In situ monitoring of biofilm formations ofEscherichia coli andPseudomonas putida by use of lux and GFP reporters

A plasmid vector containing two reporter genes,mer-lux andlac-GFP, was transformed to bothEscherichia coli andPseudomonas putida. Their cellular activities and biofilm characteristics were investigated in flow-cell units by measuring bioluminescent lights and fluorescent levels of GFP. Bioluminescence was effective to monitor temporal cell activities, whereas fluorescent level of GFP was useful to indicate the overall cell activities during biofilm development. The light production rates ofE. coli andP. putida cultures were dependent upon concentrations of HgCl₂. Mercury molecules entrapped inP. putida biofilms were hardly washed out in comparison with those inE. coli biofilms, indicating thatP. putida biofilms may have higher affinity to mercury molecules thanE. coli biofilms. It was observed thatP. putida expressed GFP cDNA in biofilms but not in liquid cultures. This may indicate that the genetic mechanisms ofP. putida were favorably altered in biofilm conditions to make a foreign gene expression possible.     

Choice of microbial host for the naphthalene dioxygenase bioconversion

The use of whole cell biotransformations for single and multistep enzyme conversions is gaining widespread application. In this study the naphthalene dioxygenasenah A gene was transferred intoPseudomonas aeruginosa PAC 1R,Escherichia coli JM107 andPseudomonas putida PpG 277. The effect of ethanol on these genetically engineered Gram-negative bacteria was studied by measurement of enzyme activity, stability and cell integrity. Ethanol has been used in biotransformations as a co-substrate carbon source for co-factor recycling and as a co-solvent increasing dissolved substrate and product levels. Ethanol increased the dissolved substrate (naphthalene) concentration slightly and dissolved product ((+)-cis-(1R, 2S)-dihydroxy-1,2-dihydronaphthalene) by approximately 30% at 4% (w/v) ethanol. BothP. aeruginosa PAC 1R andP. putida PpG 277 showed decreased activity with increasing ethanol concentration whilstE. coli enzyme activity increased with increasing ethanol concentration being comparable to that when glucose was used as a carbon source. This project highlighted the many factors involved in the selection of microbial hosts for whole cell biotransformation processes.     

Use of haloacetate dehalogenase genes as selection markers forEscherichia coli andPseudomonas vectors

The haloacetate dehalogenase gene,dehH2, cloned fromMoraxella sp. strain B could be used as a selection marker gene for vectors inEscherichia coli andPseudomonas putida. Haloacetates, especially iodoacetate, inhibit the growth of some microorganisms. ThedehH2 gene introduced into the cells conferred iodoacetate resistance on them. Therefore,E. coli andP. putida transformed with vectors marked withdehH2 could be easily selected on plates containing iodoacetate.     

Cytosine deaminase that hydrolyzes creatinine to N-methylhydantoin in various cytosine deaminase-forming microorganisms

Creatinine deimination has been newly detected in the following various cytosine deaminase-forming microorganisms: Escherichia coli, Proteus mirabilis, Pseudomonas aureofaciens, Pseudomonas chlororaphis and Pseudomonas cruciviae. All these microorganisms, except for E. coli, formed cytosine deaminase in a constitutive or repressive way. P. putida 77 and E. coli showed highly increased formation of creatinine deiminase in the presence of creatinine and cytosine. Throughout serial DEAE-Sephacel and Sephacryl S-300 column chromatographies, the cytosine deaminases of these microorganisms, except for that of P. ovalis, were found to hydrolyze both creatinine and cytosine at comparable rates. No concrete evidence was obtained for the presence of any other protein that hydrolyzed creatine and/or cytosine than the cytosine deaminases in the three test microorganisms randomly selected for investigation.Different from P. putida 77, none of the test microorganisms degraded N-methylhydantoin; neither N-methylhydantoin amidohydrolase nor N-carbamoylsarcosine amidohydrolase was formed in the presence of creatinine in these microorganisms. As a result, the wide occurrence of cytosine deaminases in microorganisms was found to be related to the wide distribution of those microorganisms which hydrolyze creatinine to N-methylhydantoin without further degradation.     

Impacts of gene bioaugmentation with pJP4-harboring bacteria of 2,4-D-contaminated soil slurry on the indigenous microbial community

Gene bioaugmentation is a bioremediation strategy that enhances biodegradative potential via dissemination of degradative genes from introduced microorganisms to indigenous microorganisms. Bioremediation experiments using 2,4-dichlorophenoxyacetic acid (2,4-D)-contaminated soil slurry and strains of Pseudomonas putida or Escherichia coli harboring a self-transmissible 2,4-D degradative plasmid pJP4 were conducted in microcosms to assess possible effects of gene bioaugmentation on the overall microbial community structure and ecological functions (carbon source utilization and nitrogen transformation potentials). Although exogenous bacteria decreased rapidly, 2,4-D degradation was stimulated in bioaugmented microcosms, possibly because of the occurrence of transconjugants by the transfer of pJP4. Terminal restriction fragment length polymorphism analysis revealed that, although the bacterial community structure was disturbed immediately after introducing exogenous bacteria to the inoculated microcosms, it gradually approached that of the uninoculated microcosms. Biolog assay, nitrate reduction assay, and monitoring of the amoA gene of ammonia-oxidizing bacteria and nirK and nirS genes of denitrifying bacteria showed no irretrievable depressive effects of gene bioaugmentation on the carbon source utilization and nitrogen transformation potentials. These results may suggest that gene bioaugmentation with P. putida and E. coli strains harboring pJP4 is effective for the degradation of 2,4-D in soil without large impacts on the indigenous microbial community.     

Thiosulfate oxidation by obligately heterotrophic bacteria

Thiosulfate was oxidized stoichiometrically to tetrathionate during growth on glucose byKlebsiella aerogenes, Bacillus globigii, B. megaterium, Pseudomonas putida, two strains each ofP. fluorescens andP. aeruginosa, and anAeromonas sp. A gram-negative, rod-shaped soil isolate, Pseudomonad H_w, converted thiosulfate to tetrathionate during growth on acetate. None of the organisms could use thiosulfate as sole energy source. The quantitative recovery of all the thiosulfate supplied to heterotrophic cultures either as tetrathionate alone or as tetrathionate and unused thiosulfate demonstrated that no oxidation to sulfate occurred with any of the strains tested. Two strains ofEscherichia coli did not oxidize thiosulfate. Thiosulfate oxidation in batch culture occurred at different stages of the growth cycle for different organisms:P. putida oxidized thiosulfate during lag and early exponential phase,K. aerogenes oxidized thiosulfate at all stages of growth, andB. megaterium andAeromonas oxidized thiosulfate during late exponential phase. The relative rates of oxidation byP. putida andK. aerogenes were apparently determined by different concentrations of thiosulfate oxidizing enzyme. Thiosulfate oxidation byP. aeruginosa grown in chemostat culture was inducible, since organisms pregrown on thiosulfate-containing media oxidized thiosulfate, but those pregrown on glucose only could not oxidize thiosulfate. Steady state growth yield ofP. aeruginosa in glucose-limited chemostat culture increased about 23% in the presence of 5–22 mM thiosulfate, with complete or partial concomitant oxidation to tetrathionate. The reasons for this stimulation are unclear. The results suggest that heterotrophic oxidation of thiosulfate to tetrathionate is widespread across several genera and may even stimulate bacterial growth in some organisms.     

Degradation of trichloroethylene by a growth-arrestedPseudomonas putida

A toluene-oxidizing strain ofPseudomonas mendocina KR1 containing toluene-4-mono-oxygenase (TMO) completely degrades TCE with the addition of toluene as a co-substrate in aerobic condition. In order to constructin situ bioremediation system for TCE degradation without any growth-stimulating nutrients or toxic inducers such as toluene, we used the carbon-starvation promoter ofPseudomonas putida MK1 (Kim, Y.et al., J. bacteriol., 1995). Upon entry into the stationary phase due to the deprivation of nutrients, this promoter is strongly induced without further cell growth. The TMO gene cluster (4.5 kb) was spliced downstream of the carbon starvation promoter ofPseudomona putida MK1, already cloned in pUC19. TMO under the carbon starvation promoter was not expressed inE. coli cells either in stationary phase or exponential phase. For TMO expression inPseudomonas strains,tmo and carbon starvation promoter region were recloned into a modified broad-host range vector pMMB67HES which was made from pMMB67HE (8.9 kb) by deletion oftac promoter andlacI ^q (about 1.5 kb). Indigo was produced by TMO under the carbon starvation promoter in aPseudomonas strain of post-exponential phase on M9 (0.2% glucose and 1mM indole) or LB. 18% of TCE was degraded in 14 hours after entering the stationary phase at the initial concentration of 6.6μ M in liquid phase.     

The mechanism of action of hexahydro-1,3,5-triethyl-s-triazine

Summary The mechanism of antimicrobial action of hexahydro-1,3,5-triethyl-s-triazine (HHTT) was studied using the HHTT-resistant isolate,Pseudomonas putida 3-T-15², its HHTT-sensitive, novobiocin-cured derivative,P. putida 3-T-15² 11:21,P. putida ATCC 12633,Pseudomonas aeruginosa PA01 andEscherichia coli J53 (RP4). HHTT was oxidized byP. putida 3-T-15², while respiration ofP. putida 3-T-15² 11:21 was inhibited by HHTT. Chemical assays showed that HHTT released formaldehyde.P. putida 3-T-15² was highly resistant to formaldehyde, whileP. putida 3-T-15² 11:21 was highly sensitive to formaldehyde. Both HHTT and formaldehyde acted similarly to inhibit proline uptake in bacterial cells and to inhibit the synthesis of the inducible enzymes, -galactosidase and glucose-6-phosphate dehydrogenase. HHTT did not have uncoupler-like activity.P. putida 3-T-15² used either HHTT or ethylamine, a component of HHTT, as a nitrogen source for growth, but neither HHTT, ethylamine or formaldehyde served as a carbon and energy source for growth. We concluded that a major mechanism of antimicrobial action of HHTT was through its degradation product, formaldehyde.     

Effect of aeration on ethylene production by soil bacteria and soil samples cultivated in a closed system

Summary Ethylene production was studied in shaken cultures ofPseudomonas putida andPseudomonas fluorescens isolated from soil and in unsterile garden soil samples moistened to 60% of the water holding capacity. The highest ethylene accumulation in bacterial cultures was reached under conditions of delayed aeration,i.e. when the culture was closed and the aeration started after the oxygen content decreased to 4%. The ethylene production rose immediately after the beginning of aeration. Under these conditions ethylene production was inP. fluorescens 2–3 times and in glucosecultivatedP. putida 6 times higher than in the fully aerated cultures. Methionine stimulated ethylene production byP. fluorescens, whereas glucose proved to be more suitable forP. putida. This strain was incapable of growth on methionine as the sole carbon source. Samples of nonsterile garden soil produced the highest amounts of ethylene under anaerobic conditions. Artificial inoculation of soil samples byP. putida resulted in an increase of ethylene formation in samples with delayed aeration. Addition of glucose or glucose with methionine stimulated ethylene production in all soil samples.     

Chemotaxis of free-living nitrogen-fixing bacteria towards maize mucilage

Summary A method for collecting sterile mucilage from maize root tips growing in sterile conditions has been devised.Enterobacter andAzospirillum strains were isolated from the rhizosphere of maize and rice using the spermosphere model method. To evaluate chemotaxis of these strains, a modification of Adler's microcapillary method was used. Under these conditions, the number of attracted bacteria was proportional to the concentration of mucilage. When comparing the chemotaxis ofA. lipoferum andE. cloacae from the rhizosphere of maize and from the rhizosphere of rice, it appeared that the strains isolated from maize were strongly attracted by maize mucilage whereas strains isolated from rice were not more attracted than the control (E. coli K12). Thus, bacteria of the same species are not equivalent in their chemotactic behaviour. This could imply that some degree of specificity exists in the establishment of plant-bacteria associations.     

Engineering sucrose metabolism in Pseudomonas putida highlights the importance of porins

Using agricultural wastes as a substrate for biotechnological processes is of great interest in industrial biotechnology. A prerequisite for using these wastes is the ability of the industrially relevant microorganisms to metabolize the sugars present therein. Therefore, many metabolic engineering approaches are directed towards widening the substrate spectrum of the workhorses of industrial biotechnology like Escherichia coli, yeast or Pseudomonas putida. For instance, neither xylose or arabinose from cellulosic residues, nor sucrose, the main sugar in waste molasses, can be metabolized by most E. coli and P. putida wild types. We evaluated a new, so far uncharacterized gene cluster for sucrose metabolism from Pseudomonas protegens Pf-5 and showed that it enables P. putida to grow on sucrose as the sole carbon and energy source. Even when integrated into the genome of P. putida, the resulting strain grew on sucrose at rates similar to the rate of the wild type on glucose – making it the fastest growing, plasmid-free P. putida strain known so far using sucrose as substrate. Next, we elucidated the role of the porin, an orthologue of the sucrose porin ScrY, in the gene cluster and found that in P. putida, a porin is needed for sucrose transport across the outer membrane. Consequently, native porins were not sufficient to allow unlimited growth on sucrose. Therefore, we concluded that the outer membrane can be a considerable barrier for substrate transport, depending on strain, genotype and culture conditions, all of which should be taken into account in metabolic engineering approaches. We additionally showed the potential of the engineered P. putida strains by growing them on molasses with efficiencies twice as high as obtained with the wild-type P. putida. This can be seen as a further step towards the production of low-value chemicals and biofuels with P. putida from alternative and more affordable substrates in the future.     

Differential Rhizosphere Establishment and Cyanide Production by Alginate-Formulated Weed-Deleterious Rhizobacteria

The effects of Pseudomonas putida ATH2-1RI/9 and Acidovorax delafieldii ATH2-2RS/1 on rhizosphere colonization, cyanide production, and growth of velvetleaf and corn was examined. When formulated in alginate beads and inoculated onto velvetleaf and corn plants (10⁹ CFU/plant), only P. putida ATH2-1RI/9 consistently reduced velvetleaf growth. Neither isolate inhibited corn growth. Interestingly the levels of P. putida ATH2-1RI/9 in the velvetleaf rhizosphere were 1000-fold higher (7 × 10⁷ CFU/g root) than the A. delafieldii ATH2-2RS/1 populations. Cyanide (53–68 mM/g root) was recovered from the P. putida ATH2-1RI/9-inoculated velvetleaf plants. In contrast both A. delafieldii ATH2-2RS/1 and P. putida ATH2-1RI/9 colonized the corn rhizosphere to the same extent (1–5 × 10⁷ CFU/g root), producing 1 mM and 14 mM/g root respectively. These results suggest that bacterial formulation methods can influence the effectiveness of deleterious rhizobacteria in reducing weed growth.     

The acetoin assimilation pathway of Pseudomonas putida KT2440 is regulated by overlapping global regulatory elements that respond to nutritional cues

Many microorganisms produce and excrete acetoin (3-hydroxy-2-butanone) when growing in environments that contain glucose or other fermentable carbon sources. This excreted compound can then be assimilated by other bacterial species such as pseudomonads. This work shows that acetoin is not a preferred carbon source of Pseudomonas putida, and that the induction of genes required for its assimilation is down-modulated by different, independent, global regulatory systems when succinate, glucose or components of the LB medium are also present. The expression of the acetoin degradation genes was found to rely on the RpoN alternative sigma factor and to be modulated by the Crc/Hfq, Cyo and PTS^Ntr regulatory elements, with the impact of the latter three varying according to the carbon source present in addition to acetoin. Pyruvate, a poor carbon source for P. putida, did not repress acetoin assimilation. Indeed, the presence of acetoin significantly improved growth on pyruvate, revealing these compounds to have a synergistic effect. This would provide a clear competitive advantage to P. putida when growing in environments in which all the preferred carbon sources have been depleted and pyruvate and acetoin remain as leftovers from the fermentation of sugars by other microorganisms.     

Characterization of type II protein secretion (xcp) genes in the plant growth-stimulatingPseudomonas putida, strain WCS358

InPseudomonas aeruginosa, the products of thexcp genes are required for the secretion of exoproteins across the outer membrane. Despite structural conservation of the Xcp components, secretion of exoproteins via the Xcp pathway is generally not found in heterologous organisms. To study the specificity of this protein secretion pathway, thexcp genes of another fluorescent pseudomonad, the plant growth-promotingPseudomonas putida strain WCS358, were cloned and characterized. Nucleotide sequence analysis revealed the presence of at least five genes, i.e.,xcpP, Q, R, S, andT, with homology toxcp genes ofP. aeruginosa. Unlike the genetic organization inP. aeruginosa, where thexcp cluster consists of two divergently transcribed operons, thexcp genes inP. putida are all oriented in the same direction, and probably comprise a single operon. Upstream ofxcpP inP. putida, an additional open reading frame, with no homolog inP. aeruginosa, was identified, which possibly encodes a lipoprotein. Mutational inactivation ofxcp genes inP. putida did not affect secretion, indicating that no proteins are secreted via the Xcp system under the growth conditions tested, and that an alternative secretion system is operative. To obtain some insight into the secretory pathway involved, the amino acid sequence of the N-terminus of the major extracellular protein was determined. The protein could be identified as flagellin. Mutations in thexcpQ andR genes ofP. aeruginosa could not be complemented by introduction of the correspondingxcp genes ofP. putida. However, expression of a hybrid XcpR protein, composed of the N-terminal one-third ofP. aeruginosa XcpR and the C-terminal two-thirds ofP. putida XcpR, did restore protein secretion in aP. aeruginosa xcpR mutant.     

Effects of Pseudomonas putida modified to produce phenazine-1-carboxylic acid and 2,4-diacetylphloroglucinol on the microflora of field grown wheat

Pseudomonas putida WCS358r, genetically modified to have improved activity against soil-borne pathogens, was released into the rhizosphere of wheat. Two genetically modified derivatives carried the phzor the phl biosynthetic gene loci and constitutively produced either the antifungal compound phenazine-1-carboxylic acid (PCA) or the antifungal and antibacterial compound 2,4-diacetylphloroglucinol (DAPG). In 1997 and 1998, effects of single introductions of PCA producing derivatives on the indigenous microflora were studied. A transient shift in the composition of the total fungal microflora, determined by amplified ribosomal DNA restiction analysis (ARDRA), was detected. Starting in 1999, effects of repeated introduction of genetically modified microorganisms (GMMs) were studied. Wheat seeds coated with the PCA producer, the DAPG producer, a mixture of the PCA and DAPG producers, or WCS358r, were sown and the densities, composition and activities of the rhizosphere microbial populations were measured. All introduced strains decreased from 10⁷CFU per gram of rhizosphere sample to below the detection limit after harvest of the wheat plants. The phz genes were stably maintained in the PCA producers, and PCA was detected in rhizosphere extracts of plants treated with this strain or with the mixture of the PCA and DAPG producers. The phl genes were also stably maintained in the DAPG producing derivative of WCS358r. Effects of the genetically modified bacteria on the rhizosphere fungi and bacteria were analyzed by using amplified ribosomal DNA restriction analysis. Introduction of the genetically modified bacterial strains caused a transient change in the composition of the rhizosphere microflora. However, introduction of the GMMs did not affect the several soil microbial activities that were investigated in this study. This revised version was published online in August 2006 with corrections to the Cover Date.     

Inoculation of potatoes with microorganisms under field conditions

The effect of inoculation of potatoes with isolates ofPseudomonas putida andTrichoderma sp. suspension and in preparations with kaolin and peat carriers on growth of potatoes, yields and physiological proporties of tubers was investigated on seven locations of the potato-rye and sugar-beet regions. In 57.5% of experiments increased yields could be detected. More favorable results were obtained in the sugar-beet region and on commercially utilized fields when using suspensions of the isolates. Variability of the results can be partially explained by soil-climatic factors affecting colonization of the rhizosphere by the microorganisms and their effect on the environment. Physiological properties and the quality of the harvested tubers were comparable with those of the control. The results are discussed from the point of view of a possible inoculation of potatoes with rhizobacteria and, in the presence ofTrichoderma sp., improvement of their growth and yields.     

Effects of a clay mineral on microbial predation and parasitism ofEscherichia coli

Montmorillonitic clay influences the biological control ofEscherichia coli in aquatic systems, the magnitude of the effects being dependent on the state of the clay and the type of host-antagonist interaction. The interaction ofBdellovibrio andE. coli was partially inhibited by the presence of montmorillonite. Because it is highly motile,Bdellovibrio apparently could penetrate any colloidal clay barrier aroundE. coli if the clay envelope was thin enough. Colloidal clay had little effect on predation ofE. coli by the myxobacteriumPolyangium, and had no effect on the activity of the amoebaVexillifera. Crude clay, on the other hand, resulted in a physical separation of predator and prey, and this completely inhibited theE. coli-Polyangium interaction and slowed the rate of engulfment ofE. coli byVexillifera.The interference of natural biological control by clays may alter the microbial balance favoring survival of fecal microorganisms and resulting in their accumulation in saline sediments. This could constitute a health hazard if these organisms were released by upwelling of bottom waters or were desorbed in estuarine systems by dilution during heavy rains.     

Poly(3-hydroxyalkanoate) polymerase synthesis and in vitro activity in recombinant Escherichia coli and Pseudomonas putida

We tested the synthesis and in vitro activity of the poly(3-hydroxyalkanoate) (PHA) polymerase 1 from Pseudomonas putida GPo1 in both P. putida GPp104 and Escherichia coli JMU193. The polymerase encoding gene phaC1 was expressed using the inducible PalkB promoter. It was found that the production of polymerase could be modulated over a wide range of protein levels by varying inducer concentrations. The optimal inducer dicyclopropylketone concentrations for PHA production were at 0.03% (v/v) for P. putida and 0.005% (v/v) for E. coli. Under these concentrations the maximal polymerase level synthesized in the E. coli host (6% of total protein) was about three- to fourfold less than that in P. putida (20%), whereas the maximal level of PHA synthesized in the E. coli host (8% of total cell dry weight) was about fourfold less than that in P. putida (30%). In P. putida, the highest specific activity of polymerase was found in the mid-exponential growth phase with a maximum of 40 U/g polymerase, whereas in E. coli, the maximal specific polymerase activity was found in the early stationary growth phase (2 U/g polymerase). Our results suggest that optimal functioning of the PHA polymerase requires factors or a molecular environment that is available in P. putida but not in E. coli.     

Application of biotinylated and32P probes for detection of P-fimbriae in urinaryE. coli

Escherichia coli is the common causative agent of urinary tract infections. Twenty-six strains ofEscherichia coli were isolated from children with pyelonephritis, symptomatic urinary tract infections and asymptomatic bacteriuria. Biotinylated and³²P-DNA probes were prepared for detection of P-fimbriae in the isolates. Of the 13 strains isolated from patients with pyelonephritis 11 were positive for the presence of the P gene by both probes. Strains isolated from cases of symptomatic urinary tract infections revealed the presence of P gene only in three samples of the total of nine isolated. None of the isolatedE. coli strains from asymptomatic bacteriuria was found positive for the presence of the P gene. The biotynylated probe was simple and easily applicable in standard laboratory conditions and therefore the authors recommend it for use in diagnostic laboratories.