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Benaissa A. Rhizosphere: Role of bacteria to manage plant diseases and sustainable agriculture-A review. J Basic Microbiol 2024; 64:e2300361. [PMID: 37800617 DOI: 10.1002/jobm.202300361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/05/2023] [Accepted: 09/17/2023] [Indexed: 10/07/2023]
Abstract
General plant diseases as well as soil-borne pathogens severely reduce agricultural yield. The rhizosphere (the region of the soil that includes and surrounds the roots) is an important niche for microbial diversity in particular phytobeneficial bacteria including plant growth-promoting rhizobacteria (PGPR) which have been used for a very long time to combat plant diseases. Pathogen control and crop productivity can both be improved through the use of PGPR several mechanisms, including iron-based nutrition, antibiotics, volatile substances, enzymes, biofilm, allelochemicals, and so on. Their modes of action and molecular mechanisms have improved our comprehension of how they are used to control crop disease. Therefore, there is a lot of literal information available regarding PGPR, but this review stands out since it starts with the fundamentals: the concept of the rhizosphere and the colonization process of the latter, particularly because it covers the most mechanisms. A broad figure is used to present the study's findings. The advantages of using PGPR as bioinoculants in sustainable agriculture are also mentioned.
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Affiliation(s)
- Asmaa Benaissa
- Laboratory of Biology and Physiology of Organisms, Faculty of Biological Sciences, University of Sciences and Technology of Houari Boumediene-El-Alia Bab Ezzouar Algiers, Algeria
- Department of Biology, University of Amine Elokkal ElHadj Moussa Eg. Akhamoukh, Sersouf, Tamanrasset, Algeria
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2
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Boo A, Toth T, Yu Q, Pfotenhauer A, Fields BD, Lenaghan SC, Stewart CN, Voigt CA. Synthetic microbe-to-plant communication channels. Nat Commun 2024; 15:1817. [PMID: 38418817 PMCID: PMC10901793 DOI: 10.1038/s41467-024-45897-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.
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Affiliation(s)
- Alice Boo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tyler Toth
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Qiguo Yu
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexander Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brandon D Fields
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Wiehlmann L, Klockgether J, Hammerbacher AS, Salunkhe P, Horatzek S, Munder A, Peilert JF, Gulbins E, Eberl L, Tümmler B. A VirB4 ATPase of the mobile accessory genome orchestrates core genome-encoded features of physiology, metabolism, and virulence of Pseudomonas aeruginosa TBCF10839. Front Cell Infect Microbiol 2023; 13:1234420. [PMID: 37577372 PMCID: PMC10413270 DOI: 10.3389/fcimb.2023.1234420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Pseudomonas aeruginosa TBCF10839 is a highly virulent strain that can persist and replicate in human neutrophils. Screening of a signature-tagged mutagenesis (STM) TBCF10839 transposon library in phagocytosis tests identified a mutant that carried the transposon in the VirB4 homolog 5PG21 of an integrative and conjugative element (ICE)-associated type IV secretion system of the pKLC102 subtype. 5P21 TBCF10839 insertion mutants were deficient in metabolic versatility, secretion, quorum sensing, and virulence. The mutants were efficiently killed in phagocytosis tests in vitro and were avirulent in an acute murine airway infection model in vivo. The inactivation of 5PG21 silenced the rhl, las, and pqs operons and the gene expression for the synthesis of hydrogen cyanide, the antimetabolite l-2-amino-4-methoxy-trans-3-butenoic acid, and the H2- and H3-type VI secretion systems and their associated effectors. The mutants were impaired in the utilization of carbon sources and stored compounds that are not funneled into intermediary metabolism. This showcase demonstrates that a single gene of the mobile accessory genome can become an essential element to operate the core genome-encoded features of metabolism and virulence.
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Affiliation(s)
- Lutz Wiehlmann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Jens Klockgether
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Anna-Silke Hammerbacher
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Prabhakar Salunkhe
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sonja Horatzek
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Antje Munder
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | | | - Erich Gulbins
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Institute of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Burkhard Tümmler
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
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Uroz S, Geisler O, Fauchery L, Lami R, Rodrigues AMS, Morin E, Leveau JHJ, Oger P. Genomic and transcriptomic characterization of the Collimonas quorum sensing genes and regulon. FEMS Microbiol Ecol 2022; 98:6679101. [PMID: 36040340 DOI: 10.1093/femsec/fiac100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/13/2022] [Accepted: 08/26/2022] [Indexed: 01/21/2023] Open
Abstract
Collimonads are well-adapted to nutrient-poor environments. They are known to hydrolyse chitin, produce antifungal metabolites, weather minerals, and are effective biocontrol agents protecting plants from fungal diseases. The production of N-acyl homoserine lactones (AHLs) was suggested to be a conserved trait of collimonads, but little is known about the genes that underlie this production or the genes that are controlled by AHLs. To improve our understanding of the role of AHLs in the ecology of collimonads, we carried out transcriptomic analyses, combined with chemical and functional assays, on strain Collimonas pratensis PMB3(1). The main AHLs produced by this strain were identified as 3-hydroxy-hexa- and octa-noyl-homoserine lactone. Genome analysis permitted to identify putative genes coding for the autoinducer synthase (colI) and cognate transcriptional regulator (colR). The ability to produce AHLs was lost in ΔcolI and ΔcolR mutants. Functional assays revealed that the two mutants metabolized glucose, formate, oxalate, and leucine better than the wild-type (WT) strain. Transcriptome sequencing analyses revealed an up-regulation of different metabolic pathways and of motility in the QS-mutants compared to the WT strain. Overall, our results provide insights into the role of the AHL-dependent regulation system of Collimonas in environment colonization, metabolism readjustment, and microbial interactions.
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Affiliation(s)
- Stephane Uroz
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France.,INRAE, UR1138 "Biogéochimie des écosystèmes forestiers", F-54280 Champenoux, France
| | - Océane Geisler
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France
| | - Laure Fauchery
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France
| | - Raphaël Lami
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM, USR3579), Fédération de Recherche FR3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Alice M S Rodrigues
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM, USR3579), Fédération de Recherche FR3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France
| | - Johan H J Leveau
- Department of Plant Pathology, University of California - Davis, Davis, CA 95616, United States
| | - Philippe Oger
- Université Lyon, INSA de Lyon, CNRS UMR 5240, F-69622 Villeurbanne, France
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Probing patterning in microbial consortia with a cellular automaton for spatial organisation. Sci Rep 2022; 12:17159. [PMID: 36229548 PMCID: PMC9563066 DOI: 10.1038/s41598-022-20705-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/16/2022] [Indexed: 01/04/2023] Open
Abstract
Microbial consortia exhibit spatial patterning across diverse environments. Since probing the self-organization of natural microbial communities is limited by their inherent complexity, synthetic models have emerged as attractive alternatives. In this study, we develop novel frameworks of bacterial communication and explore the emergent spatiotemporal organization of microbes. Specifically, we built quorum sensing-mediated models of microbial growth that are utilized to characterize the dynamics of communities from arbitrary initial configurations and establish the effectiveness of our communication strategies in coupling the growth rates of microbes. Our simulations indicate that the behavior of quorum sensing-coupled consortia can be most effectively modulated by the rates of secretion of acyl homoserine lactones. Such a mechanism of control enables the construction of desired relative populations of constituent species in spatially organized populations. Our models accurately recapitulate previous experiments that have investigated pattern formation in synthetic multi-cellular systems. Additionally, our software tool enables the easy implementation and analysis of our frameworks for a variety of initial configurations and simplifies the development of sophisticated gene circuits facilitating distributed computing. Overall, we demonstrate the potential of spatial organization as a tunable parameter in synthetic biology by introducing a communication paradigm based on the location and strength of coupling of microbial strains.
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Applying molecular and phenotypic screening assays to identify efficient quorum quenching lactonases. Enzyme Microb Technol 2022; 160:110092. [DOI: 10.1016/j.enzmictec.2022.110092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
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7
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Pseudomonas putida mediates bacterial killing, biofilm invasion and biocontrol with a type IVB secretion system. Nat Microbiol 2022; 7:1547-1557. [PMID: 36123439 PMCID: PMC9519443 DOI: 10.1038/s41564-022-01209-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/21/2022] [Indexed: 11/24/2022]
Abstract
Many bacteria utilize contact-dependent killing machineries to eliminate rivals in their environmental niches. Here we show that the plant root colonizer Pseudomonas putida strain IsoF is able to kill a wide range of soil and plant-associated Gram-negative bacteria with the aid of a type IVB secretion system (T4BSS) that delivers a toxic effector into bacterial competitors in a contact-dependent manner. This extends the range of targets of T4BSSs—so far thought to transfer effectors only into eukaryotic cells—to prokaryotes. Bioinformatic and genetic analyses showed that this killing machine is entirely encoded by the kib gene cluster located within a rare genomic island, which was recently acquired by horizontal gene transfer. P. putida IsoF utilizes this secretion system not only as a defensive weapon to kill bacterial competitors but also as an offensive weapon to invade existing biofilms, allowing the strain to persist in its natural environment. Furthermore, we show that strain IsoF can protect tomato plants against the phytopathogen Ralstonia solanacearum in a T4BSS-dependent manner, suggesting that IsoF can be exploited for pest control and sustainable agriculture. Pseudomonas putida uses a type IVB secretion system to kill a broad range of Gram-negative bacteria, invade biofilms and prevent phytopathogen Ralstonia solanacearum infection in tomato plants.
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Rosier A, Bais HP. Protocol: a simple method for biosensor visualization of bacterial quorum sensing and quorum quenching interaction on Medicago roots. PLANT METHODS 2022; 18:112. [PMID: 36114554 PMCID: PMC9479286 DOI: 10.1186/s13007-022-00944-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Defining interactions of bacteria in the rhizosphere (encompassing the area near and on the plant root) is important to understand how they affect plant health. Some rhizosphere bacteria, including plant growth promoting rhizobacteria (PGPR) engage in the intraspecies communication known as quorum sensing (QS). Many species of Gram-negative bacteria use extracellular autoinducer signal molecules called N-acyl homoserine lactones (AHLs) for QS. Other rhizobacteria species, including PGPRs, can interfere with or disrupt QS through quorum quenching (QQ). Current AHL biosensor assays used for screening and identifying QS and QQ bacteria interactions fail to account for the role of the plant root. METHODS Medicago spp. seedlings germinated on Lullien agar were transferred to soft-agar plates containing the broad-range AHL biosensor Agrobacterium tumefaciens KYC55 and X-gal substrate. Cultures of QS and QQ bacteria as well as pure AHLs and a QQ enzyme were applied to the plant roots and incubated for 3 days. RESULTS We show that this expanded use of an AHL biosensor successfully allowed for visualization of QS/QQ interactions localized at the plant root. KYC55 detected pure AHLs as well as AHLs from live bacteria cultures grown directly on the media. We also showed clear detection of QQ interactions occurring in the presence of the plant root. CONCLUSIONS Our novel tri-trophic system using an AHL biosensor is useful to study QS interspecies interactions in the rhizosphere.
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Affiliation(s)
- Amanda Rosier
- Department of Plant and Soil Sciences, University of Delaware, 311 AP Biopharma, 590 Avenue 1743, Newark, DE, 19713, USA.
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, 311 AP Biopharma, 590 Avenue 1743, Newark, DE, 19713, USA
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RclS Sensor Kinase Modulates Virulence of Pseudomonas capeferrum. Int J Mol Sci 2022; 23:ijms23158232. [PMID: 35897798 PMCID: PMC9331949 DOI: 10.3390/ijms23158232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Signal transduction systems are the key players of bacterial adaptation and survival. The orthodox two-component signal transduction systems perceive diverse environmental stimuli and their regulatory response leads to cellular changes. Although rarely described, the unorthodox three-component systems are also implemented in the regulation of major bacterial behavior such as the virulence of clinically relevant pathogen P. aeruginosa. Previously, we described a novel three-component system in P. capeferrum WCS358 (RclSAR) where the sensor kinase RclS stimulates the intI1 transcription in stationary growth phase. In this study, using rclS knock-out mutant, we identified RclSAR regulon in P. capeferrum WCS358. The RNA sequencing revealed that activity of RclSAR signal transduction system is growth phase dependent with more pronounced regulatory potential in early stages of growth. Transcriptional analysis emphasized the role of RclSAR in global regulation and indicated the involvement of this system in regulation of diverse cellular activities such as RNA binding and metabolic and biocontrol processes. Importantly, phenotypic comparison of WCS358 wild type and ΔrclS mutant showed that RclS sensor kinase contributes to modulation of antibiotic resistance, production of AHLs and siderophore as well as host cell adherence and cytotoxicity. Finally, we proposed the improved model of interplay between RclSAR, RpoS and LasIR regulatory systems in P. capeferrum WCS358.
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Kusada H, Arita M, Tohno M, Tamaki H. Bile Salt Hydrolase Degrades β-Lactam Antibiotics and Confers Antibiotic Resistance on Lactobacillus paragasseri. Front Microbiol 2022; 13:858263. [PMID: 35733973 PMCID: PMC9207391 DOI: 10.3389/fmicb.2022.858263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Bile salt hydrolase (BSH) is a well-characterized probiotic enzyme associated with bile detoxification and colonization of lactic acid bacteria in the human gastrointestinal tract. Here, we isolated a putative BSH (LpBSH) from the probiotic bacterium Lactobacillus paragasseri JCM 5343T and demonstrated its bifunctional activity that allows it to degrade not only bile salts but also the antibiotic (penicillin). Although antibiotic resistance and bile detoxification have been separately recognized as different microbial functions, our findings suggest that bifunctional BSHs simultaneously confer ecological advantages to host gut bacteria to improve their survival in the mammalian intestine by attaining a high resistance to bile salts and β-lactams. Strain JCM 5343T showed resistance to both bile salts and β-lactam antibiotics, suggesting that LpBSH may be involved in this multi-resistance of the strain. We further verified that such bifunctional enzymes were broadly distributed among the phylogeny, suggesting that the bifunctionality may be conserved in other BSHs of gut bacteria. This study revealed the physiological role and phylogenetic diversity of bifunctional enzymes degrading bile salts and β-lactams in gut bacteria. Furthermore, our findings suggest that the hitherto-overlooked penicillin-degrading activity of penicillin acylase could be a potential new target for the probiotic function of gut bacteria.
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Affiliation(s)
- Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Masanori Tohno
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Japan
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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N-acyl-homoserine lactone produced by Rahnella inusitata isolated from the gut of Galleria mellonella influences Salmonella phenotypes. Braz J Microbiol 2022; 53:819-829. [PMID: 35048318 PMCID: PMC9151966 DOI: 10.1007/s42770-022-00681-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/10/2022] [Indexed: 02/01/2023] Open
Abstract
The most studied mechanism of quorum sensing in Gram-negative bacteria is mediated by autoinducer 1 (AI-1), namely, acyl-homoserine lactone (AHL). This system allows communication among different bacterial species and regulates the expression of virulence genes in many pathogens. Although AHL-producing bacteria have been detected in the intestines of humans and other animals, no report was found about AHL-producing bacteria in the insect gut and the possible effects of these autoinducers on enteropathogenic bacteria. Therefore, this study aimed to identify AHL-producing bacteria in the gut of larvae of Galleria mellonella and to evaluate the influence of this quorum sensing signal on the regulation of adhesion and motility phenotypes in the intestinal pathogen Salmonella. Sequencing of the 16S rRNA gene, 16S rRNA gene-based phylogenetic analyses, and phenotypic characterization of gut isolates was performed. The profile of AHLs produced by the isolates was determined using thin-layer chromatography (TLC) and revealed with the biosensor strain Chromobacterium violaceum CV026. Sequencing, phylogenetic analyses and phenotypic characterization of gut isolates showed that the three AHL-producing strains belong to the species Rahnella inusitata, named GM34, GM56, and GM60. The TLC showed that R. inusitata produces a six-carbon AHL. In the presence of cell-free extract of R. inusitata containing AHL and under anaerobic conditions, Salmonella enterica increased the adhesion to stainless steel coupons and presented swarming motility. Extracts from the culture medium of R. inusitata isolates containing AHL increased the adhesion on stainless steel coupons and swarming motility of Salmonella enterica serovar Enteritidis PT4 under anaerobic conditions. The results suggest the possibility of communication between members of the G. mellonella intestinal microbiota with pathogens such as Salmonella.
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Moraskie M, Roshid MHO, O'Connor G, Dikici E, Zingg JM, Deo S, Daunert S. Microbial whole-cell biosensors: Current applications, challenges, and future perspectives. Biosens Bioelectron 2021; 191:113359. [PMID: 34098470 PMCID: PMC8376793 DOI: 10.1016/j.bios.2021.113359] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/22/2022]
Abstract
Microbial Whole-Cell Biosensors (MWCBs) have seen rapid development with the arrival of 21st century biological and technological capabilities. They consist of microbial species which produce, or limit the production of, a reporter protein in the presence of a target analyte. The quantifiable signal from the reporter protein can be used to determine the bioavailable levels of the target analyte in a variety of sample types at a significantly lower cost than most widely used and well-established analytical instrumentation. Furthermore, the versatile and robust nature of MWCBs shows great potential for their use in otherwise unavailable settings and environments. While MWCBs have been developed for use in biomedical, environmental, and agricultural monitoring, they still face various challenges before they can transition from the laboratory into industrialized settings like their enzyme-based counterparts. In this comprehensive and critical review, we describe the underlying working principles of MWCBs, highlight developments for their use in a variety of fields, detail challenges and current efforts to address them, and discuss exciting implementations of MWCBs helping redefine what is thought to be possible with this expeditiously evolving technology.
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Affiliation(s)
- Michael Moraskie
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Md Harun Or Roshid
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA
| | - Gregory O'Connor
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Jean-Marc Zingg
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sapna Deo
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA; The Miami Clinical and Translational Science Institute, University of Miami, Miami, FL, 33146, USA; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33146, USA.
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Bourigault Y, Rodrigues S, Crépin A, Chane A, Taupin L, Bouteiller M, Dupont C, Merieau A, Konto-Ghiorghi Y, Boukerb AM, Turner M, Hamon C, Dufour A, Barbey C, Latour X. Biocontrol of Biofilm Formation: Jamming of Sessile-Associated Rhizobial Communication by Rhodococcal Quorum-Quenching. Int J Mol Sci 2021; 22:ijms22158241. [PMID: 34361010 PMCID: PMC8347015 DOI: 10.3390/ijms22158241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Biofilms are complex structures formed by a community of microbes adhering to a surface and/or to each other through the secretion of an adhesive and protective matrix. The establishment of these structures requires a coordination of action between microorganisms through powerful communication systems such as quorum-sensing. Therefore, auxiliary bacteria capable of interfering with these means of communication could be used to prevent biofilm formation and development. The phytopathogen Rhizobium rhizogenes, which causes hairy root disease and forms large biofilms in hydroponic crops, and the biocontrol agent Rhodococcus erythropolis R138 were used for this study. Changes in biofilm biovolume and structure, as well as interactions between rhizobia and rhodococci, were monitored by confocal laser scanning microscopy with appropriate fluorescent biosensors. We obtained direct visual evidence of an exchange of signals between rhizobia and the jamming of this communication by Rhodococcus within the biofilm. Signaling molecules were characterized as long chain (C14) N-acyl-homoserine lactones. The role of the Qsd quorum-quenching pathway in biofilm alteration was confirmed with an R. erythropolis mutant unable to produce the QsdA lactonase, and by expression of the qsdA gene in a heterologous host, Escherichia coli. Finally, Rhizobium biofilm formation was similarly inhibited by a purified extract of QsdA enzyme.
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Affiliation(s)
- Yvann Bourigault
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Sophie Rodrigues
- Laboratoire de Biotechnologie et Chimie Marines, LBCM IUEM, EA 3884, Université de Bretagne-Sud, F-56100 Lorient, France; (S.R.); (L.T.); (A.D.)
| | - Alexandre Crépin
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, F-86073 Poitiers, France;
| | - Andrea Chane
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
| | - Laure Taupin
- Laboratoire de Biotechnologie et Chimie Marines, LBCM IUEM, EA 3884, Université de Bretagne-Sud, F-56100 Lorient, France; (S.R.); (L.T.); (A.D.)
| | - Mathilde Bouteiller
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Charly Dupont
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Annabelle Merieau
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Yoan Konto-Ghiorghi
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Amine M. Boukerb
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
| | - Marie Turner
- Vegenov, F-29250 Saint-Pol-de-Léon, France; (M.T.); (C.H.)
- Biocontrol Consortium, F-75007 Paris, France
| | - Céline Hamon
- Vegenov, F-29250 Saint-Pol-de-Léon, France; (M.T.); (C.H.)
| | - Alain Dufour
- Laboratoire de Biotechnologie et Chimie Marines, LBCM IUEM, EA 3884, Université de Bretagne-Sud, F-56100 Lorient, France; (S.R.); (L.T.); (A.D.)
| | - Corinne Barbey
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Xavier Latour
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
- Biocontrol Consortium, F-75007 Paris, France
- Correspondence: ; +33-235-146-000
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14
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Friends or Foes-Microbial Interactions in Nature. BIOLOGY 2021; 10:biology10060496. [PMID: 34199553 PMCID: PMC8229319 DOI: 10.3390/biology10060496] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary Microorganisms like bacteria, archaea, fungi, microalgae, and viruses mostly form complex interactive networks within the ecosystem rather than existing as single planktonic cells. Interactions among microorganisms occur between the same species, with different species, or even among entirely different genera, families, or even domains. These interactions occur after environmental sensing, followed by converting those signals to molecular and genetic information, including many mechanisms and classes of molecules. Comprehensive studies on microbial interactions disclose key strategies of microbes to colonize and establish in a variety of different environments. Knowledge of the mechanisms involved in the microbial interactions is essential to understand the ecological impact of microbes and the development of dysbioses. It might be the key to exploit strategies and specific agents against different facing challenges, such as chronic and infectious diseases, hunger crisis, pollution, and sustainability. Abstract Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell–cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications.
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15
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Bourigault Y, Chane A, Barbey C, Jafra S, Czajkowski R, Latour X. Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol. Microorganisms 2021; 9:microorganisms9020295. [PMID: 33535657 PMCID: PMC7912877 DOI: 10.3390/microorganisms9020295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/31/2022] Open
Abstract
Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future.
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Affiliation(s)
- Yvann Bourigault
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Andrea Chane
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
| | - Corinne Barbey
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Sylwia Jafra
- Division of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, ul. A. Abrahama 58, 80-307 Gdansk, Poland;
| | - Robert Czajkowski
- Division of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, ul. A. Abrahama 58, 80-307 Gdansk, Poland
- Correspondence: (R.C.); (X.L.); Tel.: +48-58-523-63-33 (R.C.); +33-235-146-000 (X.L.)
| | - Xavier Latour
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
- Correspondence: (R.C.); (X.L.); Tel.: +48-58-523-63-33 (R.C.); +33-235-146-000 (X.L.)
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16
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Vandana UK, Rajkumari J, Singha LP, Satish L, Alavilli H, Sudheer PD, Chauhan S, Ratnala R, Satturu V, Mazumder PB, Pandey P. The Endophytic Microbiome as a Hotspot of Synergistic Interactions, with Prospects of Plant Growth Promotion. BIOLOGY 2021; 10:101. [PMID: 33535706 PMCID: PMC7912845 DOI: 10.3390/biology10020101] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
The plant root is the primary site of interaction between plants and associated microorganisms and constitutes the main components of plant microbiomes that impact crop production. The endophytic bacteria in the root zone have an important role in plant growth promotion. Diverse microbial communities inhabit plant root tissues, and they directly or indirectly promote plant growth by inhibiting the growth of plant pathogens, producing various secondary metabolites. Mechanisms of plant growth promotion and response of root endophytic microorganisms for their survival and colonization in the host plants are the result of complex plant-microbe interactions. Endophytic microorganisms also assist the host to sustain different biotic and abiotic stresses. Better insights are emerging for the endophyte, such as host plant interactions due to advancements in 'omic' technologies, which facilitate the exploration of genes that are responsible for plant tissue colonization. Consequently, this is informative to envisage putative functions and metabolic processes crucial for endophytic adaptations. Detection of cell signaling molecules between host plants and identification of compounds synthesized by root endophytes are effective means for their utilization in the agriculture sector as biofertilizers. In addition, it is interesting that the endophytic microorganism colonization impacts the relative abundance of indigenous microbial communities and suppresses the deleterious microorganisms in plant tissues. Natural products released by endophytes act as biocontrol agents and inhibit pathogen growth. The symbiosis of endophytic bacteria and arbuscular mycorrhizal fungi (AMF) affects plant symbiotic signaling pathways and root colonization patterns and phytohormone synthesis. In this review, the potential of the root endophytic community, colonization, and role in the improvement of plant growth has been explained in the light of intricate plant-microbe interactions.
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Affiliation(s)
- Udaya Kumar Vandana
- Department of Biotechnology, Assam University Silchar, Assam 788011, India; (U.K.V.); (P.B.M.)
| | - Jina Rajkumari
- Department of Microbiology, Assam University Silchar, Assam 788011, India; (J.R.); (L.P.S.)
| | - L. Paikhomba Singha
- Department of Microbiology, Assam University Silchar, Assam 788011, India; (J.R.); (L.P.S.)
| | - Lakkakula Satish
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Hemasundar Alavilli
- Department of Biochemistry and Molecular Biology, College of Medicine, Korea Molecular Medicine and Nutrition Research Institute, Korea University, Seoul 02841, Korea;
| | - Pamidimarri D.V.N. Sudheer
- Amity Institute of Biotechnology, Amity University Chhattisgarh, Raipur 493225, India; (P.D.V.N.S.); (S.C.)
| | - Sushma Chauhan
- Amity Institute of Biotechnology, Amity University Chhattisgarh, Raipur 493225, India; (P.D.V.N.S.); (S.C.)
| | - Rambabu Ratnala
- TATA Institute for Genetics and Society, Bangalore 560065, India;
| | - Vanisri Satturu
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India;
| | - Pranab Behari Mazumder
- Department of Biotechnology, Assam University Silchar, Assam 788011, India; (U.K.V.); (P.B.M.)
| | - Piyush Pandey
- Department of Microbiology, Assam University Silchar, Assam 788011, India; (J.R.); (L.P.S.)
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17
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Nawaz MS, Arshad A, Rajput L, Fatima K, Ullah S, Ahmad M, Imran A. Growth-Stimulatory Effect of Quorum Sensing Signal Molecule N-Acyl-Homoserine Lactone-Producing Multi-Trait Aeromonas spp. on Wheat Genotypes Under Salt Stress. Front Microbiol 2020; 11:553621. [PMID: 33117303 PMCID: PMC7550764 DOI: 10.3389/fmicb.2020.553621] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/17/2020] [Indexed: 01/23/2023] Open
Abstract
Salinity is one of the major threats to agricultural productivity worldwide. Soil and plant management practices, along with inoculation with plant-beneficial bacteria, play a key role in the plant’s tolerance toward salinity stress. The present study demonstrates the potential of acyl homoserine lactone (AHL)-producing plant growth promoting rhizobacteria (PGPR) strains of Aeromonas sp., namely, SAL-17 (accession no. HG763857) and SAL-21 (accession no. HG763858), for growth promotion of two wheat genotypes inherently different for salt tolerance potential. AHLs are the bacterial signal molecules that regulate the expression of various genes in bacteria and plants. Both Aeromonas spp., along with innate plant-growth-promoting (PGP) and salt tolerance traits, showed AHL production which was identified on tandem mass spectrometry as C6-HSL, 3-OH-C5-HSL, 3-OH-C6-HSL, 3-oxo-C7-HSL C10-HSL, 3-oxo-C10-HSL, 3-OH-C10-HSL, 3-oxo-C12-HSL and C6-HSL, and 3-oxo-C10-HSL. The exogenous application of purified AHLs (mix) significantly improved various root parameters at 200 mM NaCl in both salt-sensitive (SSG) and salt-tolerant (STG) genotypes, where the highest increase (≈80%) was observed where a mixture of both strains of AHLs was used. Confocal microscopic observations and root overlay assay revealed a strong root colonization potential of the two strains under salt stress. The inoculation response of both STG and SSG genotypes was evaluated with two AHL-producing strains (SAL-17 and SAL-21) and compared to non-AHL-producing Aeromonas sp. SAL-12 (accession no. HG763856) in saline (EC = 7.63 ms/cm2) and non-saline soil. The data reveal that plants inoculated with the bacterial consortium (SAL-21 + SAL-17) showed a maximum increase in leaf proline content, nitrate reductase activity, chlorophyll a/b, stomatal conductance, transpiration rate, root length, shoot length, and grain weight over non-inoculated plants grown in saline soil. Both STG and SSG showed relative effectiveness toward inoculation (percent increase for STG: 165–16%; SSG: 283–14%) and showed a positive correlation of grain yield with proline and nitrate reductase activity. Furthermore, principal component analysis (PCA) and categorical PCA analysis clearly showed an inoculation response in both genotypes, revealing the effectiveness of AHL-producing Aeromonas spp. than the non-AHL-producing strain. The present study documents that the consortium of salt-tolerant AHL-producing Aeromonas spp. is equally effective for sustaining the growth of STG as well as SSG wheat genotypes in saline soil, but biosafety should be fully ensured before field release.
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Affiliation(s)
- Muhammad Shoib Nawaz
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Ayesha Arshad
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Lubna Rajput
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Plant Physiology and Biotechnology Institute, Agriculture Research Centre, Tandojam, Pakistan
| | - Kaneez Fatima
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Department of Life Sciences, University of Management and Technology, Lahore, Pakistan
| | - Sami Ullah
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Department of Botany, Women University of Azad Jammu & Kashmir, Bagh, Bagh, Pakistan
| | - Muhammad Ahmad
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
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18
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Rémy B, Plener L, Decloquement P, Armstrong N, Elias M, Daudé D, Chabrière É. Lactonase Specificity Is Key to Quorum Quenching in Pseudomonas aeruginosa. Front Microbiol 2020; 11:762. [PMID: 32390993 PMCID: PMC7193897 DOI: 10.3389/fmicb.2020.00762] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/30/2020] [Indexed: 12/31/2022] Open
Abstract
The human opportunistic pathogen Pseudomonas aeruginosa orchestrates the expression of many genes in a cell density-dependent manner by using quorum sensing (QS). Two acyl-homoserine lactones (AHLs) are involved in QS circuits and contribute to the regulation of virulence factors production, biofilm formation, and antimicrobial sensitivity. Disrupting QS, a strategy referred to as quorum quenching (QQ) can be achieved using exogenous AHL-degrading lactonases. However, the importance of enzyme specificity on quenching efficacy has been poorly investigated. Here, we used two lactonases both targeting the signal molecules N-(3-oxododecanoyl)-L-homoserine lactone (3-oxo-C12 HSL) and butyryl-homoserine lactone (C4 HSL) albeit with different efficacies on C4 HSL. Interestingly, both lactonases similarly decreased AHL concentrations and comparably impacted the expression of AHL-based QS genes. However, strong variations were observed in Pseudomonas Quinolone Signal (PQS) regulation depending on the lactonase used. Both lactonases were also found to decrease virulence factors production and biofilm formation in vitro, albeit with different efficiencies. Unexpectedly, only the lactonase with lower efficacy on C4 HSL was able to inhibit P. aeruginosa pathogenicity in vivo in an amoeba infection model. Similarly, proteomic analysis revealed large variations in protein levels involved in antibiotic resistance, biofilm formation, virulence and diverse cellular mechanisms depending on the chosen lactonase. This global analysis provides evidences that QQ enzyme specificity has a significant impact on the modulation of QS-associated behavior in P. aeruginosa PA14.
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Affiliation(s)
- Benjamin Rémy
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France.,Gene&GreenTK, Marseille, France
| | | | - Philippe Decloquement
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics - BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | | | - Éric Chabrière
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
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19
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Vesty EF, Whitbread AL, Needs S, Tanko W, Jones K, Halliday N, Ghaderiardakani F, Liu X, Cámara M, Coates JC. Cross-kingdom signalling regulates spore germination in the moss Physcomitrella patens. Sci Rep 2020; 10:2614. [PMID: 32054953 PMCID: PMC7018845 DOI: 10.1038/s41598-020-59467-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/17/2020] [Indexed: 01/10/2023] Open
Abstract
Plants live in close association with microorganisms that can have beneficial or detrimental effects. The activity of bacteria in association with flowering plants has been extensively analysed. Bacteria use quorum-sensing as a way of monitoring their population density and interacting with their environment. A key group of quorum sensing molecules in Gram-negative bacteria are the N-acylhomoserine lactones (AHLs), which are known to affect the growth and development of both flowering plants, including crops, and marine algae. Thus, AHLs have potentially important roles in agriculture and aquaculture. Nothing is known about the effects of AHLs on the earliest-diverging land plants, thus the evolution of AHL-mediated bacterial-plant/algal interactions is unknown. In this paper, we show that AHLs can affect spore germination in a representative of the earliest plants on land, the Bryophyte moss Physcomitrella patens. Furthermore, we demonstrate that sporophytes of some wild isolates of Physcomitrella patens are associated with AHL-producing bacteria.
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Affiliation(s)
- Eleanor F Vesty
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,University Centre Shrewsbury, Guildhall, Frankwell Quay, Shrewsbury, Shropshire, UK
| | - Amy L Whitbread
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,Karlsruhe Institute of Technology, Karlsruhe, Baden-Württemberg, Germany
| | - Sarah Needs
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,School of Life, Health and Chemical Sciences, Open University, Walton Hall, Kents Hill, Milton Keynes, UK
| | - Wesal Tanko
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Kirsty Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Nigel Halliday
- National Biofilm Innovations Centre, University of Nottingham Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | | | - Xiaoguang Liu
- National Biofilm Innovations Centre, University of Nottingham Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.,Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Miguel Cámara
- National Biofilm Innovations Centre, University of Nottingham Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
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20
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Prescott RD, Decho AW. Flexibility and Adaptability of Quorum Sensing in Nature. Trends Microbiol 2020; 28:436-444. [PMID: 32001099 DOI: 10.1016/j.tim.2019.12.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/28/2019] [Accepted: 12/09/2019] [Indexed: 02/02/2023]
Abstract
Quorum sensing (QS), a type of chemical communication, allows bacteria to sense and coordinate activities in natural biofilm communities using N-acyl homoserine lactones (AHLs) as one type of signaling molecule. For AHL-based communication to occur, bacteria must produce and recognize the same signals, which activate similar genes in different species. Our current understanding of AHL-QS suggests that signaling between species would arise randomly, which is not probable. We propose that AHL-QS signaling is a mutable and adaptable process, within limits. AHLs are highly-conserved signals, however, their corresponding receptor proteins (LuxR) are highly variable. We suggest that both flexibility and adaptation occur among receptor proteins, allowing for complex signaling networks to develop in biofilms over time.
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Affiliation(s)
- Rebecca D Prescott
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK; Microbial Interactions Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA.
| | - Alan W Decho
- Microbial Interactions Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
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21
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Chane A, Barbey C, Robert M, Merieau A, Konto-Ghiorghi Y, Beury-Cirou A, Feuilloley M, Pátek M, Gobert V, Latour X. Biocontrol of Soft Rot: Confocal Microscopy Highlights Virulent Pectobacterial Communication and Its Jamming by Rhodococcal Quorum-Quenching. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:802-812. [PMID: 30645157 DOI: 10.1094/mpmi-11-18-0314-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Confocal laser-scanning microscopy was chosen to observe the colonization and damage caused by the soft rot Pectobacterium atrosepticum and the protection mediated by the biocontrol agent Rhodococcus erythropolis. We developed dual-color reporter strains suited for monitoring quorum-sensing and quorum-quenching activities leading to maceration or biocontrol, respectively. A constitutively expressed cyan or red fluorescent protein served as a cell tag for plant colonization, while an inducible expression reporter system based on the green fluorescent protein gene enabled the simultaneous recording of signaling molecule production, detection, or degradation. The dual-colored pathogen and biocontrol strains were used to coinoculate potato tubers. At cellular quorum, images revealed a strong pectobacterial quorum-sensing activity, especially at the plant cell walls, as well as a concomitant rhodococcal quorum-quenching response, at both the single-cell and microcolony levels. The generated biosensors appear to be promising and complementary tools useful for molecular and cellular studies of bacterial communication and interference.
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Affiliation(s)
- Andrea Chane
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Corinne Barbey
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
- 2 Seeds Innovation Protection Research and Environment, Route de la petite chaussée, 76110 Bretteville du Grand-Caux and Rue des Champs Potez, 62217 Achicourt, France
| | - Magalie Robert
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Annabelle Merieau
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Yoan Konto-Ghiorghi
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Amélie Beury-Cirou
- 2 Seeds Innovation Protection Research and Environment, Route de la petite chaussée, 76110 Bretteville du Grand-Caux and Rue des Champs Potez, 62217 Achicourt, France
- 3 French Federation of seed potato growers (FN3PT/RD3PT), 43-45 rue de Naples, 75008 Paris, France
| | - Marc Feuilloley
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Miroslav Pátek
- 4 Institute of Microbiology of the CAS, v.v.i. Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Virginie Gobert
- 2 Seeds Innovation Protection Research and Environment, Route de la petite chaussée, 76110 Bretteville du Grand-Caux and Rue des Champs Potez, 62217 Achicourt, France
- 3 French Federation of seed potato growers (FN3PT/RD3PT), 43-45 rue de Naples, 75008 Paris, France
| | - Xavier Latour
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
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Singh D, Raina TK, Kumar A, Singh J, Prasad R. Plant microbiome: A reservoir of novel genes and metabolites. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.plgene.2019.100177] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kusada H, Zhang Y, Tamaki H, Kimura N, Kamagata Y. Novel N-Acyl Homoserine Lactone-Degrading Bacteria Isolated From Penicillin-Contaminated Environments and Their Quorum-Quenching Activities. Front Microbiol 2019; 10:455. [PMID: 30923518 PMCID: PMC6426785 DOI: 10.3389/fmicb.2019.00455] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/20/2019] [Indexed: 01/28/2023] Open
Abstract
N-Acyl homoserine lactones (AHLs) are signaling molecules used in the quorum sensing (QS) of Gram-negative bacteria. Some bacteria interfere with the QS system using AHL-inactivating enzymes, commonly known as quorum-quenching (QQ) enzymes. We have recently isolated a new QQ bacterium showing high resistance to multiple β-lactam antibiotics, and its QQ enzyme (MacQ) confers β-lactam antibiotic resistance and exhibits QQ activities. This observation suggests the possibility of isolating novel QQ bacteria from β-lactam antibiotic-resistant bacteria. In this direction, we attempted to isolate penicillin G (PENG)-resistant bacteria from penicillin-contaminated river sediments and activated sludge treating penicillin-containing wastewater and characterize their QQ activities. Of 19 PENG-resistant isolates, six isolates showed high QQ activity toward a broad range of AHLs, including AHLs with 3-oxo substituents. Five of the six AHL-degraders showed AHL-acylase activity and hydrolyzed the amide bond of AHLs, whereas the remaining one strain did not show AHL-acylase activity, suggesting that this isolate may likely possess alternative degradation mechanism such as AHL-lactonase activity hydrolyzing the lactone ring of AHLs. The 16S rRNA gene sequence analysis results categorized these six AHL-degrading isolates into at least five genera, namely, Sphingomonas (Alphaproteobacteria), Diaphorobacter (Betaproteobacteria), Acidovorax (Betaproteobacteria), Stenotrophomonas (Gammaproteobacteria), and Mycobacterium (Actinobacteria); of these, Mycobacterium sp. M1 has never been known as QQ bacteria. Moreover, multiple β-lactam antibiotics showed high minimum inhibitory concentrations (MICs) when tested against all of isolates. These results strongly demonstrate that a wide variety of β-lactam antibiotic-resistant bacteria possess QQ activities. Although the genetic and enzymatic elements are yet unclear, this study may infer the functional and evolutionary correlation between β-lactam antibiotic resistance and QQ activities.
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Affiliation(s)
- Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yu Zhang
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, Tsukuba, Japan
| | - Nobutada Kimura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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Abstract
Bacterial cells use the quorum sensing system to communicate with each other. The gram-negative species very often use N-acyl homoserine lactones for this purpose. One of the easiest ways to detect these molecules is the use of particular reporter strains, which possess different kinds of reporter genes under the control of AHL-responsive promoters. Here we present some of the possibilities available today, even for not specialized researchers.
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Affiliation(s)
- Elke Stein
- Institute for Phytopathology, IFZ, Justus Liebig University Giessen, Gießen, Germany
| | - Adam Schikora
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
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25
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Palla M, Battini F, Cristani C, Giovannetti M, Squartini A, Agnolucci M. Quorum sensing in rhizobia isolated from the spores of the mycorrhizal symbiont Rhizophagus intraradices. MYCORRHIZA 2018; 28:773-778. [PMID: 29938366 DOI: 10.1007/s00572-018-0847-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
Most beneficial services provided by arbuscular mycorrhizal fungi (AMF), encompassing improved crop performance and soil resource availability, are mediated by AMF-associated bacteria, showing key-plant growth-promoting (PGP) traits, i.e., the production of indole acetic acid, siderophores and antibiotics, and activities increasing the availability of plant nutrients by nitrogen fixation and phosphate mobilization. Such functions may be affected by the ability of AMF-associated bacteria to communicate through the production and secretion of extracellular small diffusible chemical signals, N-acyl homoserine lactone signal molecules (AHLs), that regulate bacterial behavior at the community level (quorum sensing, QS). This work investigated the occurrence and extent of QS among rhizobia isolated from AMF spores, using two different QS reporter strains, Agrobacterium tumefaciens NTL4 pZRL4 and Chromobacterium violaceum CV026. We also assessed the quorum quenching (QQ) activity among Bacillus isolated from the same AMF spores. Most rhizobia were found to be quorum-signaling positive, including six isolates producing very high levels of AHLs. The results were confirmed by microtiter plate assay, which detected 65% of the tested bacteria as medium/high AHL producers. A 16S rDNA sequence analysis grouped the rhizobia into two clusters, consistent with the QS phenotype. None of the tested bacteria showed QQ activity able to disrupt the QS signaling, suggesting the absence of antagonism among bacteria living in AMF sporosphere. Our results provide the first evidence of the ability of AMF-associated rhizobia to communicate through QS, suggesting further studies on the potential importance of such a behavior in association with key-plant growth-promoting functions.
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Affiliation(s)
- Michela Palla
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Fabio Battini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Caterina Cristani
- "E. Avanzi" Research Center, University of Pisa, Via Vecchia di Marina 6, 56122, Pisa, Italy
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Viale dell'Università 16, Legnaro, PD, Italy
| | - Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
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26
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Liu J, Fu K, Wu C, Qin K, Li F, Zhou L. "In-Group" Communication in Marine Vibrio: A Review of N-Acyl Homoserine Lactones-Driven Quorum Sensing. Front Cell Infect Microbiol 2018; 8:139. [PMID: 29868495 PMCID: PMC5952220 DOI: 10.3389/fcimb.2018.00139] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/18/2018] [Indexed: 12/26/2022] Open
Abstract
N-Acyl Homoserine Lactones (N-AHLs) are an important group of small quorum-sensing molecules generated and released into the surroundings by Gram-negative bacteria. N-AHLs play a crucial role in various infection-related biological processes of marine Vibrio species, including survival, colonization, invasion, and pathogenesis. With the increasing problem of antibiotic abuse and subsequently the emergence of drug-resistant bacteria, studies on AHLs are therefore expected to bring potential new breakthroughs for the prevention and treatment of Vibrio infections. This article starts from AHLs generation in marine Vibrio, and then discusses the advantages, disadvantages, and trends in the future development of various detection methods for AHLs characterization. In addition to a detailed classification of the various marine Vibrio-derived AHL types that have been reported over the years, the regulatory mechanisms of AHLs and their roles in marine Vibrio biofilms, pathogenicity and interaction with host cells are also highlighted. Intervention measures for AHLs in different stages are systematically reviewed, and the prospects of their future development and application are examined.
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Affiliation(s)
- Jianfei Liu
- Central Laboratory, Navy General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Kaifei Fu
- Central Laboratory, Navy General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Chenglin Wu
- Central Laboratory, Navy General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Kewei Qin
- Central Laboratory, Navy General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Fei Li
- Central Laboratory, Navy General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Lijun Zhou
- Central Laboratory, Navy General Hospital of Chinese People's Liberation Army, Beijing, China
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27
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 485] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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28
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Bifunctional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides. Sci Rep 2017; 7:8946. [PMID: 28827579 PMCID: PMC5566955 DOI: 10.1038/s41598-017-09399-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/26/2017] [Indexed: 12/18/2022] Open
Abstract
Understanding the molecular mechanisms of bacterial antibiotic resistance will help prepare against further emergence of multi-drug resistant strains. MacQ is an enzyme responsible for the multi-drug resistance of Acidovorax sp. strain MR-S7. MacQ has acylase activity against both N-acylhomoserine lactones (AHLs), a class of signalling compounds involved in quorum sensing, and β-lactam antibiotics. Thus, MacQ is crucial as a quencher of quorum sensing as well as in conferring antibiotic resistance in Acidovorax. Here, we report the X-ray structures of MacQ in ligand-free and reaction product complexes. MacQ forms a 170-kDa capsule-shaped molecule via face-to-face interaction with two heterodimers consisting of an α-chain and a β-chain, generated by the self-cleaving activity of a precursor polypeptide. The electron density of the spacer polypeptide in the hollow of the molecule revealed the close orientation of the peptide-bond atoms of Val20SP-Gly21SP to the active-site, implying a role of the residues in substrate binding. In mutational analyses, uncleaved MacQ retained degradation activity against both AHLs and penicillin G. These results provide novel insights into the mechanism of self-cleaving maturation and enzymatic function of N-terminal nucleophile hydrolases.
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29
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A Novel Quorum-Quenching N-Acylhomoserine Lactone Acylase from Acidovorax sp. Strain MR-S7 Mediates Antibiotic Resistance. Appl Environ Microbiol 2017; 83:AEM.00080-17. [PMID: 28455333 PMCID: PMC5478981 DOI: 10.1128/aem.00080-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/03/2017] [Indexed: 11/22/2022] Open
Abstract
N-Acylhomoserine lactone acylase (AHL acylase) is a well-known enzyme responsible for disrupting cell-cell communication (quorum sensing) in bacteria. Here, we isolated and characterized a novel and unique AHL acylase (designated MacQ) from a multidrug-resistant bacterium, Acidovorax sp. strain MR-S7. The purified MacQ protein heterologously expressed in Escherichia coli degraded a wide variety of AHLs, ranging from C6 to C14 side chains with or without 3-oxo substitutions. We also observed that AHL-mediated virulence factor production in a plant pathogen, Pectobacterium carotovorum, was dramatically attenuated by coculture with MacQ-overexpressing Escherichia coli, whereas E. coli with an empty vector was unable to quench the pathogenicity, which strongly indicates that MacQ can act in vivo as a quorum-quenching enzyme and interfere with the quorum-sensing system in the pathogen. In addition, this enzyme was found to be capable of degrading a wide spectrum of β-lactams (penicillin G, ampicillin, amoxicillin, carbenicillin, cephalexin, and cefadroxil) by deacylation, clearly indicating that MacQ is a bifunctional enzyme that confers both quorum quenching and antibiotic resistance on strain MR-S7. MacQ has relatively low amino acid sequence identity to any of the known acylases (<39%) and has among the broadest substrate range. Our findings provide the possibility that AHL acylase genes can be an alternative source of antibiotic resistance genes posing a threat to human health if they migrate and transfer to pathogenic bacteria. IMPORTANCEN-Acylhomoserine lactones (AHLs) are well-known signal molecules for bacterial cell-cell communication (quorum sensing), and AHL acylase, which is able to degrade AHLs, has been recognized as a major target for quorum-sensing interference (quorum quenching) in pathogens. In this work, we succeeded in isolating a novel AHL acylase (MacQ) from a multidrug-resistant bacterium and demonstrated that the MacQ enzyme could confer multidrug resistance as well as quorum quenching on the host organism. Indeed, the purified MacQ protein was found to be bifunctional and capable of degrading not only various AHL derivatives but also multiple β-lactam antibiotics by deacylation activities. Although quorum quenching and antibiotic resistance have been recognized to be distinct biological functions, our findings clearly link the two functions by discovering the novel bifunctional enzyme and further providing the possibility that a hitherto-overlooked antibiotic resistance mechanism mediated by the quorum-quenching enzyme may exist in natural environments and perhaps in clinical settings.
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30
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Wilson CE, Lopatkin AJ, Craddock TJA, Driscoll WW, Eldakar OT, Lopez JV, Smith RP. Cooperation and competition shape ecological resistance during periodic spatial disturbance of engineered bacteria. Sci Rep 2017; 7:440. [PMID: 28348396 PMCID: PMC5428654 DOI: 10.1038/s41598-017-00588-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/06/2017] [Indexed: 12/17/2022] Open
Abstract
Cooperation is fundamental to the survival of many bacterial species. Previous studies have shown that spatial structure can both promote and suppress cooperation. Most environments where bacteria are found are periodically disturbed, which can affect the spatial structure of the population. Despite the important role that spatial disturbances play in maintaining ecological relationships, it remains unclear as to how periodic spatial disturbances affect bacteria dependent on cooperation for survival. Here, we use bacteria engineered with a strong Allee effect to investigate how the frequency of periodic spatial disturbances affects cooperation. We show that at intermediate frequencies of spatial disturbance, the ability of the bacterial population to cooperate is perturbed. A mathematical model demonstrates that periodic spatial disturbance leads to a tradeoff between accessing an autoinducer and accessing nutrients, which determines the ability of the bacteria to cooperate. Based on this relationship, we alter the ability of the bacteria to access an autoinducer. We show that increased access to an autoinducer can enhance cooperation, but can also reduce ecological resistance, defined as the ability of a population to resist changes due to disturbance. Our results may have implications in maintaining stability of microbial communities and in the treatment of infectious diseases.
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Affiliation(s)
- Cortney E Wilson
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, Florida, 33314, USA.,Guy Harvey Oceanographic Center, Nova Southeastern University, 8000 North Ocean Dr, Dania Beach, Florida, 33004, USA
| | - Allison J Lopatkin
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Durham, North Carolina, USA
| | - Travis J A Craddock
- Clinical Systems Biology Group, Institute for Neuro-Immune Medicine, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, Florida, 33314, USA.,Department of Psychology & Neuroscience, College of Psychology, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, Florida, 33314, USA.,Department of Computer Science, College of Engineering and Computing, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, Florida, 33314, USA.,Department of Clinical Immunology, College of Osteopathic Medicine, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, Florida, 33314, USA
| | - William W Driscoll
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St. Paul, Minnesota, 55108, USA
| | - Omar Tonsi Eldakar
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, Florida, 33314, USA
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, Florida, 33314, USA.,Guy Harvey Oceanographic Center, Nova Southeastern University, 8000 North Ocean Dr, Dania Beach, Florida, 33004, USA
| | - Robert P Smith
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, Florida, 33314, USA.
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31
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Foster ZSL, Sharpton TJ, Grünwald NJ. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol 2017; 100:1738-50. [PMID: 28222096 DOI: 10.3732/ajb.1200572] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/07/2017] [Accepted: 02/10/2017] [Indexed: 05/20/2023] Open
Abstract
Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.
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Affiliation(s)
- Zachary S L Foster
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, Oregon, United States of America
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32
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Ma ZP, Lao YM, Jin H, Lin GH, Cai ZH, Zhou J. Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove ( Kandelia obovata) Rhizosphere Environment. Front Microbiol 2016; 7:1957. [PMID: 27994584 PMCID: PMC5136546 DOI: 10.3389/fmicb.2016.01957] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/22/2016] [Indexed: 11/25/2022] Open
Abstract
Mangrove rhizosphere environment harbors diverse populations of microbes, and some evidence showed that rhizobacteria behavior was regulated by quorum sensing (QS). Investigating the diverse profiles of QS molecules in mangrove ecosystems may shed light on the bacterial roles and lead to a better understanding of the symbiotic interactions between plants and microbes. The aims of the current study focus on identifying AI-1 type QS signals, i.e., acyl homoserine lactones (AHLs), in Kandelia obovata rhizosphere environment. Approximately 1200 rhizobacteria were screened and 184 strains (15.3%) tested were positive. Subsequent 16s rRNA gene sequencing and dereplication analyses identified 24 species from the positive isolates, which were affiliated to three different phyla, including Proteobacteria, Firmicutes, and Actinobacteria. Thin-layer chromatography separation of extracts revealed diverse AHL profiles and detected at least one active compound in the supernatant of these 24 cultivable AHL-producers. The active extracts from these bacterial isolates were further evaluated by ultra performance liquid chromatography-mass spectrometry, and the carbon side chain length ranged from C4 to C14. This is the first report on the diversity of AI-1 type auto-inducers in the mangrove plant K. obovata, and it is imperative to expand our knowledge of plant-bacteria interactions with respect to the maintenance of wetland ecosystem health.
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Affiliation(s)
- Zhi P Ma
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Yong M Lao
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Hui Jin
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Guang H Lin
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University Shenzhen, China
| | - Zhong H Cai
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Jin Zhou
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
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33
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Braga RM, Dourado MN, Araújo WL. Microbial interactions: ecology in a molecular perspective. Braz J Microbiol 2016; 47 Suppl 1:86-98. [PMID: 27825606 PMCID: PMC5156507 DOI: 10.1016/j.bjm.2016.10.005] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/07/2016] [Indexed: 02/06/2023] Open
Abstract
The microorganism–microorganism or microorganism–host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial–host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community.
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Affiliation(s)
- Raíssa Mesquita Braga
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Manuella Nóbrega Dourado
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Welington Luiz Araújo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil.
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de Carvalho MP, Gulotta G, do Amaral MW, Lünsdorf H, Sasse F, Abraham WR. Coprinuslactone protects the edible mushroom Coprinus comatus against biofilm infections by blocking both quorum-sensing and MurA. Environ Microbiol 2016; 18:4254-4264. [PMID: 27696655 DOI: 10.1111/1462-2920.13560] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/28/2016] [Indexed: 12/23/2022]
Abstract
Pathogens embedded in biofilms are involved in many infections and are very difficult to treat with antibiotics because of higher resistance compared with planktonic cells. Therefore, new approaches for their control are urgently needed. One way to search for biofilm dispersing compounds is to look at defense strategies of organisms exposed to wet environments, which makes them prone to biofilm infections. It is reasonable to assume that mushrooms have developed mechanisms to control biofilms on their sporocarps (fruiting bodies). A preliminary screening for biofilms on sporocarps revealed several species with few or no bacteria on their sporocarps. From the edible mushroom Coprinus comatus where no bacteria on the sporocarp could be detected (3R,4S)-2-methylene-3,4-dihydroxypentanoic acid 1,4-lactone, named coprinuslactone, was isolated. Coprinuslactone interfered with quorum-sensing and dispersed biofilms of Pseudomonas aeruginosa, where it also reduced the formation of the pathogenicity factors pyocyanin and rhamnolipid B. Coprinuslactone also damaged Staphylococcus aureus cells in biofilms at subtoxic concentrations. Furthermore, it inhibited UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), essential for bacterial cell wall synthesis. These two modes of action ensure the inhibition of a broad spectrum of pathogens on the fruiting body but may also be useful for future clinical applications.
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Affiliation(s)
- Maira P de Carvalho
- Chemical Microbiology, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Giuseppe Gulotta
- Microbial Interactions and Processes, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Matheus W do Amaral
- Chemical Microbiology, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Heinrich Lünsdorf
- Central Facility for Microscopy, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Florenz Sasse
- Chemical Biology, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
| | - Wolf-Rainer Abraham
- Chemical Microbiology, Helmholtz Center for Infection Research, Braunschweig, 38124, Germany
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Moreira AS, Mil-Homens D, Sousa SA, Coutinho CP, Pinto-de-Oliveira A, Ramos CG, Dos Santos SC, Fialho AM, Leitão JH, Sá-Correia I. Variation of Burkholderia cenocepacia virulence potential during cystic fibrosis chronic lung infection. Virulence 2016; 8:782-796. [PMID: 27652671 DOI: 10.1080/21505594.2016.1237334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
During long-term lung infection in cystic fibrosis (CF) patients, Burkholderia cenocepacia faces multiple selective pressures in this highly stressful and fluctuating environment. As a consequence, the initial infecting strain undergoes genetic changes that result in the diversification of genotypes and phenotypes. Whether this clonal expansion influences the pathogenic potential is unclear. The virulence potential of 39 sequential B. cenocepacia (recA lineage IIIA) isolates, corresponding to 3 different clones retrieved from 3 chronically infected CF patients was compared in this study using the non-mammalian infection hosts Galleria mellonella and Caenorhabditis elegans. The isolates used in this retrospective study were picked randomly from selective agar plates as part of a CF Center routine, from the onset of infection until patients' death after 3.5 and 7.5 y or the more recent isolation date after 12.5 y of chronic infection. The infection models proved useful to assess virulence potential diversification, but for some isolates the relative values diverged in C. elegans and G. mellonella. Results also reinforce the concept of the occurrence of clonal diversification and co-existence of multiple phenotypes within the CF lungs, also with respect to pathogenicity. No clear trend of decrease (or increase) of the virulence potential throughout long-term infection was found but there is an apparent tendency for a clone/patient-dependent decrease of virulence when the G. mellonella model was used. The sole avirulent variant in both infection hosts was found to lack the small third replicon previously associated to virulence. Although possible, the in vivo loss of this nonessential megaplasmid was found to be a rare event (1 among a total of 64 isolates examined).
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Affiliation(s)
- Ana S Moreira
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Dalila Mil-Homens
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Sílvia A Sousa
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Carla P Coutinho
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Ana Pinto-de-Oliveira
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Christian G Ramos
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Sandra C Dos Santos
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Arsénio M Fialho
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Jorge H Leitão
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Isabel Sá-Correia
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
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Nievas FL, Bogino PC, Giordano W. Programmed Lab Experiments for Biochemical Investigation of Quorum-Sensing Signal Molecules in Rhizospheric Soil Bacteria. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:256-262. [PMID: 27027267 DOI: 10.1002/bmb.20949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/29/2015] [Indexed: 06/05/2023]
Abstract
Biochemistry courses in the Department of Molecular Biology at the National University of Río Cuarto, Argentina, are designed for undergraduate students in biology, microbiology, chemistry, agronomy, and veterinary medicine. Microbiology students typically have previous coursework in general, analytical, and organic chemistry. Programmed sequences of lab experiments allow these students to investigate biochemical problems whose solution is feasible within the context of their knowledge and experience. We previously designed and reported a programmed lab experiment that familiarizes microbiology students with techniques for detection and characterization of quorum-sensing (QS) and quorum-quenching (QQ) signal molecules. Here, we describe a sequence of experiments designed to expand the understanding and capabilities of biochemistry students using techniques for extraction and identification of QS and QQ signal molecules from peanut rhizospheric soil bacteria, including culturing and manipulation of bacteria under sterile conditions. The program provides students with an opportunity to perform useful assays, draw conclusions from their results, and discuss possible extensions of the study. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:256-262, 2016.
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Affiliation(s)
- Fiorela L Nievas
- Departamento De Biología Molecular, Universidad Nacional De Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Pablo C Bogino
- Departamento De Biología Molecular, Universidad Nacional De Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Walter Giordano
- Departamento De Biología Molecular, Universidad Nacional De Río Cuarto, Río Cuarto, Córdoba, Argentina
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Veselova MA, Romanova YM, Lipasova VA, Koksharova OA, Zaitseva YV, Chernukha MU, Gintsburg AL, Khmel IA. The effect of mutation in the clpX gene on the synthesis of N-acyl-homoserine lactones and other properties of Burkholderia cenocepacia 370. Microbiol Res 2016; 186-187:90-8. [PMID: 27242147 DOI: 10.1016/j.micres.2016.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/24/2016] [Accepted: 03/31/2016] [Indexed: 10/22/2022]
Abstract
In order to study the regulation of N-acyl-homoserine lactones synthesis (AHLs, the signal molecules of Quorum Sensing regulation) in Burkholderia cenocepacia strain 370 we obtained mutants with increased AHL production. One of the mutants, named BC-B6, was obtained by TnMod-RKm(r) plasposon mutagenesis. The plasposon insertion was located within the clpX gene encoding the ATPase subunit ClpX of the ClpXP protease. The mutation reduced bacterial virulence in mice intranasal infection. The results of proteomic analysis demonstrated that the expression of at least 19 proteins differed not less than 2-fold between the parental and mutant strains. 18 of the proteins were upregulated in the mutant, and one protein was downregulated. The proteins included those that involved in protein synthesis and modification, in energy production, in general metabolism, in transport and regulation. To check the effect of the clpX mutation on the AHL synthesis, a mutant with inactivated clpX gene (BC-clpX:Km(r)) was constructed by gene replacement method. This mutant also exhibited increased AHLs production. A swarming motility of both mutants was reduced compared to the original strain. Thus, the obtained results show that the clpX gene was involved in the regulation of AHL production and a number of cellular processes in B. cenocepacia 370.
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Affiliation(s)
- M A Veselova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia
| | - Yu M Romanova
- The Gamaleya Scientific Research Centre of Epidemiology and Microbiology, Gamaleya Str. 18, Moscow 123098, Russia
| | - V A Lipasova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia
| | - O A Koksharova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia; M.V. Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-Chemical Biology, Leninskie Gory 1-40, Moscow 119991, Russia
| | - Yu V Zaitseva
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia
| | - M U Chernukha
- The Gamaleya Scientific Research Centre of Epidemiology and Microbiology, Gamaleya Str. 18, Moscow 123098, Russia
| | - A L Gintsburg
- The Gamaleya Scientific Research Centre of Epidemiology and Microbiology, Gamaleya Str. 18, Moscow 123098, Russia
| | - I A Khmel
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia.
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Rosier A, Bishnoi U, Lakshmanan V, Sherrier DJ, Bais HP. A perspective on inter-kingdom signaling in plant-beneficial microbe interactions. PLANT MOLECULAR BIOLOGY 2016; 90:537-48. [PMID: 26792782 DOI: 10.1007/s11103-016-0433-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 01/06/2016] [Indexed: 05/14/2023]
Abstract
Recent work has shown that the rhizospheric and phyllospheric microbiomes of plants are composed of highly diverse microbial species. Though the information pertaining to the diversity of the aboveground and belowground microbes associated with plants is known, an understanding of the mechanisms by which these diverse microbes function is still in its infancy. Plants are sessile organisms, that depend upon chemical signals to interact with the microbiota. Of late, the studies related to the impact of microbes on plants have gained much traction in the research literature, supporting diverse functional roles of microbes on plant health. However, how these microbes interact as a community to confer beneficial traits to plants is still poorly understood. Recent advances in the use of "biologicals" as bio-fertilizers and biocontrol agents for sustainable agricultural practices is promising, and a fundamental understanding of how microbes in community work on plants could help this approach be more successful. This review attempts to highlight the importance of different signaling events that mediate a beneficial plant microbe interaction. Fundamental research is needed to understand how plants react to different benign microbes and how these microbes are interacting with each other. This review highlights the importance of chemical signaling, and biochemical and genetic events which determine the efficacy of benign microbes to promote the development of beneficial traits in plants.
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Affiliation(s)
- Amanda Rosier
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
- Delaware Biotechnology Institute, Newark, DE, 19711, USA
| | - Usha Bishnoi
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
- Delaware Biotechnology Institute, Newark, DE, 19711, USA
| | - Venkatachalam Lakshmanan
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
- Delaware Biotechnology Institute, Newark, DE, 19711, USA
| | - D Janine Sherrier
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
- Delaware Biotechnology Institute, Newark, DE, 19711, USA
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA.
- Delaware Biotechnology Institute, Newark, DE, 19711, USA.
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Helman Y, Chernin L. Silencing the mob: disrupting quorum sensing as a means to fight plant disease. MOLECULAR PLANT PATHOLOGY 2015; 16:316-29. [PMID: 25113857 PMCID: PMC6638422 DOI: 10.1111/mpp.12180] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Bacteria are able to sense their population's density through a cell-cell communication system, termed 'quorum sensing' (QS). This system regulates gene expression in response to cell density through the constant production and detection of signalling molecules. These molecules commonly act as auto-inducers through the up-regulation of their own synthesis. Many pathogenic bacteria, including those of plants, rely on this communication system for infection of their hosts. The finding that the countering of QS-disrupting mechanisms exists in many prokaryotic and eukaryotic organisms offers a promising novel method to fight disease. During the last decade, several approaches have been proposed to disrupt QS pathways of phytopathogens, and hence to reduce their virulence. Such studies have had varied success in vivo, but most lend promising support to the idea that QS manipulation could be a potentially effective method to reduce bacterial-mediated plant disease. This review discusses the various QS-disrupting mechanisms found in both bacteria and plants, as well as the different approaches applied artificially to interfere with QS pathways and thus protect plant health.
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Affiliation(s)
- Yael Helman
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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40
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Cárcamo-Oyarce G, Lumjiaktase P, Kümmerli R, Eberl L. Quorum sensing triggers the stochastic escape of individual cells from Pseudomonas putida biofilms. Nat Commun 2015; 6:5945. [PMID: 25592773 PMCID: PMC4309448 DOI: 10.1038/ncomms6945] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 11/24/2014] [Indexed: 12/18/2022] Open
Abstract
The term ‘quorum sensing’ (QS) is generally used to describe the phenomenon that bacteria release and perceive signal molecules to coordinate cooperative behaviour in response to their population size. QS-based communication has therefore been considered a social trait. Here we show that QS signals (N-acyl-homoserine lactones, AHLs) are stochastically produced in young biofilms of Pseudomonas putida and act mainly as self-regulatory signals rather than inducing neighbouring cells. We demonstrate that QS induces the expression of putisolvin biosurfactants that are not public goods, thereby triggering asocial motility of induced cells out of microcolonies. Phenotypic heterogeneity is most prominent in the early stages of biofilm development, whereas at later stages behaviour patterns across cells become more synchronized. Our findings broaden our perspective on QS by showing that AHLs can control the expression of asocial (self-directed) traits, and that heterogeneity in QS can serve as a mechanism to drive phenotypic heterogeneity in self-directed behaviour. Bacteria secrete signalling molecules (AHLs) to coordinate actions such as biofilm formation and the release of public goods, in a process called quorum sensing. Here, the authors show that AHLs are stochastically produced and control asocial (self-directed) traits in young biofilms of P. putida.
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Affiliation(s)
- Gerardo Cárcamo-Oyarce
- Department of Microbiology, Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland
| | - Putthapoom Lumjiaktase
- Department of Microbiology, Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland
| | - Rolf Kümmerli
- Department of Microbial Evolutionary Ecology, Institute of Plant Biology, University of Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
| | - Leo Eberl
- Department of Microbiology, Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland
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Martins ML, Pinto UM, Riedel K, Vanetti MCD, Mantovani HC, de Araújo EF. Lack of AHL-based quorum sensing in Pseudomonas fluorescens isolated from milk. Braz J Microbiol 2014; 45:1039-46. [PMID: 25477941 PMCID: PMC4204945 DOI: 10.1590/s1517-83822014000300037] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 12/13/2013] [Indexed: 11/22/2022] Open
Abstract
Numerous bacteria coordinate gene expression in response to small signalling molecules in many cases known as acylhomoserine lactones (AHLs), which accumulate as a function of cell density in a process known as quorum sensing. This work aimed to determine if phenotypes that are important to define microbial activity in foods such as biofilm formation, swarming motility and proteolytic activity of two Pseudomonas fluorescens strains, isolated from refrigerated raw milk, are influenced by AHL molecules. The tested P. fluorescens strains did not produce AHL molecules in none of the evaluated media. We found that biofilm formation was dependent on the culture media, but it was not influenced by AHLs. Our results indicate that biofilm formation, swarming motility and proteolytic activity of the tested P. fluorescens strains are not regulated by acyl-homoserine lactones. It is likely that AHL-dependent quorum sensing system is absent from these strains.
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Affiliation(s)
- Maurilio L Martins
- Instituto Federal de Educação Ciência e Tecnologia do Sudeste de Minas Gerais Campus Rio Pomba Belo HorizonteMG Brazil Instituto Federal de Educação, Ciência e Tecnologia do Sudeste de Minas Gerais, Campus Rio Pomba, Belo Horizonte, MG, Brazil
| | - Uelinton M Pinto
- Departamento de Alimentos Universidade Federal de Ouro Preto Ouro PretoMG Brazil Departamento de Alimentos, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Kathrin Riedel
- Institute of Microbiology Ernst-Moritz-Arndt University of Greifswald Germany Institute of Microbiology Ernst-Moritz-Arndt University of Greifswald, Germany
| | - Maria C D Vanetti
- Departamento de Microbiologia Universidade Federal de Viçosa ViçosaMG Brazil Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Hilário C Mantovani
- Departamento de Microbiologia Universidade Federal de Viçosa ViçosaMG Brazil Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Elza F de Araújo
- Departamento de Microbiologia Universidade Federal de Viçosa ViçosaMG Brazil Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Buddrus-Schiemann K, Rieger M, Mühlbauer M, Barbarossa MV, Kuttler C, Hense BA, Rothballer M, Uhl J, Fonseca JR, Schmitt-Kopplin P, Schmid M, Hartmann A. Analysis of N-acylhomoserine lactone dynamics in continuous cultures of Pseudomonas putida IsoF by use of ELISA and UHPLC/qTOF-MS-derived measurements and mathematical models. Anal Bioanal Chem 2014; 406:6373-83. [PMID: 25116602 DOI: 10.1007/s00216-014-8063-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/24/2014] [Accepted: 07/24/2014] [Indexed: 01/12/2023]
Abstract
In this interdisciplinary approach, the dynamics of production and degradation of the quorum sensing signal 3-oxo-decanoylhomoserine lactone were studied for continuous cultures of Pseudomonas putida IsoF. The signal concentrations were quantified over time by use of monoclonal antibodies and ELISA. The results were verified by use of ultra-high-performance liquid chromatography. By use of a mathematical model we derived quantitative values for non-induced and induced signal production rate per cell. It is worthy of note that we found rather constant values for different rates of dilution in the chemostat, and the values seemed close to those reported for batch cultures. Thus, the quorum-sensing system in P. putida IsoF is remarkably stable under different environmental conditions. In all chemostat experiments, the signal concentration decreased strongly after a peak, because emerging lactonase activity led to a lower concentration under steady-state conditions. This lactonase activity probably is quorum sensing-regulated. The potential ecological implication of such unique regulation is discussed.
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Affiliation(s)
- Katharina Buddrus-Schiemann
- Research Unit Microbe-Plant Interactions, Helmholtz Zentrum München, German Research Centre for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
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Grube M, Cernava T, Soh J, Fuchs S, Aschenbrenner I, Lassek C, Wegner U, Becher D, Riedel K, Sensen CW, Berg G. Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics. ISME JOURNAL 2014; 9:412-24. [PMID: 25072413 DOI: 10.1038/ismej.2014.138] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 11/09/2022]
Abstract
Symbioses represent a frequent and successful lifestyle on earth and lichens are one of their classic examples. Recently, bacterial communities were identified as stable, specific and structurally integrated partners of the lichen symbiosis, but their role has remained largely elusive in comparison to the well-known functions of the fungal and algal partners. We have explored the metabolic potentials of the microbiome using the lung lichen Lobaria pulmonaria as the model. Metagenomic and proteomic data were comparatively assessed and visualized by Voronoi treemaps. The study was complemented with molecular, microscopic and physiological assays. We have found that more than 800 bacterial species have the ability to contribute multiple aspects to the symbiotic system, including essential functions such as (i) nutrient supply, especially nitrogen, phosphorous and sulfur, (ii) resistance against biotic stress factors (that is, pathogen defense), (iii) resistance against abiotic factors, (iv) support of photosynthesis by provision of vitamin B12, (v) fungal and algal growth support by provision of hormones, (vi) detoxification of metabolites, and (vii) degradation of older parts of the lichen thallus. Our findings showed the potential of lichen-associated bacteria to interact with the fungal as well as algal partner to support health, growth and fitness of their hosts. We developed a model of the symbiosis depicting the functional multi-player network of the participants, and argue that the strategy of functional diversification in lichens supports the longevity and persistence of lichens under extreme and changing ecological conditions.
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Affiliation(s)
- Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Jung Soh
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Stephan Fuchs
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Ines Aschenbrenner
- 1] Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria [2] Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Christian Lassek
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Uwe Wegner
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Christoph W Sensen
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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N-acyl homoserine lactone-mediated quorum sensing with special reference to use of quorum quenching bacteria in membrane biofouling control. BIOMED RESEARCH INTERNATIONAL 2014; 2014:162584. [PMID: 25147787 PMCID: PMC4131561 DOI: 10.1155/2014/162584] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/04/2014] [Accepted: 07/06/2014] [Indexed: 11/17/2022]
Abstract
Membrane biofouling remains a severe problem to be addressed in wastewater treatment systems affecting reactor performance and economy. The finding that many wastewater bacteria rely on N-acyl homoserine lactone-mediated quorum sensing to synchronize their activities essential for biofilm formations; the quenching bacterial quorum sensing suggests a promising approach for control of membrane biofouling. A variety of quorum quenching compounds of both synthetic and natural origin have been identified and found effective in inhibition of membrane biofouling with much less environmental impact than traditional antimicrobials. Work over the past few years has demonstrated that enzymatic quorum quenching mechanisms are widely conserved in several prokaryotic organisms and can be utilized as a potent tool for inhibition of membrane biofouling. Such naturally occurring bacterial quorum quenching mechanisms also play important roles in microbe-microbe interactions and have been used to develop sustainable nonantibiotic antifouling strategies. Advances in membrane fabrication and bacteria entrapment techniques have allowed the implication of such quorum quenching bacteria for better design of membrane bioreactor with improved antibiofouling efficacies. In view of this, the present paper is designed to review and discuss the recent developments in control of membrane biofouling with special emphasis on quorum quenching bacteria that are applied in membrane bioreactors.
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Kusada H, Hanada S, Kamagata Y, Kimura N. The effects of N-acylhomoserine lactones, β-lactam antibiotics and adenosine on biofilm formation in the multi-β-lactam antibiotic-resistant bacterium Acidovorax sp. strain MR-S7. J Biosci Bioeng 2014; 118:14-9. [DOI: 10.1016/j.jbiosc.2013.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/03/2013] [Accepted: 12/13/2013] [Indexed: 10/25/2022]
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Koch G, Nadal-Jimenez P, Cool RH, Quax WJ. Deinococcus radiodurans can interfere with quorum sensing by producing an AHL-acylase and an AHL-lactonase. FEMS Microbiol Lett 2014; 356:62-70. [PMID: 24863934 DOI: 10.1111/1574-6968.12479] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/13/2014] [Accepted: 05/19/2014] [Indexed: 11/29/2022] Open
Abstract
Bacterial communication via the secretion of small diffusible compounds allows microorganisms to regulate gene expression in a coordinated manner. As many virulence traits are regulated in this fashion, disruption of chemical communication has been proposed as novel antimicrobial therapy. Quorum-quenching enzymes have been a promising discovery in this field as they interfere with the communication of Gram-negative bacteria. AHL-lactonases and AHL-acylases have been described in a variety of bacterial strains; however, usually only one of these two groups of enzymes has been described in a single species. We report here the presence of a member of each group of enzymes in the extremophile bacterium Deinococcus radiodurans. Co-occurrence of both enzymes in a single species increases the chance of inactivating foreign AHL signals under different conditions. We demonstrate that both enzymes are able to degrade the quorum-sensing molecules of various pathogens subsequently affecting virulence gene expression. These studies add the quorum-quenching enzymes of D. radiodurans to the list of potent quorum-quenchers and highlight the idea that quorum quenching could have evolved in some bacteria as a strategy to gain a competitive advantage by altering gene expression in other species.
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Affiliation(s)
- Gudrun Koch
- Department of Pharmaceutical Biology, University of Groningen, Groningen, the Netherlands
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Berg G, Grube M, Schloter M, Smalla K. Unraveling the plant microbiome: looking back and future perspectives. Front Microbiol 2014; 5:148. [PMID: 24926286 PMCID: PMC4045152 DOI: 10.3389/fmicb.2014.00148] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 03/20/2014] [Indexed: 11/16/2022] Open
Abstract
Most eukaryotes develop close interactions with microorganisms that are essential for their performance and survival. Thus, eukaryotes and prokaryotes in nature can be considered as meta-organisms or holobionts. Consequently, microorganisms that colonize different plant compartments contain the plant's second genome. In this respect, many studies in the last decades have shown that plant-microbe interactions are not only crucial for better understanding plant growth and health, but also for sustainable crop production in a changing world. This mini-review acting as editorial presents retrospectives and future perspectives for plant microbiome studies as well as information gaps in this emerging research field. In addition, the contribution of this research topic to the solution of various issues is discussed.
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Affiliation(s)
- Gabriele Berg
- Austrian Centre of Industrial BiotechnologyGraz, Austria
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Martin Grube
- Institute of Plant Sciences, University of GrazGraz, Austria
| | - Michael Schloter
- Environmental Genomics, Helmholtz Zentrum MünchenOberschleissheim, Germany
| | - Kornelia Smalla
- Julius Kühn-Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Federal Research Centre for Cultivated PlantsBraunschweig, Germany
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Schenk ST, Hernández-Reyes C, Samans B, Stein E, Neumann C, Schikora M, Reichelt M, Mithöfer A, Becker A, Kogel KH, Schikora A. N-Acyl-Homoserine Lactone Primes Plants for Cell Wall Reinforcement and Induces Resistance to Bacterial Pathogens via the Salicylic Acid/Oxylipin Pathway. THE PLANT CELL 2014; 26:2708-2723. [PMID: 24963057 PMCID: PMC4114961 DOI: 10.1105/tpc.114.126763] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/27/2014] [Accepted: 05/31/2014] [Indexed: 05/18/2023]
Abstract
The ability of plants to monitor their surroundings, for instance the perception of bacteria, is of crucial importance. The perception of microorganism-derived molecules and their effector proteins is the best understood of these monitoring processes. In addition, plants perceive bacterial quorum sensing (QS) molecules used for cell-to-cell communication between bacteria. Here, we propose a mechanism for how N-acyl-homoserine lactones (AHLs), a group of QS molecules, influence host defense and fortify resistance in Arabidopsis thaliana against bacterial pathogens. N-3-oxo-tetradecanoyl-l-homoserine lactone (oxo-C14-HSL) primed plants for enhanced callose deposition, accumulation of phenolic compounds, and lignification of cell walls. Moreover, increased levels of oxylipins and salicylic acid favored closure of stomata in response to Pseudomonas syringae infection. The AHL-induced resistance seems to differ from the systemic acquired and the induced systemic resistances, providing new insight into inter-kingdom communication. Consistent with the observation that short-chain AHLs, unlike oxo-C14-HSL, promote plant growth, treatments with C6-HSL, oxo-C10-HSL, or oxo-C14-HSL resulted in different transcriptional profiles in Arabidopsis. Understanding the priming induced by bacterial QS molecules augments our knowledge of plant reactions to bacteria and suggests strategies for using beneficial bacteria in plant protection.
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Affiliation(s)
- Sebastian T Schenk
- Institute of Phytopathology and Applied Zoology, IFZ, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Casandra Hernández-Reyes
- Institute of Phytopathology and Applied Zoology, IFZ, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Birgit Samans
- Department of Plant Breeding, IFZ, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Elke Stein
- Institute of Phytopathology and Applied Zoology, IFZ, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Christina Neumann
- Institute of Phytopathology and Applied Zoology, IFZ, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Marek Schikora
- Department of Sensor Data and Information Fusion, Fraunhofer FKIE, 53343 Wachtberg, Germany
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Axel Mithöfer
- Department of Bioorganic Chemistry, Plant Defense, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Annette Becker
- Plant Developmental Biology Group, Institute of Botany, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology and Applied Zoology, IFZ, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Adam Schikora
- Institute of Phytopathology and Applied Zoology, IFZ, Justus Liebig University Giessen, 35392 Giessen, Germany
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Thomanek H, Schenk ST, Stein E, Kogel KH, Schikora A, Maison W. Modified N-acyl-homoserine lactones as chemical probes for the elucidation of plant-microbe interactions. Org Biomol Chem 2014; 11:6994-7003. [PMID: 24057134 DOI: 10.1039/c3ob41215f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Gram-negative bacteria often use N-acyl-homoserine lactones (AHLs) as signal molecules to monitor their local population densities and to regulate gene-expression in a process called "Quorum Sensing" (QS). This cell-to-cell communication allows bacteria to adapt to environmental changes and to behave as multicellular communities. QS plays a key role in both bacterial virulence towards the host and symbiotic interactions with other organisms. Plants also perceive AHLs and respond to them with changes in gene expression or modifications in development. Herein, we report the synthesis of new AHL-derivatives for the investigation and identification of AHL-interacting proteins. We show that our new compounds are still recognised by different bacteria and that a novel biotin-tagged-AHL derivative interacts with a bacterial AHL receptor.
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Affiliation(s)
- Heike Thomanek
- Pharmaceutical and Medicinal Chemistry, University of Hamburg, Bundesstr. 45, 20146 Hamburg, Germany.
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Fazli M, Almblad H, Rybtke ML, Givskov M, Eberl L, Tolker-Nielsen T. Regulation of biofilm formation in Pseudomonas and Burkholderia species. Environ Microbiol 2014; 16:1961-81. [PMID: 24592823 DOI: 10.1111/1462-2920.12448] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/12/2014] [Accepted: 02/28/2014] [Indexed: 01/28/2023]
Abstract
In the present review, we describe and compare the molecular mechanisms that are involved in the regulation of biofilm formation by Pseudomonas putida, Pseudomonas fluorescens, Pseudomonas aeruginosa and Burkholderia cenocepacia. Our current knowledge suggests that biofilm formation is regulated by cyclic diguanosine-5'-monophosphate (c-di-GMP), small RNAs (sRNA) and quorum sensing (QS) in all these bacterial species. The systems that employ c-di-GMP as a second messenger regulate the production of exopolysaccharides and surface proteins which function as extracellular matrix components in the biofilms formed by the bacteria. The systems that make use of sRNAs appear to regulate the production of exopolysaccharide biofilm matrix material in all these species. In the pseudomonads, QS regulates the production of extracellular DNA, lectins and biosurfactants which all play a role in biofilm formation. In B.cenocepacia QS regulates the expression of a large surface protein, lectins and extracellular DNA that all function as biofilm matrix components. Although the three regulatory systems all regulate the production of factors used for biofilm formation, the molecular mechanisms involved in transducing the signals into expression of the biofilm matrix components differ between the species. Under the conditions tested, exopolysaccharides appears to be the most important biofilm matrix components for P.aeruginosa, whereas large surface proteins appear to be the most important biofilm matrix components for P.putida, P.fluorescens, and B.cenocepacia.
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Affiliation(s)
- Mustafa Fazli
- Department of International Health, Immunology, and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark; Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, Turkey
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