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E. M, S. U, R. K, M.W. R, J. P, F. A, J. H. J. L. Draft genome sequence of Collimonas sp. strain H4R21, an effective mineral-weathering bacterial strain isolated from the beech rhizosphere. Microbiol Resour Announc 2024; 13:e0030824. [PMID: 39037313 PMCID: PMC11320959 DOI: 10.1128/mra.00308-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024] Open
Abstract
We present the draft genome sequence of Collimonas sp. strain H4R21, isolated from the rhizosphere of Fagus sylvatica in the forest experimental site of Montiers (France). This genome features coding capacity for plant growth promotion, such as the ability to solubilize minerals, to produce siderophores and antifungal secondary metabolites.
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Affiliation(s)
- Morin E.
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, France
| | - Uroz S.
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, France
- INRAE, UR1138 « Biogéochimie des Ecosystèmes Forestiers », Champenoux, France
| | - Kumar R.
- Novozymes Inc., Davis, California, USA
| | - Rey M.W.
- Novozymes Inc., Davis, California, USA
| | - Pham J.
- Novozymes Inc., Davis, California, USA
| | - Akum F.
- Department of Plant Pathology, University of California, Davis, California, USA
| | - Leveau J. H. J.
- Department of Plant Pathology, University of California, Davis, California, USA
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Uroz S, Bouche S, Morin E, Bocquart M, Kumar R, Rey MW, Pham J, Akum F, Leveau JHJ. Collimonas rhizosphaerae sp. nov., a novel species isolated from the beech rhizosphere. Int J Syst Evol Microbiol 2024; 74:006481. [PMID: 39078398 PMCID: PMC11288634 DOI: 10.1099/ijsem.0.006481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/20/2024] [Indexed: 07/31/2024] Open
Abstract
Bacterial strain H4R21T was isolated from beech rhizosphere soil sampled in the forest experimental site of Montiers (Meuse, France). It effectively weathers minerals, hydrolyses chitin and produces quorum sensing signal molecules. The strain is aerobic and Gram-stain-negative. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain H4R21T belongs to the genus Collimonas with high sequence similarity to C. arenae Ter10T (99.38 %), C. fungivorans Ter6T(98.97 %), C. pratensis Ter91T (98.76 %), C. humicola RLT1W51T (98.46 %) and C. silvisoli RXD178 T (98.46 %), but less than 98 % similarity to other strains of the genus Collimonas. The predominant quinone in H4R21T is ubiquinone-8 (Q8). The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and lipid. The major fatty acids identified were C12 : 0, C12:0 3-OH, C16 : 0 and C17:0 cyclo. The digital DNA G+C content of the genomic DNA was 59.5 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by a combination of phylogenomic and in silico DNA-DNA hybridization results, and phenotypic characteristics. Therefore, strain H4R21T represents a novel species within the genus Collimonas, for which the name Collimonas rhizosphaerae sp. nov. is proposed, with strain H4R21T (=CFBP 9203T=DSM 117599T) as the type strain.
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Affiliation(s)
- Stephane Uroz
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres-Microorganismes, 54000 Nancy, France
- INRAE, UR1138, Biogéochimie des Ecosystèmes Forestiers, F-54280 Champenoux, France
| | - Ségolène Bouche
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres-Microorganismes, 54000 Nancy, France
- INRAE, UR1138, Biogéochimie des Ecosystèmes Forestiers, F-54280 Champenoux, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres-Microorganismes, 54000 Nancy, France
| | - Mathilde Bocquart
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres-Microorganismes, 54000 Nancy, France
| | - Ravi Kumar
- Novozymes Inc., 1445 Drew Ave., Davis, CA 95618, USA
| | | | - Jonathan Pham
- Novozymes Inc., 1445 Drew Ave., Davis, CA 95618, USA
| | - Fidel Akum
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Johan H. J. Leveau
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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Uroz S, Geisler O, Fauchery L, Lami R, Rodrigues AMS, Morin E, Leveau JHJ, Oger P. Genomic and transcriptomic characterization of the Collimonas quorum sensing genes and regulon. FEMS Microbiol Ecol 2022; 98:6679101. [PMID: 36040340 DOI: 10.1093/femsec/fiac100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/13/2022] [Accepted: 08/26/2022] [Indexed: 01/21/2023] Open
Abstract
Collimonads are well-adapted to nutrient-poor environments. They are known to hydrolyse chitin, produce antifungal metabolites, weather minerals, and are effective biocontrol agents protecting plants from fungal diseases. The production of N-acyl homoserine lactones (AHLs) was suggested to be a conserved trait of collimonads, but little is known about the genes that underlie this production or the genes that are controlled by AHLs. To improve our understanding of the role of AHLs in the ecology of collimonads, we carried out transcriptomic analyses, combined with chemical and functional assays, on strain Collimonas pratensis PMB3(1). The main AHLs produced by this strain were identified as 3-hydroxy-hexa- and octa-noyl-homoserine lactone. Genome analysis permitted to identify putative genes coding for the autoinducer synthase (colI) and cognate transcriptional regulator (colR). The ability to produce AHLs was lost in ΔcolI and ΔcolR mutants. Functional assays revealed that the two mutants metabolized glucose, formate, oxalate, and leucine better than the wild-type (WT) strain. Transcriptome sequencing analyses revealed an up-regulation of different metabolic pathways and of motility in the QS-mutants compared to the WT strain. Overall, our results provide insights into the role of the AHL-dependent regulation system of Collimonas in environment colonization, metabolism readjustment, and microbial interactions.
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Affiliation(s)
- Stephane Uroz
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France.,INRAE, UR1138 "Biogéochimie des écosystèmes forestiers", F-54280 Champenoux, France
| | - Océane Geisler
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France
| | - Laure Fauchery
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France
| | - Raphaël Lami
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM, USR3579), Fédération de Recherche FR3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Alice M S Rodrigues
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM, USR3579), Fédération de Recherche FR3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France
| | - Johan H J Leveau
- Department of Plant Pathology, University of California - Davis, Davis, CA 95616, United States
| | - Philippe Oger
- Université Lyon, INSA de Lyon, CNRS UMR 5240, F-69622 Villeurbanne, France
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Chen MX, He XY, Li HY. Muricauda chongwuensis sp. nov., isolated from coastal seawater of China. Arch Microbiol 2021; 203:6245-6252. [PMID: 34609527 DOI: 10.1007/s00203-021-02591-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/02/2021] [Accepted: 09/21/2021] [Indexed: 11/26/2022]
Abstract
In the course of screening for bacterial predators, a Gram-stain-negative, non-flagellated, gliding, long rod-shaped, and yellow-pigmented bacterium, designated strain HICWT, was isolated from coastal seawater of China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HICWT represented a member of the genus Muricauda and showed the highest sequence similarity to M. aquimarina JCM11811T (98.8%) and M. ruestringensis DSM13258T (98.1%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain HICWT and M. aquimarina JCM11811T were 79.2% and 34.1%, respectively. NaCl was required for growth. Optimum growth occurred at 25-30 °C, 2.0-3.0% (w/v) NaCl with pH 7.0. Strain HICWT showed some similar characteristics to the nonobligate bacterial predators, and the cells can attach to the prey cells. Strain HICWT contained MK-6 as the predominant respiratory quinone and had iso-C15:0, iso-C15:1 G, and iso-C17:0 3-OH as the major cellular fatty acids. The polar lipids contained phosphatidylethanolamine (PE), three unidentified phospholipids (PL1-PL3), one unidentified amino lipids (AL), and three unidentified polar lipids (L1-L3). The genome size of strain HICWT was approximately 3.8 Mbp, with a G + C content of 41.4%. Based on the polyphasic evidence, strain HICWT is proposed as representing a new species of the genus Muricauda, for which the name Muricauda chongwuensis sp. nov. is proposed. The type strain is HICWT (= JCM 33643 T = MCCC 1K03769T).
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Affiliation(s)
- Ming-Xia Chen
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Xiamen, 361021, Fujian, People's Republic of China.
| | - Xiao-Yu He
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Xiamen, 361021, Fujian, People's Republic of China
| | - He-Yang Li
- Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen, 361005, Fujian, People's Republic of China.
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, 361005, Fujian, People's Republic of China.
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