-based study aimed at (1) characterizing the environmental drivers (rhizosphere physico-chemical properties, plant type and season) of the AM fungal community along an environmental gradient and (2) identifying the AM fungal taxa that might explain the S. robustus-mediated benefits to P. juliflora. Glomeraceae predominated in the two plants, but a higher richness was observed for S. robustus. The pH and salinity were the main drivers of AM fungal community associated with the two plants, negatively impacting richness and diversity. However, while a negative impact was also observed on mycorrhizal colonization for S. robustus, P. juliflora showed opposite colonization patterns. Furthermore, no change was observed in terms of AM fungal community dissimilarity between the two plants along the environmental gradient as would be expected according to the stress-gradient and complementary hypotheses when a facilitation process occurs. However, changes in intraspecific diversity of shared AM fungal community between the two plants were observed, highlighting 23 AM fungal OTUs associated with both plants and the highest salinity levels. Consequently, the increase of their abundance and frequency along the environmental gradient might suggest their potential role in the facilitation process that can take place between the two plants. Their use in ecological engineering could also represent promising avenues for improving vegetation restoration in saline Senegalese's lands.
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Affiliation(s)
- Fatoumata Fall
- LCM Laboratoire Commun de Microbiologie, IRD, ISRA, UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal
- LAPSE Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux, Dakar, Senegal
| | - Hervé Sanguin
- CIRAD, UMR PHIM, 34090, Montpellier, France.
- PHIM Plant Health Institute, CIRAD, INRAE, Institut Agro, IRD, Univ Montpellier, Montpellier, France.
| | - Dioumacor Fall
- LCM Laboratoire Commun de Microbiologie, IRD, ISRA, UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal
- Institut Sénégalais de Recherches Agricoles (ISRA), Centre National de Recherches Agronomiques (CNRA), Bambey, Senegal
| | - Estelle Tournier
- CIRAD, UMR PHIM, 34090, Montpellier, France
- PHIM Plant Health Institute, CIRAD, INRAE, Institut Agro, IRD, Univ Montpellier, Montpellier, France
| | - Niokhor Bakhoum
- LCM Laboratoire Commun de Microbiologie, IRD, ISRA, UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal
- LAPSE Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux, Dakar, Senegal
- Département Environnement, Biodiversité Et Développement Durable, Université du Sine Saloum El-Hadj Ibrahima NIASS (USSEIN), Kaolack, Senegal
| | - Cheikh Ndiaye
- Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Diégane Diouf
- Département Environnement, Biodiversité Et Développement Durable, Université du Sine Saloum El-Hadj Ibrahima NIASS (USSEIN), Kaolack, Senegal
| | - Amadou Mustapha Bâ
- Laboratoire de Biologie Et Physiologie Végétales, Université Des Antilles, Guadeloupe, France
- LSTM, CIRAD, INRAE, IRD, Institut Agro, Univ Montpellier, Montpellier, France
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3
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Alonso P, Blondin L, Gladieux P, Mahé F, Sanguin H, Ferdinand R, Filloux D, Desmarais E, Cerqueira F, Jin B, Huang H, He X, Morel JB, Martin DP, Roumagnac P, Vernière C. Heterogeneity of the rice microbial community of the Chinese centuries-old Honghe Hani rice terraces system. Environ Microbiol 2020; 22:3429-3445. [PMID: 32510843 PMCID: PMC7497281 DOI: 10.1111/1462-2920.15114] [Citation(s) in RCA: 8] [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: 03/03/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 11/30/2022]
Abstract
The Honghe Hani rice terraces system (HHRTS) is a traditional rice cultivation system where Hani people cultivate remarkably diverse rice varieties. Recent introductions of modern rice varieties to the HHRTS have significantly increased the severity of rice diseases within the terraces. Here, we determine the impacts of these recent introductions on the composition of the rice-associated microbial communities. We confirm that the HHRTS contains a range of both traditional HHRTS landraces and introduced modern rice varieties and find differences between the microbial communities of these two groups. However, this introduction of modern rice varieties has not strongly impacted the overall diversity of the HHRTS rice microbial community. Furthermore, we find that the rice varieties (i.e. groups of closely related genotypes) have significantly structured the rice microbial community composition (accounting for 15%-22% of the variance) and that the core microbial community of HHRTS rice plants represents less than 3.3% of all the microbial taxa identified. Collectively, our study suggests a highly diverse HHRTS rice holobiont (host with its associated microbes) where the diversity of rice hosts mirrors the diversity of their microbial communities. Further studies will be needed to better determine how such changes might impact the sustainability of the HHRTS.
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Affiliation(s)
- Pascal Alonso
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Laurence Blondin
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Pierre Gladieux
- BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France.,INRA, BGPI, Montpellier, France
| | - Frédéric Mahé
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Hervé Sanguin
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Romain Ferdinand
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Denis Filloux
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Eric Desmarais
- ISEM, CNRS, University of Montpellier, IRD, EPHE, Montpellier, France
| | | | - Baihui Jin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Southwest Forestry University, Kunming, China
| | - Jean-Benoit Morel
- BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France.,INRA, BGPI, Montpellier, France
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 4579, South Africa
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Christian Vernière
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
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Robin A, Pradier C, Sanguin H, Mahé F, Lambais GR, de Araujo Pereira AP, Germon A, Santana MC, Tisseyre P, Pablo AL, Heuillard P, Sauvadet M, Bouillet JP, Andreote FD, Plassard C, de Moraes Gonçalves JL, Cardoso EJBN, Laclau JP, Hinsinger P, Jourdan C. How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation. Mycorrhiza 2019; 29:637-648. [PMID: 31732817 DOI: 10.1007/s00572-019-00917-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 03/02/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.
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Affiliation(s)
- Agnès Robin
- CIRAD, UMR Eco&Sols, Piracicaba, SP, 13418-900, Brazil.
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France.
- ESALQ, University São Paulo, Piracicaba, SP, 13418-900, Brazil.
| | - Céline Pradier
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR Eco&Sols, F-34398, Montpellier, France
| | - Hervé Sanguin
- CIRAD, UMR BGPI, F-34398, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Frédéric Mahé
- CIRAD, UMR BGPI, F-34398, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | | | - Amandine Germon
- UNESP, University São Paulo, Botucatu, SP, 18610-300, Brazil
| | | | - Pierre Tisseyre
- LSTM, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Anne-Laure Pablo
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Pauline Heuillard
- INRA, US 1426, GeT-PlaGe, Genotoul, F-31320, Castanet-Tolosan, France
| | - Marie Sauvadet
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Bouillet
- CIRAD, UMR Eco&Sols, Piracicaba, SP, 13418-900, Brazil
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | - Claude Plassard
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | | | - Jean-Paul Laclau
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR Eco&Sols, F-34398, Montpellier, France
| | - Philippe Hinsinger
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Christophe Jourdan
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR Eco&Sols, F-34398, Montpellier, France
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5
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Viruel J, Haguenauer A, Juin M, Mirleau F, Bouteiller D, Boudagher‐Kharrat M, Ouahmane L, La Malfa S, Médail F, Sanguin H, Nieto Feliner G, Baumel A. Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae). Appl Plant Sci 2018; 6:e01201. [PMID: 30598859 PMCID: PMC6303155 DOI: 10.1002/aps3.1201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/28/2018] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected. METHODS In this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results. RESULTS The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates. DISCUSSION Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.
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Affiliation(s)
- Juan Viruel
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Anne Haguenauer
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Marianick Juin
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Fatma Mirleau
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Delphine Bouteiller
- Institut du Cerveau et de la Moelle épinière (ICM)Hôpital Pitié Salpêtrière47 Boulevard de l'Hôpital75013ParisFrance
| | - Magda Boudagher‐Kharrat
- Laboratoire Caractérisation Génétique des PlantesFaculté des sciencesUniversité Saint‐JosephB.P. 11‐514 Riad El SolhBeirut1107 2050Lebanon
| | - Lahcen Ouahmane
- Laboratoire d'Ecologie et EnvironnementFaculté des Sciences SemlaliaUniversité Cadi AyyadMarrakeshMorocco
| | - Stefano La Malfa
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A)Università degli Studi di CataniaVia Valdisavoia 595123CataniaItaly
| | - Frédéric Médail
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Hervé Sanguin
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD)Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM)MontpellierFrance
- LSTM [LSTM is sponsored by University of Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro]TA A‐82/J Campus International de BaillarguetFR‐34398Montpellier CEDEX 5France
| | | | - Alex Baumel
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
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Maghnia FZ, Abbas Y, Mahé F, Kerdouh B, Tournier E, Ouadji M, Tisseyre P, Prin Y, El Ghachtouli N, Bakkali Yakhlef SE, Duponnois R, Sanguin H. Habitat- and soil-related drivers of the root-associated fungal community of Quercus suber in the Northern Moroccan forest. PLoS One 2017; 12:e0187758. [PMID: 29155841 PMCID: PMC5695781 DOI: 10.1371/journal.pone.0187758] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 01/27/2017] [Accepted: 10/25/2017] [Indexed: 12/25/2022] Open
Abstract
Soil fungi associated with plant roots, notably ectomycorrhizal (EcM) fungi, are central in above- and below-ground interactions in Mediterranean forests. They are a key component in soil nutrient cycling and plant productivity. Yet, major disturbances of Mediterranean forests, particularly in the Southern Mediterranean basin, are observed due to the greater human pressures and climate changes. These disturbances highly impact forest cover, soil properties and consequently the root-associated fungal communities. The implementation of efficient conservation strategies of Mediterranean forests is thus closely tied to our understanding of root-associated fungal biodiversity and environmental rules driving its diversity and structure. In our study, the root-associated fungal community of Q. suber was analyzed using high-throughput sequencing across three major Moroccan cork oak habitats. Significant differences in root-associated fungal community structures of Q. suber were observed among Moroccan cork oak habitats (Maâmora, Benslimane, Chefchaoun) subjected to different human disturbance levels (high to low disturbances, respectively). The fungal community structure changes correlated with a wide range of soil properties, notably with pH, C:N ratio (P = 0.0002), and available phosphorus levels (P = 0.0001). More than 90 below-ground fungal indicators (P < 0.01)-either of a type of habitat and/or a soil property-were revealed. The results shed light on the ecological significance of ubiquitous ectomycorrhiza (Tomentella, Russula, Cenococcum), and putative sclerotia-associated/ericoid mycorrhizal fungal taxa (Cladophialophora, Oidiodendron) in the Moroccan cork oak forest, and their intraspecific variability regarding their response to land use and soil characteristics.
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Affiliation(s)
- Fatima Zahra Maghnia
- Forestry research center, Rabat, Morocco
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
- IRD, UMR LSTM, Montpellier, France
| | - Younes Abbas
- Polyvalent Laboratory, Multidisciplinary Faculty, University of Sultan Moulay Slimane, Béni Mellal, Morocco
| | - Frédéric Mahé
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Estelle Tournier
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Pierre Tisseyre
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
- IRD, UMR LSTM, Montpellier, France
| | - Yves Prin
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
| | - Naïma El Ghachtouli
- Laboratory of Microbial Biotechnology, Faculty of Sciences and Technology, University of Sidi Mohamed Ben Abdellah, Fez, Morocco
| | | | - Robin Duponnois
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
- IRD, UMR LSTM, Montpellier, France
| | - Hervé Sanguin
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
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7
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Geoffroy A, Sanguin H, Galiana A, Bâ A. Molecular Characterization of Arbuscular Mycorrhizal Fungi in an Agroforestry System Reveals the Predominance of Funneliformis spp. Associated with Colocasia esculenta and Pterocarpus officinalis Adult Trees and Seedlings. Front Microbiol 2017; 8:1426. [PMID: 28804479 PMCID: PMC5532380 DOI: 10.3389/fmicb.2017.01426] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/14/2017] [Indexed: 11/13/2022] Open
Abstract
Pterocarpus officinalis (Jacq.) is a leguminous forestry tree species endemic to Caribbean swamp forests. In Guadeloupe, smallholder farmers traditionally cultivate flooded taro (Colocasia esculenta) cultures under the canopy of P. officinalis stands. The role of arbuscular mycorrhizal (AM) fungi in the sustainability of this traditional agroforestry system has been suggested but the composition and distribution of AM fungi colonizing the leguminous tree and/or taro are poorly characterized. An in-depth characterization of root-associated AM fungal communities from P. officinalis adult trees and seedlings and taro cultures, sampled in two localities of Guadeloupe, was performed by pyrosequencing (GS FLX+) of partial 18S rRNA gene. The AM fungal community was composed of 215 operational taxonomic units (OTUs), belonging to eight fungal families dominated by Glomeraceae, Acaulosporaceae, and Gigasporaceae. Results revealed a low AM fungal community membership between P. officinalis and C. esculenta. However, certain AM fungal community taxa (10% of total community) overlapped between P. officinalis and C. esculenta, notably predominant Funneliformis OTUs. These findings provide new perspectives in deciphering the significance of Funneliformis in nutrient exchange between P. officinalis and C. esculenta by forming a potential mycorrhizal network.
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Affiliation(s)
- Alexandre Geoffroy
- Laboratoire de Biologie et Physiologie Végétales, L’Unité de Formation des Sciences Exactes et Naturelles, Unité Mixte de Recherche LSTM, Université des AntillesPointe-à-Pitre, France
- Unité Mixte de Recherche LTSM, Centre de Coopération Internationale en Recherche Agronomique Pour le DéveloppementMontpellier, France
| | - Hervé Sanguin
- Unité Mixte de Recherche LTSM, Centre de Coopération Internationale en Recherche Agronomique Pour le DéveloppementMontpellier, France
| | - Antoine Galiana
- Unité Mixte de Recherche LTSM, Centre de Coopération Internationale en Recherche Agronomique Pour le DéveloppementMontpellier, France
| | - Amadou Bâ
- Laboratoire de Biologie et Physiologie Végétales, L’Unité de Formation des Sciences Exactes et Naturelles, Unité Mixte de Recherche LSTM, Université des AntillesPointe-à-Pitre, France
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Maghnia FZ, Sanguin H, Abbas Y, Verdinelli M, Kerdouh B, El Ghachtouli N, Lancellotti E, Bakkali Yakhlef SE, Duponnois R. [Impact of cork oak management on the ectomycorrhizal fungal diversity associated with Quercus suber in the Mâamora forest (Morocco)]. C R Biol 2017; 340:298-305. [PMID: 28506468 DOI: 10.1016/j.crvi.2017.04.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 11/28/2022]
Abstract
The cork oak forest is an ecosystem playing a major role in Moroccan socio-economy and biodiversity conservation. However, this ecosystem is negatively impacted by extensive human- and climate-driven pressures, causing a strong decrease in its distribution and a worsening of the desertification processes. This study aims at characterising the impact of cork oak forest management on a major actor of its functioning, the ectomycorrhizal (EcM) fungal community associated with Quercus suber, and the determination of EcM bio-indicators. The EcM fungal community has been monitored during spring and winter seasons in two sites of the Moroccan Mâamora forest, corresponding to a forest site either impacted by human activities or protected. A significant impact of cork oak forest management on the EcM fungal community has been revealed, with major differences during the summer season. The results confirmed the potential ecological significance of several EcM fungi (e.g., Cenococcum) in the sustainability of the cork oak forest functioning, but also the significant association of certain EcM fungi (Pachyphloeus, Russula, Tomentella) with a perturbation or a season, and consequently to the cork oak forest status or to climatic conditions, respectively. The development of study at the Mediterranean scale may improve the robustness of ecological models to predict the impact of global changes on this emblematic ecosystem of Mediterranean basin.
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Affiliation(s)
- Fatima Z Maghnia
- CIRAD, UMR LSTM, 34398 Montpellier, France; Centre de la recherche forestière, Rabat, Maroc; Laboratoire de biotechnologie microbienne, faculté des sciences et techniques, université Sidi-Mohamed-Ben-Abdellah, Fès, Maroc
| | | | - Younes Abbas
- Centre de la recherche forestière, Rabat, Maroc; Département de biologie-géologie, faculté polydisciplinaire, université Sultan-Moulay-Slimane, Béni Mellal, Maroc
| | | | | | - Naima El Ghachtouli
- Laboratoire de biotechnologie microbienne, faculté des sciences et techniques, université Sidi-Mohamed-Ben-Abdellah, Fès, Maroc
| | | | - Salah Eddine Bakkali Yakhlef
- Direction de l'enseignement, de la formation et de la recherche, ministère de l'Agriculture et de la Pêche maritime, Rabat, Maroc
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9
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Wahbi S, Prin Y, Thioulouse J, Sanguin H, Baudoin E, Maghraoui T, Oufdou K, Le Roux C, Galiana A, Hafidi M, Duponnois R. Impact of Wheat/Faba Bean Mixed Cropping or Rotation Systems on Soil Microbial Functionalities. Front Plant Sci 2016; 7:1364. [PMID: 27695462 PMCID: PMC5023684 DOI: 10.3389/fpls.2016.01364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/29/2016] [Indexed: 05/21/2023]
Abstract
Cropping systems based on carefully designed species mixtures reveal many potential advantages in terms of enhancing crop productivity, reducing pest and diseases, and enhancing ecological services. Associating cereals and legume production either through intercropping or rotations might be a relevant strategy of producing both type of culture, while benefiting from combined nitrogen fixed by the legume through its symbiotic association with nitrogen-fixing bacteria, and from a better use of P and water through mycorrhizal associations. These practices also participate to the diversification of agricultural productions, enabling to secure the regularity of income returns across the seasonal and climatic uncertainties. In this context, we designed a field experiment aiming to estimate the 2 years impact of these practices on wheat yield and on soil microbial activities as estimated through Substrate Induced Respiration method and mycorrhizal soil infectivity (MSI) measurement. It is expected that understanding soil microbial functionalities in response to these agricultural practices might allows to target the best type of combination, in regard to crop productivity. We found that the tested cropping systems largely impacted soil microbial functionalities and MSI. Intercropping gave better results in terms of crop productivity than the rotation practice after two cropping seasons. Benefits resulting from intercrop should be highly linked with changes recorded on soil microbial functionalities.
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Affiliation(s)
- Sanâa Wahbi
- IRD, UMR LSTMMontpellier, France
- Laboratoire Ecologie et Environnement (Unité Associée au CNRST, URAC 32), Faculté des Sciences Semlalia, Université Cadi AyyadMarrakech, Morocco
| | | | - Jean Thioulouse
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie EvolutiveVilleurbanne, France
| | | | | | - Tasnime Maghraoui
- IRD, UMR LSTMMontpellier, France
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie EvolutiveVilleurbanne, France
- Laboratoire de Biologie et de Biotechnologie des Microorganisms, Faculté des Sciences Semlalia, Université Cadi AyyadMarrakech, Morocco
| | - Khalid Oufdou
- Laboratoire de Biologie et de Biotechnologie des Microorganisms, Faculté des Sciences Semlalia, Université Cadi AyyadMarrakech, Morocco
| | | | | | - Mohamed Hafidi
- Laboratoire Ecologie et Environnement (Unité Associée au CNRST, URAC 32), Faculté des Sciences Semlalia, Université Cadi AyyadMarrakech, Morocco
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Le Roux C, Tournier E, Lies A, Sanguin H, Chevalier G, Duponnois R, Mousain D, Prin Y. Bacteria of the genus Rhodopseudomonas (Bradyrhizobiaceae): obligate symbionts in mycelial cultures of the black truffles Tuber melanosporum and Tuber brumale. Springerplus 2016; 5:1085. [PMID: 27468385 PMCID: PMC4947074 DOI: 10.1186/s40064-016-2756-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/05/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND This work aimed at characterizing 12 isolates of the genus Tuber including Tuber melanosporum (11 isolates) and Tuber brumale (one isolate). This was done using internal transcribed spacer (ITS) sequences, confirming their origin. RESULTS Analysis of their mating type revealed that both MAT1-1 and MAT1-2 exist within these isolates (with 3 and 8 of each, respectively). We observed that each of these cultures was consistently associated with one bacterium that was intimately linked to fungal growth. These bacterial associates failed to grow in the absence of fungus. We extracted DNA from bacterial colonies in the margin of mycelium and sequenced a nearly complete 16S rDNA gene and a partial ITS fragment. We found they all belonged to the genus Rhodopseudomonas, fitting within different phylogenetic clusters. No relationships were evidenced between bacterial and fungal strains or mating types. Rhodopseudomonas being a sister genus to Bradyrhizobium, we tested the nodulation ability of these bacteria on a promiscuously nodulating legume (Acacia mangium), without success. We failed to identify any nifH genes among these isolates, using two different sets of primers. CONCLUSIONS While the mechanisms of interaction between Tuber and Rhodopseudomonas remain to be elucidated, their interdependency for in vitro growth seems a novel feature of this fungus.
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Affiliation(s)
| | | | - Adrien Lies
- />CIRAD, UMR LSTM, 34398 Montpellier Cedex 5, France
| | - Hervé Sanguin
- />CIRAD, UMR LSTM, 34398 Montpellier Cedex 5, France
| | - Gérard Chevalier
- />INRA Centre de Recherche de Clermont-Theix, 63039 Clermont-Ferrand Cedex, France
| | | | - Daniel Mousain
- />Société d’Horticulture et d’Histoire Naturelle de l’Hérault, Parc à Ballon 1, bâtiment B, 125 rue du Moulin de Sémalen, 34000 Montpellier, France
| | - Yves Prin
- />CIRAD, UMR LSTM, 34398 Montpellier Cedex 5, France
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11
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Ouaryi A, Boularbah A, Sanguin H, Hafidi M, Baudoin E, Ouahmane L, Le Roux C, Galiana A, Prin Y, Duponnois R. High potential of symbiotic interactions between native mycorrhizal fungi and the exotic tree Eucalyptus camaldulensis for phytostabilization of metal-contaminated arid soils. Int J Phytoremediation 2016; 18:41-47. [PMID: 26529094 DOI: 10.1080/15226514.2015.1058335] [Citation(s) in RCA: 2] [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] [Indexed: 06/05/2023]
Abstract
Waste dumps generated by mining activities contain heavy metals that are dispersed into areas leading to significant environmental contamination. The objectives of this study were (i) to survey native plants and their associated AM fungal communities from waste soils in a Moroccan mine site and (ii) to follow Eucalyptus growth in soil collected from the waste-mine. AM spores from native plant species were collected from the mining site and the surrounding uncontaminated areas were multiplied and inoculated onto Eucalyptus camaldulensis. The results showed that (i) the native plant species recorded in the waste did not show an active metal uptake, (ii) the selected native plant species are associated with AM mycorrhizal fungi and (iii) the use of AM fungi adapted to these drastic conditions can improve the growth of the fast-growing tree, E. camaldulensis and its tolerance to high soil Cu content. In conclusion, it is suggested that in order to define efficient low-cost phytostabilization processes, the use of native resources (i.e., mixtures of native mycorrhizal fungi) in combination with fast-growing tree species such as Eucalyptus, could be used to optimize the establishment of a permanent cover plant in contaminated areas.
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Affiliation(s)
- A Ouaryi
- a Laboratoire Ecologie & Environnement (Unité associée au CNRST, URAC), Faculté des Sciences Semlalia, Université Cadi Ayyad , Marrakech , Maroc
- b Laboratoire d'Aliment, Environnement et Santé, Département de Biologie, Faculté des Sciences et Techniques-Marrakech, Université CadiAyyad , Marrakech , Maroc
| | - A Boularbah
- b Laboratoire d'Aliment, Environnement et Santé, Département de Biologie, Faculté des Sciences et Techniques-Marrakech, Université CadiAyyad , Marrakech , Maroc
| | - H Sanguin
- c CIRAD, UMR LSTM , Montpellier , France
| | - M Hafidi
- a Laboratoire Ecologie & Environnement (Unité associée au CNRST, URAC), Faculté des Sciences Semlalia, Université Cadi Ayyad , Marrakech , Maroc
| | - E Baudoin
- d IRD, UMR LSTM , Montpellier , France
| | - L Ouahmane
- a Laboratoire Ecologie & Environnement (Unité associée au CNRST, URAC), Faculté des Sciences Semlalia, Université Cadi Ayyad , Marrakech , Maroc
| | - C Le Roux
- c CIRAD, UMR LSTM , Montpellier , France
| | - A Galiana
- c CIRAD, UMR LSTM , Montpellier , France
| | - Y Prin
- c CIRAD, UMR LSTM , Montpellier , France
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12
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Drogue B, Sanguin H, Chamam A, Mozar M, Llauro C, Panaud O, Prigent-Combaret C, Picault N, Wisniewski-Dyé F. Plant root transcriptome profiling reveals a strain-dependent response during Azospirillum-rice cooperation. Front Plant Sci 2014; 5:607. [PMID: 25414716 PMCID: PMC4222233 DOI: 10.3389/fpls.2014.00607] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/18/2014] [Indexed: 05/07/2023]
Abstract
Cooperation involving Plant Growth-Promoting Rhizobacteria results in improvements of plant growth and health. While pathogenic and symbiotic interactions are known to induce transcriptional changes for genes related to plant defense and development, little is known about the impact of phytostimulating rhizobacteria on plant gene expression. This study aims at identifying genes significantly regulated in rice roots upon Azospirillum inoculation, considering possible favored interaction between a strain and its original host cultivar. Genome-wide analyzes of Oryza sativa japonica cultivars Cigalon and Nipponbare were performed, by using microarrays, seven days post-inoculation with Azospirillum lipoferum 4B (isolated from Cigalon) or Azospirillum sp. B510 (isolated from Nipponbare) and compared to the respective non-inoculated condition. A total of 7384 genes were significantly regulated, which represent about 16% of total rice genes. A set of 34 genes is regulated by both Azospirillum strains in both cultivars, including a gene orthologous to PR10 of Brachypodium, and these could represent plant markers of Azospirillum-rice interactions. The results highlight a strain-dependent response of rice, with 83% of the differentially expressed genes being classified as combination-specific. Whatever the combination, most of the differentially expressed genes are involved in primary metabolism, transport, regulation of transcription and protein fate. When considering genes involved in response to stress and plant defense, it appears that strain B510, a strain displaying endophytic properties, leads to the repression of a wider set of genes than strain 4B. Individual genotypic variations could be the most important driving force of rice roots gene expression upon Azospirillum inoculation. Strain-dependent transcriptional changes observed for genes related to auxin and ethylene signaling highlight the complexity of hormone signaling networks in the Azospirillum-rice cooperation.
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Affiliation(s)
- Benoît Drogue
- Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, Université Lyon 1Villeurbanne, France
| | - Hervé Sanguin
- Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, Université Lyon 1Villeurbanne, France
| | - Amel Chamam
- Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, Université Lyon 1Villeurbanne, France
| | - Michael Mozar
- Laboratoire de Génome et Développement des Plantes, UMR 5096 CNRS/IRD/Université de Perpignan Via DomitiaPerpignan, France
| | - Christel Llauro
- Laboratoire de Génome et Développement des Plantes, UMR 5096 CNRS/IRD/Université de Perpignan Via DomitiaPerpignan, France
| | - Olivier Panaud
- Laboratoire de Génome et Développement des Plantes, UMR 5096 CNRS/IRD/Université de Perpignan Via DomitiaPerpignan, France
| | | | - Nathalie Picault
- Laboratoire de Génome et Développement des Plantes, UMR 5096 CNRS/IRD/Université de Perpignan Via DomitiaPerpignan, France
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Héry M, Rizoulis A, Sanguin H, Cooke DA, Pancost RD, Polya DA, Lloyd JR. Microbial ecology of arsenic-mobilizing Cambodian sediments: lithological controls uncovered by stable-isotope probing. Environ Microbiol 2014; 17:1857-69. [PMID: 24467551 DOI: 10.1111/1462-2920.12412] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 01/20/2014] [Indexed: 11/29/2022]
Abstract
Microbially mediated arsenic release from Holocene and Pleistocene Cambodian aquifer sediments was investigated using microcosm experiments and substrate amendments. In the Holocene sediment, the metabolically active bacteria, including arsenate-respiring bacteria, were determined by DNA stable-isotope probing. After incubation with (13) C-acetate and (13) C-lactate, active bacterial community in the Holocene sediment was dominated by different Geobacter spp.-related 16S rRNA sequences. Substrate addition also resulted in the enrichment of sequences related to the arsenate-respiring Sulfurospirillum spp. (13) C-acetate selected for ArrA related to Geobacter spp. whereas (13) C-lactate selected for ArrA which were not closely related to any cultivated organism. Incubation of the Pleistocene sediment with lactate favoured a 16S rRNA-phylotype related to the sulphate-reducing Desulfovibrio oxamicus DSM1925, whereas the ArrA sequences clustered with environmental sequences distinct from those identified in the Holocene sediment. Whereas limited As(III) release was observed in Pleistocene sediment after lactate addition, no arsenic mobilization occurred from Holocene sediments, probably because of the initial reduced state of As, as determined by X-ray Absorption Near Edge Structure. Our findings demonstrate that in the presence of reactive organic carbon, As(III) mobilization can occur in Pleistocene sediments, having implications for future strategies that aim to reduce arsenic contamination in drinking waters by using aquifers containing Pleistocene sediments.
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Affiliation(s)
- Marina Héry
- School of Earth, Atmospheric and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, University of Manchester, Manchester, UK
| | - Athanasios Rizoulis
- School of Earth, Atmospheric and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, University of Manchester, Manchester, UK
| | - Hervé Sanguin
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - David A Cooke
- Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, UK
| | - Richard D Pancost
- Organic Geochemistry Unit, The Cabot Institute, Bristol Biogeochemistry Research Centre, School of Chemistry, Cantock's Close, Bristol University, Bristol, UK
| | - David A Polya
- School of Earth, Atmospheric and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, University of Manchester, Manchester, UK
| | - Jonathan R Lloyd
- School of Earth, Atmospheric and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, University of Manchester, Manchester, UK
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14
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Drogue B, Sanguin H, Borland S, Prigent-Combaret C, Wisniewski-Dyé F. Genome wide profiling of Azospirillum lipoferum 4B gene expression during interaction with rice roots. FEMS Microbiol Ecol 2013; 87:543-55. [PMID: 24283406 DOI: 10.1111/1574-6941.12244] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [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: 06/07/2013] [Revised: 08/18/2013] [Accepted: 10/31/2013] [Indexed: 01/02/2023] Open
Abstract
Azospirillum-plant cooperation has been mainly studied from an agronomic point of view leading to a wide description of mechanisms implicated in plant growth-promoting effects. However, little is known about genetic determinants implicated in bacterial adaptation to the host plant during the transition from free-living to root-associated lifestyles. This study aims at characterizing global gene expression of Azospirillum lipoferum 4B following a 7-day-old interaction with two cultivars of Oryza sativa L. japonica (cv. Cigalon from which it was originally isolated, and cv. Nipponbare). The analysis was done on a whole genome expression array with RNA samples obtained from planktonic cells, sessile cells, and root-adhering cells. Root-associated Azospirillum cells grow in an active sessile-like state and gene expression is tightly adjusted to the host plant. Adaptation to rice seems to involve genes related to reactive oxygen species (ROS) detoxification and multidrug efflux, as well as complex regulatory networks. As revealed by the induction of genes encoding transposases, interaction with root may drive bacterial genome rearrangements. Several genes related to ABC transporters and ROS detoxification display cultivar-specific expression profiles, suggesting host specific adaptation and raising the question of A. lipoferum 4B/rice cv. Cigalon co-adaptation.
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Affiliation(s)
- Benoît Drogue
- UMR5557 CNRS, Ecologie Microbienne, Université de Lyon, Villeurbanne, France
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15
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Duponnois R, Ramanankierana H, Hafidi M, Baohanta R, Baudoin E, Thioulouse J, Sanguin H, Bâ A, Galiana A, Bally R, Lebrun M, Prin Y. [Native plant resources to optimize the performances of forest rehabilitation in Mediterranean and tropical environment: some examples of nursing plant species that improve the soil mycorrhizal potential]. C R Biol 2013; 336:265-72. [PMID: 23916201 DOI: 10.1016/j.crvi.2013.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The overexploitation of natural resources, resulting in an increased need for arable lands by local populations, causes a serious dysfunction in the soil's biological functioning (mineral deficiency, salt stress, etc.). This dysfunction, worsened by the climatic conditions (drought), requires the implementation of ecological engineering strategies allowing the rehabilitation of degraded areas through the restoration of essential ecological services. The first symptoms of weathering processes of soil quality in tropical and Mediterranean environments result in an alteration of the plant cover structure with, in particular, the pauperization of plant species diversity and abundance. This degradation is accompanied by a weakening of soils and an increase of the impact of erosion on the surface layer resulting in reduced fertility of soils in terms of their physicochemical characteristics as well as their biological ones (e.g., soil microbes). Among the microbial components particularly sensitive to erosion, symbiotic microorganisms (rhizobia, Frankia, mycorrhizal fungi) are known to be key components in the main terrestrial biogeochemical cycles (C, N and P). Many studies have shown the importance of the management of these symbiotic microorganisms in rehabilitation and revegetation strategies of degraded environments, but also in improving the productivity of agrosystems. In particular, the selection of symbionts and their inoculation into the soil were strongly encouraged in recent decades. These inoculants were selected not only for their impact on the plant, but also for their ability to persist in the soil at the expense of the residual native microflora. The performance of this technique was thus evaluated on the plant cover, but its impact on soil microbial characteristics was totally ignored. The role of microbial diversity on productivity and stability (resistance, resilience, etc.) of eco- and agrosystems has been identified relatively recently and has led to a questioning of the conceptual bases of controlled inoculation in sustainable land management. It has been suggested that the environmental characteristics of the area to rehabilitate should be taken into account, and more particularly its degradation level in relation to the threshold of ecological resilience. This consideration should lead to the optimization of the cultural practices to either (i) restore the original properties of an ecosystem in case of slightly degraded environments or (ii) transform an ecosystem in case of highly degraded soils (e.g., mine soils). In this chapter, we discuss, through various examples of experiments conducted in tropical and Mediterranean areas, the performance of different strategies to manage the microbial potential in soils (inoculation of exotic vs. native species, inoculation or controlled management potential microbial stratum via aboveground vegetation, etc.) based on the level of environmental degradation.
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Affiliation(s)
- Robin Duponnois
- IRD, UMR 113, laboratoire des symbioses tropicales et méditerranéennes, campus Cirad de Baillarguet, 98 Montpellier cedex 5, France.
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16
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Chamam A, Sanguin H, Bellvert F, Meiffren G, Comte G, Wisniewski-Dyé F, Bertrand C, Prigent-Combaret C. Plant secondary metabolite profiling evidences strain-dependent effect in the Azospirillum-Oryza sativa association. Phytochemistry 2013; 87:65-77. [PMID: 23266268 DOI: 10.1016/j.phytochem.2012.11.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 11/08/2012] [Accepted: 11/15/2012] [Indexed: 05/21/2023]
Abstract
Azospirillum is a plant growth-promoting rhizobacterium (PGPR) able to enhance growth and yield of cereals such as rice, maize and wheat. The growth-promoting ability of some Azospirillum strains appears to be highly specific to certain plant species and cultivars. In order to ascertain the specificity of the associative symbiosis between rice and Azospirillum, the physiological response of two rice cultivars, Nipponbare and Cigalon, inoculated with two rice-associated Azospirillum was analyzed at two levels: plant growth response and plant secondary metabolic response. Each strain of Azospirillum (Azospirillum lipoferum 4B isolated from Cigalon and Azospirillum sp. B510 isolated from Nipponbare) preferentially increased growth of the cultivar from which it was isolated. This specific effect is not related to a defect in colonization of host cultivar as each strain colonizes effectively both rice cultivars, either at the rhizoplane (for 4B and B510) and inside the roots (for B510). The metabolic profiling approach showed that, in response to PGPR inoculation, profiles of rice secondary metabolites were modified, with phenolic compounds such as flavonoids and hydroxycinnamic derivatives being the main metabolites affected. Moreover, plant metabolic changes differed according to Azospirillum strain×cultivar combinations; indeed, 4B induced major secondary metabolic profile modifications only on Cigalon roots, while B510, probably due to its endophytic feature, induced metabolic variations on shoots and roots of both cultivars, triggering a systemic response. Plant secondary metabolite profiling thereby evidences the specific interaction between an Azospirillum strain and its original host cultivar.
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Affiliation(s)
- Amel Chamam
- CNRS, UMR 5557, Ecologie Microbienne, Université Lyon 1, Université de Lyon, Villeurbanne, France
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Prigent-Combaret C, Sanguin H, Champier L, Bertrand C, Monnez C, Colinon C, Blaha D, Ghigo JM, Cournoyer B. The bacterial thiopurine methyltransferase tellurite resistance process is highly dependent upon aggregation properties and oxidative stress response. Environ Microbiol 2012; 14:2645-60. [PMID: 22708879 DOI: 10.1111/j.1462-2920.2012.02802.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Bacterial thiopurine methyltransferases (bTPMTs) can favour resistance towards toxic tellurite oxyanions through a pathway leading to the emission of a garlic-like smell. Gene expression profiling completed by genetic, physiological and electron microscopy analyses was performed to identify key bacterial activities contributing to this resistance process. Escherichia coli strain MG1655 expressing the bTPMT was used as a cell model in these experiments. This strain produced a garlic-like smell which was found to be due to dimethyl telluride, and cell aggregates in culture media supplemented with tellurite. Properties involved in aggregation were correlated with cell attachment to polystyrene, which increased with tellurite concentrations. Gene expression profiling supported a role of adhesins in the resistance process with 14% of the tellurite-regulated genes involved in cell envelope, flagella and fimbriae biogenesis. Other tellurite-regulated genes were, at 27%, involved in energy, carbohydrate and amino acid metabolism including the synthesis of antioxidant proteins, and at 12% in the synthesis of transcriptional regulators and signal transduction systems. Escherichia coli mutants impaired in tellurite-regulated genes showed ubiquinone and adhesins synthesis, oxidative stress response, and efflux to be essential in the bTPMT resistance process. High tellurite resistance required a synergistic expression of these functions and an efficient tellurium volatilization by the bTPMT.
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Affiliation(s)
- Claire Prigent-Combaret
- Research group on «Bacterial Opportunistic Pathogens and Environment», Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Villeurbanne, F-69622, France
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Héry M, Sanguin H, Perez Fabiel S, Lefebvre X, Vogel TM, Paul E, Alfenore S. Monitoring of bacterial communities during low temperature thermal treatment of activated sludge combining DNA phylochip and respirometry techniques. Water Res 2010; 44:6133-6143. [PMID: 20673948 DOI: 10.1016/j.watres.2010.07.003] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 05/30/2010] [Accepted: 07/04/2010] [Indexed: 05/29/2023]
Abstract
Sludge reduction is one of the major challenges in biological wastewater treatment. One approach is to increase the sludge degradation yield together with the biodegradation kinetics. Among the various sludge pretreatment strategies proposed, thermal pretreatment at around 65 °C was described as promising. The enhancement in the biodegradation activity due to the selection of thermophilic hydrolytic bacteria was proposed, but further experiments are needed to demonstrate the specific role of these bacteria. In this study, concentrated activated sludge grown at 20 °C was subjected to thermal treatment at 65 °C for different periods. The originality of the work relied on a polyphasic approach based on the correlation between kinetics (chemical oxygen demand, COD; mixed liquor suspended solids, MLSS), bacterial activity (respirometry) and bacterial community structure (phylochip monitoring) in order to characterize the mechanisms involved in the thermal reduction of sludge. The bacterial activity in the aeration basin decreased to a very low level when recycling sludge was treated at 65 °C from 13 to 60 h, but then, started to increase after 60 h. In parallel to these fluctuations in activity, a drastic shift occurred in the bacterial community structure with the selection of thermophilic bacteria (mainly related to genera Paenibacillus and Bacillus), which are known for their specific hydrolases.
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Affiliation(s)
- Marina Héry
- Université de Toulouse, F-31077, Toulouse, France.
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Sanguin H, Sarniguet A, Gazengel K, Moënne-Loccoz Y, Grundmann GL. Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture. New Phytol 2009; 184:694-707. [PMID: 19732350 DOI: 10.1111/j.1469-8137.2009.03010.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The decline of take-all disease (Gaeumannomyces graminis var. tritici), which may take place during wheat monocropping, involves plant-protecting, root-colonizing microorganisms. So far, however, most work has focused on antagonistic fluorescent pseudomonads. Our objective was to assess the changes in rhizobacterial community composition during take-all decline of field-grown wheat. The study was based on the development and utilization of a taxonomic 16S rRNA-based microarray of 575 probes, coupled with cloning-sequencing and quantitative PCR. Plots from one experimental field grown with wheat for 1 yr (low level of disease), 5 yr (high level of disease) or 10 yr (low level of disease, suppressiveness reached) were used. Microarray data discriminated between the three stages. The outbreak stage (5 yr) was mainly characterized by the prevalence of Proteobacteria, notably Pseudomonas (Gammaproteobacteria), Nitrosospira (Betaproteobacteria), Rhizobacteriaceae, Sphingomonadaceae, Phyllobacteriaceae (Alphaproteobacteria), as well as Bacteroidetes and Verrucomicrobia. By contrast, suppressiveness (10 yr) correlated with the prevalence of a broader range of taxa, which belonged mainly to Acidobacteria, Planctomycetes, Nitrospira, Chloroflexi, Alphaproteobacteria (notably Azospirillum) and Firmicutes (notably Thermoanaerobacter). In conclusion, take-all decline correlated with multiple changes in rhizobacterial community composition, far beyond the sole case of pseudomonads.
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Affiliation(s)
- H Sanguin
- Université de Lyon, F-69003, Lyon, France
- Université Lyon 1, F-69003 Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - A Sarniguet
- INRA, Agrocampus Ouest, Université Rennes 1, UMR 1099 BiO3P 'Biologie des Organismes et des Populations appliquée à la Protection des Plantes', F-35653 Le Rheu, France
| | - K Gazengel
- INRA, Agrocampus Ouest, Université Rennes 1, UMR 1099 BiO3P 'Biologie des Organismes et des Populations appliquée à la Protection des Plantes', F-35653 Le Rheu, France
| | - Y Moënne-Loccoz
- Université de Lyon, F-69003, Lyon, France
- Université Lyon 1, F-69003 Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - G L Grundmann
- Université de Lyon, F-69003, Lyon, France
- Université Lyon 1, F-69003 Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, F-69622 Villeurbanne, France
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Sanguin H, Remenant B, Dechesne A, Thioulouse J, Vogel TM, Nesme X, Moënne-Loccoz Y, Grundmann GL. Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities. Appl Environ Microbiol 2006; 72:4302-12. [PMID: 16751545 PMCID: PMC1489601 DOI: 10.1128/aem.02686-05] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. The high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. Here, the power of this technology was evidenced through methodological verifications and analysis of maize rhizosphere effect based on a 16S rRNA-based microarray developed from the prototype of H. Sanguin et al. (Environ. Microbiol. 8:289-307, 2006). The current probe set was composed of 170 probes (41 new probes in this work) that targeted essentially the Proteobacteria. Cloning and sequencing of 16S rRNA amplicons were carried out on maize rhizosphere and bulk soil DNA. All tested clones that had a perfect match with corresponding probes were positive in the hybridization experiment. The hierarchically nested probes were reliable, but the level of taxonomic identification was variable, depending on the probe set specificity. The comparison of experimental and theoretical hybridizations revealed 0.91% false positives and 0.81% false negatives. The microarray detection threshold was estimated at 0.03% of a given DNA type based on DNA spiking experiments. A comparison of the maize rhizosphere and bulk soil hybridization results showed a significant rhizosphere effect, with a higher predominance of Agrobacterium spp. in the rhizosphere, as well as a lower prevalence of Acidobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes, a new taxon of interest in soil. In addition, well-known taxonomic groups such as Sphingomonas spp., Rhizobiaceae, and Actinobacteria were identified in both microbial habitats with strong hybridization signals. The taxonomic microarray developed in the present study was able to discriminate and characterize bacterial community composition in related biological samples, offering extensive possibilities for systematic exploration of bacterial diversity in ecosystems.
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Affiliation(s)
- Hervé Sanguin
- UMR CNRS 5557/USC INRA 1193 Ecologie Microbienne, Université Claude Bernard (Lyon 1), 43 bd du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
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Sanguin H, Herrera A, Oger-Desfeux C, Dechesne A, Simonet P, Navarro E, Vogel TM, Moënne-Loccoz Y, Nesme X, Grundmann GL. Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ Microbiol 2006; 8:289-307. [PMID: 16423016 DOI: 10.1111/j.1462-2920.2005.00895.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microarray approach has been proposed for high throughput analysis of the microbial community by providing snapshots of the microbial diversity under different environmental conditions. For this purpose, a prototype of a 16S rRNA-based taxonomic microarray was developed and evaluated for assessing bacterial community diversity. The prototype microarray is composed of 122 probes that target bacteria at various taxonomic levels from phyla to species (mostly Alphaproteobacteria). The prototype microarray was first validated using bacteria in pure culture. Differences in the sequences of probes and potential target DNAs were quantified as weighted mismatches (WMM) in order to evaluate hybridization reliability. As a general feature, probes having a WMM > 2 with target DNA displayed only 2.8% false positives. The prototype microarray was subsequently tested with an environmental sample, which consisted of an Agrobacterium-related polymerase chain reaction amplicon from a maize rhizosphere bacterial community. Microarray results were compared to results obtained by cloning-sequencing with the same DNA. Microarray analysis enabled the detection of all 16S rRNA gene sequences found by cloning-sequencing. Sequences representing only 1.7% of the clone library were detected. In conclusion, this prototype 16S rRNA-based taxonomic microarray appears to be a promising tool for the analysis of Alphaproteobacteria in complex ecosystems.
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Affiliation(s)
- Hervé Sanguin
- UMR CNRS 5557/USC INRA 1193 Ecologie Microbienne, Université Claude Bernard (Lyon 1), Villeurbanne, France
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Blaha D, Sanguin H, Robe P, Nalin R, Bally R, Moënne-Loccoz Y. Physical organization of phytobeneficial genesnifHandipdCin the plant growth-promoting rhizobacteriumAzospirillum lipoferum4VI. FEMS Microbiol Lett 2005; 244:157-63. [PMID: 15727835 DOI: 10.1016/j.femsle.2005.01.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Revised: 01/17/2005] [Accepted: 01/20/2005] [Indexed: 10/25/2022] Open
Abstract
The physical organization of phytobeneficial genes was investigated in the plant growth-promoting rhizobacterium Azospirillum lipoferum 4VI by hybridization screening of a bacterial artificial chromosome (BAC) library. Pulsed-field gel electrophoresis gave an estimated 5.7-Mb genome size for strain 4VI and a coverage level of 9 for the BAC library. The phytobeneficial genes nifH (associative nitrogen fixation) and ipdC (synthesis of the phytohormone indoleacetic acid) are chromosomal, but no BAC clone containing both genes was found, pointing to the absence of any genetic island containing nifH and ipdC. A 11.8-kb fragment containing nifH was analyzed. Neighboring genes implicated in nitrogen fixation (nifH, draT, draG) or not (arsC, yafJ and acpD) were organized as in A. brasilense. In contrast, the region located downstream of acpD contained four housekeeping genes (i.e. genes encoding DapF-, MiaB- and FtsY-like proteins, as well as gene amn) and differed totally from the one found in A. brasilense.
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Affiliation(s)
- Didier Blaha
- UMR CNRS 5557 Ecologie Microbienne, Université Claude Bernard (Lyon 1), 43 bd du 11 Novembre, 69622 Villeurbanne cedex, France
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