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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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Guyonnet JP, Vautrin F, Meiffren G, Labois C, Cantarel AAM, Michalet S, Comte G, Haichar FEZ. The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites. FEMS Microbiol Ecol 2017; 93:3003321. [PMID: 28334144 DOI: 10.1093/femsec/fix022] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/17/2017] [Indexed: 11/12/2022] Open
Abstract
The aim of this study was to determine (i) whether plant nutritional strategy affects the composition of primary metabolites exuded into the rhizosphere and (ii) the impact of exuded metabolites on denitrification activity in soil. We answered this question by analysing primary metabolite content extracted from the root-adhering soil (RAS) and the roots of three grasses representing different nutrient management strategies: conservative (Festuca paniculata), intermediate (Bromus erectus) and exploitative (Dactylis glomerata). We also investigated the impact of primary metabolites on soil microbial denitrification enzyme activity without carbon addition, comparing for each plant RAS and bulk soils. Our data show that plant nutritional strategy impacts on primary metabolite composition of root extracts or RAS. Further we show, for the first time, that RAS-extracted primary metabolites are probably better indicators to explain plant nutrient strategy than root-extracted ones. In addition, our results show that some primary metabolites present in the RAS were well correlated with soil microbial denitrification activity with positive relationships found between denitrification and the presence of some organic acids and negative ones with the presence of xylose. We demonstrated that the analysis of primary metabolites extracted from the RAS is probably more pertinent to evaluate the impact of plant on soil microbial community functioning.
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Simonin M, Richaume A, Guyonnet JP, Dubost A, Martins JMF, Pommier T. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers. Sci Rep 2016; 6:33643. [PMID: 27659196 PMCID: PMC5034236 DOI: 10.1038/srep33643] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/31/2016] [Indexed: 11/08/2022] Open
Abstract
Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg-1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function.
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Affiliation(s)
- Marie Simonin
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
- LTHE, UMR 5564 CNRS – Univ. Grenoble Alpes 38041 Grenoble Cedex 9, France
| | - Agnès Richaume
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Julien P. Guyonnet
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Jean M. F. Martins
- LTHE, UMR 5564 CNRS – Univ. Grenoble Alpes 38041 Grenoble Cedex 9, France
| | - Thomas Pommier
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
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Haichar FEZ, Heulin T, Guyonnet JP, Achouak W. Stable isotope probing of carbon flow in the plant holobiont. Curr Opin Biotechnol 2016; 41:9-13. [PMID: 27019410 DOI: 10.1016/j.copbio.2016.02.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/27/2023]
Abstract
Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with 13C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.
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Affiliation(s)
- Feth El Zahar Haichar
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France.
| | - Thierry Heulin
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
| | - Julien P Guyonnet
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
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Simonin M, Guyonnet JP, Martins JMF, Ginot M, Richaume A. Influence of soil properties on the toxicity of TiO₂ nanoparticles on carbon mineralization and bacterial abundance. J Hazard Mater 2015; 283:529-35. [PMID: 25464292 DOI: 10.1016/j.jhazmat.2014.10.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/27/2014] [Accepted: 10/03/2014] [Indexed: 05/12/2023]
Abstract
Information regarding the impact of low concentration of engineered nanoparticles on soil microbial communities is currently limited and the importance of soil characteristics is often neglected in ecological risk assessment. To evaluate the impact of TiO2 nanoparticles (NPs) on soil microbial communities (measured on bacterial abundance and carbon mineralization activity), 6 agricultural soils exhibiting contrasted textures and organic matter contents were exposed for 90 days to a low environmentally relevant concentration or to an accidental spiking of TiO2-NPs (1 and 500mgkg(-1) dry soil, respectively) in microcosms. In most soils, TiO2-NPs did not impact the activity and abundance of microbial communities, except in the silty-clay soil (high OM) where C-mineralization was significantly lowered, even with the low NPs concentration. Our results suggest that TiO2-NPs toxicity does not depend on soil texture but likely on pH and OM content. We characterized TiO2-NPs aggregation and zeta potential in soil solutions, in order to explain the difference of TiO2-NPs effects on soil C-mineralization. Zeta potential and aggregation of TiO2-NPs in the silty-clay (high OM) soil solution lead to a lower stability of TiO2-NP-aggregates than in the other soils. Further experiments would be necessary to evaluate the relationship between TiO2-NPs stability and toxicity in the soil.
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Affiliation(s)
- Marie Simonin
- Université de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, Université Lyon 1, Villeurbanne, France; UJF-Grenoble/CNRS-INSU/G-INP/IRD, LTHE UMR 5564, Grenoble F-38041, France
| | - Julien P Guyonnet
- Université de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, Université Lyon 1, Villeurbanne, France
| | - Jean M F Martins
- UJF-Grenoble/CNRS-INSU/G-INP/IRD, LTHE UMR 5564, Grenoble F-38041, France
| | - Morgane Ginot
- Université de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, Université Lyon 1, Villeurbanne, France
| | - Agnès Richaume
- Université de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, Université Lyon 1, Villeurbanne, France.
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Leporq B, Membré JM, Dervin C, Buche P, Guyonnet JP. The “Sym'Previus” software, a tool to support decisions to the foodstuff safety. Int J Food Microbiol 2005; 100:231-7. [PMID: 15854708 DOI: 10.1016/j.ijfoodmicro.2004.10.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [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: 09/27/2004] [Accepted: 10/06/2004] [Indexed: 11/25/2022]
Abstract
Describing the Sym'Previus project, the software and its deliverable facilities is the aim of this present paper. This software concerns all the partners of the food industry who are involved in the management of food safety and allows food-borne pathogen behaviour in food to be predicted, as function of the environment (nature of the food, manufacturing process, conditions of conservation). This analysis of microbial behaviour has been possible thanks to the progress made in predictive microbiology since the 1980s. Sym'Previus offers to food industry professionals and their partners the possibility of applying this progress, by giving access to a database, to simulation systems and expertise.
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Affiliation(s)
- B Leporq
- Institut National de Recherche Agronomique, 369 rue Jules Guesde BP 39, F-59651 Villeneuve d'Ascq cédex, France
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Le Marc Y, Huchet V, Bourgeois CM, Guyonnet JP, Mafart P, Thuault D. Modelling the growth kinetics of Listeria as a function of temperature, pH and organic acid concentration. Int J Food Microbiol 2002; 73:219-37. [PMID: 11934031 DOI: 10.1016/s0168-1605(01)00640-7] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.1] [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: 10/18/2022]
Abstract
The combined effects of temperature, pH and organic acids (lactic, acetic and propionic) on the growth kinetics of Listeria innocua ATCC 33090 were studied. First, a multiplicative model was built assuming independent effects of all environmental factors. Thus, the model was expanded by the inclusion of a novel term describing the effects of interactions on the growth/no growth limits. The proposed approach allows an accurate description of the boundary between growth and no growth of Listeria.
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Affiliation(s)
- Y Le Marc
- Département Recherche Innovation--ADRIA, Creac'h Gwen, Quimper, France
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