Environmental factors modulating antibiotic and siderophore biosynthesis by Pseudomonas fluorescens biocontrol strains.

Understanding the environmental factors that regulate the biosynthesis of antimicrobial compounds by disease-suppressive strains of Pseudomonas fluorescens is an essential step toward improving the level and reliability of their biocontrol activity. We used liquid culture assays to identify several minerals and carbon sources which had a differential influence on the production of the antibiotics 2,4-diacetylphloroglucinol (PHL), pyoluteorin (PLT), and pyrrolnitrin and the siderophores salicylic acid and pyochelin by the model strain CHA0, which was isolated from a natural disease-suppressive soil in Switzerland. Production of PHL was stimulated by Zn2+, NH4Mo2+, and glucose; the precursor compound mono-acetylphloroglucinol was stimulated by the same factors as PHL. Production of PLT was stimulated by Zn2+, Co2+, and glycerol but was repressed by glucose. Pyrrolnitrin production was increased by fructose, mannitol, and a mixture of Zn2+ and NH4Mo2+. Pyochelin production was increased by Co2+, fructose, mannitol, and glucose. Interestingly, production of its precursor salicylic acid was increased by different factors, i.e., NH4Mo2+, glycerol, and glucose. The mixture of Zn2+ and NH4Mo2+ with fructose, mannitol, or glycerol further enhanced the production of PHL and PLT compared with either the minerals or the carbon sources used alone, but it did not improve siderophore production. Extending fermentation time from 2 to 5 days increased the accumulation of PLT, pyrrolnitrin, and pyochelin but not of PHL. When findings with CHA0 were extended to an ecologically and genetically diverse collection of 41 P. fluorescens biocontrol strains, the effect of certain factors was strain dependent, while others had a general effect. Stimulation of PHL by Zn2+ and glucose was strain dependent, whereas PLT production by all strains that can produce this compound was stimulated by Zn2+ and transiently repressed by glucose. Inorganic phosphate reduced PHL production by CHA0 and seven other strains tested but to various degrees. Production of PLT but not pyrrolnitrin by CHA0 was also reduced by 100 mM phosphate. The use of 1/10-strength nutrient broth-yeast extract, compared with standard nutrient broth-yeast extract, amended with glucose and/or glycerol resulted in dramatically increased accumulations of PHL (but not PLT), pyochelin, and salicylic acid, indicating that the ratio of carbon source to nutrient concentration played a key role in the metabolic flow. The results of this study (i) provide insight into the biosynthetic regulation of antimicrobial compounds, (ii) limit the number of factors for intensive study in situ, and (iii) indicate factors that can be manipulated to improve bacterial inoculants.     

Draft genome sequences of Helicobacter pylori strains 17874 and P79

Helicobacter pylori is a human pathogen that colonizes the human gastric mucosa, causing gastritis, duodenal and gastric ulcers, and gastric carcinoma. Here we announce the draft genomes of H. pylori strain 17874, commonly used for studying motility, and P79, a strain for which plasmid vectors have been developed.     

荧光假单胞菌生防机理的研究进展

荧光假单胞菌是植物根际促生细菌(Plant Growth Promoting Rhizobacteria,PGPR)具有分布广、数量多、营养需要简单、繁殖快、竞争定殖力强的特点。它们能通过产生多种次生代谢物及有效的根际定殖防治植物病害,成为植物生防控制的重要研究对象。主要论述了荧光假单胞菌对植物病害生物防治机理的研究进展。     

Draft genome sequences of the biocontrol bacterium Mitsuaria sp. strain H24L5A

Mitsuaria sp. strain H24L5A is a plant-associated bacterium with proven capacities to suppress plant pathogens. Here, we report the draft genome sequences and automatic annotation of H24L5A. Comparative genomic analysis indicates H24L5A's similarity to the Leptothrix and Methylibium species, as well as several genes potentially contributing to its biocontrol activities.     

Draft genome sequences of two Legionella dumoffii strains, TEX-KL and NY-23

Legionella (Fluoribacter) dumoffii is one of the agents causing Legionnaires' disease. Here, we used Illumina second-generation sequencing technology to decipher for the first time the whole-genome sequences of two strains of this species, TEX-KL and NY-23. The assembly results for both strains consist of one chromosome and two plasmids.     

Genome sequence of the biocontrol strain Pseudomonas fluorescens F113

Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) that has biocontrol activity against fungal plant pathogens and is a model for rhizosphere colonization. Here, we present its complete genome sequence, which shows that besides a core genome very similar to those of other strains sequenced within this species, F113 possesses a wide array of genes encoding specialized functions for thriving in the rhizosphere and interacting with eukaryotic organisms.     

Draft genome sequence of the polycyclic aromatic hydrocarbon-degrading, genetically engineered bioluminescent bioreporter Pseudomonas fluorescens HK44

Pseudomonas fluorescens strain HK44 (DSM 6700) is a genetically engineered lux-based bioluminescent bioreporter. Here we report the draft genome sequence of strain HK44. Annotation of ～6.1 Mb of sequence indicates that 30% of the traits are unique and distributed over five genomic islands, a prophage, and two plasmids.     

Draft genome sequences of two Pseudomonas aeruginosa clinical isolates with different antibiotic susceptibilities

Pseudomonas aeruginosa is a primary cause of opportunistic infections. We have sequenced and annotated the genomes of two P. aeruginosa clinical isolates evidencing different antibiotic susceptibilities. Registered differences in the composition of their accessory genomes may provide clues on P. aeruginosa strategies to thrive in different environments like infection loci.     

Novel lectin-like bacteriocins of biocontrol strain Pseudomonas fluorescens Pf-5

Bacteriocin LlpA, produced by Pseudomonas sp. strain BW11M1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (A. H. A. Parret, G. Schoofs, P. Proost, and R. De Mot, J. Bacteriol. 185:897-908, 2003). Biocontrol strain Pseudomonas fluorescens Pf-5 contains two llpA-like genes, named llpA1(Pf-5) and llpA2(Pf-5). Recombinant Escherichia coli cells expressing llpA1(Pf-5) or llpA2(Pf-5) acquired bacteriocin activity and secreted a 31-kDa protein cross-reacting with LlpA(BW11M1) antibodies. Antibacterial activity of the recombinant proteins was evidenced by gel overlay assays. Analysis of the antimicrobial spectrum indicated that LlpA1(Pf-5) and LlpA2(Pf-5) are able to inhibit P. fluorescens strains, as well as the related mushroom pathogen Pseudomonas tolaasii. LlpA-type bacteriocins are characterized by a domain structure consisting of tandem monocot mannose-binding lectin (MMBL) domains. Molecular phylogeny of these MMBL domains suggests that the individual MMBL domains within an LlpA protein have evolved separately toward a specific, as yet unknown, function or, alternatively, were acquired from different ancestral sources. Our observations are consistent with earlier observations, which hinted that MMBL-like bacteriocins represent a new family of antibacterial proteins, probably with a novel mode of action.     

Draft genome sequences of the diarrheagenic Escherichia coli collection

We report the draft genome sequences of the collection referred to as the Escherichia coli DECA collection, which was assembled to contain representative isolates of the 15 most common diarrheagenic clones in humans (http://shigatox.net/new/). These genomes represent a valuable resource to the community of researchers who examine these enteric pathogens.     

Genome sequences of two plant growth-promoting fluorescent Pseudomonas strains, R62 and R81

Plant growth-promoting rhizobacterial (PGPR) strains R62 and R81 have previously been isolated and characterized as part of the Indo-Swiss Collaboration in Biotechnology. Here we present the draft genome sequences of these two PGPR strains, with the aim of unraveling the mechanisms behind their ability to promote wheat growth.     

Draft Genome Sequence of the Cyanide-Utilizing Bacterium Pseudomonas fluorescens Strain NCIMB 11764

We report here the 6.97-Mb draft genome sequence of Pseudomonas fluorescens strain NCIMB 11764, which is capable of growth on cyanide as the sole nitrogen source. The draft genome sequence allowed the discovery of several genes implicated in enzymatic cyanide turnover and provided additional information contributing to a better understanding of this organism''s unique cyanotrophic ability. This is the first sequenced genome of a cyanide-assimilating bacterium.     

Pseudomonas fluorescens and closely-related fluorescent pseudomonads as biocontrol agents of soil-borne phytopathogens

Many strains of Pseudomonas fluorescens show potential for biological control of phytopathogens especially root pathogens. In taxonomic terms, several of them are indeed P. fluorescens sensu stricto , while others belong in fact to neighbouring species of the ' P. fluorescens ' complex or to ill-defined related species within the fluorescent Pseudomonas spp. These bacteria have become prominent models for rhizosphere ecological studies and analysis of bacterial secondary metabolism, and in recent years knowledge on their plant-beneficial traits has been considerably enhanced by widening the focus beyond the case of phytopathogen-directed antagonism. Current genomic analyses of rhizosphere competence and biocontrol traits will likely lead to the development of novel tools for effective management of indigenous and inoculated P. fluorescens biocontrol agents and a better exploitation of their plant-beneficial properties for sustainable agriculture.     

Identification of differences in genome content among phlD-positive Pseudomonas fluorescens strains by using PCR-based subtractive hybridization

Certain 2,4-diacetylphloroglucinol-producing strains of Pseudomonas fluorescens colonize roots and suppress soilborne diseases more effectively than others from which they are otherwise phenotypically almost indistinguishable. We recovered DNA fragments present in the superior colonizer P. fluorescens Q8r1-96 but not in the less rhizosphere-competent strain Q2-87. Of the open reading frames in 32 independent Q8r1-96-specific clones, 1 was similar to colicin M from Escherichia coli, 3 resembled known regulatory proteins, and 28 had no significant match with sequences of known function. Seven clones hybridized preferentially to DNA from strains with superior rhizosphere competence, and sequences in two others were highly expressed in vitro and in the rhizosphere.     

Endophytic colonization of olive roots by the biocontrol strain Pseudomonas fluorescens PICF7

Confocal microscopy combined with three-dimensional olive root tissue sectioning was used to provide evidence of the endophytic behaviour of Pseudomonas fluorescens PICF7, an effective biocontrol strain against Verticillium wilt of olive. Two derivatives of the green fluorescent protein (GFP), the enhanced green and the red fluorescent proteins, have been used to visualize simultaneously two differently fluorescently tagged populations of P. fluorescens PICF7 within olive root tissues at the single cell level. The time-course of colonization events of olive roots cv. Arbequina by strain PICF7 and the localization of tagged bacteria within olive root tissues are described. First, bacteria rapidly colonized root surfaces and were predominantly found in the differentiation zone. Thereafter, microscopy observations showed that PICF7-tagged populations eventually disappeared from the root surface, and increasingly colonized inner root tissues. Localized and limited endophytic colonization by the introduced bacteria was observed over time. Fluorescent-tagged bacteria were always visualized in the intercellular spaces of the cortex region, and no colonization of the root xylem vessels was detected at any time. To the best of our knowledge, this is the first time this approach has been used to demonstrate endophytism of a biocontrol Pseudomonas spp. strain in a woody host such as olive using a nongnotobiotic system.     

Survival of the rhizosphere-competent biocontrol strain Pseudomonas fluorescens NBRI2650 in the soil and phytosphere

Pseudomonas fluorescens NBRI2650 was isolated after screening 360 bacterial strains from the rhizosphere of chickpea (Cicer arietinum L.) grown in fungal-disease-suppressive field soil. The strain was selected because of its high rhizosphere competence and ability to inhibit the growth of Fusarium oxysporum f.sp. ciceri, Rhizoctonia bataticola, and Pythium sp. under in vitro conditions. Survival and colonization of NBRI2650 in the phytosphere of chickpea, cotton (Gossypium hirsutum L.), cucumber (Cucumis sativus L.), and tomato (Lycopersicon seculentum Mill.) were monitored using a chromosomally located rifampicin-marked mutant P. fluorescens NBRI2650R. The strain showed variable ability to invade and survive in the phytosphere of different plants. Chickpea was used as a tester plant for further work, as it was not invaded by NBRI2650R. The interaction between NBRI2650R and F oxysporum fsp. ciceri was studied by both light microscopy and scanning electron microscopy. The lysis of the fungal cell wall by NBRI2650R was clearly demonstrated. Treatment of the chickpea seeds with NBRI2650R in prerelease experiments in the greenhouse using disease-conducive field soils from Jhansi and Kanpur resulted in increased plant growth and did not result in any perturbation of the indigenous microbial community that inhabited the rhizosphere of chickpea compared with nonbacterized seeds. Direct fermentation of diluted NBRI2650R on vermiculite without the need of expensive fermentors offers a reliable process for manufacturing bacterial inoculants in developing countries. Under field conditions, the horizontal and vertical movement of NBRI2650R was restricted to 30 and 60 cm, respectively, and the strain could not survive in the field during the 7 months before the chickpea could be planted for next cropping season. Field trials conducted at Jhansi, Kanpur, and Pantnagar resulted in higher grain yield increase in the bacteria-treated seed compared with the nonbacterized control. Seed and furrow treatment of the two chickpeas ('Radhey' and 'H-208') at Pantnagar resulted in significantly (P = 0.05) greater seedling mortality in nonbacterized seedlings compared with bacterized ones. The seed dry weight and yield for each variety were also significantly higher in bacterized seedlings than in nonbacterized ones. The population of NBRI2650R persisted throughout the growing season of chickpea in the range of 5.4-6.4 log10 CFU/g root.     

Draft genome sequence of the biocontrol bacterium Chromobacterium sp. strain C-61

Chromobacterium sp. strain C-61 is a plant-associated bacterium with proven capacities to suppress plant diseases. Here, we report the draft genome sequence and automatic annotation of strain C-61. A comparison of this sequence to the sequenced genome of Chromobacterium violaceum ATCC 12472 indicates the novelty of C-61 and a subset of gene functions that may be related to its biocontrol activities.     

Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35

Lactobacillus rhamnosus is a facultative, lactic acid bacterium in the phylum Firmicutes. Lactobacillus spp. are generally considered beneficial, and specific strains of L. rhamnosus are validated probiotics. We describe the draft genomes of three L. rhamnosus strains (L31, L34, and L35) isolated from the feces of Thai breastfed infants, which exhibit anti-inflammatory properties in vitro. The three genomes range between 2.8 – 2.9 Mb, and contain approximately 2,700 protein coding genes.     

Inactivation of Salmonella serovars by Pseudomonas chlororaphis and Pseudomonas fluorescens strains on tomatoes

Salmonella enterica and its serovars have been associated with pathogen contamination of tomatoes with numerous outbreaks of salmonellosis. To improve food safety, pathogen control is of immediate concern. The aim of this research was to assess the populations of natural microflora (aerobic mesophilic bacteria, lactic acid bacteria, yeasts and moulds and Pseudomonas species) on tomatoes, and evaluate the efficacy of Pseudomonas fluorescens (Pf) and Pseudomonas chlororaphis (Pc) for inactivation of Salmonella on tomatoes. Microflora were determined on sanitised and unsanitised produce and enumerated on Plate Count Agar, de Man, Rogosa and Sharpe medium, Potato Dextrose Agar and Pseudomonas Agar F media. The efficacy of Pc and Pf for inactivation of S. enterica serovars Montevideo, Typhimurium and Poona was determined on spot-inoculated tomato stem scars. The effects of storage time on bacterial populations were also investigated. On unsanitised tomatoes, lactic acid bacteria, Pseudomonas sp., aerobic mesophilic bacteria and yeasts and moulds ranged from 3.31–4.84, 3.93–4.77, 4.09–4.80 and 3.83–4.67 log CFU/g of produce, respectively. The microflora were similar at 0 and 24 storage hours on sanitised produce. The suppression of Salmonella Montevideo by P. chlororaphis and P. fluorescens on tomatoes ranged from 0.51 to 2.00 log CFU/g of produce. On Salmonella Montevideo and S. Typhimurium, the suppressive effects ranged from 0.51 to 0.95 and 0.46 to 2.00 log CFU/g of produce, respectively. The pathogen suppressive effects may be attributed to competition ability of Pseudomonas relative to Salmonella strains. Pseudomonas strains may be effective against Salmonella strains as a post-harvest application, but strain synergy is required to optimise pathogen reductions.