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Biochemistry, Genetics and Molecular Biology » "Microbiology in Agriculture and Human Health", book edited by Mohammad Manjur Shah , ISBN 978-953-51-2144-2, Published: July 16, 2015 under CC BY 3.0 license. © The Author(s).

Chapter 5

An Insight Into Beneficial Pseudomonas bacteria

By Galina Novik, Victoria Savich and Elena Kiseleva
DOI: 10.5772/60502

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An Insight Into Beneficial Pseudomonas bacteria

Galina Novik1, Victoria Savich1 and Elena Kiseleva1

1. Introduction

Pseudomonas is one of the most studied species of bacteria. They were first identified at the end of 19th century by Migula as Gram-negative, rod-shaped and polar-flagellated bacteria. Since that time description of genus Pseudomonas has widened; development of new methods allowed to study in detail the morphology and physiology of these bacteria. However, the morphological characteristics of Pseudomonas are common to many bacterial genera and so are of little value in the positive identification of members of the genus. Advanced nucleic acid-based methods allow to differentiate it from other similar genera and reveal taxonomic relationships among various bacterial species including Pseudomonas.

Genus Pseudomonas is represented by species that occupy a wide range of niches owing to metabolic and physiological diversity. This diversity allows pseudomonads to adapt to challenging environment, resist to adverse conditions caused by abiotic and biotic factors such as high and low temperature, moisture, oxygen and nutrients availability, antibiotics, etc. Elevated resistance provides for ubiquitous distribution of Pseudomonas in soil and water, as well as plant growth-promoting rhizobacteria (PGPR), animal and plant pathogens. The bacterium is capable of utilizing a broad spectrum of organic compounds as sources of carbon and energy, hence it is able to colonize habitats where nutrients are limited.

Diversity of Pseudomonas determines vast research interest in this genus. Some species like P. aeruginosa are opportunistic human pathogens showing enhanced antibiotic resistance, so that studies of pathogenic strains are centered on mechanisms of this antibiotic resistance. Other species are able to degrade a number of compounds that are toxic or recalcitrant to other bacterial species, or produce a wide range of secondary metabolites and biopolymers. It makes these strains perspective for industrial applications.

2. Morphology and physiology of Pseudomonas bacteria

Pseudomonas are Gram-negative, aerobic, motile by one or several polar flagella, non-spore-forming straight or slightly curved rods. In addition to the polar flagella, some species (P. stutzeri, P. mendocina) have shorter lateral flagella. Solid media favor the formation of lateral flagella which are closely related with swarming of cells on solid surfaces [1]. The number of flagella has taxonomic importance. Most P. aeruginosa cells carry only one flagellum, although some cells hold two or three flagella. P. alcaligenes, P. mendocina, P. pseudoalcaligenes, and P. stutzeri are also characterized by a single flagellum. The majority of species possess more than one flagella [2].

Some Pseudomonas species also form pili (P. aeruginosa, P. alcaligenes, P. syringae). Type IV pili of P. aeruginosa similar to pili of other pathogenic bacteria are involved in cell adhesion to epithelial cells [3, 4]. Pili are essential for the normal development of P. aeruginosa biofilms, and they also function as receptors for bacteriophage binding [5-7]. The adhesive region is located at the tip of the pilus. Pili of phytopathogenic P. syringae serve as a conduit for the long-distance translocation of effector proteins in plant cells [8].

Bacterial cells don’t produce prosthecae and aren’t surrounded by sheaths, but they can form biofilms that provide attachment of cells to the substrate and increase stability under adverse conditions [9].

Another important Pseudomonas feature is production of variety of pigments. Character of pigmentation remains significant factor among the diagnostic traits of Pseudomonas. Pigments may be soluble in water and diffusible into the medium or may be associated with the cells. Pseudomonads can produce diffusible pigments that fluoresce in short wavelength (254 nm) ultraviolet light. Some of these pigments, like yellow-green pyoverdine (fluorescein), are siderophores that play an important physiological role in satisfying the iron requirement. The synthesis of pyoverdine is strongly related to iron starvation. It can be demonstrated by cultivating the bacteria in media such as King’s medium B. Pyoverdine binds iron (III) ions very tightly, and that ferripyoverdine complex is actively transported into the bacterial cell [10, 11]. Pyoverdine from P. aeruginosa is essential for virulence in animal models [12]. Pyoverdine also can be a tool for identification of Pseudomonas because each genomic group is characterized by a specific pyoverdine [13]. Other pigments produced by species of Pseudomonas include pyocyanin (P. aeruginosa, blue color), pyorubin (P. aeruginosa, red color), chlororaphin (P. chlororaphis, green color), pyomelanin (P. aeruginosa, brown/black color). P. mendocina is able to produce carotenoid pigment [14, 15].

Pseudomonas are aerobic bacteria, but in some cases they can use nitrate as alternate electron acceptor and carry out denitrification (P. aeruginosa, P. stutzeri, and some P. fluorescens biovars), reducing nitrate to N2O or N2. Additionally, P. chloritidismutans can utilize chlorate (ClO3) as an alternative energy-yielding electron acceptor [16].

Pseudomonas tends to utilize organic acids in preference to more complex organic compounds. It represses many inducible peripheral catabolic enzymes. Most of Pseudomonas species have incomplete glycolytic pathways, lacking 6-phosphofructokinase, therefore sugars and organic acids are dissimilated prevalently via the Entner-Doudoroff pathway. Representatives of the genus can utilize common monosaccharides (glucose, fructose, galactose, l-arabinose), but growth of some species (P. stutzeri, P. mendocina, P. syringae) may be slow. Most hexoses and related compounds are also degraded by the Entner-Doudoroff pathway and various peripheral pathways [2, 14, 17].

Strains of Pseudomonas can grow in minimal media with ammonium ions or nitrate as nitrogen source and a single organic compound as the sole carbon and energy source, not requiring organic growth factors. Some species like strains of phytopathogenic P. syringae grow very slowly in comparison with strains of the saprophytic species, but their growth can be enhanced by addition of small amounts of complex organic materials (yeast extract, peptones). Significant systematic feature of Pseudomonas is inability to accumulate polyhydroxybutyrate, but polyhydroxyalkanoates of monomer lengths higher than C4 may be accumulated when growing on alkanes or gluconate. Optimal temperature for growth is approximately 28ºC, although some species can grow at 4ºC or 41ºC. Most species can’t tolerate acid conditions (pH 4.5 or lower) [14].

Members of the genus Pseudomonas are known for their degrading ability on a whole range of substrates, like hydrocarbons, aromatic compounds, and their derivatives. Some of these compounds are natural (toluene, styrene, naphthalene, phenol), other compounds are final products or intermediates from industrial activities (polychlorobiphenyls, dioxins, nitrotoluenes). A considerable number of these compounds is toxic to microorganisms of other groups and to higher organisms. Research revealed 11 central pathways to which many different peripheral pathways converge. Peripheral pathways transform substrates into a few central intermediates (usually dihydroxybenzenes or dihydroxyaromatic acids), which are then ring-cleaved and converted to tricarboxylic acid (TCA) cycle intermediates through the corresponding central pathways. P. putida contains 9 out of the 11 identified central pathways, which is in agreement with the wide range of niches that this species can colonize. The ability to degrade aromatic compounds is a strain-specific feature, therefore several pathways that are found in some strains are missing in other strains of the same species [18].

The β-ketoadipate pathway is the most widespread Pseudomonas pathway of the degradation of aromatic compounds. It includes ortho-cleavage protocatechuate (pca genes) and catechol (cat genes) branches. Both cat and pca branches are usually present in most organisms, but the cat branch is absent in the three available genomes of P. syringae. Quinate, p-hydroxybenzoate, and phenylpropenoids (p-coumarate, caffeate, cinnamate, ferulate, etc.) are degraded via the intermediate protocatechuate. Protocatechuate is cleaved by 3,4-dioxygenase to carboxy-cis,cis-muconate that is converted to β-ketoadipate enol-lactone by PcaC and PcaD enzymes. The pca genes are gathered in a single cluster in P. fluorescens, but they are organized in different clusters in other Pseudomonas strains [19]. Benzoate, tryptophan, aniline, salicylate, naphthalene, biphenyl, phenol, benzene, toluene, 4-nitrotoluene, and nitrobenzene are degraded via catechol. Benzoate is an intermediate in the catabolism of several aromatic compounds. Its degradation to catechol involves the benABCD genes which were identified in the Pseudomonas genomes carrying cat genes. Cat genes encode enzymes involved in catechol ortho-cleavage. CatA, catB, and catC encode catechol 1,2-dioxygenase, cis,cis–muconate cycloisomerase, and muconolactone isomerase, respectively. The ben and cat genes are located together in the genomes of P. fluorescens, P. aeruginosa, P. stutzeri, and P. entomophila. Reverse situation is observed in most P. putida strains.

Genus Pseudomonas also displays other metabolic pathways for aromatic compounds: phenylacetyl-CoA (phenylethylamine, phenylethanol, styrene, tropate), homogentisate (phenylalanine, tyrosine), gentisate (salicylate, 3-hydroxybenzoate, m-cresol), homoprotocatechuate (4-hydroxyphenylacetate), nicotinate (nicotinic acid), etc [18].

3. Taxonomy and identification of Pseudomonas bacteria

The genus Pseudomonas belongs to phylum Proteobacteria, class Gammaproteobacteria, order Pseudomonadales, family Pseudomonadaceae with type species P. aeruginosa. At present the genus includes about 216 species with 18 subspecies and the number of species constantly increases [20].

The identification of Pseudomonas is a necessary step preceding further use of these bacteria because of pathogenicity of some strains to plants and animals, including humans, and its wide metabolic diversity. Since the discovery of Pseudomonas, a large number of species was assigned to the genus. First classification of Pseudomonas species was based on phenotypic characteristics. The most significant work providing phenotypic description of this genus was performed by Stanier et al. Strains of different species were subjected to many phenotypic tests, the most important of which was the nutritional screening [21].

In the 1960s studies on nucleic acid similarity have been started. DNA–DNA hybridization (DDH) has shown high degree of genomic heterogeneity among the species assigned to the genus [14, 22]. DDH is a universal technique that could offer truly genome-wide comparisons between organisms, but it demands large quantities of high-quality DNA (in comparison with PCR-based techniques). It makes DDH time-consuming and labour-intensive [23].

Evidence of the high level of conservatism among ribosomal RNA molecules [24, 25] allowed to divide this genus into five rRNA groups using rRNA–DNA hybridization [26]. Only rRNA group I that included the type species P. aeruginosa, all the fluorescent (P. fluorescens, P. putida, P. syringae), and some non-fluorescent species (P. stutzeri, P. alcaligenes, P. pseudoalcaligenes, P. mendocina) reserved the name Pseudomonas. Later the residuary rRNA groups were affiliated to other genera. The species of rRNA group II were transferred to the genera Burkholderia and Ralstonia, the species of rRNA group III were transferred to the genera Acidovorax, Comamonas, and Hydrogenophaga, the species of rRNA group IV and group V were transferred to the genera Brevundimonas and Stenotrophomonas, respectively [27-33].

Sequential development of molecular methods has emphasized the role of 16S rRNA in the identification and classification of bacteria, including Pseudomonas. Reasons that allow wide use of 16S rRNA for taxonomic studies include: presence in almost all bacteria, often existing as a multigene family, or operons; the function of the 16S rRNA gene over time has not changed, suggesting that random sequence changes are a more accurate measure of time (evolution); the 16S rRNA gene (1500 bp) is large enough for informatics purposes [34]. 23S rRNA is excessively conserved and 5S rRNA is too small for research.

As a result of 16S rRNA sequencing by Moore et al., the genus Pseudomonas was grouped into 2 distinct intrageneric divisions. These divisions are designated the "P. aeruginosa intrageneric cluster" and the "P. fluorescens intrageneric cluster" including four (P. aeruginosa, P. resinovorans, P. mendocina, P. flavescens) and five (P. fluorescens, P. syringae, P. cichorii, P. putida, P. agarici) lineages, respectively. Sequence similarities between the species ranged from 93.3% (between P. cichorii and P. cirtonellolis) to 99.9% (between P. oloevorans and P. pseudoalcaligenes). It was observed that 148 positions of 16S rRNA were variable among 1492 nucleotide positions, and 65 positions of these nucleotides were located within three hypervariable regions. Approximately 44% of the total gene sequence variability of Pseudomonas species occurs in 6% of the 16S rRNA sequence. Regions other than the variable regions are crucial for ribosome functions [35]. In the research of Anzai et al. genus Pseudomonas was divided into two clusters using 16S rRNA sequencing. Six groups were defined within the first cluster: P. syringae, P. chlororaphis, P. fluorescens, P. stutzeri, P. aeruginosa, and P. putida groups. P. agarici and P. asplenii belong to first cluster, but they were not included into any group. The second cluster contained only P. pertucinogena group [36].

Although 16S rRNA gene sequencing is useful for classification and identification, it has some resolution problems at the genus and species level. These problematic groups include the family Enterobacteriaceae (in particular, Enterobacter and Pantoea), the Acinetobacter baumannii-A. calcoaceticus complex, genera Achromobacter, Stenotrophomonas, Actinomyces, and some species such as Bacillus anthracis, Bacillus cereus, Bacillus globisporus, Bacillus psychrophilus, Burkholderia cocovenenans, Burkholderia gladioli, Burkholderia pseudomallei, Burkholderia thailandensis, Neisseria cinerea, Neisseria meningitides, Pseudomonas fluorescens, Pseudomonas jessenii, Streptococcus mitis, Streptococcus oralis, Streptococcus pneumonia, etc. Some of these problems are related to bacterial nomenclature and taxonomy; others are related to sequence identity and very high similarity scores. Some species, like Aeromonas veronii, could contain up to six copies of the 16S rRNA gene that differ by up to 1.5% among themselves which might cause identification problems [37].

Some conservative genes such as gyrB (DNA gyrase B subunit) and rpoD70 factor) also can be used for the identification because protein-encoding genes evolve much faster than rRNA genes and provide higher resolution of intrageneric relationships than 16S rRNA sequencing. Using these genes, two major intrageneric clusters were identified. These intrageneric divisions are consistent with the clusters that have been defined using 16S rRNA gene sequence analysis by Moore, but phylogenetic relationships within the clusters differ in comparison with 16S rRNA sequencing. GyrB and rpoD nucleotide sequences can be also used to design specific PCR primers due to the high evolution rates [38, 39]. OprI, rpoB, atpD, carA, recA, and oprF also can serve as alternative phylogenetic markers when studying Pseudomonas taxonomy [40-43].

Another recently introduced method for taxonomic investigations of bacteria is multilocus sequence typing/analysis (MLST/MLSA). MLSA is a molecular typing method that consists of sequencing 400-600 bp long fragments of some housekeeping genes, i.e., genes that are present in most bacteria. MLSA has two important advantages over 16S rRNA sequencing: 1) the higher variability of housekeeping genes as compared to the 16S rRNA sequence and increased length of the total analyzed sequence even allow differentiation of strains; 2) sequencing of some genes reduces the risk that horizontal gene transfer obscures the resulting phylogeny [44]. According to the recent MLSA research (16S rRNA, gyrB, rpoB, and rpoD genes) the genus Pseudomonas, as before, is divided into two lineages (P. aeruginosa and P. fluorescens), which are subdivided into three and nine groups, respectively. The P. oryzihabitans group (two species) and the type strains of P. luteola, P. pachastrellae, and P. pertucinogena are the most phylogenetically distant from all other Pseudomonas and therefore they aren’t included in these lineages [45].

In addition to sequencing of different genes it’s possible to use a number of other methods. Restriction fragment length polymorphism (RFLP) is related to the polymorphic nature of the locations of restriction enzyme sites within defined genetic regions. As a result of RFLP, restriction profile is revealed. RFLP procedure is simple in manipulation and it doesn’t require sequence information allowing to identify bacteria at species or subspecies level. On the other hand, it’s time consuming and requires large amounts of DNA. The method was applied to determine genomovars and biotypes of various Pseudomonas species using 16S rRNA or 16S-23S spacer regions [46, 47]. The intergenic 16S-23S internally transcribed spacer (ITS1) regions are less susceptible to selection pressure because of their non-coding function and should have accumulated a higher percentage of mutations than the rRNA genes [46].

It’s possible to use polymerase chain reaction-reverse cross-blot hybridization (PCR-RCBH) in detection and identification studies. 16S-23S intergenic spacer region was amplified and used in hybridization assay with specific oligonucleotide probes to fluorescent pseudomonads and certain species of the genus. Positive reactions were observed if studied bacteria at least belonged to genus Pseudomonas. It was demonstrated that the identification of pseudomonads by PCR-RCBH is highly specific and less time-consuming than the conventional bacterial culture method [48].

Pulsed-field gel electrophoresis (PFGE) can be used for differentiation and identification of single strains [49, 50]. PFGE is often considered the “gold standard” of molecular typing methods. PFGE has the high discriminatory power, however, this method is time-consuming and labour-intensive, and some point mutations can change banding patterns, resulting in misleading results [51]. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) is also an effective method for identification of Pseudomonas genotypes. ERIC-PCR is quick, easy to perform and cost effective, but it has low reproducibility compared to PFGE [52-54].

As mentioned above, some chemotaxonomic markers like pyoverdines also can be taxonomic tools for the identification of Pseudomonas. Strains belonging to a well-defined genomic group produce an identical pyoverdine, and each genomic group is characterized by a specific pyoverdine. The same conclusions are valid for nonfluorescent Pseudomonas species and their siderophores. Strains are analyzed by two siderotyping methods: siderophore isoelectrofocusing and siderophore-mediated iron uptake. Correlation between DNA-DNA hybridization and siderotyping data was established. Compared to conventional phenotypic and genomic methods, siderotyping is the fast, accurate, and easy-to-perform technique allowing to identify at the species level. Two siderotyping methods can be improved by mass spectrometric determination of the molecular mass of pyoverdines [13, 55, 56].

Another possible tool for Pseudomonas taxonomy is fluorescence spectroscopy. In the study of Tourkya et al. analysis of emission spectra of three intrinsic fluorophores (NADH, tryptophan, and the complex of aromatic amino acids and nucleic acid) allowed to clearly discriminate Pseudomonas at genus level from Burkholderia, Xanthomonas and Stenotrophomonas. These results correlate with the classification based on 16S rRNA comparison. Fluorescence spectroscopy also allowed to discriminate P. lundensis, P. taetrolens, P. fragi, P. chlororaphis, and P. stutzeri species from the others. Clustering of these species is also concordant with data from 16S rRNA gene sequence comparison affiliating the four species to the same P. chlororaphis group [57].

There are many methods allowing to identify and classify the Pseudomonas genus, but gene sequencing procedures proved the most advanced and sophisticated. Great diversity of genus Pseudomonas urges further progress of taxonomic methodology.

4. Criteria for selection of Pseudomonas bacteria

As mentioned above, pseudomonads are able to degrade a broad spectrum of compounds. They are also characterized by an enormous biosynthesis capacity resulting in the production of a wide range of secondary metabolites and biopolymers. Ability to degrade and synthesize various substances is a vital technological merit of Pseudomonas. It promotes practical interest in various biotechnological processes such as bioremediation, production of polymers, biotransformation, synthesis of low-molecular-weight compounds and recombinant proteins, biocontrol agents [58]. The above-mentioned applications demand formulation of criteria for selection of pseudomonads.

5. Safety of Pseudomonas bacteria

Pseudomonas is known to display a range of pathogenic and toxicological characteristics in regard to humans, animals, and plants. The infections pseudomonads cause to humans are generally opportunistic. Individuals most at risk from Pseudomonas infection are the immunocompromised, patients with cystic fibrosis, and patients suffering major trauma or burns. The predominant Pseudomonas species isolated from clinical sources are P. aeruginosa [59]. P. aeruginosa is an opportunistic pathogen that may induce severe infections in humans and other vertebrates. Some P. aeruginosa strains, like PA14, also cause disease in a variety of nonvertebrate hosts, including plants, Caenorhabditis elegans, and the greater wax moth, Galleria mellonella [60]. The other Pseudomonas infection cases are rare.

Important feature of Pseudomonas is antibiotic resistance. Antibiotic resistance in the bacterial community constantly increases, and more multiple drug resistant strains appear. The best studied organism among pseudomonads is P. aeruginosa. The species is known for multiple drug resistance. P. aeruginosa has acquired resistance via multiple mechanisms, including production of β-lactamases and carbapenemases, upregulation of multidrug efflux pumps, and cell wall mutations leading to a reduction in porin channels [61].

Antibiotics used to treat P. aeruginosa infections have to cross the cell wall to reach their targets. The resistance of P. aeruginosa to these antibiotics is connected, first of all, with low permeability of the outer cell membrane and the efficient removal of antibiotics by efflux pumps. The above-mentioned mechanisms are common components of the resistance phenotype for β-lactams, aminoglycosides, and quinolone antibiotics. The agents that break down the outer-membrane permeability barrier (cationic antimicrobial peptides [62] or mutations that create large channels in the outer membrane [63]) make cells more susceptible to antibiotics.

The outer membrane contains proteins (porins) which form water-filled channels for diffusion of hydrophilic molecules. Porins play an important physiological role in the transport of various compounds. β-lactams, aminoglycosides, tetracyclines, and some fluoroquinolones can pass through porin channels [64, 65]. The loss of these porin channels can decrease the susceptibility of P. aeruginosa to antibiotics. Approximately 163 known or predicted outer membrane proteins were identified with 64 of these outer membrane proteins grouped into three families of porins [66]. OprF is a major porin of P. aeruginosa that forms a majority of small channels and a minority of larger channels [67]. OprF is present in high abundance as a closed conformer, and exists as an open channel only at very low levels. Therefore, it was shown that resistance to β-lactam antibiotics does not seem to involve loss or modification of OprF [68].

Porin OprD takes part in uptake of basic amino acids, small peptides and carbapenems (such as imipenem and meropenem) [69, 70]. Any substitution or deletion within external loop 2 and loop 3 of OprD results in changes of conformation and can cause imipenem resistance. Functional deletion of loop 2 at H729 induced partial resistance to imipenem and meropenem. Imipenam was found to bind to sites in loop 2 to block channel function. Deletion of loops 3 and 4 in OprD also results in failed expression. However, loop 3 is more likely to serve as a passage channel within OprD for imipenem, but not a direct binding site. Loop 1, loop 5, loop 6, loop 7, and loop 8 are not involved in the passage of imipenem, but either the deletion or amino acid substitutions of loop 5, loop 7, and loop 8 resulted in increased susceptibility to β-lactams, quinolones, chloramphenicol, carbapenems and tetracycline [71-76]. Amino acids including histidine, arginine, and lysine, its analogs, and peptides containing lysine can inhibit the penetration of imipenem in P. aeruginosa cells [70]. Culture medium containing basic amino acids significantly increased the minimum inhibitory concentration (MIC) of carbapenems against clinical isolates of P. aeruginosa [77].

Polycationic antibiotics, such as polymyxin B and aminoglycosides, and EDTA can pass through outer membrane without porins [78]. They displace divalent cations from lipopolysaccharide (LPS) molecules and destabilize the outer membrane increasing susceptibility to these antibiotics [79, 80]. Overexpression of OprH as a result of mutation or adaptation to low Mg2+ concentrations increases membrane resistance. OprH binds to LPS sites which are occupied by divalent cations and prevents access of polymyxin, gentamicin, and EDTA to these sites [78].

Besides porins, P. aeruginosa has numerous and highly efficient efflux mechanisms to resist to antibiotics. Efflux pumps include five superfamilies, based on energy source, the phylogenic relationship and the substrate specificity. There are five superfamilies: SMR (Small Multidrug Resistance), MET (Multidrug Endosomal Transporter), MAR (Multi Antimicrobial Resistance), RND (Resistance Nodulation Division), and MFS (Major Facilitator Superfamily) [81]. P. aeruginosa has efflux systems from all five superfamilies, but the largest number of predicted pumps belongs to the RND family with a total of 12 RND systems including two divalent metal cation transporters [82]. The efflux systems are composed of three protein components: an energy-dependent pump located in the cytoplasmic membrane, an outer membrane porin, and a linker protein which couples the two membrane components together. The 10 RND pumps of P. aeruginosa without the metal cation transporters are MexAB-OprM, MexCD-OprJ, MexEF-OprN, MexXY, MexJK, MexGHI-OpmD, MexVW, MexPQ-OpmE, MexMN, and TriABC, however, not all of these systems are well studied. These systems provide for intrinsic resistance to a number of antibiotics. Deletion, disruption or overexpression of pumps can make strains more or less sensitive to antibiotics or both effects can be shown (in case of MexCD-oprJ) [83].

Additionally, P. aeruginosa has a number of β-lactamases that are able to hydrolyze such antibiotics as penicillins, monobactams, cephalosporins, and carbapenems. β-lactamases divide into four classes, each including types that are usually plasmid-mediated or chromosomal [84]. The most common imported β-lactamases of P. aeruginosa are penicillinases from the molecular class A serine β-lactamases (PSE, CARB, and TEM families). The most prevalent enzymes of this group belong to the PSE family. Class A extended-spectrum β-lactamases also include enzymes from the TEM, SHV, CTX-M, PER, VEB, GES, and IBC families. Extended-spectrum β-lactamases from the class D, metallo-β-lactamases from the class B with four major families (IMP, VIM, SPM, and GIM families), OXA-type enzymes, class A carbapenemases of the KPC family also have been found within P. aeruginosa. P. aeruginosa has an inducible AmpC cephalosporinase which is similar to AmpC of several members of the Enterobacteriaceae. Increasing AmpC production provides for resistance to all β-lactams, except the carbapenems. However, lack of AmpC increases susceptibility to imipenem and doripenem but not to meropenem. Overproduction of AmpC can occur either by induction of the ampC gene or through a process of derepression. Overproduction via induction occurs under the influence of specific β-lactams and β-lactamase inhibitors (cefoxitin, imipenem, and clavulanate), but the process is reversible after removal of the inducing agent. AmpC derepression is related to chromosomal mutations, and therefore concentration of AmpC enzyme remains at an elevated level [83].

Another mechanism of antibiotic resistance is modification of antibiotics such as aminoglycosides. Modifying enzymes phosphorylate (aminoglycoside phosphoryltransferase), acetylate (aminoglycoside acetyltransferase), or adenylate (aminoglycoside nucleotidyltransferase) these antibiotics. Aminoglycoside acetyltransferases (AAC) acetylate compounds such as gentamicin, tobramycin, netilmicin, and amikacin at the 1, 3, 6′, and 2′ amino groups. Aminoglycoside phosphoryltransferases (APH) inactivate kanamycin, neomycin, and streptomycin by modification of the 3′-OH of these antibiotics. Primary role of some phosphotransferases such as APH(3′)-IIb may be participation in metabolism, and resistance to aminoglycosides may be provided fortuitously. Aminoglycoside nucleotidyltransferases (ANT) modify aminoglycosides such as streptomycin and gentamicin. ANT(2")-I with AAC(6′) and AAC(3) are the most common enzymes providing for aminoglycoside resistance in P. aeruginosa. Enzymes that modify aminoglycosides can be associated with transposons which additionally carry genes for resistance to other compounds. aac(3) and aac(6′) genes are often associated with transposons or integrons carrying genes for extended-spectrum β-lactamases, metallo-β-lactamases or genes encoding other aminoglycoside-modifying enzymes [85].

Antibiotic resistance can be provided by changes in targets. Mutations in genes gyrA and parC (topoisomerases II and IV, respectively) increase resistance to fluoroquinolones. Mainly changes of gyrA especially in the Thr-83 codon provide reduced fluoroquinolone sensitivity in P. aeruginosa. Usually mutations in parC are found jointly with highly resistant gyrA mutants [86-88].

Biofilm-forming ability provides resistance to adverse conditions, like antibiotic tolerance in P. aeruginosa. Biofilm bacteria are usually embedded in an extracellular polymeric substance (EPS) matrix composed of polysaccharides, proteins, and nucleic acid [89-92]. The composition of the matrix depends on the environmental conditions, the age of the biofilm, and the particular P. aeruginosa strain forming the biofilm. At least three exopolysaccharides have been shown to be produced by P. aeruginosa: alginate, Psl, and Pel. Alginates are linear polyanionic exopolysaccharides composed of uronic acids. These compounds decrease susceptibility of biofilms to antibiotic treatment. The Psl polysaccharide is rich in mannose and galactose and is connected with initial attachment and mature biofilm formation. Pel is a glucose-rich, cellulose-like polymer that plays a role in cell-to-cell interactions [93]. Several mechanisms in biofilm increase resistance to antimicrobial agents. These are binding and sequestration of antimicrobial agents by EPS components, stationary phase or slow growth of cells because of nutrient and oxygen limitation within the depths of a biofilm [94, 95]. Alginate produced by P. aeruginosa can retard the diffusion of some antimicrobials (piperacillin, amikacin, gentamicin), whereas others penetrate readily (ciprofloxacin, levofloxacin, sparfloxacin, ofloxacin) [96, 97]. Addition of alginate lyase and DNase increase activity of antibiotics [98]. Biofilms are characterized by the heterogeneity: cells close to the substratum exhibit low metabolic activity and cells on top exhibit high metabolic activity. Antimicrobial agents such as ciprofloxacin, tetracycline, tobramycin, and gentamicin interfere with physiological processes of bacterial cells and specifically kill the metabolically active cells in the top layer of biofilms. Other antimicrobial agents such as colistin, EDTA, and SDS interfere with bacterial membrane structures and kill the cells of the deeper layer [99, 100]. However, a small number of bacteria can survive under simultaneous action of both treatments [99].

Thereby P. aeruginosa have many mechanisms allowing to survive negative effects of antibiotics. As a result Pseudomonas infections are hard to get rid of.

6. Waste as media for growth of Pseudomonas bacteria

As mentioned above, Pseudomonas can grow in minimal media and can utilize a large variety of organic molecules. It appears attractive to use waste as media for Pseudomonas cultivation, biodegradation or production of necessary compounds, hence further experiments were carried out.

Frying oil is produced in large quantities by the food industry and private households. The used cooking oil changes its composition and contains more than 30% of polar compounds depending on the variety of food, the type of frying and the number of cycles used. The utilization of these compounds is a growing problem, arousing expanding interest in the use of waste in microbial transformation [101]. Most of the tested Pseudomonas showed satisfactory growth on basal medium with 2% or 4% used olive oil or used sunflower oil. Used olive oil also induced biosurfactant production. Sunflower oil was worse substrate for cell growth and biosurfactant production [102].

Biosurfactants are the surface-active compounds that find use in the cosmetic and food production, healthcare, pulp and paper processing, coal, ceramic, and metal industries. They also may be applied in cleaning of oil-contaminated tankers, oil spill removal, transportation and recovery of crude oil, and bioremediation of contaminated sites. Biosurfactants show advantages over chemical analogs owing to their low toxicity and biodegradable nature. Pseudomonas is able to synthesize these compounds from cheap carbon sources such as vegetable oils and wastes from the food industry [58, 103].

P. aeruginosa LBI strain was grown on media containing one of residues from soybean, corn, babassu, cottonseed, and palm oil refinery. The soybean soapstock waste was the preferred substrate generating 11.7 g/L of rhamnolipids with the best surface-active properties compared with the products from other oil wastes. Biosurfactant from palm oil waste shows a good emulsification index against kerosene suggesting its potential use for bioremediation [104].

Similar experiments showed that waste motor lubricant oil and peanut oil cake [105], waste frying rice bran oil [106], distillery and whey wastes [107], waste frying coconut oil [108], olive oil mill wastewater [109] and molasses [110] can be used as cheap carbon sources for production of biosurfactants by Pseudomonas. Additionally, these substrates may help solve waste disposal problem.

Glycerol, cassava wastewater, waste cooking oil and cassava wastewater with waste frying oils were evaluated as alternative low-cost carbon substrates for the production of rhamnolipids and polyhydroxyalkanoates (PHAs) by various P. aeruginosa strains. Cassava wastewater with added waste cooking oil provides higher levels of rhamnolipids and PHAs compared with the other carbon substrates [111].

PHAs are composed of medium-chain length (R)-3-hydroxyfatty acids characterized by thermoplastic properties, biodegradability and biocompatibility. They make PHAs suitable for use in the packaging, medicine, pharmacy, agriculture and food industries [58]. Technical oleic acid and waste frying oil were shown to be suitable substrates for PHAs production by P. aeruginosa strain NCIB 40045 [112]. Glycerol by-product generated during the production of biodiesel from kitchen chimney dump lard was a better carbon source for PHA synthesis by P. aeruginosa JQ866912 as compared with commercial glycerol, sugarcane molasses and glucose. Using this glycerol by-product as a carbon source for PHA production could be both environmentally benign and cost-effective coupling of biodiesel and PHA production [113]. P. oleovorans is able to produce PHAs using the residual oil from biotechnological rhamnose production as the sole carbon source. PHAs isolated from P. oleovorans are more diverse than PHAs from Ralstonia eutropha H16 growing under the same conditions [114]. P. putida KT2442 produces PHAs in wastewater from olive oil mills (called alpechín), supplemented with glucose, yeast extract and NH4Cl [115].

Wastes can be used as media in melanin production. Melanins represent a group of macromolecules, synthesized in living organisms by oxidative polymerization of various phenolic substances in the process of adaption [116]. Melanins act as photoprotectants against UV and visible light, charge transport mediators, free-radical scavengers, antioxidants, metal ion balancers [117]. Melanins find applications in agriculture, medicine, cosmetic and pharmaceutical industries. Some bacteria are able to synthesize these compounds. Marine melanin producer Pseudomonas sp. (closely related to P. guinea) was incubated in marine broth, vegetable waste from cabbage leftovers supplemented with 1.9 % NaCl to maintain salinity and marine broth - vegetable waste medium blended in 30:70 ratio for melanin production. The sole vegetable waste generated no pigmentation. Marine broth medium demonstrated more melanin production than the marine broth - vegetable waste blended medium (5.35 ± 0.4 and 2.79 ± 0.2 mg/mL after 72h of incubation, respectively). However, melanin from both sources after purification looked alike in appearance. This study confirms that the pigment can be produced from the cheaper substrates without any functional variation [118].

Another possible waste substrate as fermentation media is animal fleshing, the solid waste produced in large amounts by tanning industry. The studied P. aeruginosa strain can digest the media and produce alkaline protease, an industrially important enzyme from waste material. Alkaline proteases have considerable application in leather tanning industry [119]. Strain showed maximum alkaline protease production after 20 hours of incubation at the end of exponential growth phase [120].

P. aeruginosa MN7 was found to produce proteases when it was grown in media containing only shrimp waste powder, indicating that it can obtain its carbon, nitrogen, and salts requirements directly from shrimp waste. Protease production increased with increasing concentration of shrimp waste powder and reached a maximum value at 60 g/L [121]. Shrimp shell powder can be used for low-cost production of chitinase and chitosanase showing potential applications in the biocontrol of plant pathogenic fungi and insects. Shrimp shell powder (10 mU/mL) was more suitable as an inducer of chitinase production than squid pen powder (7.2 mU/mL), shrimp and crab shell powder (2.8 mU/mL), katsuobushi from mackerel (<0.1 mU/mL), katsuobushi from bonito (<0.1 mU/mL), and chitin (<0.1 mU/mL) [122].

The potential use of keratinous and chitinous wastes, such as chicken-feathers and shrimp wastes for oil-remediation was shown. Cultures were grown in minimal media with crude oil, or oil supplemented with chicken-feathers or shrimp wastes. The presence of organic wastes, mainly keratinous ones, enhanced the oil-hydrocarbons removal to an extent of 90%. Keratinolytic bacteria were better enzyme producers than the chitinolytic ones, and oil removal in the presence of chicken-feathers was 3.8 times higher than with shrimp wastes, and almost twice, in comparison with oil-only added cultures [123].

Various combinations of agricultural wastes can be tested to promote P. fluorescence production. Seven different variants were checked to detect the increased production of P. fluorescence. Composition containing rice straw, rice husk, wheat husk, cow dung, coconut water was found to be the optimal substrate for cultivation. The chosen combination also favored a high rate of green pigment production in this medium [124].

Toner waste black powder (TWBP) from copiers and printers is considered to be toxic for environment, and introduction of bacteria can alleviate the problem of TWBP disposal. It was stated that P. spp. and P. aeuroginosa utilize TWBP for growth. TWBP was mixed with soil at different concentrations (2g TWBP + 10g soil, 4g TWBP + 10 g soil, 6g TWBP + 10g soil, 8g TWBP + 10g soil and 10g TWBP + 10g soil) and inoculated in minimal salt medium. Among the various tested TWBP concentrations, 2g TWBP dose provoked significant stimulation of bacterial growth [125].

Tobacco-related processes can release wastes saturated with water-soluble nicotine posing biological and ecological hazard. P. sp. ZUTSKD consumed nicotine as sole source of carbon, nitrogen and energy when grown in basic inorganic salt medium. Growth and nicotine degradation were observed at substrate concentrations of 2–5.8 g/L. The strain degraded nicotine completely when the concentration of reducing sugar in TWE (tobacco waste extract) was lower than 8 g/L. Glucose concentration above 10 g/L inhibited nicotine degradation. Yeast extract and phosphate additions improved nicotine degradation in 5% TWE [126].

7. Stress resistance of Pseudomonas bacteria

Pseudomonas species thrive under moist conditions in soil (particularly in association with plants), in sewage sediments and the aquatic environments. Environmental conditions which will affect their growth include nutrient availability, moisture, temperature, competition, UV irradiation, oxygen availability, salinity and the presence of inhibitory or toxic compounds, but nutritional demands of Pseudomonas are modest [59].

There are some ways that allow pseudomonads to resist to adverse conditions. The alternative sigma factors RpoS (σs) and RpoE (σ22; also referred to as AlgU or AlgT in fluorescent pseudomonads) are involved in bacterial survival under stress conditions. The sigma factor encoded by the rpoS gene is known to be important for survival under stressful conditions in several bacterial species. Studies of rpoS mutant P. aeruginosa PAOl revealed a two- to threefold increase in the rate of kill of stationary-phase cells following exposure to heat, low pH, high osmolarity, hydrogen peroxide and ethanol. However, stationary-phase RpoS-negative cells of P. aeruginosa were much more resistant than exponentially growing RpoS-positive cells [127]. RpoS gene also is involved in tolerance to antibiotics in P. aeruginosa during the stationary phase and heat stress [128].

The sigma factor AlgU contributes to tolerance towards osmotic, oxidative, and heat stresses in the pathogens P. aeruginosa and P. syringae [129-133]. AlgU in P. aeruginosa also plays part in regulation of biosynthesis of EPS alginate. AlgU is essential for adaptation of plant-associated P. fluorescens to osmotic and desiccation stresses [134]. mucABCD genes ensure tight control of AlgU activity [135]. The mucA gene encoding a transmembrane protein, and mucB gene encoding a periplasmic protein are negative regulators of AlgU. Stress conditions destabilize the MucB-MucA-AlgU complex, leading to release of AlgU into the cytosol where AlgU becomes active [136].

Production of some compounds can provide bacterial resistance to adverse conditions. PHA-negative mutants were more sensitive to heat treatment than non-mutated cells. The similar effect was revealed in biofilms of PHA-negative mutants as compared to non-mutated strains [137]. PHA availability enhances the ATP and ppGpp levels, and ppGpp has been shown to induce expression of the rpoS gene involved in regulation of stress tolerance [138].

P. putida NBAII-RPF9 can survive under saline shock (1 M NaCl for 1 h) or heat shock (45°C for 20 min). It was identified 13 upregulated proteins and one downregulated protein under heat shock, 6 upregulated proteins under heat tolerance, 11 upregulated proteins under saline shock, and 6 upregulated proteins under saline tolerance. During heat shock, heat stress responsive molecular chaperones and membrane proteins, and during salt stress, proteins upregulated to favor growth and adaptation of the bacterium were revealed. Heat shock chaperones DnaK and DnaJ were expressed under both saline and heat stress. The expression of different classes of proteins under abiotic stress can help this organism to adapt and survive under harsh environmental conditions [139].

Study of P. aeruginosa culture exposed to steady-state hyperosmotic stress demonstrated increased gene expression (at least threefold) in cells grown in the presence of 0.3 M NaCl and 0.7 M sucrose. Research revealed that 66 genes changed expression level in response to both stressors [140]. Also 40 of those 66 genes are associated with virulence factor expression, encoding proteins of a type III secretion system (TTSS), the type III cytotoxins ExoT and ExoY, and two ancillary chaperones [141, 142]. It has been shown that P. aeruginosa accumulated K+, glutamate, trehalose as cytoplasmic osmoprotectants coupled to major organic osmoprotectant N-acetylglutaminylglutamine amide (NAGGN). Exogenous betaine was found to increase the growth rate and to partially replace NAGGN in osmotically stressed wild-type P. aeruginosa cells [143].

Organic solvents are extremely toxic to microbial cells, even at very low concentration. The cell membrane is the primary target for these compounds. Solvents penetrate into and disrupt the lipid bilayer of membrane. Concentration plays a crucial role in determining toxicity of organic solvents. Since Gram-negative bacteria have an additional outer membrane, and Gram-positive bacteria have a single cytoplasmic membrane, it was assumed that Gram-negative bacteria are better equipped to resist to organic solvents. Gram-negative bacteria including some strains of Pseudomonas possess various adaptive mechanisms of organic solvent tolerance. There are modifications in cell envelope to increase cell membrane rigidity and decrease permeability, enzymes increasing rate of membrane repair, special solvent-inactivating enzymes, action of efflux pumps, release of membrane vesicles with adhered solvent molecules. These mechanisms help bacteria to overcome the toxic effects of organic solvents [144].

As mentioned above, ability to form biofilm provides resistance to adverse conditions, like antibiotic exposure of P. aeruginosa. Biofilm beneficial impact is not limited exclusively to antibiotics. Biofilm cells were found to be more resistant to heavy metals than an equal number of free-floating cells. The degree of increased resistance varied depending on the element. EPS binds heavy metals and retards their diffusion within biofilm, protecting cells from stress [145].

8. Application of Pseudomonas bacteria

Due to simple requirements of growth conditions and medium composition, capacity to produce and degrade a number of compounds, Pseudomonas species are regarded as promising microorganisms in various biotechnological applications. As mentioned above, Pseudomonas is able to produce biosurfactants and PHAs characterized by low toxicity and biodegradability for further use in different technological areas. It’s possible to apply waste in these processes as low-cost media.

Pseudomonas is also an excellent source of various enzymes acting as catalysts in specific biochemical reactions. High efficiency and specificity facilitate introduction of enzymes in diverse industrial processes. Enzymes produced by Pseudomonas species can be used in leather processing for dehairing of hides [119, 146], hydrolysis of oils to concentrate the derived fatty acids for medical purpose [147], production of monoacylglycerols and hydrocinnamic esters used in food, pharmaceutical and cosmetic industries [148, 149], manufacturing of detergents [150], production of biodiesel [151], remediation [152], etc.

Another possible application of Pseudomonas is bioremediation. Pseudomonas is able to remove various toxic pollutants from natural environment. Crude oil is known to alter physical and biochemical characteristics of soil. Petroleum contains numerous components including alkanes, aromatics, resins and asphaltenes. Action of some Pseudomonas cultures was shown to degrade constituents of crude oil, automobile oil effluent, and diesel fuel [153-155]. Moreover, pseudomonads can remove heavy metals released into the environment with industrial and domestic wastewaters. The studies proved that Pseudomonas strains are able to dispose of such metals as Cr, Cd, Mn, Fe, Cu, Ni, Pb from wastes [156-158]. Some species possess enormous potential for the detoxification of pollutants containing pesticides and phenols [157].

The textile industry makes extensive use of synthetic chemicals as dyes. A significant proportion of these dyes entering the surrounding media via wastewater is toxic to the environment and humans [159]. Dyes obstruct light penetration and oxygen transfer in water reservoirs. They retain stability and persistence in the environment for a long term [160]. Various physicochemical methods have been used for decolorization of dyes in wastewater, but these methods are distinguished by low efficiency, high cost, limited application scope, and production of recalcitrant wastes [161]. Application of bacteria can solve problems typical to physicochemical methods. It was shown that different Pseudomonas species efficiently decolorize and degrade dyes. It’s possible to increase decolorization rates by changing cultural conditions. The optimum pH and temperature values for color removal are 7–9 and about 37°C, respectively. Immobilization, anaerobic conditions and addition of some compounds, like yeast extract, promote enhanced decolorization rate. Elevated concentrations of dyes and oxygen decelerate color removal [162-167].

Pseudomonas may be used as biocontrol agents that reduce disease severity and promote plant growth. They stimulate growth by several mechanisms. The bacteria can produce some compounds that inhibit spread of plant pathogens. These compounds are siderophores, hydrogen cyanide, pyrrolnitrin, phenazine, 2,4-diacetyl phloroglucinol and lytic enzymes (chitinase, β-1,3-glucanase). The inhibitors can act on pathogens directly like chitinase degrading the fungal cell wall or indirectly like siderophore that binds iron (III) ions in the environment and restrains access of pathogen to these ions. Additionally, Pseudomonas provides activation of induced systemic resistance (ISR) or systemic acquired resistance (SAR) in plants. Resistance reveals as oxidative burst which can lead to cell death and prevention of pathogen spreading, changes in cell wall composition, production of phytoalexins and PR proteins [168-173].

9. Conclusion

Genus Pseudomonas represents a diverse group of bacteria including a large number of species. On the one hand, Pseudomonas is characterized by ability to grow in minimal media without growth factors; on the other hand, these bacteria are able to produce and degrade a broad spectrum of compounds. Pseudomonas is equipped with several mechanisms allowing to resist and survive under adverse conditions. Currently the genus became the attractive object of intensive research.

Pseudomonas can be used in bioremediation allowing to degrade toxic compounds and solve problems concerning utilization of wastes hazardous for environment and humans. It was shown that 11 central and many different peripheral pathways provide for bacterial degradation of a whole range of compounds. Pseudomonas promising application is bioremediation of oil-contaminated environment. Crude oil causes changes of soil valuable properties such as fertility, water-holding and binding capacity, permeability, and bioremediation appears the best way to treat the oil contamination problem.

Pseudomonas species are capable of synthesizing both low-molecular-weight compounds (rhamnolipids, enzymes) and polymers (polyhydroxyalkanoates) that are often characterized by better properties than chemical analogs. Their potential usage is manufacturing cosmetics, food, oil refining, leather and paper processing, coal, ceramic, metal industries, agriculture, biodiesel production and medicine. Experiments revealed that agricultural and industrial wastes are suitable substrates for production of biosurfactants, polyhydroxyalkanoates, enzymes, melanin, etc. Application of these substrates will solve problems related to utilization of wastes.

Vast potential of pseudomonads as biocontrol agents was demonstrated. Pseudomonas decrease negative influence of plant pathogens by various ways. They can either produce compounds that directly affect pathogens or stimulate development of induced resistance in plants. Summing up, Pseudomonas species and their products find applications in various fields primarily because they are capable to utilize a wide range of organic and inorganic compounds.

The recent technological advances in the area of genomics and proteomics are now beginning to lay out important avenue of research focused on the role of Pseudomonas bacteria and the molecular mechanisms of their beneficial action.


1 - Shinoda S, Okamoto K. Formation and function of Vibrio parahemolyticus lateral flagella. Journal of Bacteriology 1977;129(3) 1266-1271.
2 - Moore ERB, Tindall BJ, Martins Dos Santos VAP, Pieper DH, Ramos JL, Palleroni NJ. Nonmedical: Pseudomonas. In: Dworkin M, Falkow S, Rosenberg E., Schleifer KH, Stackebrandt E. (eds.) The Prokaryotes Volume 6: Proteobacteria: Gamma Subclass. Springer New York; 2006. p.646-703. DOI: 10.1007/0-387-30746-X_21.
3 - Woods DE, Straus DC, Johanson WG, Berry VK, Bass JA. Role of pili in adherence of Pseudomonas aeruginosa to mammalian buccal epithelial-cells. Infection and Immunity 1980;29(3) 1146-1151.
4 - Doig P, Todd T, Sastry PA, Lee KK, Hodges RS, Paranchych W, Irvin RT. Role of pili in adhesion of Pseudomonas aeruginosa to human respiratory epithelial-cells. Infection and Immunity 1988:56(6) 1641-1646.
5 - Bradley DE. A function of Pseudomonas aeruginosa PAO polar pili: twitching motility. Can Journal of Bacteriology 1980;26(2) 146-154. DOI: 10.1139/m80-022.
6 - Klausen M, Heydorn A, Ragas P, Lambertsen L, Aaes-Jørgensen A, Molin S, Tolker-Nielsen T. Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants. Molecular Microbiology 2003;48(6) 1511-1524. DOI: 10.1046/j.1365-2958.2003.03525.x.
7 - O'Toole GA, Kolter R. Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Molecular Microbiology 1998;30(2) 295-304. DOI: 10.1046/j.1365-2958.1998.01062.x.
8 - Li CM, Brown I, Mansfield J, Stevens C, Boureau T, Romantschuk M, Taira S. The Hrp pilus of Pseudomonas syringae elongates from its tip and acts as a conduit for translocation of the effector protein HrpZ. The EMBO Journal 2002;21(8) 1909-1915. DOI: 10.1093/emboj/21.8.1909.
9 - Ghafoor A, Hay ID, Rehm BH. Role of exopolysaccharides in Pseudomonas aeruginosa biofilm formation and architecture. Applied and Environmental Microbiology 2011;77(15) 5238-5246. DOI: 10.1128/AEM.00637-11.
10 - Meyer JM, Abdallah MA. The fluorescent pigment of Pseudomonas fluorescens: biosynthesis, purification and physicochemical properties. Journal of General Microbiology 1978;107(2) 319-328. DOI: 10.1099/00221287-107-2-319.
11 - Meyer JM, Hornsperger JM. Role of pyoverdine Pf, the iron binding fluorescent pigment of Pseudomonas fluorescens in iron transport. Journal of General Microbiology 1978;107(2) 329-331. DOI: 10.1099/00221287-107-2-329.
12 - Takase H, Nitanai H, Hoshino K, Otani T. Impact of siderophore production on Pseudomonas aeruginosa infections in immunosuppressed mice. Infection and Immunity 2000;68(4) 1834-1839. DOI: 10.1128/IAI.68.4.1834-1839.2000.
13 - Meyer JM, Geoffroy VA, Baida N, Gardan L, Izard D, Lemanceau P, Achouak W, Palleroni NJ. Siderophore typing, a powerful tool for the identification of fluorescent and nonfluorescent pseudomonads. Applied and Environmental Microbiology 2002;68(6) 2745-2753. DOI: 10.1128/AEM.68.6.2745-2753.2002.
14 - Palleroni NJ. Pseudomonas. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM. (eds.) Bergey’s Manual of Systematic Bacteriology, Volume Two the Proteobacteria Part B the Gammaproteobacteria. 2nd ed. Springer US; 2005. p.323-379. DOI: 10.1007/0-387-28022-7.
15 - Blondel-Hill E, Henry DA, David P. Pseudomonas. In: Murray PR, Baron EJ, Jorgensen JH, Landry ML, Pfaller MA. (eds.) Manual of Clinical Microbiology. 9th ed. Washington, DC: ASM Press. 2007; p.734-748.
16 - Wolterink AFWM., Jonker AB, Kengen SWM, Stams AJM. Pseudomonas chloritidismutans sp. nov., a non-denitrifying, chlorate-reducing bacterium. International Journal of Systematic and Evolutionary Microbiology 2002;52(Pt 6) 2183-2190. DOI: 10.1099/ijs.0.02102-0.
17 - Lessie TG, Phibbs PV Jr. Alternative pathways of carbohydrate utilization in pseudomonads. Annual Review of Microbiology 1984;38: 359-388. DOI: 10.1146/annurev.mi.38.100184.002043.
18 - Jiménez JI, Nogales J, García JL, Díaz E. A genomic view of the catabolism of aromatic compounds in Pseudomonas. In: Timmis KN. (ed.) Handbook of Hydrocarbon and Lipid Microbiology. Springer Berlin Heidelberg; 2010. p.1297-1325. DOI: 10.1007/978-3-540-77587-4_91.
19 - Jiménez JI, Miñambres B, Garcı́a JL, Dı́az E. Genomic insights in the metabolism of aromatic compounds in Pseudomonas. In: Ramos JL. (ed.) Pseudomonas, Volume 3 Biosynthesis of Macromolecules and Molecular Metabolism. Springer US; 2004. p.425-462. DOI: 10.1007/978-1-4419-9088-4_15.
20 - List of prokaryotic names with standing in nomenclature. (accessed 30 January 2015).
21 - Stanier RY, Palleroni NJ, Doudoroff M. The aerobic pseudomonads: a taxonomic study. Journal of General Microbiology 1966;43(2) 159-271. DOI: 10.1099/00221287-43-2-159.
22 - Palleroni NJ. The Pseudomonas story. Environmental Microbiology 2010;12(6) 1377-1383. DOI: 10.1111/j.1462-2920.2009.02041.x.
23 - Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology 2007;57(Pt 1) 81-91. DOI: 10.1099/ijs.0.64483-0.
24 - Doi RH, Igarashi RT. Conservation of ribosomal and messenger ribonucleic acid cistrons in Bacillus species. Journal of Bacteriology 1965; 90(2) 384-390.
25 - Dubnau D, Smith I, Porell P, Marmur J. Gene conservation in Bacillus species. I. Conserved genetic and nucleic acid base sequence homologies. Proceedings of the National Academy of Sciences of the United States of America 1965;54(2) 491-498. DOI: 10.2307/72742.
26 - Palleroni NJ, Kunisawa R, Contopoulou R, Doudoroff M. Nucleic acid homologies in the genus Pseudomonas. International Journal of Systematic Bacteriology 1973;23(4) 333-339. DOI: 10.1099/00207713-23-4-333.
27 - Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H, Hashimoto Y, Ezaki T, Arakawa M. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiology and Immunology 1992;36(12) 1251-1275. DOI: 10.1111/j.1348-0421.1992.tb02129.x.
28 - Yabuuchi E, Kosako Y, Yano I, Hotta I, Nishiuchi Y. Transfer of two Burkholderia and an Alcaligenes species to Ralstonia gen. nov.: proposal of Ralstonia pickettii (Ralston, Palleroni and Doudoroff 1973) comb. nov., Ralstonia solanacearum (Smith 1896) comb. nov. and Ralstonia eutropha (Davis 1969) comb. nov. Microbiology and Immunology 1995;39(11) 897-904. DOI: 10.1111/j.1348-0421.1995.tb03275.x.
29 - Willems A, Busse J, Goor M, Pot B, Falsen E, Jantzen E, Hoste B, Gillis M, Kersters K, Auling G, De Ley J. Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (formerly Pseudomonas flava), Hydrogenophaga palleroni (formerly Pseudomonas palleroni), Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava and ‘‘Pseudomonas carboxydoflava’’), and Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis). International Journal of Systematic Bacteriology 1989;39(3) 319-333. DOI: 10.1099/00207713-39-3-319.
30 - Willems A, Falsen E, Pot B, Jantzen E, Hoste B, Vandamme P, Gillis M, Kersters K, De Ley J. Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldeii comb. nov., and Acidovorax temperans sp. nov. International Journal of Systematic Bacteriology 1990;40(4) 384-398. DOI: 10.1099/00207713-40-4-384.
31 - Tamaoka J, Ha D-M, Komagata K. Reclassification of Pseudomonas acidovorans den Dooren de Jong 1926 and Pseudomonas testosteroni Marcus and Talalay 1956 as Comamonas acidovorans comb. nov. and Comamonas testosterone comb. nov., with an emended description of the genus Comamonas. International Journal of Systematic Bacteriology 1987;37(1) 52-59. DOI: 10.1099/00207713-37-1-52.
32 - Segers P, Vancanneyt M, Pot B, Torck U, Hoste B, Dewettinck D, Felsen E, Kersters K, De Vos P. Classification of Pseudomonas diminuta Leifson and Hugh 1954 and Pseudomonas vesicularis Büsing, Döll, and Freytag 1953 in Brevundimonas gen. nov. as Brevundimonas diminuta comb. nov. and Brevundimonas vesicularis comb. nov., respectively. International Journal of Systematic Bacteriology 1994;44(3) 499-510. DOI: 10.1099/00207713-44-3-499.
33 - Palleroni NJ, Bradbury JF. Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983. International Journal of Systematic Bacteriology 1993;43(3) 606-609. DOI: 10.1099/00207713-43-3-606.
34 - Patel JB. 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Molecular Diagnosis 2001;6(4) 313-321. DOI: 10.1007/BF03262067.
35 - Moore ERB, Mau M, Arnscheidt A, Böttger EC, Hutson RA, Collins MD, van de Peer Y, De Wachter R, Timmis KN. The determination and comparison of the 16S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Systematic and Applied Microbiology 1996;19(4) 478-492. DOI: 10.1016/S0723-2020(96)80021-X.
36 - Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. International Journal of Systematic and Evolutionary Microbiology 2000;50(Pt 4) 1563-1589. DOI: 10.1099/00207713-50-4-1563.
37 - Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. Journal of Clinical Microbiology 2007;45(9) 2761-2764. DOI: 10.1128/JCM.01228-07.
38 - Yamamoto S, Harayama S. Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. International Journal of Systematic Bacteriology 1998;48(Pt 3) 813-819. DOI: 10.1099/00207713-48-3-813.
39 - Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A, Harayama S. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 2000;146 (Pt 10) 2385-2394.
40 - De Vos D, Bouton C, Sarniguet A, De Vos P, Vauterin M, Cornelis P. Sequence diversity of the oprI gene, coding for major outer membrane lipoprotein I, among rRNA group I pseudomonads. Journal of Bacteriology 1998;180(24) 6551-6556.
41 - Ait Tayeb L, Ageron E, Grimont F, Grimont PAD. Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Research in Microbiology 2005;156(5-6) 763-773. DOI: 10.1016/j.resmic.2005.02.009.
42 - Hilario E, Buckley TR, Young JM. Improved resolution on the phylogenetic relationships among Pseudomonas by the combined analysis of atp D, car A, rec A and 16S rDNA. Antonie Van Leeuwenhoek. 2004;86(1) 51-64. DOI: 10.1023/B:ANTO.0000024910.57117.16.
43 - Bodilis J, Barray S. Molecular evolution of the major outer-membrane protein gene (oprF) of Pseudomonas. Microbiology 2006;152(Pt 4) 1075-1088. DOI: 10.1099/mic.0.28656-0.
44 - Vinatzer BA, Bull CT. The impact of genomic approaches on our understanding of diversity and taxonomy of plant pathogenic bacteria. In: Jackson RW. (ed.) Plant Pathogenic Bacteria: Genomics and Molecular Biology. Horizon Scientific Press; 2009. p.37-61.
45 - Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environmental Microbiology 2010;12(6) 1513-1530. DOI: 10.1111/j.1462-2920.2010.02181.x.
46 - Guasp C, Moore ER, Lalucat J, Bennasar A. Utility of internally transcribed 16S-23S rDNA spacer regions for the definition of Pseudomonas stutzeri genomovars and other Pseudomonas species. International Journal of Systematic and Evolutionary Microbiology 2000;50(Pt 4) 1629-1639. DOI: 10.1099/00207713-50-4-1629.
47 - Scarpellini M, Franzetti L, Galli A. Development of PCR assay to identify Pseudomonas fluorescens and its biotype. FEMS Microbiology Letters 2004;236(2) 257-260. DOI: 10.1111/j.1574-6968.2004.tb09655.x.
48 - Jaturapahu T., Puttinaowarat S., Somsiri T. Detection and identification of Pseudomonas Spp. by polymerase chain reaction-reverse cross-blot hybridization (PCR-RCBH) with 16S-23S ribosomal RNA intergenic spacer probes. In: Walker P, Lester R, Bondad-Reantaso MG. (eds.) Diseases in Asian Aquaculture: Proceedings of the Fifth symposium on Diseases in Asian Aquaculture, 24-28 November 2002, Queensland, Australia. Fish Health Section, Asian Fisheries Society, Manila, Philippines. 2005. p.447-456.
49 - Geider K. Differentiation and identification of Pseudomonas syringae pathovars by PCR- and PFGE-Analyses. In: Rudolph K, Burr TJ, Mansfield JW, Stead D, Vivian A, von Kietzell J. (eds.) Developments in Plant Pathology, Volume 9: Pseudomonas syringae Pathovars and Related Pathogens. Springer Netherlands; 1997. p.459-464. DOI: 10.1007/978-94-011-5472-7_82.
50 - Spencker FB, Haupt S, Claros MC, Walter S, Lietz T, Schille R, Rodloff AC. Epidemiologic characterization of Pseudomonas aeruginosa in patients with cystic fibrosis. Clinical Microbiology and Infection 2000;6(11) 600-607. DOI: 10.1046/j.1469-0691.2000.00171.x.
51 - Fothergill JL, White J, Foweraker JE, Walshaw MJ, Ledson MJ, Mahenthiralingam E, Winstanley C. Impact of Pseudomonas aeruginosa genomic instability on the application of typing methods for chronic cystic fibrosis infections. Journal of Clinical Microbiology 2010;48(6) 2053-2059. DOI: 10.1128/JCM.00019-10.
52 - Wolska K, Szweda P. A comparative evaluation of PCR ribotyping and ERIC PCR for determining the diversity of clinical Pseudomonas aeruginosa isolates. Polish Journal of Microbiology 2008;57(2) 157-163.
53 - Syrmis MW, O'Carroll MR, Sloots TP, Coulter C, Wainwright CE, Bell SC, Nissen MD. Rapid genotyping of Pseudomonas aeruginosa isolates harboured by adult and paediatric patients with cystic fibrosis using repetitive-element-based PCR assays. Journal of Medical Microbiology 2004;53(Pt 11): 1089-1096. DOI: 10.1099/jmm.0.45611-0.
54 - Han MM, Mu LZ, Liu XP, Zhao J, Liu XF, Liu H. ERIC-PCR genotyping of Pseudomonas aeruginosa isolates from haemorrhagic pneumonia cases in mink. Veterinary Record Open 2014;1(1): e000043. DOI: 10.1136/vropen-2014-000043.
55 - Meyer JM. Siderotyping and bacterial taxonomy: a siderophore bank for a rapid identification at the species level of fluorescent and non-fluorescent Pseudomonas. In: Varma A, Chincholkar SB. (eds.) Soil Biology, Microbial Siderophores, Volume 12. Springer Berlin Heidelberg; 2007. p.43-66. DOI: 10.1007/978-3-540-71160-5_2.
56 - Meyer JM, Gruffaz C, Raharinosy V, Bezverbnaya I, Schäfer M, Budzikiewicz H. Siderotyping of fluorescent Pseudomonas: molecular mass determination by mass spectrometry as a powerful pyoverdine siderotyping method. Biometals 2008;21(3) 259-271. DOI: 10.1007/s10534-007-9115-6.
57 - Tourkya B, Boubellouta T, Dufour E, Leriche F. Fluorescence spectroscopy as a promising tool for a polyphasic approach to pseudomonad taxonomy. Current Microbiology 2009;58(1) 39-46. DOI: 10.1007/s00284-008-9263-0.
58 - Rehm BHA. Biotechnological relevance of Pseudomonads. In: Rehm BHA. (ed.) Pseudomonas: Model Organism, Pathogen, Cell Factory. Wiley-Blackwell; 2008. p.377-395. DOI: 10.1002/9783527622009.ch14.
59 - OECD. Section 2 – Pseudomonas. In: Safety Assessment of Transgenic Organisms, Volume 2: OECD Consensus Documents. OECD Publishing; 2006. p.312-393. DOI: 10.1787/9789264095403-10-en.
60 - Choi JY, Sifri CD, Goumnerov BC, Rahme LG, Ausubel FM, Calderwood SB. Identification of virulence genes in a pathogenic strain of Pseudomonas aeruginosa by representational difference analysis. Journal of Bacteriology 2002;184(4): 952-961. DOI: 10.1128/jb.184.4.952-961.2002.
61 - Lambert PA. Mechanisms of antibiotic resistance in Pseudomonas aeruginosa. Journal of the Royal Society of Medicine 2002;95(Suppl 41) 22-26.
62 - Scott MG, Yan H, Hancock REW. Biological properties of structurally related α-helical cationic antimicrobial peptides. Infection and Immunity 1999;67(4) 2005-2009.
63 - Huang H, Hancock REW. The role of specific surface loop regions in determining the function of the imipenem-specific pore protein OprD of Pseudomonas aeruginosa. Journal of Bacteriology 1996;178(11) 3085-3090.
64 - Nikaido H. Outer membrane barrier as a mechanism of antimicrobial resistance. Antimicrobial Agents and Chemotherapy 1989;33(11): 1831-1836. DOI: 10.1128/AAC.33.11.1831.
65 - Yoshimura F, Nikaido H. Diffusion of beta-lactam antibiotics through the porin channels of Escherichia coli K-12. Antimicrobial Agents and Chemotherapy 1985;27(1) 84-92. DOI: 10.1128/AAC.27.1.84.
66 - Hancock REW, Brinkman FS. Function of pseudomonas porins in uptake and efflux. Annual Review of Microbiology 2002;56 17-38. DOI: 10.1146/annurev.micro.56.012302.160310.
67 - Brinkman FS, Bains M, Hancock RE. The amino terminus of Pseudomonas aeruginosa outer membrane protein OprF forms channels in lipid bilayer membranes: correlation with a three-dimensional model. Journal of Bacteriology 2000;182(18) 5251-5255. DOI: 10.1128/JB.182.18.5251-5255.2000.
68 - Bratu S, Landman D, Gupta J, Quale J. Role of AmpD, OprF and penicillin-binding proteins in beta-lactam resistance in clinical isolates of Pseudomonas aeruginosa. Journal of Medical Microbiology 2007;56(6) 809-814. DOI: 10.1099/jmm.0.47019-0.
69 - Trias J, Nikaido H. Outer membrane protein D2 catalyzes facilitated diffusion of carbapenems and penems through the outer membrane of Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy 1990;34(1) 52-57. DOI: 10.1128/AAC.34.1.52.
70 - Trias J, Nikaido H. Protein D2 channel of the Pseudomonas aeruginosa outer membrane has a binding site for basic amino acids and peptides. Journal of Biological Chemistry 1990;265(26) 15680-15684.
71 - Ochs MM, Bains M, Hancock REW. Role of putative loops 2 and 3 in imipenem passage through the specific porin OprD of Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy 2000;44(7) 1983-1985. DOI: 10.1128/AAC.44.7.1983-1985.2000.
72 - Huang H, Jeanteur D, Pattus F, Hancock REW. Membrane topology and site specific mutagenesis of Pseudomonas aeruginosa porin OprD. Molecular Microbiology 1995;16(5) 931–941. DOI: 10.1111/j.1365-2958.1995.tb02319.x.
73 - Huang H, Hancock RW. The role of specific surface loop regions in determining the function of the imipenem-specific pore protein OprD of Pseudomonas aeruginosa. Journal of Bacteriology 1996;178(11) 3085-3090.
74 - Pirnay JP, De Vos D, Mossialos D, Vanderkelen A, Cornelis P, Zizi M. Analysis of the Pseudomonas aeruginosa oprD gene from clinical and environmental isolates. Environmental Microbiology 2002;4(12) 872-882. DOI: 10.1046/j.1462-2920.2002.00281.x.
75 - Chevalier S, Bodilis J, Jaouen T, Barray S, Feuilloley MGJ, Orange N. Sequence diversity of the OprD protein of environmental Pseudomonas strains. Environmental Microbiology 2007;9(3) 824-835. DOI: 10.1111/j.1462-2920.2006.01191.x.
76 - Epp SF, Köhler T, Plésiat P, Michéa-Hamzehpour M, Frey J, Pechère JC. C-terminal region of Pseudomonas aeruginosa outer membrane porin OprD modulates susceptibility to meropenem. Antimicrobial Agents and Chemotherapy 2001;45(6) 1780-1787. DOI: 10.1128/AAC.45.6.1780-1787.2001.
77 - Muramatsu H, Horii T, Morita M, Hashimoto H, Kanno T, Maekawa M. Effect of basic amino acids on susceptibility to carbapenems in clinical Pseudomonas aeruginosa isolates. International Journal of Medical Microbiology 2003;293(2-3) 191-197. DOI: 10.1078/1438-4221-00256.
78 - Young ML, Bains M, Bell A, Hancock RE. Role of Pseudomonas aeruginosa outer membrane protein OprH in polymyxin and gentamicin resistance: isolation of an OprH-deficient mutant by gene replacement techniques. Antimicrobial Agents and Chemotherapy 1992;36(11) 2566-2568. DOI: 10.1128/AAC.36.11.2566.
79 - Hancock RE, Chan L. Outer membranes of environmental isolates of Pseudomonas aeruginosa. Journal of Clinical Microbiology 1988;26(11) 2423-2424.
80 - M Vaara. Agents that increase the permeability of the outer membrane. Microbiological Reviews 1992;56(3) 395-411.
81 - Van Bambeke R, Balzi E, Tulkens PM. Antibiotic efflux pumps. Biochemical Pharmacology 2000;60(4) 457-470. DOI: 10.1016/S0006-2952(00)00291-4.
82 - Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S, Olson MV. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 2000;406(6799) 959-964. DOI: 10.1038/35023079.
83 - Lister PD, Wolter DJ, Hanson ND. Antibacterial-resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms. Clinical Microbiology Reviews 2009;22(4) 582-610. DOI: 10.1128/CMR.00040-09.
84 - Livermore DM, Woodford N. The beta-lactamase threat in Enterobacteriaceae, Pseudomonas and Acinetobacter. Trends in Microbiology 2006;14(9) 413-420. DOI: 10.1016/j.tim.2006.07.008.
85 - Poole K. Aminoglycoside resistance in Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy 2005;49(2) 479-487. DOI: 10.1128/AAC.49.2.479-487.2005.
86 - Yonezawa M, Takahata M, Matsubara N, Watanabe Y, Narita H. DNA gyrase gyrA mutations in quinolone-resistant clinical isolates of Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy 1995;39(9) 1970-1972. DOI: 10.1128/AAC.39.9.1970.
87 - Higgins PG, Fluit AC, Milatovic D, Verhoef J, Schmitz FJ. Mutations in GyrA, ParC, MexR and NfxB in clinical isolates of Pseudomonas aeruginosa. The International Journal of Antimicrobial Agents 2003;21(5) 409-413. DOI: 10.1016/S0924-8579(03)00009-8.
88 - Salma R, Dabboussi F, Kassaa I, Khudary R, Hamze M. gyrA and parC mutations in quinolone-resistant clinical isolates of Pseudomonas aeruginosa from Nini Hospital in north Lebanon. Journal of Infection and Chemotherapy 2013;19(1) 77-81. DOI: 10.1007/s10156-012-0455-y.
89 - Flemming HC, Wingender J. Relevance of microbial extracellular polymeric substances (EPSs)-Part I: Structural and ecological aspects. Water Science and Technology 2001;43(6) 1-8.
90 - Sutherland IW. Exopolysaccharides in biofilms, flocs and related structures. Water Science and Technology 2001;43(6) 77-86.
91 - Whitchurch CB, Tolker-Nielsen T, Ragas PC, Mattick JS. Extracellular DNA required for bacterial biofilm formation. Science 2002;295(5559) 1487. DOI: 10.1126/science.295.5559.1487.
92 - Toyofuku M, Roschitzki B, Riedel K, Eberl L. Identification of proteins associated with the Pseudomonas aeruginosa biofilm extracellular matrix. Journal of Proteome Research 2012;11(10) 4906-4915. DOI: 10.1021/pr300395j.
93 - Ghafoor A, Hay ID, Rehm BH. Role of exopolysaccharides in Pseudomonas aeruginosa biofilm formation and architecture. Applied and Environmental Microbiology 2011;77(15) 5238-5246. DOI: 10.1128/AEM.00637-11.
94 - Borriello G, Werner E, Roe F, Kim AM, Ehrlich GD, Stewart PS. Oxygen limitation contributes to antibiotic tolerance of Pseudomonas aeruginosa in biofilms. Antimicrobial Agents and Chemotherapy 2004;48(7) 2659-2664. DOI: 10.1128/AAC.48.7.2659-2664.2004.
95 - Brown MRW, Allison DG, Gilbert P. Resistance of bacterial biofilms to antibiotics: a growth-rate related effect? Journal of Antimicrobial Chemotherapy 1988;22(6) 777-783. DOI: 10.1093/jac/22.6.777.
96 - Hoyle BD, Alcantara J, Costerton JW. Pseudomonas aeruginosa biofilm as a diffusion barrier to piperacillin. Antimicrobial Agents and Chemotherapy 1992;36(9) 2054-2056. DOI: 10.1128/AAC.36.9.2054.
97 - Shigeta M, Tanaka G, Komatsuzawa H, Sugai M, Suginaka H, Usui T. Permeation of antimicrobial agents through Pseudomonas aeruginosa biofilms: a simple method. Chemotherapy 1997;43(5) 340-345.
98 - Alipour M, Suntres ZE, Omri A. Importance of DNase and alginate lyase for enhancing free and liposome encapsulated aminoglycoside activity against Pseudomonas aeruginosa. Journal of Antimicrobial Chemotherapy 2009;64(2) 317-325. DOI: 10.1093/jac/dkp165.
99 - Pamp SJ, Gjermansen M, Johansen HK, Tolker-Nielsen T. Tolerance to the antimicrobial peptide colistin in Pseudomonas aeruginosa biofilms is linked to metabolically active cells, and depends on the pmr and mexAB-oprM genes. Molecular Microbiology 2008;68(1) 223-240. DOI: 10.1111/j.1365-2958.2008.06152.x.
100 - Banin E, Brady KM, Greenberg EP. Chelator-induced dispersal and killing of Pseudomonas aeruginosa cells in a biofilm. Applied and Environmental Microbiology 2006;72(3) 2064-2069. DOI: 10.1128/AEM.72.3.2064-2069.2006.
101 - Kock JLF, Botha A, Blerh J, Nigam S. Used cooking oil: science tackles a potential health hazard. South African Journal of Science 1996;92(11-12) 513–514.
102 - Haba E, Espuny MJ, Busquets M, Manresa A. Screening and production of rhamnolipids by Pseudomonas aeruginosa 47T2 NCIB 40044 from waste frying oils. Journal of Applied Microbiology 2000;88(3) 379-387. DOI: 10.1046/j.1365-2672.2000.00961.x.
103 - Makkar RS, Cameotra SS. An update on the use of unconventional substrates for biosurfactant production and their new applications. Applied Microbiology and Biotechnology 2002;58(4) 428-434. DOI: 10.1007/s00253-001-0924-1.
104 - Nitschke M, Costa SG, Haddad R, Gonçalves LA, Eberlin MN, Contiero J. Oil wastes as unconventional substrates for rhamnolipid biosurfactant production by Pseudomonas aeruginosa LBI. Biotechnology Progress 2005;21(5) 1562-1566. DOI: 10.1021/bp050198x.
105 - Thavasi R, Subramanyam Nambaru VRM, Jayalakshmi S, Balasubramanian T, Banat IM. Biosurfactant production by Pseudomonas aeruginosa from renewable resources. Indian Journal of Microbiology 2011;51(1) 30-36. DOI: 10.1007/s12088-011-0076-7.
106 - Venkatesh NM, Vedaraman N. Remediation of soil contaminated with copper using rhamnolipids produced from Pseudomonas aeruginosa MTCC 2297 using waste frying rice bran oil. Annals of Microbiology 2012;62(1) 85-91. DOI: 10.1007/s13213-011-0230-9.
107 - Babu PS, Vaidya AN, Bal AS, Kapur R, Juwarkar A, Khanna P. Kinetics of biosurfactant production by Pseudomonas aeruginosa strain BS2 from industrial wastes. Biotechnology Letters 1996;18(3) 263-268. DOI: 10.1007/BF00142942.
108 - George S, Jayachandran K. Production and characterization of rhamnolipid biosurfactant from waste frying coconut oil using a novel Pseudomonas aeruginosa D. Journal of Applied Microbiology 2013;114(2) 373-383. DOI: 10.1111/jam.12069.
109 - Colak AK, Kahraman H. The use of raw cheese whey and olive oil mill wastewater for rhamnolipid production by recombinant Pseudomonas aeruginosa. Environmental and Experimental Biology 2013;11(3) 125-130.
110 - Rashedi H, Assadi MM, Bonakdarpour B, Jamshidi E. Environmental importance of rhamnolipid production from molasses as a carbon source. Internation Journal of Environmental Science and Technology 2005;2(1) 59-62. DOI: 10.1007/BF03325858.
111 - Costa SG, Lépine F, Milot S, Déziel E, Nitschke M, Contiero J. Cassava wastewater as a substrate for the simultaneous production of rhamnolipids and polyhydroxyalkanoates by Pseudomonas aeruginosa. Journal of Industrial Microbiology and Biotechnology 2009;36(8) 1063-1072. DOI: 10.1007/s10295-009-0590-3.
112 - Fernández D, Rodríguez E, Bassas M, Viñas M, Solanas AM, Llorens J, Marqués AM, Manresa A. Agro-industrial oily wastes as substrates for PHA production by the new strain Pseudomonas aeruginosa NCIB 40045: Effect of culture conditions. Biochemical Engineering Journal 2005;26(2) 159-167. DOI: 10.1016/j.bej.2005.04.022.
113 - Phukon P, Phukan MM, Phukan S, Konwa BK. Polyhydroxyalkanoate production by indigenously isolated Pseudomonas aeruginosa using glycerol by-product of KCDL biodiesel as an inexpensive carbon source. Annals of Microbiology 2014;64(4) 1567-1574. DOI 10.1007/s13213-014-0800-8.
114 - Füchtenbusch B, Wullbrandt D, Steinbüchel A. Production of polyhydroxyalkanoic acids by Ralstonia eutropha and Pseudomonas oleovorans from an oil remaining from biotechnological rhamnose production. Applied Microbiology and Biotechnology 2000;53(2) 167-172. DOI: 10.1007/s002530050004.
115 - Ribera RG, Monteoliva-Sanchez M, Ramos-Cormenzana A. Production of polyhydroxyalkanoates by Pseudomonas putida KT2442 harboring pSK2665 in wastewater from olive oil mills (alpechín). Electronic Journal of Biotechnology 2001;4(2) 116-119.
116 - Sajjan S, Purification and physiochemical characterization of melanin pigment from Klebsiella sp. GSK. Journal of Microbiology and Biotechnology 2010;20(11) 1513-1520.
117 - Geng J, Yuan P, Shao C, Yu SB, Zhou B, Zhou P, Chen XD. Bacterial melanin interacts with double-stranded DNA with high affinity and may inhibit cell metabolism in vivo. Archives of Microbiology 2010;192(5) 321-329. DOI: 10.1007/s00203-010-0560-1.
118 - Tarangini K, Mishra S. Production, characterization and analysis of melanin from isolated marine Pseudomonas sp. using vegetable waste. Research Journal of Engineering Sciences 2013;2(5) 40-46.
119 - Dayanandan A, Kanagaraj J, Sounderraj L, Govindaraju R., Rajkumar GS. Application of an alkaline protease in leather processing: an ecofriendly approach. Journal of Cleaner Production 2003;11(5) 533-536. DOI: 10.1016/S0959-6526(02)00056-2.
120 - Kumar AG, Swarnalatha S, Sairam B, Sekaran G. Production of alkaline protease by Pseudomonas aeruginosa using proteinaceous solid waste generated from leather manufacturing industries. Bioresource Technology 2008;99(6) 1939-1944. DOI: 10.1016/j.biortech.2007.03.025.
121 - Jellouli K, Bayoudh A, Manni L, Agrebi R, Nasri M. Purification, biochemical and molecular characterization of a metalloprotease from Pseudomonas aeruginosa MN7 grown on shrimp wastes. Applied Microbiology and Biotechnology 2008;79(6) 989-999. DOI: 10.1007/s00253-008-1517-z.
122 - Wang SL, Chen SJ, Wang CL. Purification and characterization of chitinases and chitosanases from a new species strain Pseudomonas sp. TKU015 using shrimp shells as a substrate. Carbohydrate Research 2008;19;343(7) 1171-1179. DOI: 10.1016/j.carres.2008.03.018.
123 - Cervantes-González E, Rojas-Avelizapa NG, Cruz-Camarillo R, García-Mena J, Rojas-Avelizapa LI. Oil-removal enhancement in media with keratinous or chitinous wastes by hydrocarbon-degrading bacteria isolated from oil-polluted soils. Environmental Technology 2008;29(2) 171-182. DOI: 10.1080/09593330802028659.
124 - Poorni KE, Manikandan A, Geethanjali S, Percy PK. Production of Pseudomonas fluorescence from agricultural wastes and its application in the preservation of selected vegetables. Advances in Applied Science Research 2011;2(2) 156-160.
125 - Sepperumal U, Selvanayagam S, Markandan M. Utilization of toner waste black powder for bacterial growth. Journal of Microbiology and Biotechnology Research 2014;4(1) 28-30.
126 - Zhong W, Zhu C, Shu M, Sun K, Zhao L, Wanga C, Ye Z, Chen J. Degradation of nicotine in tobacco waste extract by newly isolated Pseudomonas sp. ZUTSKD. Bioresource Technology 2010;101(18) 6935-6941. DOI: 10.1016/j.biortech.2010.03.142.
127 - Jørgensen F, Bally M, Chapon-Herve V, Michel G, Lazdunski A, Williams P, Stewart GS. RpoS-dependent stress tolerance in Pseudomonas aeruginosa. Microbiology 1999;145(Pt 4) 835-844. DOI: 10.1099/13500872-145-4-835.
128 - Murakami K, Ono T, Viducic D, Kayama S, Mori M, Hirota K, Nemoto K, Miyake Y. Role for rpoS gene of Pseudomonas aeruginosa in antibiotic tolerance. FEMS Microbiology Letters 2005;242(1) 161-167. DOI: 10.1016/j.femsle.2004.11.005.
129 - Martin DW, Schurr MJ, Yu H, Deretic V. Analysis of promoters controlled by the putative sigma factor AlgU regulating conversion to mucoidy in Pseudomonas aeruginosa: relationship to σE and stress response. Journal of Bacteriology 1994;176(21) 6688-6696.
130 - Keith LMW, Bender CL. AlgT (σ22) controls alginate production and tolerance to environmental stress in Pseudomonas syringae. Journal of Bacteriology 1999;181(23) 7176-7184.
131 - Schurr MJ, Deretic V. Microbial pathogenesis in cystic fibrosis: co-ordinate regulation of heat-shock response and conversion to mucoidy in Pseudomonas aeruginosa. Molecular Microbiology 1997;24(2) 411-420. DOI: 10.1046/j.1365-2958.1997.3411711.x.
132 - Schurr MJ, Yu H, Boucher JC, Hibler NS, Deretic V. Multiple promoters and induction by heat shock of the gene encoding the alternative sigma factor AlgU (σE) which controls mucoidy in cystic fibrosis isolates of Pseudomonas aeruginosa. Journal of Bacteriology 1995;177(19) 5670-5679.
133 - Yu H, Schurr MJ, Deretic V. Functional equivalence of Escherichia coli σE and Pseudomonas aeruginosa AlgU: E. coli rpoE restores mucoidy and reduces sensitivity to reactive oxygen intermediates in algU mutants of P. aeruginosa. Journal of Bacteriology 1995;177(11) 3259-3268.
134 - Schnider-Keel U, Lejbølle KB, Baehler E, Haas D, Keel C. The sigma factor AlgU (AlgT) controls exopolysaccharide production and tolerance towards desiccation and osmotic stress in the biocontrol agent Pseudomonas fluorescens CHA0. Applied and Environmental Microbiology 2001;67(12) 5683-5693. DOI: 10.1128/AEM.67.12.5683-5693.2001.
135 - Govan J, Deretic V. Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia. Microbiological Reviews 1996;60(3) 539-574.
136 - Mathee K, McPherson CJ, Ohman DE. Posttranslational control of the algT (algU)-encoded sigma22 for expression of the alginate regulon in Pseudomonas aeruginosa and localization of its antagonist proteins MucA and MucB (AlgN). Journal of Bacteriology 1997;179(11) 3711-3720.
137 - Pham TH, Webb JS, Rehm BHA. The role of polyhydroxyalkanoate biosynthesis by Pseudomonas aeruginosa in rhamnolipid and alginate production as well as stress tolerance and biofilm formation. Microbiology 2004;150(10) 3405-3413. DOI: 10.1099/mic.0.27357-0.
138 - Gentry DR, Hernandez VJ, Nguyen LH, Jensen DB, Cashel M. Synthesis of the stationary-phase sigma factor σs is positively regulated by ppGpp. Journal of Bacteriology 1993;175(24) 7982-7989.
139 - Rangeshwaran R, Ashwitha K, Sivakumar G, Jalali SK. Analysis of proteins expressed by an abiotic stress tolerant Pseudomonas putida (NBAII-RPF9) isolate under saline and high temperature conditions. Current Microbiology 2013;67(6) 659-667. DOI: 10.1007/s00284-013-0416-4.
140 - Aspedon A, Palmer K, Whiteley M. Microarray analysis of the osmotic stress response in Pseudomonas aeruginosa. Journal of Bacteriology 2006;188(7) 2721-2725. DOI: 10.1128/JB.188.7.2721-2725.2006.
141 - Frank DW. The exoenzyme S regulon of Pseudomonas aeruginosa. Molecular Microbiology 1997;26(4) 621-629. DOI: 10.1046/j.1365-2958.1997.6251991.x.
142 - Hueck CJ. Type III protein secretion systems in bacterial pathogens of animals and plants. Microbiology and Molecular Biology Reviews 1998;62(2) 379-433.
143 - D'Souza-Ault MR, Smith LT, Smith GM. Roles of N-acetylglutaminylglutamine amide and glycine betaine in adaptation of Pseudomonas aeruginosa to osmotic stress. Applied and Environmental Microbiology 1993;59(2) 473-478.
144 - Sardessai Y, Bhosle S. Tolerance of bacteria to organic solvents. Research in Microbiology 2002;153(5) 263-268. DOI: 10.1016/S0923-2508(02)01319-0.
145 - Teitzel GM, Parsek MR. Heavy metal resistance of biofilm and planktonic Pseudomonas aeruginosa. Applied and Environmental Microbiology 2003;69(4) 2313-2320. DOI: 10.1128/AEM.69.4.2313-2320.2003.
146 - Boopathy NR, Indhuja D, Srinivasan K, Uthirappan M, Gupta R, Ramudu KN, Chellan R. Statistical medium optimization of an alkaline protease from Pseudomonas aeruginosa MTCC 10501, its characterization and application in leather processing. Indian Journal of Experimental Biology 2013;51(4) 336-342.
147 - Kojima Y, Sakuradani E, Shimizu S. Different specificities of two types of Pseudomonas lipases for C20 fatty acids with a Δ5 unsaturated double bond and their application for selective concentration of fatty acids. Journal of Bioscience and Bioengineering 2006;101(6) 490-500. DOI: 10.1263/jbb.101.496.
148 - Cheirsilp B, Jeamjounkhaw P, Kittikun AH. Optimizing an alginate immobilized lipase for monoacylglycerol production by the glycerolysis reaction. Journal of Molecular Catalysis B: Enzymatic 2009;59(1-3) 206-211. DOI: 10.1016/j.molcatb.2009.03.001.
149 - Zhang A, Gao R, Diao N, Xie G, Gao G, Cao S. Cloning, expression and characterization of an organic solvent tolerant lipase from Pseudomonas fluorescens JCM5963. Journal of Molecular Catalysis B: Enzymatic 2009;56(2-3) 78-84. DOI: 10.1016/j.molcatb.2008.06.021.
150 - Priya K, Chadha A. Synthesis of hydrocinnamic esters by Pseudomonas cepacia lipase. Enzyme and Microbial Technology 2003;32(3-4) 885-890. DOI: 10.1016/S0141-0229(02)00340-X.
151 - Li Q, Yan Y. Production of biodiesel catalyzed by immobilized Pseudomonas cepacia lipase from Sapium sebiferum oil in micro-aqueous phase. Applied Energy 2008;87(10) 3148-3154. DOI: 03/13/201510.1016/j.apenergy.2010.02.032.
152 - Vandana P, Peter JK. Application of partially purified laccases from Pseudomonas fluorescens on dye decolourization. International Journal of Advanced Technology in Engineering and Science 2014;2(8) 317-327.
153 - Kumar V, Singh S, Manhas A, Singh J, Singla S, Kaur P, Data S, Negi P, Kalia A. Bioremediation of petroleum hydrocarbon by using Pseudomonas species isolated from petroleum contaminated soil. Oriental Journal of Chemistry 2014;30(4) 1771-1776.
154 - Sathiya-Moorthi P, Deecaraman M, Kalaichelvan PT. Bioremediation of automobile oil effluent by Pseudomonas sp. Advanced Biotech 2008;31 34-37.
155 - Roy AS, Yenn R, Singh AK, Boruah HPD, Saikia N, Deka M. Bioremediation of crude oil contaminated tea plantation soil using two Pseudomonas aeruginosa strains AS 03 and NA 108. African Journal of Biotechnology 2013;12(19) 2600-2610. DOI: 10.5897/AJB12.170
156 - Baltazar M, Gracioso L, Avanzi I, Veiga M, Gimenes L, Nascimento C, Perpetuo E. Bioremediation potential of Pseudomonas aeruginosa and Enterobacter cloacae isolated from a copper-contaminated area. BMC Proceedings 2014;8(Suppl 4) P188. DOI: 10.1186/1753-6561-8-S4-P188.
157 - Ali Khan MW, Ahmad M. Detoxification and bioremediation potential of a Pseudomonas fluorescens isolate against the major Indian water pollutants. Journal of Environmental Science and Health, Part A: Toxic/Hazardous Substances and Environmental Engineering 2006;41(4) 659-674. DOI: 10.1080/10934520600575051.
158 - Singh R, Bishnoi NR, Kirrolia A. Evaluation of Pseudomonas aeruginosa an innovative bioremediation tool in multi metals ions from simulated system using multi response methodology. Bioresource Technology 2013;138 222-234. DOI: 10.1016/j.biortech.2013.03.100.
159 - Moorthi PS, Selvam SP, Sasikalaveni A, Murugesan K, Kalaichelvan PT. Decolorization of textile dyes and their effluents using white rot fungi. African Journal of Biotechnology 2007;6(4) 424-429.
160 - Silveira E, Marques PP, Silva SS, Lima-Filho JL, Porto ALF, Tambourgi EB. Selection of Pseudomonas for industrial textile dyes decolourization. International Biodeterioration and Biodegradation 2009;63(2) 230-235. DOI: 10.1016/j.ibiod.2008.09.007.
161 - Daneshvar N, Ayazloo M, Khataee AR, Pourhassan M. Biological decolorization of dye solution containing Malachite Green by microalgae Cosmarium sp. Bioresource Technology 2007;98(6) 1176-1182. DOI: 10.1016/j.biortech.2006.05.025.
162 - Shah MP, Patel KA, Nair SS, Darji AM. Microbial decolourization of methyl orange dye by Pseudomonas spp. OA Biotechnology 2013;2(1) 10.
163 - Joe J, Kothari RK, Raval CM, Kothari CR, Akbari VG, Singh SP. Decolorization of textile dye Remazol Black B by Pseudomonas aeruginosa CR-25 isolated from the common effluent treatment plant. Journal of Bioremediation and Biodegradation 2011;2 118. DOI: 10.4172/2155-6199.1000118.
164 - Wu J, Jung BG, Kim KS, Lee YC, Sung NC. Isolation and characterization of Pseudomonas otitidis WL-13 and its capacity to decolorize triphenylmethane dyes. Journal of Environmental Sciences 2009;21(7) 960-964. DOI: 10.1016/S1001-0742(08)62368-2.
165 - Chen JP, Lin YS. Decolorization of azo dye by immobilized Pseudomonas luteola entrapped in alginate–silicate sol–gel beads. Process Biochemistry 2007;42(6) 934-942. DOI: 10.1016/j.procbio.2007.03.001.
166 - Işik M, Sponza DT. Effect of oxygen on decolorization of azo dyes by Escherichia coli and Pseudomonas sp. and fate of aromatic amines. Process Biochemistry 2003;38(8) 1183-1192. DOI: 10.1016/S0032-9592(02)00282-0.
167 - Chang JS, Chou C, Lin YC, Lin PJ, Ho JY, Hu TL. Kinetic characteristics of bacterial azo-dye decolorization by Pseudomonas luteola. Water Research 2001;35(12) 2841-2850. DOI: 10.1016/S0043-1354(00)00581-9.
168 - Voisard C, Keel C, Haas D, Dèfago G. Cyanide production by Pseudomonas fluorescens helps suppress black root rot of tobacco under gnotobiotic conditions. The EMBO Journal 1989 Feb;8(2) 351-358.
169 - Nandakumar R, Babu S, Viswanathan R, Raguchander T, Samiyappan R. Induction of systemic resistance in rice against sheath blight disease by Pseudomonas fluorescens. Soil Biology and Biochemistry 2001;33(4-5) 603-612. DOI: 10.1016/S0038-0717(00)00202-9.
170 - Samavat S, Heydari A, Zamanizadeh HR, Rezaee S, Aliabadi AA. Application of new bioformulations of Pseudomonas aureofaciens for biocontrol of cotton seedling damping-off. Journal of Plant Protection Research 2014;54(4) 334-339. DOI: 10.2478/jppr-2014-0050.
171 - Khan MR, Haque Z. Soil application of Pseudomonas fluorescens and Trichoderma harzianum reduces root-knot nematode, Meloidogyne incognita, on tobacco. Phytopathologia Mediterranea 2011;50(2) 257-266. DOI: 10.14601/Phytopathol_Mediterr-9252.
172 - Vanitha S, Ramjegathesh R. Bio control potential of Pseudomonas fluorescens against coleus root rot disease. Journal of Plant Pathology and Microbiology 2014;5(1) 1-4. DOI: 10.4172/2157-7471.1000216.
173 - Heil M, Bostock RM. Induced systemic resistance (ISR) against pathogens in the context of induced plant defences. Annals of Botany 2002:89(5) 503-512. DOI: 10.1093/aob/mcf076.