1
|
Blanco Nouche C, Paris C, Dhalleine T, Oger P, Turpault MP, Uroz S. The non-ribosomal peptide synthetase-independent siderophore (NIS) rhizobactin produced by Caballeronia mineralivorans PML1(12) confers the ability to weather minerals. Appl Environ Microbiol 2023; 89:e0045323. [PMID: 37800940 PMCID: PMC10617554 DOI: 10.1128/aem.00453-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023] Open
Abstract
To mobilize nutrients entrapped into minerals and rocks, heterotrophic bacteria living in nutrient-poor environments have developed different mechanisms based mainly on acidolysis and chelation. However, the genetic bases of these mechanisms remain unidentified. To fill this gap, we considered the model strain Caballeronia mineralivorans PML1(12) known to be effective at weathering. Based on its transcriptomics and proteomics responses in Fe-depleted conditions, we pointed a cluster of genes differentially expressed and putatively involved in the production of siderophores. In this study, we report the characterization of this gene region coding for the production of a non-ribosomal peptide synthetase-independent siderophore (NIS). Targeted mutagenesis associated with functional assays and liquid chromatography coupled to high-resolution tandem mass spectrometry demonstrated the production of a single siderophore, identified as rhizobactin. This siderophore represents the first NIS containing malic acid in its structure. The evidence for the implication of rhizobactin in mineral weathering was demonstrated during a hematite dissolution assay. This study provides the first demonstration of the synthesis of a NIS in the genus Caballeronia and its involvement in mineral weathering. Our conclusions reinforce the idea that strain PML1(12) is particularly well adapted to nutrient-poor environments. IMPORTANCE This work deciphers the molecular and genetic bases used by strain PML1(12) of Caballeronia mineralivorans to mobilize iron and weather minerals. Through the combination of bioinformatics, chemical, and phylogenetic analyses, we characterized the siderophore produced by strain PML1(12) and the related genes. This siderophore was identified as rhizobactin and classified as a non-ribosomal peptide synthetase-independent siderophore (NIS). Contrary to the previously identified NIS synthetases that form siderophores containing citric acid, α-ketoglutarate, or succinic acid, our analyses revealed that rhizobactin contains malic acid in its structure, representing, therefore, the first identified NIS with such an acid and probably a new NIS category. Last, this work demonstrates for the first time the effectiveness at weathering minerals of a siderophore of the NIS family. Our findings offer relevant information for different fields of research, such as environmental genomics, microbiology, chemistry, and soil sciences.
Collapse
Affiliation(s)
- Cintia Blanco Nouche
- Université de Lorraine, INRAE, UMR1136 Interactions Arbres-Microorganismes, Nancy, France
- INRAE, UR1138 Biogéochimie des Ecosystèmes Forestiers, Champenoux, France
| | - Cédric Paris
- Université de Lorraine, EA 4367 Laboratoire d’Ingénierie des Biomolécules, Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires (ENSAIA), Vandœuvre-lès-Nancy, France
| | - Tiphaine Dhalleine
- Université de Lorraine, INRAE, UMR1136 Interactions Arbres-Microorganismes, Nancy, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Villeurbanne, France
| | | | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR1136 Interactions Arbres-Microorganismes, Nancy, France
- INRAE, UR1138 Biogéochimie des Ecosystèmes Forestiers, Champenoux, France
| |
Collapse
|
2
|
Zhang Y, Zhao Q, Uroz S, Gao T, Li J, He F, Rosazlina R, Martin F, Xu L. The cultivation regimes of Morchella sextelata trigger shifts in the community assemblage and ecological traits of soil bacteria. Front Microbiol 2023; 14:1257905. [PMID: 37808313 PMCID: PMC10552182 DOI: 10.3389/fmicb.2023.1257905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
The successful large-scale cultivation of morel mushrooms (Morchella sextelata) requires a comprehensive understanding of the soil bacterial communities associated with morel-farming beds, as the interactions between fungi and bacteria play a crucial role in shaping the soil microbiome. In this study, we investigated the temporal distribution and ecological characteristics of soil bacteria associated with morel fruiting bodies at different stages, specifically the conidial and primordial stages, under two cropping regimes, non-continuous cropping (NCC) and continuous cropping (CC). Our findings revealed a significant reduction in the yield of morel primordia during the third year following 2 years of CC (0.29 ± 0.25 primordia/grid), in comparison to the NCC regime (12.39 ± 6.09 primordia/grid). Furthermore, inoculation with morel mycelia had a notable impact on soil bacterial diversity, decreasing it in the NCC regime and increasing the number of generalist bacterial members in the CC regime. The latter regime also led to the accumulation of nutrients in the soil beds, resulting in a shift from a stochastic to a deterministic process in the composition of the bacterial community, which differed from the NCC regime. Additionally, mycelial inoculation had a positive effect on the abundance of potential copiotrophic/denitrifying and N-fixing bacteria while decreasing the abundance of oligotrophic/nitrifying bacteria. Interestingly, this effect was more pronounced in the NCC regime than in the CC regime. These results suggest that the increase in potential copiotrophic/denitrifying and N-fixing bacteria facilitated the decomposition of nutrients in exogenous nutrient bags by morel mushrooms, thereby maintaining nitrogen balance in the soil. Overall, our study provides valuable insights into the interactions between morel mycelia and the associated soil bacteriome as well as the influence of different cultivation regimes on these interactions. These findings contribute to our understanding of the complex dynamics of the soil microbiome and can inform strategies for optimizing morel mushroom cultivation.
Collapse
Affiliation(s)
- Yan Zhang
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
| | - Qi Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, France
| | - Tianpeng Gao
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
- The Engineering Research Center of Mining Pollution Treatment and Ecological Restoration of Gansu Province, Lanzhou City University, Lanzhou, China
| | - Jing Li
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
| | - Fengqin He
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
| | - Rusly Rosazlina
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, France
| | - Lingling Xu
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, France
| |
Collapse
|
3
|
Mieszkin S, Trouche B, Ancousture J, Raouf Y, Uroz S, Alain K. Scleromatobacter humisilvae gen. nov., sp. nov., a novel bacterium isolated from oak forest soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 36884366 DOI: 10.1099/ijsem.0.005793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
A novel bacterial strain, designated BS-T2-15T, isolated from forest soil in close proximity to decaying oak wood, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences as well as phylogenomic analyses based on coding sequences of 340 concatenated core proteins indicated that strain BS-T2-15T forms a distinct and robust lineage in the Rubrivivax-Roseateles -Leptothrix-Azohydromonas -Aquincola-Ideonella branch of the order Burkholderiales. The amino acid identity and the percentage of conserved proteins between the genome of strain BS-T2-15T and genomes of closely related type strains ranged from 64.27 to 66.57% and from 40.89 to 49.27 %, respectively, providing genomic evidence that strain BS-T2-15T represents a new genus. Its cells are Gram-stain-negative, aerobic, motile by a polar flagellum, rod-shaped and form incrusted white to ivory colonies. Optimal growth is observed at 20-22 °C, pH 6 and 0% NaCl. The predominant fatty acids of strain BS-T2-15T are C16 : 1 ω7c, C16 : 0 and C14 : 0 2-OH. Its polar lipid profile consists of a mixture of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol and its main respiratory quinone is ubiquinone 8. The estimated size of its genome is 6.28 Mb with a DNA G+C content of 69.56 mol%. Therefore, on the basis of phenotypic and genotypic properties, the new strain BS-T2-15T represents a novel genus and species for which the name Scleromatobacter humisilvae gen. nov., sp. nov., is proposed. The type strain is BS-T2-15T (DSM 113115T=UBOCC-M-3373T).
Collapse
Affiliation(s)
- Sophie Mieszkin
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France.,Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France
| | - Blandine Trouche
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Julien Ancousture
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Youssef Raouf
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Stéphane Uroz
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France
| | - Karine Alain
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| |
Collapse
|
4
|
Thomas F, Le Duff N, Wu TD, Cébron A, Uroz S, Riera P, Leroux C, Tanguy G, Legeay E, Guerquin-Kern JL. Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria. ISME J 2021; 15:3062-3075. [PMID: 33953365 PMCID: PMC8443679 DOI: 10.1038/s41396-021-00987-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/25/2021] [Accepted: 04/09/2021] [Indexed: 02/03/2023]
Abstract
Algal polysaccharides constitute a diverse and abundant reservoir of organic matter for marine heterotrophic bacteria, central to the oceanic carbon cycle. We investigated the uptake of alginate, a major brown macroalgal polysaccharide, by microbial communities from kelp-dominated coastal habitats. Congruent with cell growth and rapid substrate utilization, alginate amendments induced a decrease in bacterial diversity and a marked compositional shift towards copiotrophic bacteria. We traced 13C derived from alginate into specific bacterial incorporators and quantified the uptake activity at the single-cell level, using halogen in situ hybridization coupled to nanoscale secondary ion mass spectrometry (HISH-SIMS) and DNA stable isotope probing (DNA-SIP). Cell-specific alginate uptake was observed for Gammaproteobacteria and Flavobacteriales, with carbon assimilation rates ranging from 0.14 to 27.50 fg C µm-3 h-1. DNA-SIP revealed that only a few initially rare Flavobacteriaceae and Alteromonadales taxa incorporated 13C from alginate into their biomass, accounting for most of the carbon assimilation based on bulk isotopic measurements. Functional screening of metagenomic libraries gave insights into the genes of alginolytic Alteromonadales active in situ. These results highlight the high degree of niche specialization in heterotrophic communities and help constraining the quantitative role of polysaccharide-degrading bacteria in coastal ecosystems.
Collapse
Affiliation(s)
- François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France.
| | - Nolwen Le Duff
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ting-Di Wu
- Institut Curie, Université Paris-Saclay, Paris, France
- Université Paris-Saclay, INSERM US43, CNRS UMS2016, Multimodal Imaging Center, Orsay, France
| | | | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, France
| | - Pascal Riera
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Cédric Leroux
- CNRS, Sorbonne Université, FR2424, Metabomer, Station Biologique de Roscoff, Roscoff, France
| | - Gwenn Tanguy
- CNRS, Sorbonne Université, FR2424, Genomer, Station Biologique de Roscoff, Roscoff, France
| | - Erwan Legeay
- CNRS, Sorbonne Université, FR2424, Genomer, Station Biologique de Roscoff, Roscoff, France
| | - Jean-Luc Guerquin-Kern
- Institut Curie, Université Paris-Saclay, Paris, France
- Université Paris-Saclay, INSERM US43, CNRS UMS2016, Multimodal Imaging Center, Orsay, France
| |
Collapse
|
5
|
Mieszkin S, Pouder E, Uroz S, Simon-Colin C, Alain K. Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate. Microorganisms 2021; 9:microorganisms9102053. [PMID: 34683374 PMCID: PMC8537097 DOI: 10.3390/microorganisms9102053] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 12/02/2022] Open
Abstract
Two novel strains, HW T2.11T and HW T5.17T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11T and HW T5.17T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisomacellulosilytica are, respectively, HW T2.11T (DSM 111006T; UBOCC-M-3364T) and HW T5.17T (DSM 111007T; UBOCC-M-3365T).
Collapse
Affiliation(s)
- Sophie Mieszkin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
- Correspondence:
| | - Eva Pouder
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Stéphane Uroz
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
| | - Christelle Simon-Colin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| |
Collapse
|
6
|
Picard L, Paris C, Dhalleine T, Morin E, Oger P, Turpault MP, Uroz S. The mineral weathering ability of Collimonas pratensis PMB3(1) involves a Malleobactin-mediated iron acquisition system. Environ Microbiol 2021; 24:784-802. [PMID: 33817942 DOI: 10.1111/1462-2920.15508] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/23/2021] [Accepted: 04/03/2021] [Indexed: 11/27/2022]
Abstract
Mineral weathering by microorganisms is considered to occur through a succession of mechanisms based on acidification and chelation. While the role of acidification is established, the role of siderophores is difficult to disentangle from the effect of the acidification. We took advantage of the ability of strain Collimonas pratensis PMB3(1) to weather minerals but not to acidify depending on the carbon source to address the role of siderophores in mineral weathering. We identified a single non-ribosomal peptide synthetase (NRPS) responsible for siderophore biosynthesis in the PMB3(1) genome. By combining iron-chelating assays, targeted mutagenesis and chemical analyses (HPLC and LC-ESI-HRMS), we identified the siderophore produced as malleobactin X and how its production depends on the concentration of available iron. Comparison with the genome sequences of other collimonads evidenced that malleobactin production seems to be a relatively conserved functional trait, though some collimonads harboured other siderophore synthesis systems. We also revealed by comparing the wild-type strain and its mutant impaired in the production of malleobactin that the ability to produce this siderophore is essential to allow the dissolution of hematite under non-acidifying conditions. This study represents the first characterization of the siderophore produced by collimonads and its role in mineral weathering.
Collapse
Affiliation(s)
- Laura Picard
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, F-54280, France
| | - Cédric Paris
- Université de Lorraine, EA 4367 « Laboratoire d'Ingénierie des Biomolécules », Ecole Nationale Supérieure d'Agronomie et des Industries Alimentaires (ENSAIA), Vandœuvre-lès-Nancy, F-54505, France.,Plateau d'Analyse Structurale et Métabolomique (PASM) - SF4242 EFABA, Vandœuvre-lès-Nancy, F-54505, France
| | - Tiphaine Dhalleine
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France
| | - Philippe Oger
- Université de Lyon, INSA de Lyon, CNRS UMR 5240 « Microbiologie, Adaptation et Pathogénie », Villeurbanne, F-69621, France
| | - Marie-Pierre Turpault
- INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, F-54280, France
| | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, F-54280, France
| |
Collapse
|
7
|
Picard L, Turpault MP, Oger PM, Uroz S. Identification of a novel type of glucose dehydrogenase involved in the mineral weathering ability of Collimonas pratensis strain PMB3(1). FEMS Microbiol Ecol 2020; 97:5986611. [PMID: 33201986 DOI: 10.1093/femsec/fiaa232] [Citation(s) in RCA: 2] [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] [Received: 07/16/2020] [Accepted: 11/13/2020] [Indexed: 11/12/2022] Open
Abstract
The exact molecular mechanisms as well as the genes involved in the mineral weathering (MW) process by bacteria remain poorly characterized. To date, a single type of glucose dehydrogenase (GDH) depending on a particular co-factor named pyrroloquinoline quinone (PQQ) is known. These enzymes allow the production of gluconic acid through the oxidation of glucose. However, it remains to be determined how bacteria missing PQQ-dependent GDH and/or the related pqq biogenesis genes weather minerals. In this study, we considered the very effective mineral weathering bacterial strain PMB3(1) of Collimonas pratensis. Genome analysis revealed that it does not possess the PQQ-based system. The use of random mutagenesis, gene complementation and functional assays allowed us to identify mutants impacted in their ability to weather mineral. Among them, three mutants were strongly altered on their acidification and biotite weathering abilities (58% to 75% of reduction compared to WT) and did not produce gluconic acid. The characterization of the genomic regions allowed noticeably to the identification of a Glucose/Methanol/Choline oxidoreductase. This region appeared very conserved among collimonads and related genera. This study represents the first demonstration of the implication of a PQQ-independent GDH in the mineral weathering process and explains how Collimonas weather minerals.
Collapse
Affiliation(s)
- L Picard
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres-Microorganismes, F-54280 Champenoux, France.,INRAE, UR1138, Biogéochimie des écosystèmes forestiers, F-54280 Champenoux, France
| | - M P Turpault
- INRAE, UR1138, Biogéochimie des écosystèmes forestiers, F-54280 Champenoux, France
| | - P M Oger
- Université de Lyon, INSA de Lyon, CNRS UMR 5240, Lyon, 11 Avenuue Jean Capelle 69621 Villeurbanne, France
| | - S Uroz
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres-Microorganismes, F-54280 Champenoux, France.,INRAE, UR1138, Biogéochimie des écosystèmes forestiers, F-54280 Champenoux, France
| |
Collapse
|
8
|
Uroz S, Picard L, Turpault MP, Auer L, Armengaud J, Oger P. Dual transcriptomics and proteomics analyses of the early stage of interaction between Caballeronia mineralivorans PML1(12) and mineral. Environ Microbiol 2020; 22:3838-3862. [PMID: 32656915 DOI: 10.1111/1462-2920.15159] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Minerals and rocks represent essential reservoirs of nutritive elements for the long-lasting functioning of forest ecosystems developed on nutrient-poor soils. While the presence of effective mineral weathering bacteria was evidenced in the rhizosphere of different plants, the molecular mechanisms involved remain uncharacterized. To fill this gap, we combined transcriptomic, proteomics, geo-chemical and physiological analyses to decipher the potential molecular mechanisms explaining the mineral weathering effectiveness of strain PML1(12) of Caballeronia mineralivorans. Considering the early-stage of the interaction between mineral and bacteria, we identified the genes and proteins differentially expressed when: (i) the environment is depleted of certain essential nutrients (i.e., Mg and Fe), (ii) a mineral is added and (iii) the carbon source (i.e., glucose vs mannitol) differs. The integration of these data demonstrates that strain PML1(12) is capable of (i) mobilizing iron through the production of a non-ribosomal peptide synthetase-independent siderophore, (ii) inducing chemotaxis and motility in response to nutrient availability and (iii) strongly acidifying its environment in the presence of glucose using a suite of GMC oxidoreductases to weather mineral. These results provide new insights into the molecular mechanisms involved in mineral weathering and their regulation and highlight the complex sequence of events triggered by bacteria to weather minerals.
Collapse
Affiliation(s)
- Stéphane Uroz
- INRAE, UMR1136 « Interactions Arbres-Microorganismes », Université de Lorraine, Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des écosystèmes forestiers », Champenoux, F-54280, France
| | - Laura Picard
- INRAE, UMR1136 « Interactions Arbres-Microorganismes », Université de Lorraine, Champenoux, F-54280, France.,INRAE, UR1138 « Biogéochimie des écosystèmes forestiers », Champenoux, F-54280, France
| | - Marie-Pierre Turpault
- INRAE, UR1138 « Biogéochimie des écosystèmes forestiers », Champenoux, F-54280, France
| | - Lucas Auer
- INRAE, UMR1136 « Interactions Arbres-Microorganismes », Université de Lorraine, Champenoux, F-54280, France
| | - Jean Armengaud
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, SPI, 30200 Bagnols-sur-Cèze, France
| | - Phil Oger
- Univ Lyon, INSA de Lyon, CNRS UMR 5240, Lyon, France, Univ Lyon, Villeurbanne, F-69622, France
| |
Collapse
|
9
|
Splivallo R, Vahdatzadeh M, Maciá-Vicente JG, Molinier V, Peter M, Egli S, Uroz S, Paolocci F, Deveau A. Orchard Conditions and Fruiting Body Characteristics Drive the Microbiome of the Black Truffle Tuber aestivum. Front Microbiol 2019; 10:1437. [PMID: 31316485 PMCID: PMC6611097 DOI: 10.3389/fmicb.2019.01437] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 11/28/2018] [Accepted: 06/07/2019] [Indexed: 11/21/2022] Open
Abstract
Truffle fungi are well known for their enticing aromas partially emitted by microbes colonizing truffle fruiting bodies. The identity and diversity of these microbes remain poorly investigated, because few studies have determined truffle-associated bacterial communities while considering only a small number of fruiting bodies. Hence, the factors driving the assembly of truffle microbiomes are yet to be elucidated. Here we investigated the bacterial community structure of more than 50 fruiting bodies of the black truffle Tuber aestivum in one French and one Swiss orchard using 16S rRNA gene amplicon high-throughput sequencing. Bacterial communities from truffles collected in both orchards shared their main dominant taxa: while 60% of fruiting bodies were dominated by α-Proteobacteria, in some cases the β-Proteobacteria or the Sphingobacteriia classes were the most abundant, suggesting that specific factors (i.e., truffle maturation and soil properties) shape differently truffle-associated microbiomes. We further attempted to assess the influence in truffle microbiome variation of factors related to collection season, truffle mating type, degree of maturation, and location within the truffle orchards. These factors had differential effects between the two truffle orchards, with season being the strongest predictor of community variation in the French orchard, and spatial location in the Swiss one. Surprisingly, genotype and fruiting body maturation did not have a significant effect on microbial community composition. In summary, our results show, regardless of the geographical location considered, the existence of heterogeneous bacterial communities within T. aestivum fruiting bodies that are dominated by three bacterial classes. They also indicate that factors shaping microbial communities within truffle fruiting bodies differ across local conditions.
Collapse
Affiliation(s)
- Richard Splivallo
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Maryam Vahdatzadeh
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Jose G Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt, Germany
| | - Virginie Molinier
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland.,UMR 5175 CEFE - CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, INSERM, Montpellier, France
| | - Martina Peter
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Simon Egli
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Stéphane Uroz
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 INRA - Université de Lorraine, Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, Champenoux, France
| | - Francesco Paolocci
- National Research Council (CNR), Institute of Biosciences and Bioresources, Division of Perugia, Perugia, Italy
| | - Aurélie Deveau
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 INRA - Université de Lorraine, Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, Champenoux, France
| |
Collapse
|
10
|
Uroz S, Oger P. Corrigendum to “Caballeronia mineralivorans sp. nov., isolated from oak-Scleroderma citrinum mycorrhizosphere” [Syst. Appl. Microbiol. 40 (2017) 345–351]. Syst Appl Microbiol 2019; 42:423-424. [DOI: 10.1016/j.syapm.2019.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
11
|
Plassart P, Prévost-Bouré NC, Uroz S, Dequiedt S, Stone D, Creamer R, Griffiths RI, Bailey MJ, Ranjard L, Lemanceau P. Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect. Sci Rep 2019; 9:605. [PMID: 30679566 PMCID: PMC6345909 DOI: 10.1038/s41598-018-36867-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 06/21/2018] [Accepted: 11/14/2018] [Indexed: 11/09/2022] Open
Abstract
To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.
Collapse
Affiliation(s)
- Pierre Plassart
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | | | - Stéphane Uroz
- UMR 1136 Interactions Arbres Micro-organismes, INRA Univ Lorraine, F-54280, Champenoux, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | | | - Rachel Creamer
- TEAGASC, Johnstown Castle, Wexford, Ireland.,Wageningen University and Research, Wageningen, The Netherlands
| | - Robert I Griffiths
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, UK
| | - Mark J Bailey
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, UK
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France.
| |
Collapse
|
12
|
Courty PE, Buée M, Tech JJT, Brulé D, Colin Y, Leveau JHJ, Uroz S. Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino. Mycorrhiza 2018; 28:343-356. [PMID: 29574496 DOI: 10.1007/s00572-018-0829-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.
Collapse
Affiliation(s)
- P E Courty
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - M Buée
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
| | - J J T Tech
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - D Brulé
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Y Colin
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France
| | - J H J Leveau
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - S Uroz
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France.
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France.
| |
Collapse
|
13
|
Abstract
Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS). The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material. However, environmental-derived samples from soil, wood, or litter often contain phenolic compounds, pigments, and other molecules that can be inhibitors for reactions during sequencing library construction. In this chapter, we propose an optimized protocol allowing the preparation of high quality and long fragment DNA from different samples (mycelium, fruiting body, soil) compatible with the current sequencing requirements.
Collapse
Affiliation(s)
- Laure Fauchery
- Institut National de la Recherche Agronomique, UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Champenoux, France
| | - Stéphane Uroz
- Institut National de la Recherche Agronomique, UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Champenoux, France
| | - Marc Buée
- Institut National de la Recherche Agronomique, UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Champenoux, France
| | - Annegret Kohler
- Institut National de la Recherche Agronomique, UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Champenoux, France.
| |
Collapse
|
14
|
Uroz S, Oger P. Caballeronia mineralivorans sp. nov., isolated from oak- Scleroderma citrinum mycorrhizosphere. Syst Appl Microbiol 2017; 40:345-351. [DOI: 10.1016/j.syapm.2017.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 10/19/2022]
|
15
|
Colin Y, Nicolitch O, Van Nostrand JD, Zhou JZ, Turpault MP, Uroz S. Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence. Sci Rep 2017; 7:9604. [PMID: 28851878 PMCID: PMC5574896 DOI: 10.1038/s41598-017-07639-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 02/23/2017] [Accepted: 07/13/2017] [Indexed: 11/23/2022] Open
Abstract
It has been rarely questioned as to whether the enrichment of specific bacterial taxa found in the rhizosphere of a given plant species changes with different soil types under field conditions and under similar climatic conditions. Understanding tree microbiome interactions is essential because, in contrast to annual plants, tree species require decades to grow and strongly depend on the nutritive resources of the soil. In this context, we tested using a natural toposequence the hypothesis that beech trees select specific taxa and functions in their rhizosphere based on the soil conditions and their nutritive requirements. Our 16S rRNA gene pyrosequencing analyses revealed that the soil type determines the taxa colonizing the beech rhizosphere. A rhizosphere effect was observed in each soil type, but a stronger effect was observed in the nutrient-poor soils. Although the communities varied significantly across the toposequence, we identified a core beech rhizosphere microbiome. Functionally, GeoChip analyses showed a functional redundancy across the toposequence, with genes related to nutrient cycling and to the bacterial immune system being significantly enriched in the rhizosphere. Altogether, the data suggest that, regardless of the soil conditions, trees enrich variable bacterial communities to maintain the functions necessary for their nutrition.
Collapse
Affiliation(s)
- Y Colin
- INRA, Université de Lorraine, UMR 1136 "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France
| | - O Nicolitch
- INRA, Université de Lorraine, UMR 1136 "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France
| | - J D Van Nostrand
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73072, USA
| | - J Z Zhou
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73072, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - M-P Turpault
- INRA, Université de Lorraine, UMR 1136 "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France
| | - S Uroz
- INRA, Université de Lorraine, UMR 1136 "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France.
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France.
| |
Collapse
|
16
|
Crampon M, Cébron A, Portet-Koltalo F, Uroz S, Le Derf F, Bodilis J. Low effect of phenanthrene bioaccessibility on its biodegradation in diffusely contaminated soil. Environ Pollut 2017; 225:663-673. [PMID: 28390702 DOI: 10.1016/j.envpol.2017.03.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
This study focused on the role of bioaccessibility in the phenanthrene (PHE) biodegradation in diffusely contaminated soil, by combining chemical and microbiological approaches. First, we determined PHE dissipation rates and PHE sorption/desorption isotherms for two soils (PPY and Pv) presenting similar chronic PAH contamination, but different physico-chemical properties. Our results revealed that the PHE dissipation rate was significantly higher in the Pv soil compared to the PPY soil, while PHE sorption/desorption isotherms were similar. Interestingly, increases of PHE desorption and potentially of PHE bioaccessibility were observed for both soils when adding rhamnolipids (biosurfactants produced by Pseudomonas aeruginosa). Second, using 13C-PHE incubated in the same soils, we analyzed the PHE degrading bacterial communities. The combination of stable isotope probing (DNA-SIP) and 16S rRNA gene pyrosequencing revealed that Betaproteobacteria were the main PHE degraders in the Pv soil, while a higher bacterial diversity (Alpha-, Beta-, Gammaproteobacteria and Actinobacteria) was involved in PHE degradation in the PPY soil. The amendment of biosurfactants commonly used in biostimulation methods (i.e. rhamnolipids) to the two soils clearly modified the PHE sorption/desorption isotherms, but had no significant impact on PHE degradation rates and PHE-degraders identity. These results demonstrated that increasing the bioaccessibility of PHE has a low impact on its degradation and on the functional populations involved in this degradation.
Collapse
Affiliation(s)
- M Crampon
- COBRA UMR CNRS 6014, Université de Rouen-Normandie, 55 rue saint Germain, 27000 Evreux, France; Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Université de Rouen, 76821 Mont Saint Aignan, France
| | - A Cébron
- CNRS, LIEC UMR 7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy Cedex, France; Université de Lorraine, LIEC UMR 7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy Cedex, France
| | - F Portet-Koltalo
- COBRA UMR CNRS 6014, Université de Rouen-Normandie, 55 rue saint Germain, 27000 Evreux, France
| | - S Uroz
- UMR 1138 INRA, Centre de Nancy, Biogéochimie des Ecosystèmes forestiers, Route d'Amance, 54280 Champenoux, France
| | - F Le Derf
- COBRA UMR CNRS 6014, Université de Rouen-Normandie, 55 rue saint Germain, 27000 Evreux, France
| | - J Bodilis
- Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Université de Rouen, 76821 Mont Saint Aignan, France; Université de Lyon, France, CNRS, INRA, Ecole Nationale Vétérinaire de Lyon, Université Lyon 1, UMR 5557 Ecologie Microbienne, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France.
| |
Collapse
|
17
|
|
18
|
Torres M, Uroz S, Salto R, Fauchery L, Quesada E, Llamas I. HqiA, a novel quorum-quenching enzyme which expands the AHL lactonase family. Sci Rep 2017; 7:943. [PMID: 28424524 PMCID: PMC5430456 DOI: 10.1038/s41598-017-01176-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/22/2017] [Indexed: 11/09/2022] Open
Abstract
The screening of a metagenomic library of 250,000 clones generated from a hypersaline soil (Spain) allowed us to identify a single positive clone which confers the ability to degrade N-acyl homoserine lactones (AHLs). The sequencing of the fosmid revealed a 42,318 bp environmental insert characterized by 46 ORFs. The subcloning of these ORFs demonstrated that a single gene (hqiA) allowed AHL degradation. Enzymatic analysis using purified HqiA and HPLC/MS revealed that this protein has lactonase activity on a broad range of AHLs. The introduction of hqiA in the plant pathogen Pectobacterium carotovorum efficiently interfered with both the synthesis of AHLs and quorum-sensing regulated functions, such as swarming motility and the production of maceration enzymes. Bioinformatic analyses highlighted that HqiA showed no sequence homology with the known prototypic AHL lactonases or acylases, thus expanding the AHL-degrading enzymes with a new family related to the cysteine hydrolase (CHase) group. The complete sequence analysis of the fosmid showed that 31 ORFs out of the 46 identified were related to Deltaproteobacteria, whilst many intercalated ORFs presented high homology with other taxa. In this sense, hqiA appeared to be assigned to the Hyphomonas genus (Alphaproteobacteria), suggesting that horizontal gene transfer had occurred.
Collapse
Affiliation(s)
- Marta Torres
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.,Institute of Biotechnology, Biomedical Research Center (CIBM), University of Granada, Granada, Spain
| | - Stéphane Uroz
- UMR 1136 INRA-Université de Lorraine Interactions Arbres-Microorganismes, Centre INRA de Nancy, Champenoux, France
| | - Rafael Salto
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Laure Fauchery
- UMR 1136 INRA-Université de Lorraine Interactions Arbres-Microorganismes, Centre INRA de Nancy, Champenoux, France
| | - Emilia Quesada
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.,Institute of Biotechnology, Biomedical Research Center (CIBM), University of Granada, Granada, Spain
| | - Inmaculada Llamas
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain. .,Institute of Biotechnology, Biomedical Research Center (CIBM), University of Granada, Granada, Spain.
| |
Collapse
|
19
|
Krieger C, Calvaruso C, Morlot C, Uroz S, Salsi L, Turpault MP. Identification, distribution, and quantification of biominerals in a deciduous forest. Geobiology 2017; 15:296-310. [PMID: 28130812 DOI: 10.1111/gbi.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
Biomineralization is a common process in most vascular plants, but poorly investigated for trees. Although the presence of calcium oxalate and silica accumulation has been reported for some tree species, the chemical composition, abundance, and quantification of biominerals remain poorly documented. However, biominerals may play important physiological and structural roles in trees, especially in forest ecosystems, which are characterized by nutrient-poor soils. In this context, our study aimed at investigating the morphology, distribution, and relative abundance of biominerals in the different vegetative compartments (foliage, branch, trunk, and root) of Fagus sylvatica L. and Acer pseudoplatanus L. using a combination of scanning electron microscopy and tomography analyses. Biomineral crystallochemistry was assessed by X-ray diffraction and energy-dispersive X-ray analyses, while calcium, silicon, and oxalic acid were quantified in the compartments and at the forest scale. Our analyses revealed that biominerals occurred as crystals or coating layers mostly in bark and leaves and were identified as opal, whewellite, and complex biominerals. In both tree species, opal was mostly found in the external tissues of trunk, branch, and leaves, but also in the roots of beech. In the stand, opal represents around 170 kg/ha. Whewellite was found to suit to conductive tissues (i.e., axial phloem parenchyma, vascular bundles, vessel element) in all investigated compartments of the two tree species. The shape of whewellite was prismatic and druses in beech, and almost all described shapes were seen in sycamore maple. Notably, the amount of whewellite was strongly correlated with the total calcium in all investigated compartments whatever the tree species is, suggesting a biologic control of whewellite precipitation. The amount of whewellite in the aboveground biomass of Montiers forest was more important than that of opal and was around 1170 kg/ha. Therefore, biominerals contribute in a substantial way to the biogeochemical cycles of silicon and calcium.
Collapse
Affiliation(s)
- C Krieger
- INRA - UR 1138, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, Champenoux, France
| | - C Calvaruso
- INRA - UR 1138, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, Champenoux, France
| | - C Morlot
- GéoRessources, UMR7359, Faculté des Sciences, Université de Lorraine, Vandœuvre-lès-Nancy, France
- GéoRessources, UMR7359, Faculté des Sciences, CNRS, Vandœuvre-lès-Nancy, France
| | - S Uroz
- INRA - UR 1138, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, Champenoux, France
- INRA - UMR1136, Interactions Arbres - Microorganismes, Centre INRA de Nancy, Champenoux, France
- Interactions Arbres - Microorganismes, UMR1136, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - L Salsi
- GéoRessources, UMR7359, Faculté des Sciences, Université de Lorraine, Vandœuvre-lès-Nancy, France
- GéoRessources, UMR7359, Faculté des Sciences, CNRS, Vandœuvre-lès-Nancy, France
| | - M-P Turpault
- INRA - UR 1138, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, Champenoux, France
| |
Collapse
|
20
|
Abstract
Quorum sensing (QS)-based signaling is a widespread pathway used by bacteria for the regulation of functions involved in their relation to the environment or their host. QS relies upon the production, accumulation and perception of small diffusable molecules by the bacterial population, hence linking high gene expression with high cell population densities. Among the different QS signal molecules, an important class of signal molecules is the N-acyl homoserine lactone (N-AHSL). In pathogens such as Erwinia or Pseudomonas, N-AHSL based QS is crucial to overcome the host defenses and ensure a successful infection. Interfering with QS-regulation allows the algae Delisea pulcra to avoid surface colonization by bacteria. Thus, interfering the QS-regulation of pathogenic bacteria is a promising antibiotic-free antibacterial therapeutic strategy. To date, two N-AHSL lactonases and one amidohydrolase families of N-ASHL degradation enzymes have been characterized and have proven to be efficient in vitro to control N-AHSL-based QS-regulated functions in pathogens. In this chapter, we provide methods to screen individual clones or bacterial strains as well as pool of clones for genomic and metagenomic libraries, that can be used to identify strains or clones carrying N-ASHL degradation enzymes.
Collapse
Affiliation(s)
- Stéphane Uroz
- Interactions Arbres Microorganismes, INRA Université de Lorraine, UMR1136, Champenoux, 54280, France
| | - Phil M Oger
- Univ Lyon, INSA-Lyon, UCBL, CNRS UMR5240, 69621, Villeurbanne Cedex, France. .,Univ Lyon, ENS-Lyon, CNRS UMR5276, Lyon, 69634, France.
| |
Collapse
|
21
|
Kelly LC, Colin Y, Turpault MP, Uroz S. Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing. Microb Ecol 2016; 72:428-442. [PMID: 27138048 DOI: 10.1007/s00248-016-0774-0] [Citation(s) in RCA: 8] [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: 02/05/2016] [Accepted: 04/18/2016] [Indexed: 06/05/2023]
Abstract
Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site.
Collapse
Affiliation(s)
- L C Kelly
- INRA, UMR1136 "Interactions Arbres-Microorganismes", Centre INRA de Nancy, 54280, Champenoux, France
- Université de Lorraine, UMR1136 "Interactions Arbres-Microorganismes", 54500, Vandoeuvre-lès-Nancy, France
- School of Science and the Environment, Division of Biology and Conservation Ecology, Manchester Metropolitan University, M1 5GD, Manchester, UK
| | - Y Colin
- INRA, UMR1136 "Interactions Arbres-Microorganismes", Centre INRA de Nancy, 54280, Champenoux, France
- Université de Lorraine, UMR1136 "Interactions Arbres-Microorganismes", 54500, Vandoeuvre-lès-Nancy, France
- INRA UR1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France
| | - M-P Turpault
- INRA UR1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France
| | - S Uroz
- INRA, UMR1136 "Interactions Arbres-Microorganismes", Centre INRA de Nancy, 54280, Champenoux, France.
- Université de Lorraine, UMR1136 "Interactions Arbres-Microorganismes", 54500, Vandoeuvre-lès-Nancy, France.
- INRA UR1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France.
| |
Collapse
|
22
|
Deveau A, Antony-Babu S, Le Tacon F, Robin C, Frey-Klett P, Uroz S. Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development. Mycorrhiza 2016; 26:389-399. [PMID: 26781750 DOI: 10.1007/s00572-015-0679-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [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: 10/12/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
Ectomycorrhizae create a multitrophic ecosystem formed by the association between tree roots, mycelium of the ectomycorrhizal fungus, and a complex microbiome. Despite their importance in the host tree's physiology and in the functioning of the ectomycorrhizal symbiosis, detailed studies on ectomycorrhiza-associated bacterial community composition and their temporal dynamics are rare. Our objective was to investigate the composition and dynamics of Tuber melanosporum ectomycorrhiza-associated bacterial communities from summer to winter seasons in a Corylus avellana tree plantation. We used 16S ribosomal RNA (rRNA)-based pyrosequencing to compare the bacterial community structure and the richness in T. melanosporum's ectomycorrhizae with those of the bulk soil. The T. melanosporum ectomycorrhizae harbored distinct bacterial communities from those of the bulk soil, with an enrichment in Alpha- and Gamma-proteobacteria. In contrast to the bacterial communities of truffle ascocarps that vastly varies in composition and richness during the maturation of the fruiting body and to those from the bulk soil, T. melanosporum ectomycorrhiza-associated bacterial community composition stayed rather stable from September to January. Our results fit with a recent finding from the same experimental site at the same period that a continuous supply of carbohydrates and nitrogen occurs from ectomycorrhizae to the fruiting bodies during the maturation of the ascocarps. We propose that this creates a stable niche in the ectomycorrhizosphere although the phenology of the tree changes.
Collapse
Affiliation(s)
- Aurélie Deveau
- UMR1136 INRA Université de Lorraine, Interactions Arbres - Microorganismes, F-54280, Champenoux, France.
- Université de Lorraine, UMR1136, Interactions Arbres - Microorganismes, F-54500, Vandœuvre-lès-Nancy, France.
| | - Sanjay Antony-Babu
- UMR1136 INRA Université de Lorraine, Interactions Arbres - Microorganismes, F-54280, Champenoux, France
- Université de Lorraine, UMR1136, Interactions Arbres - Microorganismes, F-54500, Vandœuvre-lès-Nancy, France
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - François Le Tacon
- UMR1136 INRA Université de Lorraine, Interactions Arbres - Microorganismes, F-54280, Champenoux, France
- Université de Lorraine, UMR1136, Interactions Arbres - Microorganismes, F-54500, Vandœuvre-lès-Nancy, France
| | - Christophe Robin
- Université de Lorraine, UMR 1121, Agronomie & Environnement, Nancy-Colmar, 54500, Vandœuvre-lès-Nancy, France
- INRA, UMR 1121, Agronomie & Environnement, Nancy-Colmar, Centre INRA de Nancy-Lorraine, 54500, Vandœuvre-lès-Nancy, France
| | - Pascale Frey-Klett
- UMR1136 INRA Université de Lorraine, Interactions Arbres - Microorganismes, F-54280, Champenoux, France
- Université de Lorraine, UMR1136, Interactions Arbres - Microorganismes, F-54500, Vandœuvre-lès-Nancy, France
| | - Stéphane Uroz
- UMR1136 INRA Université de Lorraine, Interactions Arbres - Microorganismes, F-54280, Champenoux, France
- Université de Lorraine, UMR1136, Interactions Arbres - Microorganismes, F-54500, Vandœuvre-lès-Nancy, France
- INRA, UR1138, Biogéochimie des écosystèmes forestiers, F-54280, Champenoux, France
| |
Collapse
|
23
|
Uroz S, Oger P, Tisserand E, Cébron A, Turpault MP, Buée M, De Boer W, Leveau JHJ, Frey-Klett P. Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Sci Rep 2016; 6:27756. [PMID: 27302652 PMCID: PMC4908602 DOI: 10.1038/srep27756] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [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: 01/12/2016] [Accepted: 05/25/2016] [Indexed: 11/09/2022] Open
Abstract
The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.
Collapse
Affiliation(s)
- S Uroz
- INRA-Université de Lorraine , UMR1136 « Interactions Arbres-Microorganismes », F-54280 Champenoux, France.,INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, Champenoux, France
| | - P Oger
- UMR5276 Laboratoire de Géologie de Lyon, Ecole Normale de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - E Tisserand
- INRA-Université de Lorraine , UMR1136 « Interactions Arbres-Microorganismes », F-54280 Champenoux, France
| | - A Cébron
- CNRS, LIEC UMR7360 Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France.,Université de Lorraine, LIEC UMR7360 Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France
| | - M-P Turpault
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, Champenoux, France
| | - M Buée
- INRA-Université de Lorraine , UMR1136 « Interactions Arbres-Microorganismes », F-54280 Champenoux, France
| | - W De Boer
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, The Netherlands
| | - J H J Leveau
- Department of Plant Pathology, University of California, Davis CA 95616, USA
| | - P Frey-Klett
- INRA-Université de Lorraine , UMR1136 « Interactions Arbres-Microorganismes », F-54280 Champenoux, France
| |
Collapse
|
24
|
Jeanbille M, Buée M, Bach C, Cébron A, Frey-Klett P, Turpault MP, Uroz S. Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences. Microb Ecol 2016; 71:482-93. [PMID: 26370112 DOI: 10.1007/s00248-015-0669-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 05/15/2015] [Accepted: 08/28/2015] [Indexed: 05/20/2023]
Abstract
Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.
Collapse
Affiliation(s)
- M Jeanbille
- INRA, UMR1136 Interactions Arbres-Microorganismes, Champenoux, 54280, France
- Université de Lorraine, UMR1136 Interactions Arbres-Microorganismes, Vandoeuvre-lès-Nancy, 54500, France
| | - M Buée
- INRA, UMR1136 Interactions Arbres-Microorganismes, Champenoux, 54280, France
- Université de Lorraine, UMR1136 Interactions Arbres-Microorganismes, Vandoeuvre-lès-Nancy, 54500, France
| | - C Bach
- INRA, UMR1136 Interactions Arbres-Microorganismes, Champenoux, 54280, France
| | - A Cébron
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, Champenoux, France
- CNRS, LIEC UMR7360 Faculté des Sciences et Technologies, Vandoeuvre-les-Nancy, France
| | - P Frey-Klett
- INRA, UMR1136 Interactions Arbres-Microorganismes, Champenoux, 54280, France
- Université de Lorraine, UMR1136 Interactions Arbres-Microorganismes, Vandoeuvre-lès-Nancy, 54500, France
| | - M P Turpault
- Université de Lorraine, UMR1136 Interactions Arbres-Microorganismes, Vandoeuvre-lès-Nancy, 54500, France
| | - S Uroz
- INRA, UMR1136 Interactions Arbres-Microorganismes, Champenoux, 54280, France.
- Université de Lorraine, UMR1136 Interactions Arbres-Microorganismes, Vandoeuvre-lès-Nancy, 54500, France.
- Université de Lorraine, LIEC UMR7360 Faculté des Sciences et Technologies, Vandoeuvre-les-Nancy, France.
- UMR 1136 INRA-Université de Lorraine, Interactions Arbres Micro-organismes, Champenoux, 54280, France.
| |
Collapse
|
25
|
Hervé V, Le Roux X, Uroz S, Gelhaye E, Frey-Klett P. Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay. Environ Microbiol 2013; 16:2238-52. [PMID: 24286477 DOI: 10.1111/1462-2920.12347] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/23/2013] [Indexed: 01/05/2023]
Abstract
Wood recycling is key to forest biogeochemical cycles, largely driven by microorganisms such as white-rot fungi which naturally coexist with bacteria in the environment. We have tested whether and to what extent the diversity of the bacterial community associated with wood decay is determined by wood and/or by white-rot fungus Phanerochaete chrysosporium. We combined a microcosm approach with an enrichment procedure, using beech sawdust inoculated with or without P.chrysosporium. During 18 weeks, we used 16S rRNA gene-based pyrosequencing to monitor the forest bacterial community inoculated into these microcosms. We found bacterial communities associated with wood to be substantially less diverse than the initial forest soil inoculum. The presence of most bacterial operational taxonomic units (OTUs) varied over time and between replicates, regardless of their treatment, suggestive of the stochastic processes. However, we observed two OTUs belonging to Xanthomonadaceae and Rhizobium, together representing 50% of the relative bacterial abundance, as consistently associated with the wood substrate, regardless of fungal presence. Moreover, after 12 weeks, the bacterial community composition based on relative abundance was significantly modified by the presence of the white-rot fungus. Effectively, members of the Burkholderia genus were always associated with P.chrysosporium, representing potential taxonomic bioindicators of the white-rot mycosphere.
Collapse
Affiliation(s)
- Vincent Hervé
- Interactions Arbres - Microorganismes, UMR1136, INRA, Champenoux, France; Interactions Arbres - Microorganismes, UMR1136, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | | | | | | | | |
Collapse
|
26
|
Antony-Babu S, Deveau A, Van Nostrand JD, Zhou J, Le Tacon F, Robin C, Frey-Klett P, Uroz S. Black truffle-associated bacterial communities during the development and maturation ofTuber melanosporumascocarps and putative functional roles. Environ Microbiol 2013; 16:2831-47. [DOI: 10.1111/1462-2920.12294] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Sanjay Antony-Babu
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
| | - Aurélie Deveau
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK 73072 USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK 73072 USA
- Earth Sciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control; School of Environment; Tsinghua University; Beijing 100084 China
| | - François Le Tacon
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
| | - Christophe Robin
- Agronomie & Environnement; Université de Lorraine; Nancy-Colmar UMR 1121 F-54500 Vandoeuvre-lès-Nancy France
- INRA; Agronomie & Environnement; Centre INRA de Nancy-Lorraine; Nancy-Colmar UMR 1121 F-54500 Vandoeuvre-lès-Nancy France
| | - Pascale Frey-Klett
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
| | - Stéphane Uroz
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
| |
Collapse
|
27
|
Uroz S, Courty PE, Pierrat JC, Peter M, Buée M, Turpault MP, Garbaye J, Frey-Klett P. Functional profiling and distribution of the forest soil bacterial communities along the soil mycorrhizosphere continuum. Microb Ecol 2013; 66:404-15. [PMID: 23455431 DOI: 10.1007/s00248-013-0199-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 02/08/2013] [Indexed: 05/09/2023]
Abstract
An ectomycorrhiza is a multitrophic association between a tree root, an ectomycorrhizal fungus, free-living fungi and the associated bacterial communities. Enzymatic activities of ectomycorrhizal root tips are therefore result of the contribution from different partners of the symbiotic organ. However, the functional potential of the fungus-associated bacterial communities remains unknown. In this study, a collection of 80 bacterial strains randomly selected and isolated from a soil-ectomycorrhiza continuum (oak-Scleroderma citrinum ectomycorrhizas, the ectomycorrhizosphere and the surrounding bulk soil) were characterized. All the bacterial isolates were identified by partial 16S rRNA gene sequences as members of the genera Burkholderia, Collimonas, Dyella, Mesorhizobium, Pseudomonas, Rhizobium and Sphingomonas. The bacterial strains were then assayed for β-xylosidase, β-glucosidase, N-acetyl-hexosaminidase, β-glucuronidase, cellobiohydrolase, phosphomonoesterase, leucine-aminopeptidase and laccase activities, chitin solubilization and auxin production. Using these bioassays, we demonstrated significant differences in the functional distribution of the bacterial communities living in the different compartments of the soil-ectomycorrhiza continuum. The surrounding bulk soil was significantly enriched in bacterial isolates capable of hydrolysing cellobiose and N-acetylglucosamine. In contrast, the ectomycorrhizosphere appeared significantly enriched in bacterial isolates capable of hydrolysing glucopyranoside and chitin. Notably, chitinase and laccase activities were found only in bacterial isolates belonging to the Collimonas and Pseudomonas genera. Overall, the results suggest that the ectomycorrhizal fungi favour specific bacterial communities with contrasting functional characteristics from the surrounding soil.
Collapse
Affiliation(s)
- S Uroz
- INRA, UMR1136 INRA-Nancy Université Interactions Arbres-Microorganismes, Centre INRA de Nancy, 54280, Champenoux, France.
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Antony-Babu S, Murat C, Deveau A, Le Tacon F, Frey-Klett P, Uroz S. An improved method compatible with metagenomic analyses to extract genomic DNA from soils in Tuber melanosporum orchards. J Appl Microbiol 2013; 115:163-70. [PMID: 23581622 DOI: 10.1111/jam.12205] [Citation(s) in RCA: 15] [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] [Received: 12/18/2012] [Revised: 03/01/2013] [Accepted: 03/22/2013] [Indexed: 11/29/2022]
Abstract
AIMS The development of high-throughput methods such as pyrosequencing and microarrays has greatly improved our understanding of the microbial diversity in complex environments such as soils. Nevertheless, albeit advancements in such techniques, the first major step is to obtain high quantity and good quality genomic DNA (gDNA). The work presented here aims to present an inherent problem with 260 : 230 nm ratio of extracted gDNA from calcareous soils of Tuber melanosporum orchards and a protocol to overcome this problem. METHODS AND RESULTS Using two commercial gDNA extraction kits on spatially distant truffle orchards, we demonstrated that the 260 : 230 nm ratio was very low, consequentially yielding gDNA incompatible with microarray analyses. In order to solve this problem, optimization steps were tested including several wash steps performed before and/or after lysis. These washes significantly improved the gDNA quality (ratio 260 : 230 nm >1·7) without modification of the structure of the bacterial communities as stated by temporal temperature gradient gel electrophoresis analysis. A final re-extraction with phenol/chloroform was required for one of the soil samples. CONCLUSIONS A combination of wash steps included into the extraction protocol followed by phenol: chloroform re-extraction is recommended to obtain high-quality gDNA from calcareous soils of T. melanosporum orchards. SIGNIFICANCE AND IMPACT OF THE STUDY The method recommended here significantly improves gDNA quality obtained from T. melanosporum orchards to make it acceptable for highly sensitive methods such as microarray.
Collapse
Affiliation(s)
- S Antony-Babu
- INRA, UMR 1136 INRA, Université de Lorraine Interactions Arbres Micro-organismes, Centre INRA de Nancy, Champenoux, France
| | | | | | | | | | | |
Collapse
|
29
|
Lepleux C, Uroz S, Collignon C, Churin JL, Turpault MP, Frey-Klett P. A short-term mineral amendment impacts the mineral weathering bacterial communities in an acidic forest soil. Res Microbiol 2013; 164:729-39. [PMID: 23583355 DOI: 10.1016/j.resmic.2013.03.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 03/19/2013] [Indexed: 11/29/2022]
Abstract
Mineral amendment (i.e. calcium, phosphorous, potassium and/or magnesium) is a management practice used in forestry to improve nutrient availability and recover soil fertility, especially in nutrient-poor forest ecosystems. However, whether this amendment can lead to modifications of the soil characteristics and an improvement in tree growth, and its impact on the soil bacterial communities, especially the mineral weathering bacterial communities, remains poorly documented. In this study, we investigated the short-term impact of a mineral amendment on the taxonomic and functional structure of the mineral weathering bacterial communities. To do this, a plantation of four-year old oak (Quercus petraea) trees amended with or without dolomite [CaMg(CO3)2] was established in the experimental forest site of Breuil-Chenue, which is characterized by an acidic soil and a low availability of calcium and magnesium. Three years after amendment, soil samples were used to isolate bacteria as well as to determine the soil characteristics and the metabolic potentials of these soil microbial communities. Based on a bioassay for quantifying the solubilisation of inorganic phosphorous, we demonstrate that the bacterial isolates coming from the non-amended bulk soil were significantly more efficient than those from the amended bulk soil. No difference was observed between the bacterial isolates coming from the amended and non-amended rhizospheres. Notably, the taxonomic analyses revealed a dominance of bacterial isolates belonging to the Burkholderia genus in both samples. Overall, our results suggest that the bioavailability of nutritive cations into soil impacts the distribution and the efficacy of mineral weathering bacterial communities coming from the soil but not those coming from the rhizosphere.
Collapse
Affiliation(s)
- C Lepleux
- INRA, UMR 1136 INRA Université de Lorraine Interactions Arbres Micro-organismes, Centre INRA de Nancy, 54280 Champenoux, France
| | | | | | | | | | | |
Collapse
|
30
|
Bontemps C, Toussaint M, Revol PV, Hotel L, Jeanbille M, Uroz S, Turpault MP, Blaudez D, Leblond P. Taxonomic and functional diversity of Streptomyces in a forest soil. FEMS Microbiol Lett 2013; 342:157-67. [PMID: 23489323 DOI: 10.1111/1574-6968.12126] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 03/07/2013] [Indexed: 12/26/2022] Open
Abstract
In this work we report the isolation and the characterization of 79 Streptomyces isolates from a French forest soil. The 16S rRNA gene phylogeny indicated that a great diversity of Streptomyces was present in this soil, with at least nine different and potentially new species. Growth plate assays showed that most Streptomyces lineages exhibit cellulolytic and hemicellulolytic capacities and potentially participate in wood decomposition. Molecular screening for a specific hydrogenase also indicated a widespread potential for atmospheric H2 uptake. Co-culture experiments with representative strains showed antagonistic effects between Streptomyces of the same population and between Streptomyces and various fungi. Interestingly, in certain conditions, growth promotion of some fungi also occurred. We conclude that in forest soil, Streptomyces populations exhibit many important functions involved in different biogeochemical cycles and also influence the structure of soil microbial communities.
Collapse
Affiliation(s)
- Cyril Bontemps
- Dynamique des Génomes et Adaptation Microbienne, UMR1128, Université de Lorraine, Vandoeuvre-lès-Nancy F-54506, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Cusano AM, Burlinson P, Deveau A, Vion P, Uroz S, Preston GM, Frey-Klett P. Pseudomonas fluorescens BBc6R8 type III secretion mutants no longer promote ectomycorrhizal symbiosis. Environ Microbiol Rep 2011; 3:203-210. [PMID: 23761252 DOI: 10.1111/j.1758-2229.2010.00209.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Mycorrhiza Helper Bacterium (MHB) Pseudomonas fluorescens BBc6R8 promotes the ectomycorrhizal symbiosis between Douglas fir roots and Laccaria bicolor. In this study, we identified a non-flagellar type III secretion system (T3SS) in the draft genome of BBc6R8 similar to that described in the biocontrol strain P. fluorescens SBW25. We examined whether this T3SS plays a role in the BBc6R8 mycorrhizal helper effect by creating a deletion in the rscRST genes encoding the central channel of the injectisome. The in vitro effect of BBc6R8 T3SS mutants on the radial growth rate of L. bicolor was unchanged compared with the parental strain. In contrast, T3SS mutants were unable to promote mycorrhization, suggesting that type III secretion plays an important role in the mycorrhizal helper effect of P. fluorescens BBc6R8 independent of the promotion of hyphal growth that BBc6R8 exhibits in vitro.
Collapse
Affiliation(s)
- Angela M Cusano
- INRA, UMR1136 INRA-Nancy Université, «Interactions Arbres/Micro-organismes», Centre de Nancy, IFR110, 54280 Champenoux, France. Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK. Department of Microbiology and Immunology, Dartmouth Medical School, 208 Vail Building, Hanover, NH 03755, USA
| | | | | | | | | | | | | |
Collapse
|
32
|
Calvaruso C, Turpault MP, Leclerc E, Ranger J, Garbaye J, Uroz S, Frey-Klett P. Influence of forest trees on the distribution of mineral weathering-associated bacterial communities of the Scleroderma citrinum mycorrhizosphere. Appl Environ Microbiol 2010; 76:4780-7. [PMID: 20511429 PMCID: PMC2901721 DOI: 10.1128/aem.03040-09] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [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: 12/16/2009] [Accepted: 05/18/2010] [Indexed: 11/20/2022] Open
Abstract
In acidic forest soils, availability of inorganic nutrients is a tree-growth-limiting factor. A hypothesis to explain sustainable forest development proposes that tree roots select soil microbes involved in central biogeochemical processes, such as mineral weathering, that may contribute to nutrient mobilization and tree nutrition. Here we showed, by combining soil analyses with cultivation-dependent analyses of the culturable bacterial communities associated with the widespread mycorrhizal fungus Scleroderma citrinum, a significant enrichment of bacterial isolates with efficient mineral weathering potentials around the oak and beech mycorrhizal roots compared to bulk soil. Such a difference did not exist in the rhizosphere of Norway spruce. The mineral weathering ability of the bacterial isolates was assessed using a microplaque assay that measures the pH and the amount of iron released from biotite. Using this microplate assay, we demonstrated that the bacterial isolates harboring the most efficient mineral weathering potential belonged to the Burkholderia genus. Notably, previous work revealed that oak and beech harbored very similar pHs in the 5- to 10-cm horizon in both rhizosphere and bulk soil environments. In the spruce rhizosphere, in contrast, the pH was significantly lower than that in bulk soil. Because the production of protons is one of the main mechanisms responsible for mineral weathering, our results suggest that certain tree species have developed indirect strategies for mineral weathering in nutrient-poor soils, which lie in the selection of bacterial communities with efficient mineral weathering potentials.
Collapse
Affiliation(s)
- Christophe Calvaruso
- INRA, UR1138 INRA, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, 54280 Champenoux, France, INRA, UMR1136 INRA Nancy Université, Interactions Arbres-Microorganismes, IFR 110, Centre INRA de Nancy, 54280 Champenoux, France, ANDRA, Direction Scientifique/Service Transferts, 92298 Châtenay-Malabry, France
| | - Marie-Pierre Turpault
- INRA, UR1138 INRA, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, 54280 Champenoux, France, INRA, UMR1136 INRA Nancy Université, Interactions Arbres-Microorganismes, IFR 110, Centre INRA de Nancy, 54280 Champenoux, France, ANDRA, Direction Scientifique/Service Transferts, 92298 Châtenay-Malabry, France
| | - Elisabeth Leclerc
- INRA, UR1138 INRA, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, 54280 Champenoux, France, INRA, UMR1136 INRA Nancy Université, Interactions Arbres-Microorganismes, IFR 110, Centre INRA de Nancy, 54280 Champenoux, France, ANDRA, Direction Scientifique/Service Transferts, 92298 Châtenay-Malabry, France
| | - Jacques Ranger
- INRA, UR1138 INRA, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, 54280 Champenoux, France, INRA, UMR1136 INRA Nancy Université, Interactions Arbres-Microorganismes, IFR 110, Centre INRA de Nancy, 54280 Champenoux, France, ANDRA, Direction Scientifique/Service Transferts, 92298 Châtenay-Malabry, France
| | - Jean Garbaye
- INRA, UR1138 INRA, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, 54280 Champenoux, France, INRA, UMR1136 INRA Nancy Université, Interactions Arbres-Microorganismes, IFR 110, Centre INRA de Nancy, 54280 Champenoux, France, ANDRA, Direction Scientifique/Service Transferts, 92298 Châtenay-Malabry, France
| | - Stéphane Uroz
- INRA, UR1138 INRA, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, 54280 Champenoux, France, INRA, UMR1136 INRA Nancy Université, Interactions Arbres-Microorganismes, IFR 110, Centre INRA de Nancy, 54280 Champenoux, France, ANDRA, Direction Scientifique/Service Transferts, 92298 Châtenay-Malabry, France
| | - Pascale Frey-Klett
- INRA, UR1138 INRA, Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, 54280 Champenoux, France, INRA, UMR1136 INRA Nancy Université, Interactions Arbres-Microorganismes, IFR 110, Centre INRA de Nancy, 54280 Champenoux, France, ANDRA, Direction Scientifique/Service Transferts, 92298 Châtenay-Malabry, France
| |
Collapse
|
33
|
Uroz S, Buée M, Murat C, Frey-Klett P, Martin F. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2010; 2:281-8. [PMID: 23766079 DOI: 10.1111/j.1758-2229.2009.00117.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Several reports have highlighted that forest soil samples are more phylum-rich than agricultural soil samples. However, little is known about the structure and richness of the bacterial communities in forest soil. Using high-throughput next generation 454 pyrosequencing, we deeply investigated the diversity of bacterial communities colonizing the oak rhizosphere niche and the surrounding soil. From three spatially independent soil samples, we obtained over 300 000 partial 16S rRNA gene sequences. The most abundant bacterial groups were the Acidobacteria, Proteobacteria and unclassified bacteria. Multifactorial analysis of the relative proportions of the different phyla revealed a net differentiation of the bacterial communities present in the rhizosphere and soil environments, suggesting an oak rhizosphere effect. Significantly more β-, γ- and unclassified Proteobacteria inhabited the rhizosphere when compared with the surrounding soil. Conversely, significantly more unclassified bacteria were detected in the bulk soil than in the rhizosphere, demonstrating that the soil remains a challenging reservoir of complexity. This work increases our understanding of the niche effect on bacterial diversity and on the rare phylogenetic groups inhabiting the soil.
Collapse
Affiliation(s)
- Stéphane Uroz
- INRA, UMR1136 INRA-Nancy Université'Interactions Arbres-Microorganismes', IFR 110, Centre INRA de Nancy, 54280 Champenoux, France
| | | | | | | | | |
Collapse
|
34
|
Leveau JHJ, Uroz S, de Boer W. The bacterial genusCollimonas: mycophagy, weathering and other adaptive solutions to life in oligotrophic soil environments. Environ Microbiol 2010; 12:281-92. [DOI: 10.1111/j.1462-2920.2009.02010.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
35
|
Abstract
Quorum sensing (QS)-based signaling is a widespread pathway used by bacteria for the regulation of functions involved in relation to their environment or host. QS relies upon the production, accumulation, and perception of small diffusible molecules by the bacterial population, hence linking high gene expression with high cell population densities. Amongst the different QS signal molecules, an important class of signal molecules is the N-acyl homoserine lactone (N-AHSL) class. In pathogens such as Erwinia or Pseudomonas, N-AHSL-based QS is crucial to overcome the host defenses and ensure a successful infection. Interfering with QS regulation allows the alga Delisea pulchra to avoid surface colonization by bacteria. Thus, interfering in the QS regulation of pathogenic bacteria is a promising antibiotic-free antibacterial therapeutic strategy. To date, two N-AHSL lactonase and one amidohydrolase families of N-ASHL degradation enzymes have been characterized and proven to be efficient in vitro to control N-AHSL-based QS-regulated functions in pathogens.
Collapse
Affiliation(s)
- Phil M Oger
- Laboratoire de Sciences de la Terre, Ecole Normale Supérieure, Lyon, France
| | | |
Collapse
|
36
|
Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 2009; 184:449-456. [PMID: 19703112 DOI: 10.1111/j.1469-8137.2009.03003.x] [Citation(s) in RCA: 530] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
* Soil fungi play a major role in ecological and biogeochemical processes in forests. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). * Here, we assessed the fungal diversity in six different forest soils using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1). No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units. * Most operational taxonomic units (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant operational taxonomic units showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp. * This study validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.
Collapse
Affiliation(s)
- M Buée
- INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| | - M Reich
- INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| | - C Murat
- INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| | - E Morin
- INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| | - R H Nilsson
- Department of Plant and Environmental Sciences, University of Gothenborg, Box 461, 405 30 Gothenborg, Sweden
| | - S Uroz
- INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| | - F Martin
- INRA, UMR 1136 INRA/Nancy Université Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| |
Collapse
|
37
|
Uroz S, Calvaruso C, Turpault MP, Frey-Klett P. Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol 2009; 17:378-87. [PMID: 19660952 DOI: 10.1016/j.tim.2009.05.004] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 05/15/2009] [Accepted: 05/26/2009] [Indexed: 12/31/2022]
Affiliation(s)
- Stéphane Uroz
- Institut National de la Recherche Agronomique (INRA), Nancy Université, UMR 1136 Interactions Arbres Micro-organismes, Centre INRA de Nancy, 54280 Champenoux, France.
| | | | | | | |
Collapse
|
38
|
|
39
|
Uroz S, Calvaruso C, Turpault MP, Pierrat JC, Mustin C, Frey-Klett P. Effect of the mycorrhizosphere on the genotypic and metabolic diversity of the bacterial communities involved in mineral weathering in a forest soil. Appl Environ Microbiol 2007; 73:3019-27. [PMID: 17351101 PMCID: PMC1892860 DOI: 10.1128/aem.00121-07] [Citation(s) in RCA: 211] [Impact Index Per Article: 12.4] [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: 01/17/2007] [Accepted: 02/28/2007] [Indexed: 11/20/2022] Open
Abstract
To date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. However, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. In this study, we characterized a collection of 61 bacterial strains isolated from Scleroderma citrinum mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. The ability of bacteria to weather biotite was assessed with a new microplate bioassay that measures the pH and the quantity of iron released from this mineral. We showed that weathering bacteria occurred more frequently in the vicinity of S. citrinum than in the bulk soil. Moreover, the weathering efficacy of the mycorrhizosphere bacterial isolates was significantly greater than that of the bulk soil isolates. All the bacterial isolates were identified by partial 16S rRNA gene sequence analysis as members of the genera Burkholderia, Collimonas, Pseudomonas, and Sphingomonas, and their carbon metabolism was characterized by the BIOLOG method. The most efficient isolates belonged to the genera Burkholderia and Collimonas. Multivariate analysis resulted in identification of three metabolic groups, one of which contained mainly bacterial isolates associated with S. citrinum and exhibiting high mineral-weathering potential. Therefore, our results support the hypothesis that by its carbon metabolism this fungus selects in the bulk soil reservoir a bacterial community with high weathering potential, and they also address the question of functional complementation between mycorrhizal fungi and bacteria in the ectomycorrhizal complex for the promotion of tree nutrition.
Collapse
Affiliation(s)
- S Uroz
- INRA-UHP, Interactions Arbres Micro-organismes, UMR 1136, 54280 Champenoux, France.
| | | | | | | | | | | |
Collapse
|
40
|
Uroz S, Oger P, Chhabra SR, Cámara M, Williams P, Dessaux Y. N-acyl homoserine lactones are degraded via an amidolytic activity in Comamonas sp. strain D1. Arch Microbiol 2006; 187:249-56. [PMID: 17136382 DOI: 10.1007/s00203-006-0186-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [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: 08/08/2006] [Revised: 10/05/2006] [Accepted: 10/09/2006] [Indexed: 11/27/2022]
Abstract
Comamonas strain D1 enzymatically inactivates quorum-sensing (QS) signal molecules of the N-acyl homoserine lactone (N-AHSL) family, and exhibits the broadest inactivation range of known bacteria. It degrades N-AHSL with acyl-side chains ranging from 4 to 16 carbons, with or without 3-oxo or 3-hydroxy substitutions. N-AHSL degradation yields HSL but not N-acyl homoserine: strain D1 therefore harbors an amidohydrolase activity. Strain D1 is the fifth bacterium species in which an N-AHSL amidohydrolase is described. Consistent with its N-AHSL degradation ability, strain D1 efficiently quenches various QS-dependent functions in other bacteria, such as violacein production by Chromobacterium violaceum and pathogenicity and antibiotic production in Pectobacterium.
Collapse
Affiliation(s)
- Stéphane Uroz
- CNRS, ISV, Bâtiment 23, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | | | | | | | | | | |
Collapse
|
41
|
Uroz S, Chhabra SR, Cámara M, Williams P, Oger P, Dessaux Y. N-Acylhomoserine lactone quorum-sensing molecules are modified and degraded by Rhodococcus erythropolis W2 by both amidolytic and novel oxidoreductase activities. Microbiology (Reading) 2005; 151:3313-3322. [PMID: 16207914 DOI: 10.1099/mic.0.27961-0] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [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: 11/18/2022] Open
Abstract
The Rhodococcus erythropolis strain W2 has been shown previously to degrade the N-acylhomoserine lactone (AHL) quorum-sensing signal molecule N-hexanoyl-l-homoserine lactone, produced by other bacteria. Data presented here indicate that this Gram-positive bacterium is also capable of using various AHLs as the sole carbon and energy source. The enzymic activities responsible for AHL inactivation were investigated in R. erythropolis cell extracts and in whole cells. R. erythropolis cells rapidly degraded AHLs with 3-oxo substituents but exhibited relatively poor activity against the corresponding unsubstituted AHLs. Investigation of the mechanism(s) by which R. erythropolis cells degraded AHLs revealed that 3-oxo compounds with N-acyl side chains ranging from C8 to C14 were initially converted to their corresponding 3-hydroxy derivatives. This oxidoreductase activity was not specific to 3-oxo-AHLs but also allowed the reduction of compounds such as N-(3-oxo-6-phenylhexanoyl)homoserine lactone (which contains an aromatic acyl chain substituent) and 3-oxododecanamide (which lacks the homoserine lactone ring). It also reduced both the d- and l-isomers of n-(3-oxododecanoyl)-l-homoserine lactone. A second AHL-degrading activity was observed when R. erythropolis cell extracts were incubated with N-(3-oxodecanoyl)-l-homoserine lactone (3O,C10-HSL). This activity was both temperature- and pH-dependent and was characterized as an amidolytic activity by HPLC analysis of the reaction mixture treated with dansyl chloride. This revealed the accumulation of dansylated homoserine lactone, indicating that the 3O,C10-HSL amide had been cleaved to yield homoserine lactone. R. erythropolis is therefore capable of modifying and degrading AHL signal molecules through both oxidoreductase and amidolytic activities.
Collapse
Affiliation(s)
- Stéphane Uroz
- Interactions Plantes et Micro-organismes de la Rhizosphère, Institut des Sciences du Végétal, CNRS, Bâtiment 23, Avenue de la Terrasse, 91198 Gif-sur-Yvette CEDEX, France
| | - Siri Ram Chhabra
- Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Miguel Cámara
- Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Paul Williams
- Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Phil Oger
- Laboratoire des Sciences de la Terre, École Normale Supérieure de Lyon, 43 Allée D'Italie, 69364 Lyon CEDEX 07, France
| | - Yves Dessaux
- Interactions Plantes et Micro-organismes de la Rhizosphère, Institut des Sciences du Végétal, CNRS, Bâtiment 23, Avenue de la Terrasse, 91198 Gif-sur-Yvette CEDEX, France
| |
Collapse
|
42
|
d'Angelo-Picard C, Faure D, Carlier A, Uroz S, Raffoux A, Fray R, Dessaux Y. Bacterial populations in the rhizosphere of tobacco plants producing the quorum-sensing signals hexanoyl-homoserine lactone and 3-oxo-hexanoyl-homoserine lactone. FEMS Microbiol Ecol 2004; 51:19-29. [PMID: 16329853 DOI: 10.1016/j.femsec.2004.07.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [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: 02/26/2004] [Revised: 06/21/2004] [Accepted: 07/10/2004] [Indexed: 11/15/2022] Open
Abstract
A tobacco line genetically modified to produce two N-acyl homoserine lactones and its non-transformed parental line were grown in non-sterile soil. Microbial populations inhabiting the bulk soil, and those colonizing the root system of the two tobacco lines, were analyzed using cultivation-independent (phospholipid fatty acid and denaturing gradient gel electrophoresis) and cultivation-based assays. The cell density of total cultivable bacteria, fluorescent pseudomonads, sporulated, and thermotolerant bacteria was also determined in a time-course experiment (15 weeks). A possible "rhizosphere effect" related to the development of the plant was seen. However, no dissimilarities in cell population densities or population ratios of the microbial groups were detected in the rhizosphere of the two plant lines. Similarly, bacterial communities that either produced N-acyl homoserine lactone or degraded the signal hexanoyl homoserine lactone were enumerated from the two plant lines. No noticeable differences were evidenced from one plant genotype to the other. Whilst the transgenic plants released detectable amounts of the quorum-sensing signal molecules and efficiently cross-talked with the surrounding microbial populations, the bias generated by these signals in the reported experimental conditions therefore appears to remain weak, if not non-existent.
Collapse
Affiliation(s)
- Cathy d'Angelo-Picard
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, UPR2355, Bâtiment 23, F-91198, Gif-sur-Yvette, France
| | | | | | | | | | | | | |
Collapse
|
43
|
Delalande L, Faure D, Raffoux A, Uroz S, D'Angelo-Picard C, Elasri M, Carlier A, Berruyer R, Petit A, Williams P, Dessaux Y. N-hexanoyl-L-homoserine lactone, a mediator of bacterial quorum-sensing regulation, exhibits plant-dependent stability and may be inactivated by germinating Lotus corniculatus seedlings. FEMS Microbiol Ecol 2004; 52:13-20. [PMID: 16329888 DOI: 10.1016/j.femsec.2004.10.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [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: 05/25/2004] [Revised: 09/30/2004] [Accepted: 10/06/2004] [Indexed: 11/20/2022] Open
Abstract
The half-life of N-hexanoyl-l-homoserine lactone (C6-HSL) was determined under various pH and temperature conditions, and in several plant environments. C6-HSL was sensitive to alkaline pH, a process that was also temperature-dependent. In addition, C6-HSL disappeared from plant environments, i.e. axenic monocot and dicot plants cultivated under gnotobiotic, hydroponic conditions, albeit with variable kinetics. The disappearance was rapid at the root system of legume plants such as clover or Lotus, and slow or non-existent at the root system of monocots such as wheat or corn. These variable kinetics were not dependent upon pH changes that may have affected the growth media of the plants. Furthermore, C6-HSL did not accumulate in the plant, and the plant did not produce inhibitors of the C6-HSL signal. HPLC analyses revealed that C6-HSL disappeared from the media, and hence, Lotus exhibited a natural C6-HSL inactivating ability. This ability was not specific for C6-HSL and allowed the degradation of other N-acyl-homoserine lactones such as 3-oxo-C6-HSL, 3-oxo-octanoyl-HSL and 3-oxo-decanoyl-HSL. Preliminary investigation revealed that the inactivating ability is temperature-dependant and possibly of enzymatic origin.
Collapse
Affiliation(s)
- Laurie Delalande
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette CEDEX, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Carlier A, Uroz S, Smadja B, Fray R, Latour X, Dessaux Y, Faure D. The Ti plasmid of Agrobacterium tumefaciens harbors an attM-paralogous gene, aiiB, also encoding N-Acyl homoserine lactonase activity. Appl Environ Microbiol 2003; 69:4989-93. [PMID: 12902298 PMCID: PMC169067 DOI: 10.1128/aem.69.8.4989-4993.2003] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [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
The Agrobacterium tumefaciens C58 genome contains three putative N-acyl homoserine lactone (acyl-HSL) hydrolases, which are closely related to the lactonase AiiA of Bacillus. When expressed in Escherichia coli, two of the putative acyl-HSL hydrolases, AttM and AiiB, conferred the ability to degrade acyl-HSLs on the host. In Erwinia strain 6276, the lactonases reduced the endogenous acyl-HSL level and the bacterial virulence in planta.
Collapse
Affiliation(s)
- A Carlier
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | | | | | | | | | | | | |
Collapse
|
45
|
Uroz S, D'Angelo-Picard C, Carlier A, Elasri M, Sicot C, Petit A, Oger P, Faure D, Dessaux Y. Novel bacteria degrading N-acylhomoserine lactones and their use as quenchers of quorum-sensing-regulated functions of plant-pathogenic bacteria. Microbiology (Reading) 2003; 149:1981-1989. [PMID: 12904538 DOI: 10.1099/mic.0.26375-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacteria degrading the quorum-sensing (QS) signal molecule N-hexanoylhomoserine lactone were isolated from a tobacco rhizosphere. Twenty-five isolates degrading this homoserine lactone fell into six groups according to their genomic REP-PCR and rrs PCR-RFLP profiles. Representative strains from each group were identified as members of the genera Pseudomonas, Comamonas, Variovorax and Rhodococcus: all these isolates degraded N-acylhomoserine lactones other than the hexanoic acid derivative, albeit with different specificity and kinetics. One of these isolates, Rhodococcus erythropolis strain W2, was used to quench QS-regulated functions of other microbes. In vitro, W2 strongly interfered with violacein production by Chromobacterium violaceum, and transfer of pathogenicity in Agrobacterium tumefaciens. In planta, R. erythropolis W2 markedly reduced the pathogenicity of Pectobacterium carotovorum subsp. carotovorum in potato tubers. These series of results reveal the diversity of the QS-interfering bacteria in the rhizosphere and demonstrate the validity of targeting QS signal molecules to control pathogens with natural bacterial isolates.
Collapse
Affiliation(s)
- Stéphane Uroz
- Interactions plantes et micro-organismes de la rhizosphère, Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Cathy D'Angelo-Picard
- Interactions plantes et micro-organismes de la rhizosphère, Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Aurélien Carlier
- Interactions plantes et micro-organismes de la rhizosphère, Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Miena Elasri
- Interactions plantes et micro-organismes de la rhizosphère, Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Carine Sicot
- Interactions plantes et micro-organismes de la rhizosphère, Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Annik Petit
- Interactions plantes et micro-organismes de la rhizosphère, Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Phil Oger
- Laboratoire de Sciences de la Terre, Ecole Normale Supérieure, 43 allée d'Italie, 6364 Lyon Cedex, France
- Interactions plantes et micro-organismes de la rhizosphère, Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Denis Faure
- Interactions plantes et micro-organismes de la rhizosphère, Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Yves Dessaux
- Interactions plantes et micro-organismes de la rhizosphère, Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| |
Collapse
|