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Sensors (Basel, Switzerland) 2012Initially described in 1990, Pseudomonas fluorescens HK44 served as the first whole-cell bioreporter genetically endowed with a bioluminescent (luxCDABE) phenotype... (Review)
Review
Initially described in 1990, Pseudomonas fluorescens HK44 served as the first whole-cell bioreporter genetically endowed with a bioluminescent (luxCDABE) phenotype directly linked to a catabolic (naphthalene degradative) pathway. HK44 was the first genetically engineered microorganism to be released in the field to monitor bioremediation potential. Subsequent to that release, strain HK44 had been introduced into other solids (soils, sands), liquid (water, wastewater), and volatile environments. In these matrices, it has functioned as one of the best characterized chemically-responsive environmental bioreporters and as a model organism for understanding bacterial colonization and transport, cell immobilization strategies, and the kinetics of cellular bioluminescent emission. This review summarizes the characteristics of P. fluorescens HK44 and the extensive range of its applications with special focus on the monitoring of bioremediation processes and biosensing of environmental pollution.
Topics: Biological Assay; Biosensing Techniques; Environmental Monitoring; Equipment Design; Equipment Failure Analysis; Pseudomonas fluorescens; Spectrometry, Fluorescence
PubMed: 22438725
DOI: 10.3390/s120201544 -
Clinical Microbiology Reviews Oct 2014Pseudomonas fluorescens is not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it at... (Review)
Review
Pseudomonas fluorescens is not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it at low levels in the indigenous microbiota of various body sites. With recent advances in comparative genomics, many isolates originally identified as the "species" P. fluorescens are now being reclassified as novel Pseudomonas species within the P. fluorescens "species complex." Although most widely studied for its role in the soil and the rhizosphere, P. fluorescens possesses a number of functional traits that provide it with the capability to grow and thrive in mammalian hosts. While significantly less virulent than P. aeruginosa, P. fluorescens can cause bacteremia in humans, with most reported cases being attributable either to transfusion of contaminated blood products or to use of contaminated equipment associated with intravenous infusions. Although not suspected of being an etiologic agent of pulmonary disease, there are a number of reports identifying it in respiratory samples. There is also an intriguing association between P. fluorescens and human disease, in that approximately 50% of Crohn's disease patients develop serum antibodies to P. fluorescens. Altogether, these reports are beginning to highlight a far more common, intriguing, and potentially complex association between humans and P. fluorescens during health and disease.
Topics: Genomics; Host-Pathogen Interactions; Humans; Phenotype; Pseudomonas Infections; Pseudomonas fluorescens; Quantitative Trait, Heritable; Virulence Factors
PubMed: 25278578
DOI: 10.1128/CMR.00044-14 -
FEMS Microbiology Letters Jul 2017Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static... (Review)
Review
Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation.
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function.
Topics: Adaptation, Physiological; Biofilms; Biological Evolution; Ecology; Ecosystem; Environment; Evolution, Molecular; Genotype; Mutation; Phenotype; Pseudomonas fluorescens; Radiation
PubMed: 28535292
DOI: 10.1093/femsle/fnx109 -
Scientific Reports Mar 2021The genome of Pseudomonas fluorescens F113, a model rhizobacterium and a plant growth-promoting agent, encodes three putative type VI secretion systems (T6SSs); F1-, F2-...
The genome of Pseudomonas fluorescens F113, a model rhizobacterium and a plant growth-promoting agent, encodes three putative type VI secretion systems (T6SSs); F1-, F2- and F3-T6SS. Bioinformatic analysis of the F113 T6SSs has revealed that they belong to group 3, group 1.1, and group 4a, respectively, similar to those previously described in Pseudomonas aeruginosa. In addition, in silico analyses allowed us to identify genes encoding a total of five orphan VgrG proteins and eight putative effectors (Tfe), some with their cognate immunity protein (Tfi) pairs. Genes encoding Tfe and Tfi are found in the proximity of P. fluorescens F113 vgrG, hcp, eagR and tap genes. RNA-Seq analyses in liquid culture and rhizosphere have revealed that F1- and F3-T6SS are expressed under all conditions, indicating that they are active systems, while F2-T6SS did not show any relevant expression under the tested conditions. The analysis of structural mutants in the three T6SSs has shown that the active F1- and F3-T6SSs are involved in interbacterial killing while F2 is not active in these conditions and its role is still unknown.. A rhizosphere colonization analysis of the double mutant affected in the F1- and F3-T6SS clusters showed that the double mutant was severely impaired in persistence in the rhizosphere microbiome, revealing the importance of these two systems for rhizosphere adaption.
Topics: Adaptation, Physiological; Gene Expression Regulation, Bacterial; Microbial Viability; Microbiota; Multigene Family; Phylogeny; Protein Domains; Pseudomonas fluorescens; Rhizosphere; Type VI Secretion Systems
PubMed: 33707614
DOI: 10.1038/s41598-021-85218-1 -
World Journal of Gastroenterology Feb 2013To characterize oxidase- and urease-producing bacterial isolates, grown aerobically, that originated from antral biopsies of patients suffering from acid peptic diseases.
AIM
To characterize oxidase- and urease-producing bacterial isolates, grown aerobically, that originated from antral biopsies of patients suffering from acid peptic diseases.
METHODS
A total of 258 antral biopsy specimens were subjected to isolation of bacteria followed by tests for oxidase and urease production, acid tolerance and aerobic growth. The selected isolates were further characterized by molecular techniques viz. amplifications for 16S rRNA using universal eubacterial and HSP60 gene specific primers. The amplicons were subjected to restriction analysis and partial sequencing. A phylogenetic tree was generated using unweighted pair group method with arithmetic mean (UPGMA) from evolutionary distance computed with bootstrap test of phylogeny. Assessment of acidity tolerance of bacteria isolated from antrum was performed using hydrochloric acid from 10(-7) mol/L to 10(-1) mol/L.
RESULTS
Of the 258 antral biopsy specimens collected from patients, 179 (69.4%) were positive for urease production by rapid urease test and 31% (80/258) yielded typical Helicobacter pylori (H. pylori) after 5-7 d of incubation under a microaerophilic environment. A total of 240 (93%) antral biopsies yielded homogeneous semi-translucent and small colonies after overnight incubation. The partial 16S rRNA sequences revealed that the isolates had 99% similarity with Pseudomonas species. A phylogenetic tree on the basis of 16S rRNA sequences denoted that JQ927226 and JQ927227 were likely to be related to Pseudomonas fluorescens (P. fluorescens). On the basis of HSP60 sequences applied to the UPGMA phylogenetic tree, it was observed that isolated strains in an aerobic environment were likely to be P. fluorescens, and HSP60 sequences had more discriminatory potential rather than 16S rRNA sequences. Interestingly, this bacterium was acid tolerant for hours at low pH. Further, a total of 250 (96.9%) genomic DNA samples of 258 biopsy specimens and DNA from 240 bacterial isolates were positive for the 613 bp amplicons by targeting P. fluorescens-specific conserved putative outer membrane protein gene sequences.
CONCLUSION
This study indicates that bacterial isolates from antral biopsies grown aerobically were P. fluorescens, and thus acid-tolerant bacteria other than H. pylori can also colonize the stomach and may be implicated in pathogenesis/protection.
Topics: Bacterial Proteins; Biopsy; Chaperonin 60; Humans; Hydrogen-Ion Concentration; Microbial Viability; Oxidoreductases; Phylogeny; Pseudomonas fluorescens; Pyloric Antrum; RNA, Bacterial; RNA, Ribosomal, 16S; Ribotyping; Urease
PubMed: 23466902
DOI: 10.3748/wjg.v19.i7.1056 -
Applied and Environmental Microbiology Sep 2021Within soil, bacteria are found in multispecies communities, where interactions can lead to emergent community properties. Studying bacteria in a social context is...
Exploration of Social Spreading Reveals That This Behavior Is Prevalent among and Pseudomonas fluorescens Isolates and That There Are Variations in the Induction of the Phenotype.
Within soil, bacteria are found in multispecies communities, where interactions can lead to emergent community properties. Studying bacteria in a social context is critical for investigating community-level functions. We previously showed that cocultured Pseudomonas fluorescens Pf0-1 and sp. V48 engage in interspecies social spreading (ISS) on a hard agar surface, a behavior which required close contact and depended on the nutritional environment. Here, we investigate whether social spreading is widespread among P. fluorescens and isolates and whether the requirements for interaction vary. We find that this phenotype is not restricted to the interaction between P. fluorescens Pf0-1 and sp. V48 but is a prevalent behavior found in one clade in the P. fluorescens group and two clades in the genus. We show that the interaction with certain isolates occurred without close contact, indicating induction of spreading by a putative diffusible signal. As with ISS by Pf0-1+V48, the motility of interacting pairs is influenced by the environment, with no spreading behaviors (or induction of motility) observed under high nutrient conditions. While Pf0-1+V48 require low nutrient but high NaCl conditions, in the broader range of interacting pairs, the high salt influence was variable. The prevalence of motility phenotypes observed here and found within the literature indicates that community-induced locomotion in general, and social spreading in particular, is likely important within the environment. It is crucial that we continue to study microbial interactions and their emergent properties to gain a fuller understanding of the functions of microbial communities. Interspecies social spreading (ISS) is an emergent behavior observed when Pseudomonas fluorescens Pf0-1 and sp. V48 interact, during which both species move together across a surface. Importantly, this environment does not permit the movement of either individual species. This group behavior suggests that communities of microbes can function in ways not predictable by knowledge of the individual members. Here, we have asked whether ISS is widespread and thus potentially of importance in soil microbial communities. The significance of this research is the demonstration that surface spreading behaviors are not unique to the Pf0-1-V48 interaction but rather is a more widespread phenomenon observed among members of distinct clades of both P. fluorescens and isolates. Furthermore, we identify differences in mechanisms of signaling and nutritional requirements for ISS. Emergent traits resulting from bacterial interactions are widespread, and their characterization is necessary for a complete understanding of microbial community function.
Topics: Microbial Interactions; Pedobacter; Phenotype; Phylogeny; Pseudomonas fluorescens; RNA, Ribosomal, 16S; Soil Microbiology
PubMed: 34288708
DOI: 10.1128/AEM.01344-21 -
Food Microbiology Sep 2019Pseudomonas fluorescens Ps_77 is a blue-pigmenting strain able to cause food product discoloration, causing relevant economic losses especially in the dairy industry....
Pseudomonas fluorescens Ps_77 is a blue-pigmenting strain able to cause food product discoloration, causing relevant economic losses especially in the dairy industry. Unlike non-pigmenting P. fluorescens, blue pigmenting strains previously were shown to carry a genomic region that includes homologs of trpABCDF genes, pointing at a possible role of the tryptophan biosynthetic pathway in production of the pigment. Here, we employ random mutagenesis to first identify the genes involved in blue-pigment production in P. fluorescens Ps_77 and second to investigate the biological function of the blue pigment. Genetic analyses based on the mapping of the random insertions allowed the identification of eight genes involved in pigment production, including the second copy of trpB (trpB_1) gene. Phenotypic characterization of Ps_77 white mutants demonstrated that the blue pigment increases oxidative-stress resistance. Indeed, while Ps_77 was growing at a normal rate in presence of 5 mM of HO, white mutants were completely inhibited. The antioxidative protection is not available for non-producing bacteria in co-culture with Ps_77.
Topics: Antioxidants; Bacterial Proteins; Hydrogen Peroxide; Multigene Family; Mutagenesis; Mutation; Oxidative Stress; Pigments, Biological; Pseudomonas fluorescens
PubMed: 31027811
DOI: 10.1016/j.fm.2019.03.028 -
The ISME Journal Jun 2013The bacteriovorous nematode Caenorhabditis elegans has been used to investigate many aspects of animal biology, including interactions with pathogenic bacteria. However,...
The bacteriovorous nematode Caenorhabditis elegans has been used to investigate many aspects of animal biology, including interactions with pathogenic bacteria. However, studies examining C. elegans interactions with bacteria isolated from environments in which it is found naturally are relatively scarce. C. elegans is frequently associated with cultivation of the edible mushroom Agaricus bisporus, and has been reported to increase the severity of bacterial blotch of mushrooms, a disease caused by bacteria from the Pseudomonas fluorescens complex. We observed that pseudomonads isolated from mushroom farms showed differential resistance to nematode predation. Under nutrient poor conditions, in which most pseudomonads were consumed, the mushroom pathogenic isolate P. fluorescens NZI7 was able to repel C. elegans without causing nematode death. A draft genome sequence of NZI7 showed it to be related to the biocontrol strain P. protegens Pf-5. To identify the genetic basis of nematode repellence in NZI7, we developed a grid-based screen for mutants that lacked the ability to repel C. elegans. The mutants isolated in this screen included strains with insertions in the global regulator GacS and in a previously undescribed GacS-regulated gene cluster, 'EDB' ('edible'). Our results suggest that the product of the EDB cluster is a poorly diffusible or cell-associated factor that acts together with other features of NZI7 to provide a novel mechanism to deter nematode grazing. As nematodes interact with NZI7 colonies before being repelled, the EDB factor may enable NZI7 to come into contact with and be disseminated by C. elegans without being subject to intensive predation.
Topics: Agaricales; Animals; Caenorhabditis elegans; Food Chain; Mutation; Pest Control, Biological; Pseudomonas fluorescens
PubMed: 23426012
DOI: 10.1038/ismej.2013.9 -
Mycorrhiza Jan 2017Type three secretion systems (T3SSs) mediate cell-to-cell interactions between Gram-negative bacteria and eukaryotes. We hypothesized that fluorescent pseudomonads...
Type three secretion systems (T3SSs) mediate cell-to-cell interactions between Gram-negative bacteria and eukaryotes. We hypothesized that fluorescent pseudomonads harboring T3SS (T3SS+) would be beneficial to arbuscular mycorrhizal symbiosis because non-pathogenic fluorescent pseudomonads have been previously shown to be much more abundant in mycorrhizal than in non-mycorrhizal roots. We tested this hypothesis by comparing mycorrhization and the associated rhizosphere microbial communities of Medicago truncatula grown in a non-sterile soil inoculated with either the T3SS+ mycorrhiza helper bacterium Pseudomonas fluorescens (C7R12) or a T3SS- mutant of the strain. Results showed that the bacterial secretion system was responsible for the promotion of mycorrhization because root colonization by arbuscular mycorrhizal fungi was not promoted by the T3SS- mutant. The observed T3SS-mediated promotion of mycorrhization was associated with changes in the rhizosphere bacterial communities and the increased occurrence of Claroidoglomeraceae within the intraradical arbuscular mycorrhizal fungi. Furthermore, both pseudomonad strains promoted the host-free growth of a model arbuscular mycorrhizal fungus in vitro, suggesting that T3SS-mediated promotion of mycorrhization occurs during plant-fungal interactions rather than during the pre-symbiotic phase of fungal growth. Taken together, these data provide evidence for the involvement of T3SS in promoting arbuscular mycorrhization by a model fluorescent pseudomonad and suggest the implication of interactions between the bacterium and mycorrhizas.
Topics: Fungi; Gene Expression Regulation, Bacterial; Medicago truncatula; Mutation; Mycorrhizae; Plant Roots; Pseudomonas fluorescens; Soil Microbiology; Type III Secretion Systems
PubMed: 27549437
DOI: 10.1007/s00572-016-0730-3 -
Canadian Journal of Microbiology May 2009Suppressive subtractive hybridization has been utilized to generate a cDNA library of genes differentially expressed in naphthalene grown cells of Pseudomonas...
Suppressive subtractive hybridization has been utilized to generate a cDNA library of genes differentially expressed in naphthalene grown cells of Pseudomonas fluorescens. The library was devoid of genes known to be associated with naphthalene catabolism, but was enriched in genes related to cellular uptake and efflux systems. The gene for OmpW, which was present in the cDNA library and has been proposed to encode a porin for the transport of hydrophobic molecules, was isolated, cloned, and sequenced. This gene was shown to be exclusively localized on a large catabolic plasmid possessed by the organism, and its specific mutation resulted in the loss of the organism's ability to grow on naphthalene and several other polycyclic aromatic hydrocarbons. It is proposed that a primary response by P. fluorescens to the presence of naphthalene is the elevation of the cellular mechanism(s) required for its assimilation. The presence of genes related to the uptake and efflux mechanisms present following suppressive subtractive hybridization supports this proposal.
Topics: Amino Acid Sequence; Bacterial Outer Membrane Proteins; Base Sequence; Cloning, Molecular; Gene Knockout Techniques; Gene Library; Genes, Bacterial; Molecular Sequence Data; Naphthalenes; Nucleic Acid Hybridization; Plasmids; Pseudomonas fluorescens; Sequence Analysis, DNA
PubMed: 19483784
DOI: 10.1139/w09-002