Isolation and identification of Pseudomonas spp. from Schirmacher Oasis, Antarctica

Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India

Strain HHS 22(T) was isolated from a glacial water sample from the snout of the Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Pedobacter. HHS 22(T) exhibits high 16S rRNA gene sequence similarity with Pedobacter cryoconitis (98 %). However, the level of DNA-DNA relatedness between HHS 22(T) and P. cryoconitis is only 42 %. Furthermore, HHS 22(T) differs from P. cryoconitis and the four other recognized species of Pedobacter in a number of phenotypic characteristics. These data suggest that HHS 22(T) represents a novel species of the genus Pedobacter, for which the name Pedobacter himalayensis sp. nov. is proposed. The type strain is HHS 22(T) (= JCM 12171(T) = MTCC 6384(T)).

Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India

Strain HHS 11T was isolated from a water sample collected from the snout of Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Dyadobacter. HHS 11T possessed 96 and 95 % 16S rRNA gene sequence similarity with respect to Dyadobacter crusticola and Dyadobacter fermentans, respectively. Furthermore, strain HHS 11T differs from D. crusticola and D. fermentans in a number of phenotypic characteristics. These data suggest that strain HHS 11T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter hamtensis sp. nov. is proposed. The type strain is HHS 11T (=JCM 12919T=MTCC 7023T).

Psychrobacter vallis sp. nov. and Psychrobacter aquaticus sp. nov., from Antarctica

Twelve strains of psychrophilic bacteria were isolated from cyanobacterial mat samples collected from various water bodies in the McMurdo Dry Valley region of Antarctica. All the isolates were Gram-negative, non-motile, coccoid, psychrophilic, halotolerant bacteria and had C(16 : 1)omega7c, C(17 : 1)omega8c and C(18 : 1)omega9c as the major fatty acids, ubiquinone-8 as the respiratory quinone and DNA G+C content of 41-46 mol%. Based on these characteristics, the isolates were assigned to the genus Psychrobacter. Based on their SDS-PAGE profiles, the 12 isolates could be categorized into three groups. Six isolates of Group I were identified as representing strains of Psychrobacter okhotskensis. However, using detailed phenotypic and chemotaxonomic characteristics and phylogenetic analysis based on their 16S rRNA gene sequences, strain CMS 39(T), the only strain from Group II, and strain CMS 56(T), a representative strain of Group III, were different from each other and from all recognized species of Psychrobacter. Therefore, it is proposed to classify CMS 39(T) (=DSM 15337(T)=MTCC 4208(T)) and CMS 56(T) (=DSM 15339(T)=MTCC 4386(T)) as representing the type strains of novel species of Psychrobacter, for which the names Psychrobacter vallis sp. nov. and Psychrobacter aquaticus sp. nov., respectively, are proposed.

RecD plays an essential function during growth at low temperature in the antarctic bacterium Pseudomonas syringae Lz4W

The Antarctic psychrotrophic bacterium Pseudomonas syringae Lz4W has been used as a model system to identify genes that are required for growth at low temperature. Transposon mutagenesis was carried out to isolate mutant(s) of the bacterium that are defective for growth at 4 degrees but normal at 22 degrees . In one such cold-sensitive mutant (CS1), the transposon-disrupted gene was identified to be a homolog of the recD gene of several bacteria. Trans-complementation and freshly targeted gene disruption studies reconfirmed that the inactivation of the recD gene leads to a cold-sensitive phenotype. We cloned, sequenced, and analyzed approximately 11.2 kbp of DNA from recD and its flanking region from the bacterium. recD was the last gene of a putative recCBD operon. The RecD ORF was 694 amino acids long and 40% identical (52% similar) to the Escherichia coli protein, and it could complement the E. coli recD mutation. The recD gene of E. coli, however, could not complement the cold-sensitive phenotype of the CS1 mutant. Interestingly, the CS1 strain showed greater sensitivity toward the DNA-damaging agents, mitomycin C and UV. The inactivation of recD in P. syringae also led to cell death and accumulation of DNA fragments of approximately 25-30 kbp in size at low temperature (4 degrees ). We propose that during growth at a very low temperature the Antarctic P. syringae is subjected to DNA damage, which requires direct participation of a unique RecD function. Additional results suggest that a truncated recD encoding the N-terminal segment of (1-576) amino acids is sufficient to support growth of P. syringae at low temperature.

Psychrobacter salsus sp. nov. and Psychrobacter adeliensis sp. nov. isolated from fast ice from Adelie Land, Antarctica

Nine psychrotolerant bacteria were isolated from fast ice in the middle of Geologie Archipelago, Adelie Land, Antarctica and were categorized into two groups, based on their SDS-PAGE profiles. Representatives from each of the two groups, namely strains DD 48T and SJ 14T exhibited phenotypic and chemotaxonomic characteristics confirming to the genus Psychrobacter. The 16S rRNA gene sequence indicated that the two isolates are closely related to each other and to the already reported fifteen species of Psychrobacter. Detailed studies on the phenotypic characteristics, chemotaxonomic properties and phylogenetic analysis of strains DD 48T and SJ 14T indicated that they are distinctly different from each other and the reported species of Psychrobacter. At the DNA-DNA hybridisation level, the two species exhibit less than 70% similarity. Thus, strains DD 48T and SJ 14T are identified as new species of the genus Psychrobacter for which the names Psychrobacter salsus sp. nov. and Psychrobacter adeliensis sp. nov. respectively are proposed.

Cis-trans isomerase gene in psychrophilic Pseudomonas syringae is constitutively expressed during growth and under conditions of temperature and solvent stress

In a recent study, we established that psychrophilic Pseudomonas syringae (Lz4W) requires trans-monounsaturated fatty acid for growth at higher temperatures (Kiran et al. in Extremophiles, 2004). It was also demonstrated that the cti gene was highly conserved and exhibited high sequence identity with cti of other Pseudomonas spp. (Kiran et al. in Extremophiles, 2004). Therefore it would be interesting to understand the expression of the cti gene so as to unravel the molecular basis of adaptation of microorganisms to high temperature. In the present study, the expression of cti was monitored by RT-PCR analysis during different growth stages and under conditions of high temperature and solvent stress in P. syringae. Results indicated that the cti gene is constitutively expressed during different stages of growth and the transcript level is unaltered even under conditions of temperature and solvent stress implying that the observed increase in trans-monounsaturated fatty acids (Kiran et al. in Extremophiles, 2004) is not under transcriptional control. A putative promoter present in the intergenic region of the metH and cti gene has also been characterized. The translation start site ATG, the Shine-Dalgarno sequence AGGA and the transcription start site "C" were also identified. These results provide evidence for the first time that the cti gene is constitutively expressed under normal conditions of growth and under conditions of temperature and solvent stress thus implying that the Cti enzyme is post-transcriptionally regulated.

Psychrophilic Pseudomonas syringae requires trans-monounsaturated fatty acid for growth at higher temperature

A psychrophilic bacterium, Pseudomonas syringae (Lz4W) from Antarctica, was used as a model system to establish a correlation, if any, between thermal adaptation, trans-fatty acid content and membrane fluidity. In addition, attempts were made to clone and sequence the cti gene of P. syringae (Lz4W) so as to establish its characteristics with respect to the cti of other Pseudomonas spp. and also to in vitro mutagenize the cti gene so as to generate a cti null mutant. The bacterium showed increased proportion of saturated and trans-monounsaturated fatty acids when grown at 28 degrees C compared to cells grown at 5 degrees C, and the membrane fluidity decreased with growth temperature. In the mutant, the trans-fatty acid was not synthesized, and the membrane fluidity also decreased with growth temperature, but the decrease was not to the extent that was observed in the wild-type cells. Thus, it would appear that synthesis of trans-fatty acid and modulation of membrane fluidity to levels comparable to the wild-type cells is essential for growth at higher temperatures since the mutant exhibits growth arrest at 28 degrees C. In fact, the cti null mutant-complemented strain of P. syringae (Lz4W-C30b) that was capable of synthesizing the trans-fatty acid was indeed capable of growth at 28 degrees C, thus confirming the above contention. The cti gene of P. syringae (Lz4W) that was cloned and sequenced exhibited high sequence identity with the cti of other Pseudomonas spp. and exhibited all the conserved features.

Psychrophilic pseudomonads from Antarctica: Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov

Thirty-one bacteria that belonged to the genus Pseudomonas were isolated from cyanobacterial mat samples that were collected from various water bodies in Antarctica. All 31 isolates were psychrophilic; they could be divided into three groups, based on their protein profiles. Representative strains of each of the three groups, namely CMS 35T, CMS 38T and CMS 64T, were studied in detail. Based on 16S rRNA gene sequence analysis, it was established that the strains were related closely to the Pseudomonas fluorescens group. Phenotypic and chemotaxonomic characteristics further confirmed their affiliation to this group. The three strains could also be differentiated from each other and the closely related species Pseudomonas orientalis, Pseudomonas brenneri and Pseudomonas migulae, based on phenotypic and chemotaxonomic characteristics and the level of DNA–DNA hybridization. Therefore, it is proposed that strains CMS 35T (=MTCC 4992T=DSM 15318T), CMS 38T (=MTCC 4993T=DSM 15319T) and CMS 64T (=MTCC 4994T=DSM 15321T) should be assigned to novel species of the genus Pseudomonas as Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov., respectively.

Sporosarcina macmurdoensis sp. nov., from a cyanobacterial mat sample from a pond in the McMurdo Dry Valleys, Antarctica

Strain CMS 21w(T) was isolated from a cyanobacterial mat sample taken from a pond located in the McMurdo Dry Valleys, Antarctica. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain CMS 21w(T) was identified as a member of the genus SPOROSARCINA: At the 16S rRNA gene level, CMS 21w(T) exhibited about 93-96 % similarity to all reported species of Sporosarcina and exhibited a maximum similarity of 96 % to both Sporosarcina globispora and Sporosarcina psychrophila. Based on more than 3 % difference at the 16S rRNA gene sequence level and the presence of distinct differences with respect to phenotypic, biochemical and chemotaxonomic features, strain CMS 21w(T) (=MTCC 4670(T)=DSM 15428(T)=CIP 107784(T)) is proposed as the type strain of a novel species of Sporosarcina, Sporosarcina macmurdoensis sp. nov.

Low-temperature-induced changes in composition and fluidity of lipopolysaccharides in the antarctic psychrotrophic bacterium Pseudomonas syringae

The Antarctic psychrotrophic bacterium Pseudomonas syringae was more sensitive to polymyxin B at a lower (4 degrees C) temperature of growth than at a higher (22 degrees C) temperature. The amount of hydroxy fatty acids in the lipopolysaccharides (LPS) also increased at the lower temperature. These changes correlated with the increase in fluidity of the hydrophobic phase of lipopolysaccharide aggregates in vitro.

Cloning, sequencing, and expression of the cold-inducible hutU gene from the antarctic psychrotrophic bacterium Pseudomonas syringae

A promoter-fusion study with a Tn 5-based promoter probe vector had earlier found that the hutU gene which encodes the enzyme urocanase for the histidine utilization pathway is upregulated at a lower temperature (4 degrees C) in the Antarctic psychrotrophic bacterium Pseudomonas syringae. To examine the characteristics of the urocanase gene and its promoter elements from the psychrotroph, the complete hutU and its upstream region from P. syringae were cloned, sequenced, and analyzed in the present study. Northern blot and primer extension analyses suggested that the hutU gene is inducible upon a downshift of temperature (22 to 4 degrees C) and that there is more than one transcription initiation site. One of the initiation sites was specific to the cells grown at 4 degrees C, which was different from the common initiation sites observed at both 4 and 22 degrees C. Although no typical promoter consensus sequences were observed in the flanking region of the transcription initiation sites, there was a characteristic CAAAA sequence at the -10 position of the promoters. Additionally, the location of the transcription and translation initiation sites suggested that the hutU mRNA contains a long 5'-untranslated region, a characteristic feature of many cold-inducible genes of mesophilic bacteria. A comparison of deduced amino acid sequences of urocanase from various bacteria, including the mesophilic and psychrotrophic Pseudomonas spp., suggests that there is a high degree of similarity between the enzymes. The enzyme sequence contains a signature motif (GXGX(2)GX(10)G) of the Rossmann fold for dinucleotide (NAD(+)) binding and two conserved cysteine residues in and around the active site. The psychrotrophic enzyme, however, has an extended N-terminal end.

Development of a cold resistant mutant of plant growth promoting Pseudomonas fluorescens and its functional characterization

A cold resistant mutant of plant growth promoting Pseudomonas fluorescens GRS(1), was isolated following N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) treatment. The mutant was able to grow and promote root and shoot elongation of wheat both at 25 and 10 degrees C, a temperature at which the wild type was unable to proliferate and function. In an effort to determine the mechanistic basis for this behavior, it was observed that following growth at 10 degrees C, the mutant synthesized some new proteins. SDS-polyacrylamide gel electrophoresis of the protein synthesized by the mutant revealed the presence of one major protein with a molecular mass of 13.5 kDa. However, at this point the function of this protein in not known.

A RNA polymerase with transcriptional activity at 0 degrees C from the Antarctic bacterium Pseudomonas syringae

A DNA-dependent RNA polymerase was purified from the Antarctic psychrotrophic bacterium Pseudomonas syringae. The RNA polymerase showed a typical eubacterial subunit composition with beta, beta', alpha2 and sigma subunits. The subunits cross-reacted with antibodies raised against holoenzyme and the individual subunits of the RNA polymerase of Escherichia coli. However, the enzyme was considered unique, since unlike the RNA polymerase of mesophilic E. coli it exhibited significant and consistent transcriptional activity (10-15%) even at 0 degrees C. But, similar to the enzyme from the mesophilic bacterium, the RNA polymerase from P. syringae exhibited optimum activity at 37 degrees C. The study also demonstrates that the RNA polymerase of P. syringae could preferentially transcribe the cold-inducible gene cspA of E. coli only at lower temperatures (0-22 degrees C). The polymerase was also observed to be relatively more rifampicin-resistant during transcription at lower temperature.

Studies on the cytoplasmic protein tyrosine kinase activity of the Antarctic psychrotrophic bacterium Pseudomonas syringae

The Antarctic psychrotrophic bacterium Pseudomonas syringae contains a 66-kDa cytoplasmic protein which was found to by phosphorylated on a tyrosine residue [Ray, M.K. et al. (1994) FEMS Microbiol. Lett. 122, pp. 49-54]. To investigate the nature of the cytoplasmic protein tyrosine kinase and its role in the bacterial physiology, we carried out some biochemical studies of the enzyme in vitro in the presence of exogenous peptide substrates and expression studies in vivo at low and high temperature during various phases of growth. The results suggest that the protein tyrosine kinase associated with the cytoplasmic fraction of the bacterium has certain similarities and dissimilarities with the known eukaryotic tyrosine kinases. The protein tyrosine kinase could phosphorylate exogenous substrate corresponding to the N-terminal peptide of p34cdc2 kinase but could not do so on poly(Glu:Tyr). The enzyme could not be inhibited by genistein, staurosporine and dimethyl aminopurine, but could be inhibited by piceatannol which is a known competitive inhibitor of the peptide binding site of mammalian protein tyrosine kinases. The enzyme activity in the cytoplasm is uniquely inhibited by sodium orthovanadate (IC50 = 20 microM) which is a known protein tyrosine phosphatase inhibitor. The expression studies show that the enzyme is produced more at a higher temperature (22 degrees C) of growth than at lower temperature (4 degrees C) and during the stationary phase of growth of P. syringae.

Siderotyping of fluorescent pseudomonads: characterization of pyoverdines of Pseudomonas fluorescens and Pseudomonas putida strains from Antarctica

Five independent fluorescent pseudomonad isolates originating from Antarctica were analysed for their pyoverdine systems. A pyoverdine-related siderotyping, which involved pyoverdine-induced growth stimulation, pyoverdine-mediated iron uptake, pyoverdine analysis by electrophoresis and isoelectric focusing, revealed three different pyoverdine-related siderotypes among the five isolates. One siderotype, including Pseudomonas fluorescens 1W and P. fluorescens 10CW, was identical to that of P. fluorescens ATCC 13525. Two other strains, P. fluorescens 9AW and Pseudomonas putida 9BW, showed identical pyoverdine-related behaviour to each other, whereas the fifth strain, P. fluorescens 51W, had unique features compared to the other strains or to a set of 12 fluorescent Pseudomonas strains used as comparison material. Elucidation of the structure of the pyoverdines produced by the Antarctic strains supported the accuracy of the siderotyping methodology by confirming that pyoverdines from strains 1W and 10CW had the same structures as the P. fluorescens ATCC 13525 pyoverdine, whereas the 9AW and 9BW pyoverdines are probably identical with the pyoverdine of P. fluorescens strain 244. Pyoverdine from strain 51W appeared to be a novel pyoverdine since its structure was different from all previously established pyoverdine structures. Together with the conclusion that the Antarctic Pseudomonas strains have no special features at the level of their pyoverdines and pyoverdine-mediated iron metabolism compared to worldwide strains, the present work demonstrates that siderotyping provides a rapid means of screening for novel pyoverdines.

Histidine utilisation operon (hut) is upregulated at low temperature in the antarctic psychrotrophic bacterium Pseudomonas syringae

The antarctic psychrotrophic bacterium Pseudomonas syringae was mutagenised using a transposon Tn5-OT182 which facilitates identification of promoter fusions expressing the reporter gene (lacZ) for beta-galactosidase. Most mutants expressed beta-galactosidase both at optimal growth temperature (20-22 degrees C) and at low temperature (4 degrees C). But a small percentage of the mutants (approximately 5%) were unique in that they expressed beta-galactosidase activity predominantly at low temperature. One such mutant was found to have an insertion in the gene for urocanase (hutU) of the histidine utilisation (hut) operon. Direct assay of urocanase and histidase activity in wild-type cells of various antarctic psychrotrophic strains including P. syringae, P. fluorescens and P. putida also suggested that the hut operon is expressed at an elevated level at low temperature.

Phosphorylation of lipopolysaccharides in the Antarctic psychrotroph Pseudomonas syringae: a possible role in temperature adaptation

Phosphorylation of lipopolysaccharide (LPS) from a psychrotrophic bacterium, Pseudomonas syringae, from Antarctica was studied by using sucrose gradient-separated membrane fractions. The bacterium was found to possess an LPS kinase which could phosphorylate more LPS postsynthetically at higher temperatures. The phosphorylation was low at a lower temperature and was also found to occur in vivo. After phosphorylation of LPS in vitro, it was found that the major part of the radioactivity (> 85%) was associated with the core oligosaccharide region of the LPS. The phosphate groups of this region are probably involved in the binding of metal ions, which could be removed by EDTA. The cells grown at the lower temperature probably contained fewer divalent cations because of the smaller amount of phosphate and thereby were more sensitive to EDTA. The cells were also more sensitive to cationic antibiotics at the lower temperature. A possible role of this differential phosphorylation of LPS in modulating the function of the outer membrane as a permeability barrier in the psychrotroph is discussed.

Occurrence and expression of cspA, a cold shock gene, in Antarctic psychrotrophic bacteria

The homologue of cold shock gene cspA of Escherichia coli was detected in various isolates of Antarctic psychrotrophs representing both Gram-positive and Gram-negative bacteria. The Northern hybridization study indicated that the transcript size of cspA in the psychrotrophic Gram-positive bacterium Arthrobacter protophormiae and Gram-negative Pseudomonas fluorescens was similar to that of E. coli and that the cspA homologues in these two psychrotrophs were expressed constitutively at a low level both at 4 degrees C and 22 degrees C. In P. fluorescens, the expression of cspA mRNA was inducible after shift of temperature from 22 to 4 degrees C and the maximum level of induction occurred after 1 h which correlated with the time-lag required for growth of the culture after temperature shift.

Extracellular protease from the antarctic yeast Candida humicola

The psychrotrophic, dimorphic yeast Candida humicola, isolated from Antarctic soil, secretes an acidic protease into the medium. The secretion of this protease by C. humicola was found to be dependent on the composition of the medium. In YPD or yeast nitrogen base medium containing either amino acids or ammonium sulfate as the nitrogen source, the activity of the protease in the medium was low (basal level). However, when yeast nitrogen base medium was depleted of amino acids or ammonium sulfate and supplemented with proteins, the activity of the enzyme increased. The secretion of the enzyme was greater during exponential growth at low temperatures than during growth at higher temperatures. The purified protease had a molecular mass of 36,000 Da and was inhibited by pepstatin, iodoacetamide, and sodium dodecyl sulfate. Despite the prevalent cold temperatures in Antarctica, this extracellular protease of the psychrotrophic yeast C. humicola was active at temperatures ranging from 0 to 45 degrees C, with an optimum activity at 37 degrees C.

The major carotenoid pigment of a psychrotrophic Micrococcus roseus strain: purification, structure, and interaction with synthetic membranes

The major carotenoid pigment of a psychrotrophic Micrococcus roseus strain was purified to homogeneity from methanol extracts of dried cells by reverse-phase liquid chromatography and was designated P-3. On the basis of the UV-visible, infrared, mass, and 1H nuclear magnetic resonance spectra of P-3, it was identified as bisdehydro-beta-carotene-2-carboxylic acid. The pigment interacted with synthetic membranes of phosphatidylcholine and dimyristoyl phosphatidylcholine and stabilized the membranes. These results also indicate that P-3 is different from canthaxanthin, the major carotenoid pigment from a mesophilic M. roseus strain.

Molecular analysis of deep-subsurface bacteria

Bacterial isolates from deep-sediment samples from three sites at the Savannah River site, near Aiken, S.C., were studied to determine their microbial community composition and DNA structure by using total DNA hybridization and moles percent G + C. Standard phenotypic identification underestimated the bacterial diversity at the three sites, since isolates with the same phenotype had different DNA structures in terms of moles percent G + C and DNA homology. The G + C content of deep-subsurface bacteria ranged from 20 to 77 mol%. More than 60% of the isolates tested had G + C values similar to those of Pseudomonas spp., and 12% had values similar to those of Acinetobacter spp. No isolates from deeper formations showed the same DNA composition as isolates from upper formations. Total-DNA hybridization and DNA base composition analysis provided a better resolution than phenotypic tests for the understanding of the diversity and structure of deep-subsurface bacterial communities. On the basis of the moles percent G + C values, deep-subsurface isolates tested seemed to belong to the families Pseudomonadaceae and Neisseriaceae, which might reflect a long period of adaptation to the environmental conditions of the deep subsurface.