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1 Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad – 500 007, India
2 Department of Environmental and Information Science, Otsuma Women's University, Tamashi, Tokyo 206, Japan
3 DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
Correspondence
Sisinthy Shivaji
shivas{at}ccmb.res.in
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The GenBank/EMBL/DDBJ accession numbers for the 16S rDNA sequences of strains CMS 35T, CMS 38T and CMS 64T are AJ537601, AJ537602 and AJ537603, respectively.
Tables showing the fatty acid composition of and DNA–DNA relatedness data for the novel pseudomonads are available as supplementary material in IJSEM Online.
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TOPABSTRACTMAIN TEXTREFERENCES |
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. Over the years, the genus has been redefined to differentiate it from other genera (Stanier et al., 1966; Palleroni et al., 1973; De Ley, 1992; Anzai et al., 2000). Moore et al. (1996) further delineated the genus Pseudomonas into two major intrageneric clusters, namely the Pseudomonas aeruginosa and Pseudomonas fluorescens clusters. Subsequently, based on phylogenetic analysis of 56 species of Pseudomonas sensu stricto, using 1063 bp of the 16S rRNA gene sequence, the genus was categorized into two main clusters (Anzai et al., 2000). The first cluster had six groups within it and these were designated as the Pseudomonas syringae group (with 12 species), the Pseudomonas chlororaphis group (with five species), the P. fluorescens group (with 18 species), the Pseudomonas putida group (with six species), the P. aeruginosa group (with 11 species) and the Pseudomonas stutzeri group (with three species). The second cluster had only one group, the Pseudomonas pertucinogena group, which contained two species.
Until now, about 100 species of the genus Pseudomonas have been reported from various habitats, including Antarctica. Kriss et al. (1976) were the first to report the existence of Pseudomonas species in Antarctica. However, they were not identified at species level until 1989, when Pseudomonas spp. isolated from Antarctic soil and water samples were identified as psychrophilic strains of P. aeruginosa, P. fluorescens, P. putida and P. syringae (Shivaji et al., 1989a). More recently, Maugeri et al. (1996) and Bruni et al. (1999) isolated bacteria that belonged to the genus Pseudomonas from sea water and freshwater samples from Terra Nova Bay and Wanda Lake, Antarctica. However, these were also not characterized at species level. In the present study, attempts were made to identify bacteria that belong to the genus Pseudomonas that were isolated from cyanobacterial mat samples collected from the McMurdo region, Antarctica.
Source of the organisms, media and growth conditions
Thirty-one bacterial isolates were obtained from cyanobacterial mat that were samples collected from ponds L1 (strains CMS 62–72) and L3 (CMS 33–36) of Wright Valley, Adam's glacier stream 1 (CMS 43–50), Adam's glacier stream 2 (CMS 37, CMS 38T and CMS 40) and Canada glacier stream (CMS 41–42) of Miers Valley and Lake Canopus (CMS 54, CMS 57 and CMS 60) in Antarctica. Pure cultures of the heterotrophic bacteria were set up as described previously (Reddy et al., 2000). Optimum temperature, pH and salt concentration for growth of cultures were determined by using plates of Antarctic bacterial medium (ABM) that contained 0·5 % (w/v) peptone, 0·2 % (w/v) yeast extract and 1·5 % (w/v) agar (pH 6·9) (Reddy et al., 2002, 2003).
Morphology, motility and biochemical characteristics
Bacterial cultures in the lag, exponential and stationary phases of growth were observed under a phase-contrast microscope (x1000) to ascertain their shape and motility. All biochemical tests were performed by growing cultures at 22 °C in appropriate medium (Hugh & Leifson, 1953; Stanier et al., 1966; Holding & Collee, 1971; Stolp & Gadkari, 1981). Furthermore, ability of the cultures to utilize a carbon compound as sole carbon source, sensitivity to different antibiotics and DNA G+C contents were determined as described previously (Shivaji et al., 1989b). Total protein profiles of the cultures were determined by SDS-PAGE. For this purpose, cultures were grown in 3 ml ABM broth at 25 °C and harvested at 6000 r.p.m. for 10 min at room temperature; the pellets were resuspended in 100 µl water and 100 µl SDS/sample buffer. The suspension was then boiled for 5 min and centrifuged at 10 000 r.p.m. for 10 min; 50 µl supernatant was loaded onto 12 % SDS/polyacrylamide gel (Laemmli, 1970). Bands were visualized by staining with Coomassie blue.
DNA–DNA hybridization and identification of fatty acids
DNA–DNA hybridization was performed by the membrane filter method (Tourova & Antonov, 1987) as described previously (Shivaji et al., 1992; Reddy et al., 2000). Fatty acids were identified from bacterial cell pellets by comparison with fatty acid standards that were run under similar GC conditions and also by mass spectrometry (Sato & Murata, 1988; Reddy et al., 2003).
Riboprinting
A pure colony of each of strains CMS 35T, CMS 38T and CMS 64T and Pseudomonas brenneri was picked up with a sterile toothpick and suspended in a 1·5 ml microfuge tube that contained 200 µl riboprinting buffer (DuPont Qualicon). The tube was then heated to 70 °C for 10 min in a model 480 DNA thermocycler (Perkin Elmer) and the contents were transferred to a sample carrier (DuPont Qualicon). Lysis reagent A and reagent B (5 µl each) were added before inserting the sample carrier into the characterization unit of the Qualicon Riboprinter system, where the samples were processed automatically according to the EcoRI standard protocol.
16S rRNA gene sequencing
Amplification of the 16S rRNA gene, purification of the 1·5 kb amplicon and sequencing of the amplicon were carried out by the method of Lane (1991), as described previously (Shivaji et al., 2000).
Phylogenetic analysis
16S rRNA gene sequences of the three bacteria that represented the 31 isolates were aligned with reference sequences of all species in the P. fluorescens group (obtained from GenBank/EMBL) by using the multiple sequence alignment program CLUSTAL V (Higgins et al., 1992). The aligned sequences were then checked manually for gaps. The DNADIST program was used to compute pairwise evolutionary distances for the aligned sequences by applying the Kimura two-parameter model (Kimura, 1980). Furthermore, the original sequence dataset was resampled 1000 times by using SEQBOOT and subjected to bootstrap analysis to obtain confidence values for 16S rRNA gene sequence-based genetic affiliations. The multiple distance matrices thus obtained were used to construct phylogenetic trees by using various distance matrix-based clustering algorithms, such as FITCH, KITSCH and UPGMA, as compiled in the Phylogeny Inference Package (PHYLIP; Felsenstein, 1993). Parsimony analysis was also performed for the aligned sequence dataset by using DNAPARS. In all cases, the input order of species added to the topology being constructed was randomized by using the jumble option with a random seed of 7 and ten replications. Majority-rule (50 %) consensus trees were constructed for the topologies by using CONSENSE. All these analyses were done by using the PHYLIP package, version 3.5c (Felsenstein, 1993).
Reference strains
P. brenneri CIP 106646T, Pseudomonas orientalis CIP 105540T, Pseudomonas veronii CIP 104663T, Pseudomonas marginalis ATCC 10844T, Pseudomonas rhodesiae CIP 104664T, Pseudomonas tolaasii ATCC 33618T, Pseudomonas migulae CIP 105470T and P. fluorescens ATCC 13525T were used as controls in studies that were related to the identification of fatty acids and DNA–DNA hybridization.
Conclusions
Thirty-one individual bacterial colonies were isolated from cyanobacterial mat samples that were collected from various water bodies in Antarctica. These 31 isolates could be categorized into three groups, based on their protein profiles as analysed by SDS-PAGE (data not shown), namely group I (CMS 33–36 and CMS 44–50), group II (CMS 38T) and group III (CMS 37, CMS 40–41, CMS 43, CMS 54, CMS 57, CMS 60 and CMS 62–72). Members of the same group exhibited identical protein profiles, indicating that they are probably clonal in origin. Therefore, strains CMS 35T, CMS 38T and CMS 64T were chosen as representative isolates of groups I, II and III, respectively.
These three isolates, namely CMS 35T, CMS 38T and CMS 64T, are aerobic, Gram-negative, rod-shaped and motile, possess a polar flagellum and have C16 : 0, C16 : 1
7c, C16 : 19c and C18 : 1 as their major fatty acids, indicating their affiliation to the genus Pseudomonas. They could all grow at 4–30 °C and did not accumulate polyhydroxybutyric acid. Riboprinting analysis indicated that strains CMS 35T, CMS 38T and CMS 64T are distinctly different from each other (Tables 1 and 2; Supplementary Table A, available in IJSEM Online; Fig. 1).
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) (Fig. 2). Evolutionary distances, as calculated by using the Kimura two-parameter model, indicated that the three isolates are related very closely to each other, with >99 % 16S rRNA gene sequence similarity, and also to other species of the P. fluorescens group (Anzai et al., 2000). At the DNA–DNA level, there was 40 % relatedness between strains CMS 35T and CMS 38T, 40 % between CMS 35T and CMS 64T and 43 % between CMS 38T and CMS 64T (Supplementary Table B, available in IJSEM Online).
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) and P. migulae (Verhille et al., 1999) (Fig. 2
), with a bootstrap value of 86 %. The other two Antarctic isolates, CMS 35T and CMS 38T (Fig. 2), appear to be related more closely to P. orientalis (Dabboussi et al., 1999).
Identification of strain CMS 35T as Pseudomonas antarctica sp. nov.
Strain CMS 35T can be differentiated from strains CMS 38T and CMS 64T with respect to its protein profile, riboprint, phenotypic characteristics and low (40 %) DNA–DNA relatedness (Tables 1 and 2; Supplementary Table B, available in IJSEM Online; Fig. 1). Strain CMS 35T can also be differentiated easily from the closely related species P. orientalis (Dabboussi et al., 1999), P. marginalis, P. rhodesiae and P. veronii, based on phenotypic characteristics (Table 1) and the fact that it shows <60 % relatedness at the DNA–DNA level with these species. Therefore, strain CMS 35T is proposed as the type strain of a novel species of the genus Pseudomonas, to which the name Pseudomonas antarctica sp. nov. is assigned.
Identification of strain CMS 38T as Pseudomonas meridiana sp. nov.
Strain CMS 38T, which is different from CMS 35T (Table 1), shares 99·46 % 16S rRNA gene sequence similarity with P. orientalis (Fig. 2); however, it differs from P. orientalis (Dabboussi et al., 1999) in a number of phenotypic traits (Table 1) and its protein profile and exhibits 64 % relatedness at the DNA–DNA level (Supplementary Table B, available in IJSEM Online). In addition, strain CMS 38T exhibits 52, 58 and 49 % DNA–DNA relatedness (Supplementary Table B, available in IJSEM Online) respectively with P. marginalis, P. rhodesiae and P. veronii, which are part of the main cluster of the phylogenetic tree (Fig. 2). DNA–DNA hybridization was not performed between strain CMS 38T and Pseudomonas extremorientalis (Ivanova et al., 2002), P. tolaasii (Bradbury, 1987) or Pseudomonas costantinii (Munsch et al., 2002), but they can be differentiated easily, based on phenotypic characteristics (Table 1). Thus, based on the above differences between strains CMS 38T, CMS 35T and P. orientalis, CMS 38T is proposed as the type strain of a novel species of the genus Pseudomonas, to which the name Pseudomonas meridiana sp. nov. is assigned.
Identification of strain CMS 64T as Pseudomonas proteolytica sp. nov.
Strain CMS 64T can be differentiated from strains CMS 35T and CMS 38T by phenotypic characteristics (Tables 1 and 2). In addition, these isolates differ in their protein profiles, riboprints and DNA–DNA relatedness (Supplementary Table B, available in IJSEM Online; Fig. 1). At the 16S rRNA gene sequence level, strain CMS 64T is related closely to P. brenneri (99·73 %) and P. migulae (99·75 %) (Fig. 2). Characteristics that differentiate strain CMS 64T from P. migulae (Verhille et al., 1999) and P. brenneri (Baïda et al., 2001) are listed in Table 2. Furthermore, strain CMS 64T exhibits differences in protein profile and shows only 55 % relatedness with P. migulae and 68 % with P. brenneri at the DNA–DNA level (Supplementary Table B, available in IJSEM Online). The riboprint of strain CMS 64T is also different from that of P. brenneri (Fig. 1). Thus, based on phenotypic, genotypic and phylogenetic characteristics, strain CMS 64T is proposed as the type strain of a novel species of the genus Pseudomonas, to which the name Pseudomonas proteolytica sp. nov. is assigned.
Description of Pseudomonas antarctica sp. nov.
Pseudomonas antarctica (an.tarc'ti.ca. N.L. fem. adj. antarctica pertaining to Antarctica).
Forms circular, convex, smooth and translucent colonies with a diameter of 1–2 mm. Cells are Gram-negative, motile with a polar flagellum, rod-shaped and psychrophilic (grow at 4–30 °C), can tolerate 3 % NaCl (w/v) and grow at an optimum pH of 7. Positive for catalase, oxidase, urease and phosphatase and weakly positive for lipase; reduces nitrate to nitrite; negative for 
-galactosidase, gelatinase, arginine dihydrolase, arginine decarboxylase, lysine decarboxylase, indole production, methyl red and Voges–Proskauer test. Does not hydrolyse aesculin, starch or cellulose. Acid is produced from D-fructose, D-galactose, D-glucose, D-mannose and D-mannitol, but not from L-arabinose, lactose, L-rhamnose, sucrose or D-xylose. Utilizes acetate, adonitol, citrate, meso-erythritol, D-fructose, D-galactose, D-glucose, glycerol, meso-inositol, lactic acid, D-mannose, D-mannitol, pyruvate, D-ribose, sorbitol, trehalose, L-alanine, L-arginine, L-glutamic acid, L-glutamine, L-lysine, L-serine, L-tyrosine and L-tryptophan as sole carbon sources, but not L-arabinose, D-cellobiose, cellulose, dextran, dulcitol, fumaric acid, inulin, lactose, D-maltose, D-melibiose, melezitose, D-raffinose, L-rhamnose, D-sorbose, sucrose, succinic acid, thioglycollate, D-xylose, L-aspartic acid, L-aspargine, L-cysteine, L-glycine, L-histidine, L-leucine, L-isoleucine, L-methionine, L-proline, L-threonine or L-valine. Sensitive to the antibiotics ampicillin, amoxycillin, bacitracin, carbenicillin, chloramphenicol, chlortetracycline, colistin, cotrimoxazole, erythromycin, kanamycin, gentamicin, lincomycin, nitrofurazone, nitrofurantoin, nystatin, oxytetracyclin, penicillin, polymyxin B, rifampicin, tetracycline and tobramycin, but resistant to furazolidone, furoxone and trimethoprim. DNA G+C content is 60·7 mol%.
The type strain is CMS 35T (=MTCC 4992T=DSM 15318T).
Description of Pseudomonas meridiana sp. nov.
Pseudomonas meridiana (me.ri.di.a'na. L. fem. adj. meridiana of or belonging to the south or south side, southern, southerly, meridional; pertaining to the South Pole).
Forms circular, convex, smooth and translucent colonies with a diameter of 1–2 mm. Cells are Gram-negative, motile with a polar flagellum, rod-shaped and psychrophilic (grow at 4–30 °C), can tolerate 3 % NaCl (w/v) and grow at an optimum pH of 7. Positive for catalase, oxidase and lipase and weakly positive for urease; reduces nitrate to nitrite; negative for phosphatase, -galactosidase, gelatinase, arginine dihydrolase, arginine decarboxylase, lysine decarboxylase, indole production, methyl red and Voges–Proskauer test. Does not hydrolyse aesculin, starch or cellulose. Acid is produced from D-fructose, D-galactose, D-glucose, D-mannose and D-mannitol, but not from L-arabinose, lactose, L-rhamnose, sucrose or D-xylose. Utilizes acetate, adonitol, citrate, meso-erythritol, D-fructose, D-galactose, D-glucose, L-arabinose, glycerol, meso-inositol, lactic acid, D-mannose, D-mannitol, pyruvate, D-ribose, sorbitol, trehalose, L-alanine, L-arginine, L-glutamic acid, L-glutamine, L-lysine, L-serine, L-tyrosine and L-tryptophan as sole carbon sources, but not D-cellobiose, cellulose, dextran, dulcitol, fumaric acid, inulin, lactose, D-maltose, D-melibiose, melezitose, D-raffinose, L-rhamnose, D-sorbose, sucrose, succinic acid, thioglycollate, D-xylose, L-aspartic acid, L-aspargine, L-cysteine, L-glycine, L-histidine, L-leucine, L-isoleucine, L-methionine, L-proline, L-threonine or L-valine. Resistant to ampicillin, amoxycillin, bacitracin, carbenicillin, chloramphenicol, colistin, cotrimoxazole, erythromycin, furazolidone, furoxone, gentamicin, lincomycin, nitrofurantoin, nystatin, penicillin, polymyxin B and trimethoprim, but sensitive to chlortetracycline, kanamycin, nitrofurazone, oxytetracycline, rifampicin, tetracycline and tobramycin. DNA G+C content is 63·2 mol%.
The type strain is CMS 38T (=MTCC 4993T=DSM 15319T).
Description of Pseudomonas proteolytica sp. nov.
Pseudomonas proteolytica (pro.te.o.ly'ti.ca. N.L. fem. adj. proteolytica proteolytic).
Forms circular, convex, smooth and translucent colonies with a diameter of 1–2 mm. Cells are Gram-negative, motile with a polar flagellum, rod-shaped and psychrophilic (grow at 4–30 °C), can tolerate 3 % NaCl (w/v) and grow at an optimum pH of 7. Positive for catalase, oxidase, lipase and gelatinase; reduces nitrate to nitrite; negative for phosphatase, urease, -galactosidase, arginine dihydrolase, arginine decarboxylase, lysine decarboxylase, indole production, methyl red and Voges–Proskauer test. Does not hydrolyse aesculin, starch or cellulose. Acid is produced from D-fructose, D-galactose, D-glucose, D-mannose and D-mannitol, but not from L-arabinose, lactose, L-rhamnose, sucrose or D-xylose. Utilizes acetate, adonitol, citrate, meso-erythritol, D-fructose, D-galactose, D-glucose, glycerol, meso-inositol, lactic acid, D-mannose, D-mannitol, pyruvate, D-ribose, sorbitol, trehalose, L-alanine, L-arginine, L-glutamic acid, L-glutamine, L-lysine, L-serine, L-methionine, L-phenylalanine, L-tyrosine and L-tryptophan as sole carbon sources, but not D-cellobiose, cellulose, dextran, dulcitol, fumaric acid, inulin, lactose, D-maltose, D-melibiose, melezitose, D-raffinose, L-rhamnose, D-sorbose, sucrose, succinic acid, thioglycollate, D-xylose, L-aspartic acid, L-aspargine, L-cysteine, L-glycine, L-histidine, L-leucine, L-isoleucine, L-proline, L-threonine or L-valine. Resistant to ampicillin, amoxycillin, bacitracin, carbenicillin, chloramphenicol, cotrimoxazole, erythromycin, furazolidone, furoxone, lincomycin, nitrofurazone, nitrofurantoin, nystatin, penicillin and trimethoprim, but sensitive to chlortetracycline, colistin, gentamicin, kanamycin, oxytetracycline, polymyxin B, rifampicin, tetracycline and tobramycin. DNA G+C content is 58·3 mol%.
The type strain is CMS 64T (=MTCC 4994T=DSM 15321T).
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
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