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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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2
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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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Haichar FEZ, Cernava T, Liu J, Timm CM. Editorial: Novel Insights Into the Response of the Plant Microbiome to Abiotic Factors. Front Plant Sci 2021; 12:607874. [PMID: 34122462 PMCID: PMC8193938 DOI: 10.3389/fpls.2021.607874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Univ Lyon, Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, China
| | - Collin M. Timm
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
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Galland W, Piola F, Mathieu C, Bouladra L, Simon L, Haichar FEZ. Does Biological Denitrification Inhibition (BDI) in the Field Induce an Increase in Plant Growth and Nutrition in Apium graveolens L. Grown for a Long Period? Microorganisms 2020; 8:microorganisms8081204. [PMID: 32784635 PMCID: PMC7466050 DOI: 10.3390/microorganisms8081204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/07/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 11/16/2022] Open
Abstract
Intensive agriculture uses a lot of nitrogen fertilizers to increase crop productivity. These crops are in competition with soil-denitrifying microorganisms that assimilate nitrogen in the form of nitrate and transform it into N2O, a greenhouse gas, or N2. However, certain plant species exude secondary metabolites, called procyanidins, which inhibit denitrifiers and increase the nitrate pool in the soil available for plant nutrition. This phenomenon is called biological denitrification inhibition. Previously, we showed that the addition of exogenous procyanidins to a lettuce crop induces denitrifier inhibition and increases nitrate content in the soil, affecting lettuce morphological traits. Here, the effects of procyanidin amendments in the field on a more long-term and nitrogen-consuming crop species such as celery were tested. The effects of procyanidin amendment on celery growth with those of conventional ammonium nitrate amendments were, therefore, compared. Denitrification activity, nitrate concentration, the abundance of denitrifying bacteria in the soil, and traits related to celery growth were measured. It was shown that the addition of procyanidins inhibits denitrifiers and increases the soil nitrate level, inducing an improvement in celery morphological traits. In addition, procyanidin amendment induces the lowest nitrogen concentration in tissues and reduces N2O emissions.
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Affiliation(s)
- William Galland
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA 1418, F-69622 Villeurbanne CEDEX, France; (W.G.); (L.B.)
- Université de Lyon, UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne CEDEX, France; (F.P.); (L.S.)
| | - Florence Piola
- Université de Lyon, UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne CEDEX, France; (F.P.); (L.S.)
| | - Céline Mathieu
- Station d’Expérimentation Rhône-Alpes Information Légumes (SERAIL), 123 Chemin du Finday Les Hoteaux, 69126 Brindas, France;
| | - Lyna Bouladra
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA 1418, F-69622 Villeurbanne CEDEX, France; (W.G.); (L.B.)
| | - Laurent Simon
- Université de Lyon, UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne CEDEX, France; (F.P.); (L.S.)
| | - Feth el Zahar Haichar
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA 1418, F-69622 Villeurbanne CEDEX, France; (W.G.); (L.B.)
- INSA-Lyon, Université Claude Bernard Lyon1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Univ Lyon, 10 Rue Raphaël Dubois, 69622 Villeurbanne, France
- Correspondence:
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Simon L, Haichar FEZ. Determination of Root Exudate Concentration in the Rhizosphere Using 13C Labeling. Bio Protoc 2019; 9:e3228. [PMID: 33655014 PMCID: PMC7854189 DOI: 10.21769/bioprotoc.3228] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 11/02/2022] Open
Abstract
One of the most remarkable metabolic features of plant roots is their ability to secrete a wide range of compounds into the rhizosphere, defined as the volume of soil around living roots. Around 5%-21% of total photosynthetically fixed carbon is transferred into the rhizosphere through root exudates. Until recently, studies on the quantity and quality of root exudates were conducted mostly under axenic or monoxenic in vitro conditions. Today, in situ assays are required to provide a better understanding of root exudates dynamics and role in plant-microbe interactions. By incubating plants with 13CO2 in situ for one week and quantifying 13C enrichment from the root-adhering soil using mass spectrometry, we were able to determine root exudate levels. Indeed, labeled substrate 13CO2 is converted into organic carbon via plant photosynthesis and transferred into the soil through root exudation. We assume that all 13C increases above natural abundance are mainly derived from exudates produced by 13C-labeled plants.
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Affiliation(s)
- Laurent Simon
- UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, Univ Lyon, Université Claude Bernard Lyon 1, University of Lyon, Villeurbanne Cedex, France
| | - Feth el Zahar Haichar
- UMR CNR 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, Univ Lyon, Université Claude Bernard Lyon 1, University of Lyon, Villeurbanne Cedex, France
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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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Guyonnet JP, Cantarel AAM, Simon L, Haichar FEZ. Root exudation rate as functional trait involved in plant nutrient-use strategy classification. Ecol Evol 2018; 8:8573-8581. [PMID: 30250724 PMCID: PMC6144958 DOI: 10.1002/ece3.4383] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 04/07/2018] [Revised: 05/17/2018] [Accepted: 06/27/2018] [Indexed: 11/16/2022] Open
Abstract
Plants adopt a variety of life history strategies to succeed in the Earth's diverse environments. Using functional traits which are defined as "morphological, biochemical, physiological, or phonological" characteristics measurable at the individual level, plants are classified according to their species' adaptative strategies, more than their taxonomy, from fast growing plant species to slower-growing conservative species. These different strategies probably influence the input and output of carbon (C)-resources, from the assimilation of carbon by photosynthesis to its release in the rhizosphere soil via root exudation. However, while root exudation was known to mediate plant-microbe interactions in the rhizosphere, it was not used as functional trait until recently. Here, we assess whether root exudate levels are useful plant functional traits in the classification of plant nutrient-use strategies and classical trait syndromes? For this purpose, we conducted an experiment with six grass species representing along a gradient of plant resource-use strategies, from conservative species, characterized by low biomass nitrogen (N) concentrations and a long lifespans, to exploitative species, characterized by high rates of photosynthesis and rapid rates of N acquisition. Leaf and root traits were measured for each grass and root exudate rate for each planted soil sample. Classical trait syndromes in plant ecology were found for leaf and root traits, with negative relationships observed between specific leaf area and leaf dry matter content or between specific root length and root dry matter content. However, a new root trait syndrome was also found with root exudation levels correlating with plant resource-use strategy patterns, specifically, between root exudation rate and root dry matter content. We therefore propose root exudation rate can be used as a key functional trait in plant ecology studies and plant strategy classification.
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Affiliation(s)
- Julien P. Guyonnet
- UMR CNRS 5557Laboratoire d'Ecologie MicrobienneUMR INRA 1418Univ LyonUniversité Claude Bernard Lyon 1University of LyonVilleurbanneCedexFrance
| | - Amélie A. M. Cantarel
- UMR CNRS 5557Laboratoire d'Ecologie MicrobienneUMR INRA 1418Univ LyonUniversité Claude Bernard Lyon 1University of LyonVilleurbanneCedexFrance
| | - Laurent Simon
- UMR5023 LEHNAUniversité Lyon 1CNRSENTPEUniv LyonUniversité Claude Bernard Lyon 1University of LyonVilleurbanneCedexFrance
| | - Feth el Zahar Haichar
- UMR CNRS 5557Laboratoire d'Ecologie MicrobienneUMR INRA 1418Univ LyonUniversité Claude Bernard Lyon 1University of LyonVilleurbanneCedexFrance
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9
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Bardon C, Poly F, Piola F, Pancton M, Comte G, Meiffren G, Haichar FEZ. Mechanism of biological denitrification inhibition: procyanidins induce an allosteric transition of the membrane-bound nitrate reductase through membrane alteration. FEMS Microbiol Ecol 2016; 92:fiw034. [PMID: 26906096 DOI: 10.1093/femsec/fiw034] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 12/14/2022] Open
Abstract
Recently, it has been shown that procyanidins from Fallopia spp. inhibit bacterial denitrification, a phenomenon called biological denitrification inhibition (BDI). However, the mechanisms involved in such a process remain unknown. Here, we investigate the mechanisms of BDI involving procyanidins, using the model strain Pseudomonas brassicacearum NFM 421. The aerobic and anaerobic (denitrification) respiration, cell permeability and cell viability of P. brassicacearum were determined as a function of procyanidin concentration. The effect of procyanidins on the bacterial membrane was observed using transmission electronic microscopy. Bacterial growth, denitrification, NO3- and NO2-reductase activity, and the expression of subunits of NO3- (encoded by the gene narG) and NO2-reductase (encoded by the gene nirS) under NO3 or NO2 were measured with and without procyanidins. Procyanidins inhibited the denitrification process without affecting aerobic respiration at low concentrations. Procyanidins also disturbed cell membranes without affecting cell viability. They specifically inhibited NO3- but not NO2-reductase.Pseudomonas brassicacearum responded to procyanidins by over-expression of the membrane-bound NO3-reductase subunit (encoded by the gene narG). Our results suggest that procyanidins can specifically inhibit membrane-bound NO3-reductase inducing enzymatic conformational changes through membrane disturbance and that P. brassicacearum responds by over-expressing membrane-bound NO3-reductase. Our results lead the way to a better understanding of BDI.
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Affiliation(s)
- Clément Bardon
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France Université de Lyon, UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne Cedex, France
| | - Franck Poly
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| | - Florence Piola
- Université de Lyon, UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne Cedex, France
| | - Muriel Pancton
- Université de Lyon, UMR5276 LGLTPE, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne Cedex, France
| | - Gilles Comte
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| | - Guillaume Meiffren
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| | - Feth el Zahar Haichar
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, 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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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: 291] [Impact Index Per Article: 29.1] [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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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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