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Quesada JM, Fernández M, Soriano MI, Barrientos-Moreno L, Llamas MA, Espinosa-Urgel M. Rhizosphere selection of Pseudomonas putida KT2440 variants with increased fitness associated to changes in gene expression. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:842-850. [PMID: 27487165 DOI: 10.1111/1758-2229.12447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
As the interface between plant roots and soil, the rhizosphere is a complex environment where nutrients released by the plant promote microbial growth. Increasing evidences indicate that the plant also exerts a selective pressure on microbial populations in the rhizosphere, favouring colonization by certain groups. In this work, we have designed an experimental setup to begin analysing the evolution of a specific bacterial population in the rhizosphere, using Pseudomonas putida KT2440 as model organism. After several rounds of selection without passage through laboratory growth conditions, derivatives of this strain with increased fitness in the rhizosphere were isolated. Detailed analysis of one of these clones indicated that this effect is specific for rhizosphere conditions and derives from changes in its transcriptional profile in this environment, with 43 genes being differentially expressed with respect to the parental strain. Several of these genes belong to functional categories which could affect stress adaptation and availability of particular nutrients. By inactivating two genes identified as upregulated in the selected clone (coding for a stress-response protein and a rRNA modifying protein), these functions were shown to contribute to rhizosphere fitness. Our data also suggest the existence of different evolutionary pathways leading to increased rhizosphere fitness.
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Affiliation(s)
- José Miguel Quesada
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - Matilde Fernández
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - María Isabel Soriano
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - Laura Barrientos-Moreno
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - María Antonia Llamas
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - Manuel Espinosa-Urgel
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
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Ramos-González MI, Travieso ML, Soriano MI, Matilla MA, Huertas-Rosales Ó, Barrientos-Moreno L, Tagua VG, Espinosa-Urgel M. Genetic Dissection of the Regulatory Network Associated with High c-di-GMP Levels in Pseudomonas putida KT2440. Front Microbiol 2016; 7:1093. [PMID: 27489550 PMCID: PMC4951495 DOI: 10.3389/fmicb.2016.01093] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/30/2016] [Indexed: 11/24/2022] Open
Abstract
Most bacteria grow in nature forming multicellular structures named biofilms. The bacterial second messenger cyclic diguanosine monophosphate (c-di-GMP) is a key player in the regulation of the transition from planktonic to sessile lifestyles and this regulation is crucial in the development of biofilms. In Pseudomonas putida KT2440, Rup4959, a multidomain response regulator with diguanylate cyclase activity, when overexpressed causes an increment in the intracellular levels of c-di-GMP that gives rise to a pleiotropic phenotype consisting of increased biofilm formation and crinkly colony morphology. In a broad genomic screen we have isolated mutant derivatives that lose the crinkly morphology, designed as cfc (crinkle free colony). A total of 19 different genes have been identified as being related with the emergence of the cfc phenotype either because the expression or functionality of Rup4959 is compromised, or due to a lack of transduction of the c-di-GMP signal to downstream elements involved in the acquisition of the phenotype. Discernment between these possibilities was investigated by using a c-di-GMP biosensor and by HPLC-MS quantification of the second messenger. Interestingly five of the identified genes encode proteins with AAA+ ATPase domain. Among the bacterial determinants found in this screen are the global transcriptional regulators GacA, AlgU and FleQ and two enzymes involved in the arginine biosynthesis pathway. We present evidences that this pathway seems to be an important element to both the availability of the free pool of the second messenger c-di-GMP and to its further transduction as a signal for biosynthesis of biopolimers. In addition we have identified an uncharacterized hybrid sensor histidine kinase whose phosphoaceptor conserved histidine residue has been shown in this work to be required for in vivo activation of the orphan response regulator Rup4959, which suggests these two elements constitute a two-component phosphorelay system.
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Affiliation(s)
- María Isabel Ramos-González
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - María L Travieso
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - María I Soriano
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Óscar Huertas-Rosales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Laura Barrientos-Moreno
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Víctor G Tagua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
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Identification of a Third Mn(II) Oxidase Enzyme in Pseudomonas putida GB-1. Appl Environ Microbiol 2016; 82:3774-3782. [PMID: 27084014 DOI: 10.1128/aem.00046-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/12/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The oxidation of soluble Mn(II) to insoluble Mn(IV) is a widespread bacterial activity found in a diverse array of microbes. In the Mn(II)-oxidizing bacterium Pseudomonas putida GB-1, two Mn(II) oxidase genes, named mnxG and mcoA, were previously identified; each encodes a multicopper oxidase (MCO)-type enzyme. Expression of these two genes is positively regulated by the response regulator MnxR. Preliminary investigation into putative additional regulatory pathways suggested that the flagellar regulators FleN and FleQ also regulate Mn(II) oxidase activity; however, it also revealed the presence of a third, previously uncharacterized Mn(II) oxidase activity in P. putida GB-1. A strain from which both of the Mn(II) oxidase genes and fleQ were deleted exhibited low levels of Mn(II) oxidase activity. The enzyme responsible was genetically and biochemically identified as an animal heme peroxidase (AHP) with domain and sequence similarity to the previously identified Mn(II) oxidase MopA. In the ΔfleQ strain, P. putida GB-1 MopA is overexpressed and secreted from the cell, where it actively oxidizes Mn. Thus, deletion of fleQ unmasked a third Mn(II) oxidase activity in this strain. These results provide an example of an Mn(II)-oxidizing bacterium utilizing both MCO and AHP enzymes. IMPORTANCE The identity of the Mn(II) oxidase enzyme in Pseudomonas putida GB-1 has been a long-standing question in the field of bacterial Mn(II) oxidation. In the current work, we demonstrate that P. putida GB-1 employs both the multicopper oxidase- and animal heme peroxidase-mediated pathways for the oxidation of Mn(II), rendering this model organism relevant to the study of both types of Mn(II) oxidase enzymes. The presence of three oxidase enzymes in P. putida GB-1 deepens the mystery of why microorganisms oxidize Mn(II) while providing the field with the tools necessary to address this question. The initial identification of MopA as a Mn(II) oxidase in this strain required the deletion of FleQ, a regulator involved in both flagellum synthesis and biofilm synthesis in Pseudomonas aeruginosa Therefore, these results are also an important step toward understanding the regulation of Mn(II) oxidation.
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The analysis of the antibiotic resistome offers new opportunities for therapeutic intervention. Future Med Chem 2016; 8:1133-51. [DOI: 10.4155/fmc-2016-0027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Most efforts in the development of antimicrobials have focused on the screening of lethal targets. Nevertheless, the constant expansion of antimicrobial resistance makes the antibiotic resistance determinants themselves suitable targets for finding inhibitors to be used in combination with antibiotics. Among them, inhibitors of antibiotic inactivating enzymes and of multidrug efflux pumps are suitable candidates for improving the efficacy of antibiotics. In addition, the application of systems biology tools is helping to understand the changes in bacterial physiology associated to the acquisition of resistance, including the increased susceptibility to other antibiotics displayed by some antibiotic-resistant mutants. This information is useful for implementing novel strategies based in metabolic interventions or combination of antibiotics for improving the efficacy of antibacterial therapy.
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Mwita L, Chan WY, Pretorius T, Lyantagaye SL, Lapa SV, Avdeeva LV, Reva ON. Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates. Gene 2016; 590:18-28. [PMID: 27259668 DOI: 10.1016/j.gene.2016.05.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/04/2016] [Accepted: 05/31/2016] [Indexed: 12/17/2022]
Abstract
Despite successful use of Plant Growth Promoting Rhizobacteria (PGPR) in agriculture, little is known about specific mechanisms of gene regulation facilitating the effective communication between bacteria and plants during plant colonization. Active PGPR strain Bacillus atrophaeus UCMB-5137 was studied in this research. RNA sequencing profiles were generated in experiments where root exudate stimulations were used to mimic interactions between bacteria and plants. It was found that the gene regulation in B. atrophaeus UCMB-5137 in response to the root exudate stimuli differed from the reported gene regulation at similar conditions in B. amyloliquefaciens FZB42, which was considered as a paradigm PGPR. This difference was explained by hypersensitivity of UCMB-5137 to the root exudate stimuli impelling it to a sessile root colonization behavior through the CcpA-CodY-AbrB regulation. It was found that the transcriptional factor DegU also could play an important role in gene regulations during plant colonization. A significant stress caused by the root exudates on in vitro cultivated B. atrophaeus UCMB-5137 was noticed and discussed. Multiple cases of conflicted gene regulations showed scantiness of our knowledge on the regulatory network in Bacillus. Some of these conflicted regulations could be explained by interference of non-coding RNA (ncRNA). Search through differential expressed intergenic regions revealed 49 putative loci of ncRNA regulated by the root exudate stimuli. Possible target mRNA were predicted and a general regulatory network of B. atrophaeus UCMB-5137 genome was designed.
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Affiliation(s)
- Liberata Mwita
- Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa
| | - Wai Yin Chan
- Department of Microbiology and Plant Pathology, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa
| | - Theresa Pretorius
- Department of Microbiology and Plant Pathology, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa
| | - Sylvester L Lyantagaye
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania
| | - Svitlana V Lapa
- Dep. Antibiotics, D. K. Zabolotnogo Institute of Microbiology and Virology, 154 Zabolotnogo Str., Kiev, Ukraine
| | - Lilia V Avdeeva
- Dep. Antibiotics, D. K. Zabolotnogo Institute of Microbiology and Virology, 154 Zabolotnogo Str., Kiev, Ukraine
| | - Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa.
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Blanco P, Hernando-Amado S, Reales-Calderon JA, Corona F, Lira F, Alcalde-Rico M, Bernardini A, Sanchez MB, Martinez JL. Bacterial Multidrug Efflux Pumps: Much More Than Antibiotic Resistance Determinants. Microorganisms 2016; 4:microorganisms4010014. [PMID: 27681908 PMCID: PMC5029519 DOI: 10.3390/microorganisms4010014] [Citation(s) in RCA: 366] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/22/2016] [Accepted: 01/29/2016] [Indexed: 02/07/2023] Open
Abstract
Bacterial multidrug efflux pumps are antibiotic resistance determinants present in all microorganisms. With few exceptions, they are chromosomally encoded and present a conserved organization both at the genetic and at the protein levels. In addition, most, if not all, strains of a given bacterial species present the same chromosomally-encoded efflux pumps. Altogether this indicates that multidrug efflux pumps are ancient elements encoded in bacterial genomes long before the recent use of antibiotics for human and animal therapy. In this regard, it is worth mentioning that efflux pumps can extrude a wide range of substrates that include, besides antibiotics, heavy metals, organic pollutants, plant-produced compounds, quorum sensing signals or bacterial metabolites, among others. In the current review, we present information on the different functions that multidrug efflux pumps may have for the bacterial behaviour in different habitats as well as on their regulation by specific signals. Since, in addition to their function in non-clinical ecosystems, multidrug efflux pumps contribute to intrinsic, acquired, and phenotypic resistance of bacterial pathogens, the review also presents information on the search for inhibitors of multidrug efflux pumps, which are currently under development, in the aim of increasing the susceptibility of bacterial pathogens to antibiotics.
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Affiliation(s)
- Paula Blanco
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Sara Hernando-Amado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Jose Antonio Reales-Calderon
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Fernando Corona
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Felipe Lira
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Manuel Alcalde-Rico
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Alejandra Bernardini
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Maria Blanca Sanchez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Jose Luis Martinez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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Abstract
The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.
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Corral-Lugo A, De la Torre J, Matilla MA, Fernández M, Morel B, Espinosa-Urgel M, Krell T. Assessment of the contribution of chemoreceptor-based signalling to biofilm formation. Environ Microbiol 2016; 18:3355-3372. [PMID: 26662997 DOI: 10.1111/1462-2920.13170] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/30/2015] [Indexed: 12/01/2022]
Abstract
Although it is well established that one- and two-component regulatory systems participate in regulating biofilm formation, there also exists evidence suggesting that chemosensory pathways are also involved. However, little information exists about which chemoreceptors and signals modulate this process. Here we report the generation of the complete set of chemoreceptor mutants of Pseudomonas putida KT2440 and the identification of four mutants with significantly altered biofilm phenotypes. These receptors are a WspA homologue of Pseudomonas aeruginosa, previously identified to control biofilm formation by regulating c-di-GMP levels, and three uncharacterized chemoreceptors. One of these receptors, named McpU, was found to mediate chemotaxis towards different polyamines. The functional annotation of McpU was initiated by high-throughput thermal shift assays of the receptor ligand binding domain (LBD). Isothermal titration calorimetry showed that McpU-LBD specifically binds putrescine, cadaverine and spermidine, indicating that McpU represents a novel chemoreceptor type. Another uncharacterized receptor, named McpA, specifically binds 12 different proteinogenic amino acids and mediates chemotaxis towards these compounds. We also show that mutants in McpU and WspA-Pp have a significantly reduced ability to colonize plant roots. Data agree with other reports showing that polyamines are signal molecules involved in the regulation of bacteria-plant communication and biofilm formation.
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Affiliation(s)
- Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Jesús De la Torre
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Bertrand Morel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain.
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Zhang N, Yang D, Wang D, Miao Y, Shao J, Zhou X, Xu Z, Li Q, Feng H, Li S, Shen Q, Zhang R. Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates. BMC Genomics 2015; 16:685. [PMID: 26346121 PMCID: PMC4562157 DOI: 10.1186/s12864-015-1825-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 08/07/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Bacillus amyloliquefaciens SQR9 is a plant growth-promoting rhizobacteria (PGPR) with outstanding abilities to enhance plant growth and to control soil-borne diseases. Root exudates is known to play important roles in plant-microbe interactions. To explore the rhizosphere interactions and plant-beneficial characteristics of SQR9, the complete genome sequence as well as the transcriptome in response to maize root exudates under biofilm-forming conditions were elucidated. RESULTS Maize root exudates stimulated SQR9 biofilm formation in liquid culture, which is known to be positively correlated with enhanced root colonization. Transcriptional profiling via RNA-sequencing of SQR9 under static conditions indicated that, at 24 h post-inoculation, root exudates stimulated the expression of metabolism-relevant genes, while at 48 h post-inoculation, genes related to extracellular matrix production (tapA-sipW-tasA operon) were activated by root exudates. The individual components in maize root exudates that stimulated biofilm formation included glucose, citric acid, and fumaric acid, which either promoted the growth of SQR9 cells or activated extracellular matrix production. In addition, numerous groups of genes involved in rhizosphere adaptation and in plant-beneficial traits, including plant polysaccharide utilization, cell motility and chemotaxis, secondary antibiotics synthesis clusters, and plant growth promotion-relevant, were identified in the SQR9 genome. These genes also appeared to be induced by the maize root exudates. CONCLUSIONS Enhanced biofilm formation of B. amyloliquefaciens SQR9 by maize root exudates could mainly be attributed to promoting cell growth and to inducing extracellular matrix production. The genomic analysis also highlighted the elements involved in the strain's potential as a PGPR. This study provides useful information for understanding plant-rhizobacteria interactions and hence for promoting the agricultural applications of this strain.
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Affiliation(s)
- Nan Zhang
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Dongqing Yang
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Dandan Wang
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Youzhi Miao
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Jiahui Shao
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Xuan Zhou
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Zhihui Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Qing Li
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Haichao Feng
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Shuqing Li
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Qirong Shen
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
- College of Resources & Environmental Science, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Ruifu Zhang
- Jiangsu Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China.
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
- College of Resources & Environmental Science, Nanjing Agricultural University, 210095, Nanjing, China.
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Youenou B, Favre-Bonté S, Bodilis J, Brothier E, Dubost A, Muller D, Nazaret S. Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles. Genome Biol Evol 2015; 7:2484-505. [PMID: 26276674 PMCID: PMC4607518 DOI: 10.1093/gbe/evv161] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Stenotrophomonas maltophilia, a ubiquitous Gram-negative γ-proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain's phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance-nodulation-division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.
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Affiliation(s)
- Benjamin Youenou
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Sabine Favre-Bonté
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Josselin Bodilis
- EA4312 Laboratoire de Microbiologie Signaux et Microenvironnement, Université de Rouen, Mont-Saint-Aignan, France
| | - Elisabeth Brothier
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Daniel Muller
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Sylvie Nazaret
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
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Reyes-Darias JA, García V, Rico-Jiménez M, Corral-Lugo A, Lesouhaitier O, Juárez-Hernández D, Yang Y, Bi S, Feuilloley M, Muñoz-Rojas J, Sourjik V, Krell T. Specific gamma-aminobutyrate chemotaxis in pseudomonads with different lifestyle. Mol Microbiol 2015; 97:488-501. [PMID: 25921834 DOI: 10.1111/mmi.13045] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2015] [Indexed: 02/02/2023]
Abstract
The PctC chemoreceptor of Pseudomonas aeruginosa mediates chemotaxis with high specificity to gamma-aminobutyric acid (GABA). This compound is present everywhere in nature and has multiple functions, including being a human neurotransmitter or plant signaling compound. Because P. aeruginosa is ubiquitously distributed in nature and able to infect and colonize different hosts, the physiological relevance of GABA taxis is unclear, but it has been suggested that bacterial attraction to neurotransmitters may enhance virulence. We report the identification of McpG as a specific GABA chemoreceptor in non-pathogenic Pseudomonas putida KT2440. As with PctC, GABA was found to bind McpG tightly. The analysis of chimeras comprising the PctC and McpG ligand-binding domains fused to the Tar signaling domain showed very high GABA sensitivities. We also show that PctC inactivation does not alter virulence in Caenorhabditis elegans. Significant amounts of GABA were detected in tomato root exudates, and deletion of mcpG reduced root colonization that requires chemotaxis through agar. The C. elegans data and the detection of a GABA receptor in non-pathogenic species indicate that GABA taxis may not be related to virulence in animal systems but may be of importance in the context of colonization and infection of plant roots by soil-dwelling pseudomonads.
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Affiliation(s)
- Jose Antonio Reyes-Darias
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda, 1, 18008, Granada, Spain
| | - Vanina García
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda, 1, 18008, Granada, Spain
| | - Miriam Rico-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda, 1, 18008, Granada, Spain
| | - Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda, 1, 18008, Granada, Spain
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironnement LMSM, EA 4312, Normandie Université, Université Rouen, 55 rue Saint Germain, 27000, Evreux, France
| | - Dalia Juárez-Hernández
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas-Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, 72570, Puebla, Mexico
| | - Yiling Yang
- Max Planck Institute for Terrestrial Microbiology & LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 10, D-35043, Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Shuangyu Bi
- Max Planck Institute for Terrestrial Microbiology & LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 10, D-35043, Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Marc Feuilloley
- Laboratory of Microbiology Signals and Microenvironnement LMSM, EA 4312, Normandie Université, Université Rouen, 55 rue Saint Germain, 27000, Evreux, France
| | - Jesús Muñoz-Rojas
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas-Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, 72570, Puebla, Mexico
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 10, D-35043, Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda, 1, 18008, Granada, Spain
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62
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Xie S, Wu H, Chen L, Zang H, Xie Y, Gao X. Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings. BMC Microbiol 2015; 15:21. [PMID: 25651892 PMCID: PMC4326333 DOI: 10.1186/s12866-015-0353-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 01/19/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Plant growth-promoting rhizobacteria (PGPR) are soil beneficial microorganisms that colonize plant roots for nutritional purposes and accordingly benefit plants by increasing plant growth or reducing disease. However, the mechanisms and pathways involved in the interactions between PGPR and plants remain unclear. In order to better understand these complex plant-PGPR interactions, changes in the transcriptome of the typical PGPR Bacillus subtilis in response to rice seedlings were analyzed. RESULTS Microarray technology was used to study the global transcriptionl response of B. subtilis OKB105 to rice seedlings after an interaction period of 2 h. A total of 176 genes representing 3.8% of the B. subtilis strain OKB105 transcriptome showed significantly altered expression levels in response to rice seedlings. Among these, 52 were upregulated, the majority of which are involved in metabolism and transport of nutrients, and stress responses, including araA, ywkA, yfls, mtlA, ydgG et al. The 124 genes that were downregulated included cheV, fliL, spmA and tua, and these are involved in chemotaxis, motility, sporulation and teichuronic acid biosynthesis, respectively. CONCLUSIONS We present a transcriptome analysis of the bacteria Bacillus subtilis OKB105 in response to rice seedings. Many of the 176 differentially expressed genes are likely to be involved in the interaction between Gram-positive bacteria and plants.
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Affiliation(s)
- Shanshan Xie
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Weigang No.1, Nanjing, 210095, People's Republic of China.
| | - Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Weigang No.1, Nanjing, 210095, People's Republic of China.
| | - Lina Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Weigang No.1, Nanjing, 210095, People's Republic of China.
| | - Haoyu Zang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Weigang No.1, Nanjing, 210095, People's Republic of China.
| | - Yongli Xie
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Weigang No.1, Nanjing, 210095, People's Republic of China.
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Weigang No.1, Nanjing, 210095, People's Republic of China.
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63
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Moor H, Teppo A, Lahesaare A, Kivisaar M, Teras R. Fis overexpression enhances Pseudomonas putida biofilm formation by regulating the ratio of LapA and LapF. MICROBIOLOGY-SGM 2014; 160:2681-2693. [PMID: 25253613 DOI: 10.1099/mic.0.082503-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bacteria form biofilm as a response to a number of environmental signals that are mediated by global transcription regulators and alarmones. Here we report the involvement of the global transcription regulator Fis in Pseudomonas putida biofilm formation through regulation of lapA and lapF genes. The major component of P. putida biofilm is proteinaceous and two large adhesive proteins, LapA and LapF, are known to play a key role in its formation. We have previously shown that Fis overexpression enhances P. putida biofilm formation. In this study, we used mini-Tn5 transposon mutagenesis to select potential Fis-regulated genes involved in biofilm formation. A total of 90 % of the studied transposon mutants carried insertions in the lap genes. Since our experiments showed that Fis-enhanced biofilm is mostly proteinaceous, the amounts of LapA and LapF from P. putida cells lysates were quantified using SDS-PAGE. Fis overexpression increases the quantity of LapA 1.6 times and decreases the amount of LapF at least 4 times compared to the wild-type cells. The increased LapA expression caused by Fis overexpression was confirmed by FACS analysis measuring the amount of LapA-GFP fusion protein. Our results suggest that the profusion of LapA in the Fis-overexpressed cells causes enhanced biofilm formation in mature stages of P. putida biofilm and LapF has a minor role in P. putida biofilm formation.
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Affiliation(s)
- Hanna Moor
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Annika Teppo
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Andrio Lahesaare
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Riho Teras
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
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64
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Kim J, Park W. Oxidative stress response in Pseudomonas putida. Appl Microbiol Biotechnol 2014; 98:6933-46. [PMID: 24957251 DOI: 10.1007/s00253-014-5883-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 11/30/2022]
Abstract
Pseudomonas putida is widely distributed in nature and is capable of degrading various organic compounds due to its high metabolic versatility. The survival capacity of P. putida stems from its frequent exposure to various endogenous and exogenous oxidative stresses. Oxidative stress is an unavoidable consequence of interactions with various reactive oxygen species (ROS)-inducing agents existing in various niches. ROS could facilitate the evolution of bacteria by mutating genomes. Aerobic bacteria maintain defense mechanisms against oxidative stress throughout their evolution. To overcome the detrimental effects of oxidative stress, P. putida has developed defensive cellular systems involving induction of stress-sensing proteins and detoxification enzymes as well as regulation of oxidative stress response networks. Genetic responses to oxidative stress in P. putida differ markedly from those observed in Escherichia coli and Salmonella spp. Two major redox-sensing transcriptional regulators, SoxR and OxyR, are present and functional in the genome of P. putida. However, the novel regulators FinR and HexR control many genes belonging to the E. coli SoxR regulon. Oxidative stress can be generated by exposure to antibiotics, and iron homeostasis in P. putida is crucial for bacterial cell survival during treatment with antibiotics. This review highlights and summarizes current knowledge of oxidative stress in P. putida, as a model soil bacterium, together with recent studies from molecular genetics perspectives.
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Affiliation(s)
- Jisun Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5Ga, Seungbuk-Ku, Seoul, 136-713, Republic of Korea
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65
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Holmes A, Birse L, Jackson RW, Holden NJ. An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7. Front Microbiol 2014; 5:286. [PMID: 25018749 PMCID: PMC4071639 DOI: 10.3389/fmicb.2014.00286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/23/2014] [Indexed: 01/08/2023] Open
Abstract
Analysis of microbial gene expression during host colonization provides valuable information on the nature of interaction, beneficial or pathogenic, and the adaptive processes involved. Isolation of bacterial mRNA for in planta analysis can be challenging where host nucleic acid may dominate the preparation, or inhibitory compounds affect downstream analysis, e.g., quantitative reverse transcriptase PCR (qPCR), microarray, or RNA-seq. The goal of this work was to optimize the isolation of bacterial mRNA of food-borne pathogens from living plants. Reported methods for recovery of phytopathogen-infected plant material, using hot phenol extraction and high concentration of bacterial inoculation or large amounts of infected tissues, were found to be inappropriate for plant roots inoculated with Escherichia coli O157:H7. The bacterial RNA yields were too low and increased plant material resulted in a dominance of plant RNA in the sample. To improve the yield of bacterial RNA and reduce the number of plants required, an optimized method was developed which combines bead beating with directed bacterial lysis using SDS and lysozyme. Inhibitory plant compounds, such as phenolics and polysaccharides, were counteracted with the addition of high-molecular-weight polyethylene glycol and hexadecyltrimethyl ammonium bromide. The new method increased the total yield of bacterial mRNA substantially and allowed assessment of gene expression by qPCR. This method can be applied to other bacterial species associated with plant roots, and also in the wider context of food safety.
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Affiliation(s)
- Ashleigh Holmes
- Cell and Molecular Sciences, The James Hutton Institute Invergowrie, Dundee, UK
| | - Louise Birse
- Cell and Molecular Sciences, The James Hutton Institute Invergowrie, Dundee, UK
| | - Robert W Jackson
- School of Biological Sciences, The University of Reading Knight Building, Whiteknights, Reading, UK
| | - Nicola J Holden
- Cell and Molecular Sciences, The James Hutton Institute Invergowrie, Dundee, UK
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66
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Hunter PJ, Teakle GR, Bending GD. Root traits and microbial community interactions in relation to phosphorus availability and acquisition, with particular reference to Brassica. FRONTIERS IN PLANT SCIENCE 2014; 5:27. [PMID: 24575103 PMCID: PMC3920115 DOI: 10.3389/fpls.2014.00027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/22/2014] [Indexed: 05/21/2023]
Abstract
Brassicas are among the most widely grown and important crops worldwide. Phosphorus (P) is a key mineral element in the growth of all plants and is largely supplied as inorganic rock-phosphate, a dwindling resource, which is likely to be an increasingly significant factor in global agriculture. In order to develop crops which can abstract P from the soil, utilize it more efficiently, require less of it or obtain more from other sources such as soil organic P reservoirs, a detailed understanding the factors that influence P metabolism and cycling in plants and associated soil is required. This review focuses on the current state of understanding of root traits, rhizodeposition and rhizosphere community interaction as it applies to P solubilization and acquisition, with particular reference to Brassica species. Physical root characteristics, exudation of organic acids (particularly malate and citrate) and phosphatase enzymes are considered and the potential mechanisms of control of these responses to P deficiency examined. The influence of rhizodeposits on the development of the rhizosphere microbial community is discussed and the specific features of this community in response to P deficiency are considered; specifically production of phosphatases, phytases and phosphonate hydrolases. Finally various potential approaches for improving overall P use efficiency in Brassica production are discussed.
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Affiliation(s)
- Paul J. Hunter
- School of Life Sciences, University of WarwickCoventry, UK
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67
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Yergeau E, Sanschagrin S, Maynard C, St-Arnaud M, Greer CW. Microbial expression profiles in the rhizosphere of willows depend on soil contamination. THE ISME JOURNAL 2014; 8:344-58. [PMID: 24067257 PMCID: PMC3906822 DOI: 10.1038/ismej.2013.163] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 11/09/2022]
Abstract
The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation.
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Affiliation(s)
- Etienne Yergeau
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
| | - Sylvie Sanschagrin
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
| | - Christine Maynard
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
| | - Marc St-Arnaud
- Biodiversity Center, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
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68
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Sindhu SS, Parmar P, Phour M. Nutrient Cycling: Potassium Solubilization by Microorganisms and Improvement of Crop Growth. GEOMICROBIOLOGY AND BIOGEOCHEMISTRY 2014. [DOI: 10.1007/978-3-642-41837-2_10] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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69
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Pieterse CMJ, Zamioudis C, Berendsen RL, Weller DM, Van Wees SCM, Bakker PAHM. Induced systemic resistance by beneficial microbes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:347-75. [PMID: 24906124 DOI: 10.1146/annurev-phyto-082712-102340] [Citation(s) in RCA: 1206] [Impact Index Per Article: 120.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth-promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of pathogens and insect herbivores. A wide variety of root-associated mutualists, including Pseudomonas, Bacillus, Trichoderma, and mycorrhiza species sensitize the plant immune system for enhanced defense without directly activating costly defenses. This review focuses on molecular processes at the interface between plant roots and ISR-eliciting mutualists, and on the progress in our understanding of ISR signaling and systemic defense priming. The central role of the root-specific transcription factor MYB72 in the onset of ISR and the role of phytohormones and defense regulatory proteins in the expression of ISR in aboveground plant parts are highlighted. Finally, the ecological function of ISR-inducing microbes in the root microbiome is discussed.
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Affiliation(s)
- Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3508 TB Utrecht, The Netherlands; , , , ,
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70
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Drogue B, Sanguin H, Borland S, Prigent-Combaret C, Wisniewski-Dyé F. Genome wide profiling of Azospirillum lipoferum 4B gene expression during interaction with rice roots. FEMS Microbiol Ecol 2013; 87:543-55. [PMID: 24283406 DOI: 10.1111/1574-6941.12244] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/18/2013] [Accepted: 10/31/2013] [Indexed: 01/02/2023] Open
Abstract
Azospirillum-plant cooperation has been mainly studied from an agronomic point of view leading to a wide description of mechanisms implicated in plant growth-promoting effects. However, little is known about genetic determinants implicated in bacterial adaptation to the host plant during the transition from free-living to root-associated lifestyles. This study aims at characterizing global gene expression of Azospirillum lipoferum 4B following a 7-day-old interaction with two cultivars of Oryza sativa L. japonica (cv. Cigalon from which it was originally isolated, and cv. Nipponbare). The analysis was done on a whole genome expression array with RNA samples obtained from planktonic cells, sessile cells, and root-adhering cells. Root-associated Azospirillum cells grow in an active sessile-like state and gene expression is tightly adjusted to the host plant. Adaptation to rice seems to involve genes related to reactive oxygen species (ROS) detoxification and multidrug efflux, as well as complex regulatory networks. As revealed by the induction of genes encoding transposases, interaction with root may drive bacterial genome rearrangements. Several genes related to ABC transporters and ROS detoxification display cultivar-specific expression profiles, suggesting host specific adaptation and raising the question of A. lipoferum 4B/rice cv. Cigalon co-adaptation.
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Affiliation(s)
- Benoît Drogue
- UMR5557 CNRS, Ecologie Microbienne, Université de Lyon, Villeurbanne, France
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71
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Abstract
Often referred to as the "building blocks of proteins", the 20 canonical proteinogenic amino acids are ubiquitous in biological systems as the functional units in proteins. Sometimes overlooked are their varying additional roles that include serving as metabolic intermediaries, playing structural roles in bioactive natural products, acting as cosubstrates in enzymatic transformations, and as key regulators of cellular physiology. Amino acids can also serve as biological sources of both carbon and nitrogen and are found in the rhizosphere as a result of lysis or cellular efflux from plants and microbes and proteolysis of existing peptides. While both plants and microbes apparently prefer to take up nitrogen in its inorganic form, their ability to take up and use amino acids may confer a selective advantage in certain environments where organic nitrogen is abundant. Further, certain amino acids (e.g., glutamate and proline) and their betaines (e.g., glycine betaine) serve as compatible solutes necessary for osmoregulation in plants and microbes and can undergo rapid cellular flux. This ability is of particular importance in an ecological niche such as the rhizosphere, which is prone to significant variations in solute concentrations. Amino acids are also shown to alter key phenotypes related to plant root growth and microbial colonization, symbiotic interactions, and pathogenesis in the rhizosphere. This review will focus on the sources, transport mechanisms, and potential roles of the 20 canonical proteinogenic amino acids in the rhizosphere.
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Affiliation(s)
- Luke A Moe
- Department of Plant & Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, Kentucky 40546-0312, USA
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72
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Carvalhais LC, Dennis PG, Fan B, Fedoseyenko D, Kierul K, Becker A, von Wiren N, Borriss R. Linking plant nutritional status to plant-microbe interactions. PLoS One 2013; 8:e68555. [PMID: 23874669 PMCID: PMC3713015 DOI: 10.1371/journal.pone.0068555] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 05/30/2013] [Indexed: 11/17/2022] Open
Abstract
Plants have developed a wide-range of adaptations to overcome nutrient limitation, including changes to the quantity and composition of carbon-containing compounds released by roots. Root-associated bacteria are largely influenced by these compounds which can be perceived as signals or substrates. Here, we evaluate the effect of root exudates collected from maize plants grown under nitrogen (N), phosphate (P), iron (Fe) and potassium (K) deficiencies on the transcriptome of the plant growth promoting rhizobacterium (PGPR) Bacillus amyloliquefaciens FZB42. The largest shifts in gene expression patterns were observed in cells exposed to exudates from N-, followed by P-deficient plants. Exudates from N-deprived maize triggered a general stress response in FZB42 in the exponential growth phase, which was evidenced by the suppression of numerous genes involved in protein synthesis. Exudates from P-deficient plants induced bacterial genes involved in chemotaxis and motility whilst exudates released by Fe and K deficient plants did not cause dramatic changes in the bacterial transcriptome during exponential growth phase. Global transcriptional changes in bacteria elicited by nutrient deficient maize exudates were significantly correlated with concentrations of the amino acids aspartate, valine and glutamate in root exudates suggesting that transcriptional profiling of FZB42 associated with metabolomics of N, P, Fe and K-deficient maize root exudates is a powerful approach to better understand plant-microbe interactions under conditions of nutritional stress.
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Affiliation(s)
- Lilia C. Carvalhais
- Molecular Plant Nutrition, University of Hohenheim, Stuttgart, Germany
- Bakteriengenetik, Institut für Biologie, Humboldt Universität Berlin, Berlin, Germany
| | - Paul G. Dennis
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Ben Fan
- Institute of Forest Protection, Nanjing Forestry University, Nanjing, China
| | - Dmitri Fedoseyenko
- Molecular Plant Nutrition, University of Hohenheim, Stuttgart, Germany
- Molecular Plant Nutrition, Leibniz-Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Kinga Kierul
- Bakteriengenetik, Institut für Biologie, Humboldt Universität Berlin, Berlin, Germany
| | - Anke Becker
- Molekulare Genetik, Institut für Biologie III, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Nicolaus von Wiren
- Molecular Plant Nutrition, University of Hohenheim, Stuttgart, Germany
- Molecular Plant Nutrition, Leibniz-Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Rainer Borriss
- Bakteriengenetik, Institut für Biologie, Humboldt Universität Berlin, Berlin, Germany
- ABiTEP GmbH, Berlin, Germany
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73
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Segura A, Ramos JL. Plant–bacteria interactions in the removal of pollutants. Curr Opin Biotechnol 2013; 24:467-73. [PMID: 23098915 DOI: 10.1016/j.copbio.2012.09.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
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74
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Olivares J, Bernardini A, Garcia-Leon G, Corona F, B Sanchez M, Martinez JL. The intrinsic resistome of bacterial pathogens. Front Microbiol 2013; 4:103. [PMID: 23641241 PMCID: PMC3639378 DOI: 10.3389/fmicb.2013.00103] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/11/2013] [Indexed: 11/13/2022] Open
Abstract
Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyze recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice.
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Affiliation(s)
- Jorge Olivares
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
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75
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Fernández M, Conde S, Duque E, Ramos JL. In vivo gene expression of Pseudomonas putida KT2440 in the rhizosphere of different plants. Microb Biotechnol 2013; 6:307-13. [PMID: 23433036 PMCID: PMC3815925 DOI: 10.1111/1751-7915.12037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/14/2012] [Accepted: 01/10/2013] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas putida KT2440 has the ability to colonize the rhizosphere of a wide range of plants and can reach cell densities in the range of 105–106 cfu g soil−1. Using the IVET technology we investigated which KT2440 genes were expressed in the rhizosphere of four different plants: pine, cypress, evergreen oak and rosemary. We identified 39 different transcriptional fusions containing the promoters of annotated genes that were preferentially expressed in the rhizosphere. Six of them were expressed in the rhizosphere of all the plant types tested, 11 were expressed in more than one plant and the remaining 22 fusions were found to be expressed in only one type of plant. Another 40 fusions were found to correspond to likely promoters that encode antisense RNAs of unknown function, some of which were isolated as fusions from the bacteria recovered in the rhizosphere from all of the plants, while others were specific to one or several of the plants. The results obtained in this study suggest that plant-specific signals are sensed by KT2440 in the rhizosphere and that the signals and consequent gene expression are related to the bacteria's successful establishment in this niche.
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Affiliation(s)
- Matilde Fernández
- Bio-Iliberis Research and Development, I+D Department, 18210, Peligros, Granada, Spain
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76
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Alvarez-Ortega C, Olivares J, Martínez JL. RND multidrug efflux pumps: what are they good for? Front Microbiol 2013; 4:7. [PMID: 23386844 PMCID: PMC3564043 DOI: 10.3389/fmicb.2013.00007] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/07/2013] [Indexed: 01/27/2023] Open
Abstract
Multidrug efflux pumps are chromosomally encoded genetic elements capable of mediating resistance to toxic compounds in several life forms. In bacteria, these elements are involved in intrinsic and acquired resistance to antibiotics. Unlike other well-known horizontally acquired antibiotic resistance determinants, genes encoding for multidrug efflux pumps belong to the core of bacterial genomes and thus have evolved over millions of years. The selective pressure stemming from the use of antibiotics to treat bacterial infections is relatively recent in evolutionary terms. Therefore, it is unlikely that these elements have evolved in response to antibiotics. In the last years, several studies have identified numerous functions for efflux pumps that go beyond antibiotic extrusion. In this review we present some examples of these functions that range from bacterial interactions with plant or animal hosts, to the detoxification of metabolic intermediates or the maintenance of cellular homeostasis.
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Affiliation(s)
- Carolina Alvarez-Ortega
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
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77
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Roca A, Pizarro-Tobías P, Udaondo Z, Fernández M, Matilla MA, Molina-Henares MA, Molina L, Segura A, Duque E, Ramos JL. Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1. Environ Microbiol 2012. [PMID: 23206161 DOI: 10.1111/1462-2920.12037] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Pseudomonas putida BIRD-1 is a plant growth-promoting rhizobacterium whose genome size is 5.7 Mbp. It adheres to plant roots and colonizes the rhizosphere to high cell densities even in soils with low moisture. This property is linked to its ability to synthesize trehalose, since a mutant deficient in the synthesis of trehalose exhibited less tolerance to desiccation than the parental strain. The genome of BIRD-1 encodes a wide range of proteins that help it to deal with reactive oxygen stress generated in the plant rhizosphere. BIRD-1 plant growth-promoting rhizobacteria properties derive from its ability to enhance phosphorous and iron solubilization and to produce phytohormones. BIRD-1 is capable of solubilizing insoluble inorganic phosphate forms through acid production. The genome of BIRD-1 encodes at least five phosphatases related to phosphorous solubilization, one of them being a phytase that facilitates the utilization of phytic acid, the main storage form of phosphorous in plants. Pyoverdine is the siderophore produced by this strain, a mutant that in the FvpD siderophore synthase failed to grow on medium without supplementary iron, but the mutant was as competitive as the parental strain in soils because it captures the siderophores produced by other microbes. BIRD-1 overproduces indole-3-acetic acid through convergent pathways.
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Affiliation(s)
- Amalia Roca
- Polígono Industrial Juncaril, Bio-Iliberis R&D, 18210, Peligros, Granada, Spain
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78
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Ghirardi S, Dessaint F, Mazurier S, Corberand T, Raaijmakers JM, Meyer JM, Dessaux Y, Lemanceau P. Identification of traits shared by rhizosphere-competent strains of fluorescent pseudomonads. MICROBIAL ECOLOGY 2012; 64:725-737. [PMID: 22576821 DOI: 10.1007/s00248-012-0065-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 04/21/2012] [Indexed: 05/31/2023]
Abstract
Rhizosphere competence of fluorescent pseudomonads is a prerequisite for the expression of their beneficial effects on plant growth and health. To date, knowledge on bacterial traits involved in rhizosphere competence is fragmented and derived mostly from studies with model strains. Here, a population approach was taken by investigating a representative collection of 23 Pseudomonas species and strains from different origins for their ability to colonize the rhizosphere of tomato plants grown in natural soil. Rhizosphere competence of these strains was related to phenotypic traits including: (1) their carbon and energetic metabolism represented by the ability to use a wide range of organic compounds, as electron donors, and iron and nitrogen oxides, as electron acceptors, and (2) their ability to produce antibiotic compounds and N-acylhomoserine lactones (N-AHSL). All these data including origin of the strains (soil/rhizosphere), taxonomic identification, phenotypic cluster based on catabolic profiles, nitrogen dissimilating ability, siderovars, susceptibility to iron starvation, antibiotic and N-AHSL production, and rhizosphere competence were submitted to multiple correspondence analyses. Colonization assays revealed a significant diversity in rhizosphere competence with survival rates ranging from approximately 0.1 % to 61 %. Multiple correspondence analyses indicated that rhizosphere competence was associated with siderophore-mediated iron acquisition, substrate utilization, and denitrification. However, the catabolic profile of one rhizosphere-competent strain differed from the others and its competence was associated with its ability to produce antibiotics phenazines and N-AHSL. Taken together, these data suggest that competitive strains have developed two types of strategies to survive in the rhizosphere.
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Affiliation(s)
- Sandrine Ghirardi
- INRA, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21065 Dijon Cedex, France
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79
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García-Salamanca A, Molina-Henares MA, van Dillewijn P, Solano J, Pizarro-Tobías P, Roca A, Duque E, Ramos JL. Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil. Microb Biotechnol 2012; 6:36-44. [PMID: 22883414 PMCID: PMC3815383 DOI: 10.1111/j.1751-7915.2012.00358.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 07/02/2012] [Accepted: 07/10/2012] [Indexed: 11/28/2022] Open
Abstract
Maize represents one of the main cultivar for food and energy and crop yields are influenced by soil physicochemical and climatic conditions. To study how maize plants influence soil microbes we have examined microbial communities that colonize maize plants grown in carbonate-rich soil (pH 8.5) using culture-independent, PCR-based methods. We observed a low proportion of unclassified bacteria in this soil whether it was planted or unplanted. Our results indicate that a higher complexity of the bacterial community is present in bulk soil with microbes from nine phyla, while in the rhizosphere microbes from only six phyla were found. The predominant microbes in bulk soil were bacteria of the phyla Acidobacteria, Bacteroidetes and Proteobacteria, while Gammaproteobacteria of the genera Pseudomonas and Lysobacter were the predominant in the rhizosphere. As Gammaproteobacteria respond chemotactically to exudates and are efficient in the utilization of plants exudate products, microbial communities associated to the rhizosphere seem to be plant-driven. It should be noted that Gammaproteobacteria made available inorganic nutrients to the plants favouring plant growth and then the benefit of the interaction is common.
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Affiliation(s)
- Adela García-Salamanca
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008, Granada, Spain
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80
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Fernández M, Niqui-Arroyo JL, Conde S, Ramos JL, Duque E. Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid. Appl Environ Microbiol 2012; 78:5104-10. [PMID: 22582075 PMCID: PMC3416403 DOI: 10.1128/aem.00619-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/04/2012] [Indexed: 01/16/2023] Open
Abstract
In this work, we explore the potential use of the Pseudomonas putida KT2440 strain for bioremediation of naphthalene-polluted soils. Pseudomonas putida strain KT2440 thrives in naphthalene-saturated medium, establishing a complex response that activates genes coding for extrusion pumps and cellular damage repair enzymes, as well as genes involved in the oxidative stress response. The transfer of the NAH7 plasmid enables naphthalene degradation by P. putida KT2440 while alleviating the cellular stress brought about by this toxic compound, without affecting key functions necessary for survival and colonization of the rhizosphere. Pseudomonas putida KT2440(NAH7) efficiently expresses the Nah catabolic pathway in vitro and in situ, leading to the complete mineralization of [(14)C]naphthalene, measured as the evolution of (14)CO(2), while the rate of mineralization was at least 2-fold higher in the rhizosphere than in bulk soil.
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Affiliation(s)
| | | | - Susana Conde
- Bio-Iliberis Research and Development, Granada, Spain
| | - Juan Luis Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Estrella Duque
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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81
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Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates. BMC Microbiol 2012; 12:116. [PMID: 22720735 PMCID: PMC3438084 DOI: 10.1186/1471-2180-12-116] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 05/31/2012] [Indexed: 11/21/2022] Open
Abstract
Background Plant root exudates have been shown to play an important role in mediating interactions between plant growth-promoting rhizobacteria (PGPR) and their host plants. Most investigations were performed on Gram-negative rhizobacteria, while much less is known about Gram-positive rhizobacteria. To elucidate early responses of PGPR to root exudates, we investigated changes in the transcriptome of a Gram-positive PGPR to plant root exudates. Results Bacillus amyloliquefaciens FZB42 is a well-studied Gram-positive PGPR. To obtain a comprehensive overview of FZB42 gene expression in response to maize root exudates, microarray experiments were performed. A total of 302 genes representing 8.2% of the FZB42 transcriptome showed significantly altered expression levels in the presence of root exudates. The majority of the genes (261) was up-regulated after incubation of FZB42 with root exudates, whereas only 41 genes were down-regulated. Several groups of the genes which were strongly induced by the root exudates are involved in metabolic pathways relating to nutrient utilization, bacterial chemotaxis and motility, and non-ribosomal synthesis of antimicrobial peptides and polyketides. Conclusions Here we present a transcriptome analysis of the root-colonizing bacterium Bacillus amyloliquefaciens FZB42 in response to maize root exudates. The 302 genes identified as being differentially transcribed are proposed to be involved in interactions of Gram-positive bacteria with plants.
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82
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Shidore T, Dinse T, Öhrlein J, Becker A, Reinhold-Hurek B. Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyteAzoarcussp. strain BH72. Environ Microbiol 2012; 14:2775-87. [DOI: 10.1111/j.1462-2920.2012.02777.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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83
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Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere. PLoS One 2012; 7:e35498. [PMID: 22545111 PMCID: PMC3335876 DOI: 10.1371/journal.pone.0035498] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Accepted: 03/19/2012] [Indexed: 01/26/2023] Open
Abstract
Benzoxazinoids, such as 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), are secondary metabolites in grasses. In addition to their function in plant defence against pests and diseases above-ground, benzoxazinoids (BXs) have also been implicated in defence below-ground, where they can exert allelochemical or antimicrobial activities. We have studied the impact of BXs on the interaction between maize and Pseudomonas putida KT2440, a competitive coloniser of the maize rhizosphere with plant-beneficial traits. Chromatographic analyses revealed that DIMBOA is the main BX compound in root exudates of maize. In vitro analysis of DIMBOA stability indicated that KT2440 tolerance of DIMBOA is based on metabolism-dependent breakdown of this BX compound. Transcriptome analysis of DIMBOA-exposed P. putida identified increased transcription of genes controlling benzoate catabolism and chemotaxis. Chemotaxis assays confirmed motility of P. putida towards DIMBOA. Moreover, colonisation essays in soil with Green Fluorescent Protein (GFP)-expressing P. putida showed that DIMBOA-producing roots of wild-type maize attract significantly higher numbers of P. putida cells than roots of the DIMBOA-deficient bx1 mutant. Our results demonstrate a central role for DIMBOA as a below-ground semiochemical for recruitment of plant-beneficial rhizobacteria during the relatively young and vulnerable growth stages of maize.
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84
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Duque E, de la Torre J, Bernal P, Molina-Henares MA, Alaminos M, Espinosa-Urgel M, Roca A, Fernández M, de Bentzmann S, Ramos JL. Identification of reciprocal adhesion genes in pathogenic and non-pathogenicPseudomonas. Environ Microbiol 2012; 15:36-48. [DOI: 10.1111/j.1462-2920.2012.02732.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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85
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Monteiro RA, Balsanelli E, Tuleski T, Faoro H, Cruz LM, Wassem R, Baura VA, Tadra-Sfeir MZ, Weiss V, DaRocha WD, Muller-Santos M, Chubatsu LS, Huergo LF, Pedrosa FO, Souza EM. Genomic comparison of the endophyte Herbaspirillum seropedicaeSmR1 and the phytopathogen Herbaspirillum rubrisubalbicansM1 by suppressive subtractive hybridization and partial genome sequencing. FEMS Microbiol Ecol 2012; 80:441-51. [PMID: 22268687 DOI: 10.1111/j.1574-6941.2012.01309.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 12/23/2011] [Accepted: 01/11/2012] [Indexed: 12/28/2022] Open
Affiliation(s)
- Rose A. Monteiro
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Thalita Tuleski
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Helison Faoro
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Leonardo M. Cruz
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Roseli Wassem
- Department of Genetics; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Valter A. Baura
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Michelle Z. Tadra-Sfeir
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Vinícius Weiss
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Wanderson D. DaRocha
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Marcelo Muller-Santos
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Leda S. Chubatsu
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Luciano F. Huergo
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Fábio O. Pedrosa
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Emanuel M. Souza
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
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86
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Xie F, Williams A, Edwards A, Downie JA. A plant arabinogalactan-like glycoprotein promotes a novel type of polar surface attachment by Rhizobium leguminosarum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:250-8. [PMID: 21995765 DOI: 10.1094/mpmi-08-11-0211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rhizobium leguminosarum bv. viciae can attach to the roots of legume and non-legume plants. We wanted to determine whether root exudates could affect in vitro surface attachment in a confocal microscopy assay. Root exudate from pea, other legumes, wheat, and Arabidopsis induced R. leguminosarum bv. viciae to attach end-on (in a polar manner) to glass in hexagonal close-packed arrays, rather than attaching along their long axis. This did not involve a reorientation but was probably due to altered growth. The polar attachment involves a novel bacterial component because it occurred in mutants lacking a symbiosis plasmid (and hence nodulation genes) and polar glucomannan. The major surface (acidic) exopolysaccharide was required, and mutations affecting exported proteins and flagella delayed but did not block polar attachment. The polar attachment activity was purified as a high molecular weight fraction from pea root exudate and is an arabinogalactan protein (AGP) based on its carbohydrate content, reactivity with AGP-specific monoclonal antibodies and Yariv reagent, and sensitivity to enzymes that degrade proteins and carbohydrates. We propose that this novel mode of AGP-induced attachment may be important for growth of these bacteria on the roots of both legumes and non-legumes.
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Affiliation(s)
- Fang Xie
- John Innes Centre, Norwich Research Park, Norwich, UK
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87
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Jakovleva J, Teppo A, Velts A, Saumaa S, Moor H, Kivisaar M, Teras R. Fis regulates the competitiveness of Pseudomonas putida on barley roots by inducing biofilm formation. MICROBIOLOGY-SGM 2012; 158:708-720. [PMID: 22222498 DOI: 10.1099/mic.0.053355-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An important link between the environment and the physiological state of bacteria is the regulation of the transcription of a large number of genes by global transcription factors. One of the global regulators, Fis (factor for inversion stimulation), is well studied in Escherichia coli, but the role of this protein in pseudomonads has only been examined briefly. According to studies in Enterobacteriaceae, Fis regulates positively the flagellar movement of bacteria. In pseudomonads, flagellar movement is an important trait for the colonization of plant roots. Therefore we were interested in the role of the Fis protein in Pseudomonas putida, especially the possible regulation of the colonization of plant roots. We observed that Fis reduced the migration of P. putida onto the apices of barley roots and thereby the competitiveness of bacteria on the roots. Moreover, we observed that overexpression of Fis drastically reduced swimming motility and facilitated P. putida biofilm formation, which could be the reason for the decreased migration of bacteria onto the root apices. It is possible that the elevated expression of Fis is important in the adaptation of P. putida during colonization of plant roots by promoting biofilm formation when the migration of bacteria is no longer favoured.
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Affiliation(s)
- Julia Jakovleva
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Riia 23, 51010 Tartu, Estonia
| | - Annika Teppo
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Riia 23, 51010 Tartu, Estonia
| | - Anna Velts
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Riia 23, 51010 Tartu, Estonia
| | - Signe Saumaa
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Riia 23, 51010 Tartu, Estonia
| | - Hanna Moor
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Riia 23, 51010 Tartu, Estonia
| | - Maia Kivisaar
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Riia 23, 51010 Tartu, Estonia
| | - Riho Teras
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Riia 23, 51010 Tartu, Estonia
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88
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Unraveling plant-microbe interactions: can multi-species transcriptomics help? Trends Biotechnol 2011; 30:177-84. [PMID: 22209623 DOI: 10.1016/j.tibtech.2011.11.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/04/2011] [Accepted: 11/04/2011] [Indexed: 01/17/2023]
Abstract
Plants in their natural habitats are surrounded by a large number of microorganisms. Some microbes directly interact with plants in a mutually beneficial manner whereas others colonize the plant only for their own benefit. In addition, microbes can indirectly affect plants by drastically altering their environments. Understanding the complex nature of plant-microbe interactions can potentially offer new strategies to enhance plant productivity in an environmentally friendly manner. As briefly reviewed here, the emerging area of multi-species transcriptomics holds the promise to provide knowledge on how this can be achieved. We discuss key aspects of how transcriptome analysis can be used to provide a more comprehensive picture of the complex interactions of plants with their biotic and abiotic environments.
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89
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Aromatic compounds degradation plays a role in colonization of Arabidopsis thaliana and Acacia caven by Cupriavidus pinatubonensis JMP134. Antonie van Leeuwenhoek 2011; 101:713-23. [DOI: 10.1007/s10482-011-9685-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 12/08/2011] [Indexed: 10/14/2022]
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90
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Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440. Antimicrob Agents Chemother 2011; 56:1001-9. [PMID: 22143519 DOI: 10.1128/aac.05398-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas putida KT2440 is a chloramphenicol-resistant bacterium that is able to grow in the presence of this antibiotic at a concentration of up to 25 μg/ml. Transcriptomic analyses revealed that the expression profile of 102 genes changed in response to this concentration of chloramphenicol in the culture medium. The genes that showed altered expression include those involved in general metabolism, cellular stress response, gene regulation, efflux pump transporters, and protein biosynthesis. Analysis of a genome-wide collection of mutants showed that survival of a knockout mutant in the TtgABC resistance-nodulation-division (RND) efflux pump and mutants in the biosynthesis of pyrroloquinoline (PQQ) were compromised in the presence of chloramphenicol. The analysis also revealed that an ABC extrusion system (PP2669/PP2668/PP2667) and the AgmR regulator (PP2665) were needed for full resistance toward chloramphenicol. Transcriptional arrays revealed that AgmR controls the expression of the pqq genes and the operon encoding the ABC extrusion pump from the promoter upstream of open reading frame (ORF) PP2669.
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91
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Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1. J Bacteriol 2011; 193:5539-40. [PMID: 21914867 DOI: 10.1128/jb.05717-11] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite.
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92
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Involvement of the global Crp regulator in cyclic AMP-dependent utilization of aromatic amino acids by Pseudomonas putida. J Bacteriol 2011; 194:406-12. [PMID: 22081386 DOI: 10.1128/jb.06353-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phhAB operon encodes a phenylalanine hydroxylase involved in the conversion of L-phenylalanine into L-tyrosine in Pseudomonas putida. The phhAB promoter is transcribed by RNA polymerase sigma-70 and is unusual in that the specific regulator PhhR acts as an enhancer protein that binds to two distant upstream sites (-75 to -92 and -132 to -149). There is an integration host factor (IHF) binding site that overlaps the proximal PhhR box, and, consequently, IHF acts as an inhibitor of transcription. Use of L-phenylalanine is compromised in a crp-deficient background due to reduced expression from the phhAB promoter. Electrophoretic mobility shift assays and DNase I footprinting assays reveal that Crp binds at a site centered at -109 only in the presence of cyclic AMP (cAMP). We show, using circular permutation analysis, that the simultaneous binding of Crp/cAMP and PhhR bends DNA to bring positive regulators and RNA polymerase into close proximity. This nucleoprotein complex promotes transcription from phhA only in response to L-phenylalanine.
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93
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Ramachandran VK, East AK, Karunakaran R, Downie JA, Poole PS. Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biol 2011; 12:R106. [PMID: 22018401 PMCID: PMC3333776 DOI: 10.1186/gb-2011-12-10-r106] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/19/2011] [Accepted: 10/21/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The rhizosphere is the microbe-rich zone around plant roots and is a key determinant of the biosphere's productivity. Comparative transcriptomics was used to investigate general and plant-specific adaptations during rhizosphere colonization. Rhizobium leguminosarum biovar viciae was grown in the rhizospheres of pea (its legume nodulation host), alfalfa (a non-host legume) and sugar beet (non-legume). Gene expression data were compared to metabolic and transportome maps to understand adaptation to the rhizosphere. RESULTS Carbon metabolism was dominated by organic acids, with a strong bias towards aromatic amino acids, C1 and C2 compounds. This was confirmed by induction of the glyoxylate cycle required for C2 metabolism and gluconeogenesis in all rhizospheres. Gluconeogenesis is repressed in R. leguminosarum by sugars, suggesting that although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified, of which 66% are of unknown function. Many genes were induced in the rhizosphere of the legumes, but not sugar beet, and several were plant specific. The plasmid pRL8 can be considered pea rhizosphere specific, enabling adaptation of R. leguminosarum to its host. Mutation of many of the up-regulated genes reduced competitiveness for pea rhizosphere colonization, while two genes specifically up-regulated in the pea rhizosphere reduced colonization of the pea but not alfalfa rhizosphere. CONCLUSIONS Comparative transcriptome analysis has enabled differentiation between factors conserved across plants for rhizosphere colonization as well as identification of exquisite specific adaptation to host plants.
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Affiliation(s)
| | - Alison K East
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - J Allan Downie
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Philip S Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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94
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Trivedi P, He Z, Van Nostrand JD, Albrigo G, Zhou J, Wang N. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME JOURNAL 2011; 6:363-83. [PMID: 21796220 DOI: 10.1038/ismej.2011.100] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how 'Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that 'Ca. L. asiaticus' infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in 'Ca. L. asiaticus'-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of 'Ca. L. asiaticus' infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the 'Ca. L. asiaticus'-infected citrus rhizosphere. Our results showed that the microbial community of the 'Ca. L. asiaticus'-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by 'Ca. L. asiaticus' infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability of citrus-producing agro-ecosystems.
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Affiliation(s)
- Pankaj Trivedi
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL 33850, USA
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95
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Matilla MA, Travieso ML, Ramos JL, Ramos-González MI. Cyclic diguanylate turnover mediated by the sole GGDEF/EAL response regulator in Pseudomonas putida: its role in the rhizosphere and an analysis of its target processes. Environ Microbiol 2011; 13:1745-66. [PMID: 21554519 DOI: 10.1111/j.1462-2920.2011.02499.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
GGDEF and EAL/HD-GYP protein domains are responsible for the synthesis and hydrolysis of the bacterial secondary messenger cyclic diguanylate (c-di-GMP) through their diguanylate cyclase and phosphodiesterase activities, respectively. Forty-three genes in Pseudomonas putida KT2440 are putatively involved in the turnover of c-di-GMP. Of them only rup4959 (locus PP4959) encodes a GGDEF/EAL response regulator, which was identified in a genome wide analysis as preferentially induced while this bacterium colonizes roots and adjacent soil areas (the rhizosphere). By using fusions to reporter genes it was confirmed that the rup4959 promoter is active in the rhizosphere and inducible by corn plant root exudates and microaerobiosis. Transcription of rup4959 was strictly dependent on the alternative transcriptional factor σ(S) . The inactivation of the rup4959-4957 operon altered the expression of 22 genes in the rhizosphere and had a negative effect upon oligopeptide utilization and biofilm formation. In multicopy or when overexpressed, rup4959 enhanced adhesin LapA-dependent biofilm formation, the development of wrinkly colony morphology, and increased Calcofluor stainable exopolysaccharides (EPS). Under these conditions the inhibition of swarming motility was total and plant root tip colonization considerably less efficient, whereas swimming was partially diminished. This pleiotropic phenotype, which correlated with an increase in the global level of c-di-GMP, was not acquired with increased levels of Rup4959 catalytic mutant at GGDEF as a proof of this response regulator exhibiting diguanylate cyclase activity. A screen for mutants in putative targets of c-di-GMP led to the identification of a surface polysaccharide specific to KT2440, which is encoded by the genes cluster PP3133-PP3141, as essential for phenotypes associated with increased c-di-GMP. Cellulose and alginate were discarded as the overproduced EPS, and lipopolysaccharide (LPS) core and O-antigen were found to be essential for the development of wrinkly colony morphology.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada 18008, Spain
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96
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97
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Affiliation(s)
- Pieter Van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E‐18008 Granada, Spain
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1‐1‐1 Yayoi, Bunkyo‐ku, Tokyo, Japan
| | - Jan Roelof Van Der Meer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL‐Sorge, 1015 Lausanne, Switzerland
| | - Thomas K. Wood
- Artie McFerrin Department of Chemical Engineering
- Department of Biology, and
- Zachry Department of Civil Engineering, Texas A & M University, College Station, TX 77843‐3122, USA
- *E‐mail ; Tel. (979) 862‐1588; Fax (979) 845‐6446
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98
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Affiliation(s)
- Pieter Van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Apdo. Correos 419, E-18008 Granada, Spain.
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99
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Ramos JL, Molina L, Segura A. Removal of organic toxic chemicals in the rhizosphere and phyllosphere of plants. Microb Biotechnol 2011; 2:144-6. [PMID: 21261901 PMCID: PMC3815828 DOI: 10.1111/j.1751-7915.2009.00090_13.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Juan L Ramos
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Microbiology, Granada, Spain
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100
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Van Puyvelde S, Cloots L, Engelen K, Das F, Marchal K, Vanderleyden J, Spaepen S. Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response. MICROBIAL ECOLOGY 2011; 61:723-728. [PMID: 21340736 DOI: 10.1007/s00248-011-9819-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 01/27/2011] [Indexed: 05/30/2023]
Abstract
The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.
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Affiliation(s)
- Sandra Van Puyvelde
- Centre of Microbial and Plant Genetics, K.U.Leuven, Kasteelpark Arenberg 20-Bus 2460, 3001 Heverlee, Belgium
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