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PubMed2001

Psychrobacter proteolyticus sp. nov., a psychrotrophic, halotolerant bacterium isolated from the Antarctic krill Euphausia superba Dana, excreting a cold-adapted metalloprotease.

An Antarctic marine bacterium (strain 116) excreting an extracellular cold-adapted metalloprotease was subjected to a detailed polyphasic taxonomic investigation. Strain 116 was previously isolated from the stomach of a specimen of the Antarctic krill Euphasia superba Dana and tentatively characterized as Sphingomonas paucimobilis 116. The 16S rDNA sequence analysis showed that the strain is in fact related to species of the genus Psychrobacter, next to Psychrobacter glacincola (97.4% similarity). Sequence similarities between strain 116 and other Psychrobacter species ranged from 96.9% (with P. urativorans) to 95.4% (with P. immobilis). Key phenotypic characteristics as well as chemotaxonomic features of the bacterium were congruent with the description of the genus Psychrobacter i.e. cells were strictly aerobic, strongly oxidase-positive, psychrotrophic, halotolerant, gram-negative non-motile coccobacilli, with ubiquinone-8 as the main respiratory lipoquinone and 18:1 cis 9, 16:1 cis and 17:1 (omega8c being the predominant cellular fatty acids. The G+C content of the DNA was 43.6 mol%. DNA-DNA hybridization studies showed that the relatedness between strain 116 and Psychrobacter glacinola is only 62.2%. Further differences were apparent in whole-cell SDS-PAGE protein pattern, cellular fatty acid profile and in a number of physiological and biochemical characteristics as well as in enzymatic activities. Tolerance to 5% bile salts, nitrate reduction, citrate utilization, acid production from carbohydrates, alkaline phosphatase, acid phosphatase, C4 esterase, C14 lipase and valine arylamidase were found to differentiate strain 116 from Psychrobacter glacincola. On the basis of this phenotypic and molecular evidences, strain 116, previously known as Sphingomonas paucimobilis 116, was recognized as a new species of the genus Psychrobacter for which the name Psychrobacter proteolyticus is proposed. Strain 116 has been deposited in the Collection de l'Institut Pasteur, France, as CIP106830T and in the Deutsche Sammlung von Mikroorganismen and Zellkulturen, as DSM13887.

Adaptation, Biological↗
PubMed2004

Psychrobacter nivimaris sp. nov., a heterotrophic bacterium attached to organic particles isolated from the South Atlantic (Antarctica).

An aggregate-attached bacterium, strain 88/2-7, was isolated from samples of the Southern Ocean and investigated in a polyphasic approach. The novel marine isolate is an aerobic, Gram-negative, oxidase- and catalase-positive, non-motile short rod and grows in form of cream-colored colonies. Growth was observed at 5-35 degrees C. The bacterium tolerated concentrations of 0-13% (w/v) NaCl and utilized a relatively restricted spectrum of carbon sources. The analysis of the fatty acids revealed 18:1 cis 9 (18:1omega9c) as main fatty acid. The G+C content of the DNA was approximately 42 mol%. The sequence of the 16S rDNA assigned strain 88/2-7 to the gamma-subclass of Proteobacteria with a similarity of 99.65% to Psychrobacter proteolyticus (DSM 13887T). A DNA-DNA-hybridization study showed only 26.8% renaturation to the respective strain. Based on the morphological, physiological and molecular properties of the new isolate, the name Psychrobacter nivimaris sp. nov. (type strain 88/2-7T) is proposed.

Antarctic Regions↗
PubMed1997

Spectroscopic characterization of the uptake of essential and xenobiotic metal cations in cells of the soil bacterium Azospirillum brasilense.

The results of flame (FAAS) or graphite furnace atomic absorption spectrometric (GFAAS) analyses are presented and discussed on the accumulation of essential metals (Mg, Ca, Mn and Fe contained in the cultivation medium) and traces of each one of the conventionally xenobiotic elements from the group V, Co, Ni, Cu, Zn or Pb, added to the medium in concentrations (0.2 mM) which do not essentially suppress growth of the bacterial culture, in cells of the plant root-associated nitrogen-fixing bacterium Azospirillum brasilense. Along with the essential cations assimilated by the bacterium, Zn and Cu were found to effectively accumulate in the biomass from the environment. The uptake of Co and Ni was significantly less pronounced, whereas Pb and V appeared to be present in cells in much lower concentrations than in the cultivation medium evidently showing no tendency to be assimilated by azospirilla. The effect of the above xenobiotics on the uptake level of the four essential elements provided evidence that they may compete for the formation of biologically active complexes with substances of both intracellular and extracellular localization. The analytical data obtained are compared with Fourier transform infrared (FTIR) spectra of intact vacuum-dried bacterial cells grown in a standard medium and under the conditions of an increased metal uptake.

Azospirillum brasilense↗
PubMed1977

H-2 restriction of cell-mediated immunity to an intracellular bacterium: effector T cells are specific for Listeria antigen in association with H-21 region-coded self-markers.

The protective activity of anti-Listeria-immune T cells assayed in an adoptive transfer system in H-2 restricted. As shown in the present studies, the demonstration of the restriction is directly dependent on the dose and the relative protective activity of spleen cells. In addition, some H-2-unrestricted protection is conferred predominantly by other than immunoglobulin-negative spleen cells. Thus, the activity of Listeria-immune T cells appears to be 'absolutely' restricted and is in this respect comparable to in vivo T-cell-mediated anti-viral protection. The predominant genetic region of H-2 coding for the structures which are mainly involved in this restriction in T-cell immunity to this prototype intracellular bacterium is the I region. The specificity of Listeria-immune T cells is determined by the H-2 haplotype of the donor. Thus, F1 hybrids seem to possess at least two separable sets of T cells, each specific for one parental haplotype. As is true in the virus model, the results cannot distinguish between an altered-self or a dual recognition model of T-cell recognition to explain H-2 restriction. They are, however, compatible with the idea and I-coded cell surface structures may serve as receptors for cell-specific differentiation signals, which trigger direct or lymphokin-mediated activation of macrophages to manifest increased bactericidal capacity. The interesting parallels in self-marker recognition of T cells in the virus and intracellular bacterium systems, respectively, appear to be reasonably explained by the different types of signals transmitted by T cells to various target cells via the distinctly different self-markers employed (i.e., K or D vs I).

Animals↗
PubMed2006

Identification of differentially expressed genes in Malus domestica after application of the non-pathogenic bacterium Pseudomonas fluorescens Bk3 to the phyllosphere.

Biological control of plant diseases by the application of antagonistic micro-organisms to the plant phyllosphere is only marginally understood. Suppression subtractive hybridization (SSH) was used for the identification of genes expressed after application of the non-pathogenic bacterium Pseudomonas fluorescens Bk3 to the phyllosphere of the apple scab-susceptible cultivar Malus domestica cv. Holsteiner Cox. In total, 157 expressed sequence tag (EST) clones were obtained. The sequencing of 113 ESTs which have a significantly elevated transcript level and the comparison of the obtained sequences with databases revealed similarities to different classes of pathogenesis-related proteins, for example, RNase-like PR10 protein and endochitinase, or similarities to proteins expressed under stress conditions that could have a protective function, for example, a germin-like protein, glutathione S-transferase, thioredoxin-like proteins, and heat shock proteins. In addition, several transcripts were identified that code for proteins which have a crucial role at different stages of pathogen recognition and in signalling pathways or an as yet unknown function in plant defence. The results show that a number of transcripts encoding proteins/enzymes which are known to be up-regulated after pathogen infection are also up-regulated after the application of a non-pathogenic bacterium to a M. domestica cultivar. The expression of these proteins might increase the plant resistance towards pathogen infection and damage.

Blotting, Northern↗
PubMed1996

Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae.

The entire genome of the bacterium Mycoplasma pneumoniae M129 has been sequenced. It has a size of 816,394 base pairs with an average G+C content of 40.0 mol%. We predict 677 open reading frames (ORFs) and 39 genes coding for various RNA species. Of the predicted ORFs, 75.9% showed significant similarity to genes/proteins of other organisms while only 9.9% did not reveal any significant similarity to gene sequences in databases. This permitted us tentatively to assign a functional classification to a large number of ORFs and to deduce the biochemical and physiological properties of this bacterium. The reduction of the genome size of M. pneumoniae during its reductive evolution from ancestral bacteria can be explained by the loss of complete anabolic (e.g. no amino acid synthesis) and metabolic pathways. Therefore, M. pneumoniae depends in nature on an obligate parasitic lifestyle which requires the provision of exogenous essential metabolites. All the major classes of cellular processes and metabolic pathways are briefly described. For a number of activities/functions present in M. pneumoniae according to experimental evidence, the corresponding genes could not be identified by similarity search. For instance we failed to identify genes/proteins involved in motility, chemotaxis and management of oxidative stress.

Base Sequence↗
PubMed2004

Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism.

Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to an unknown taxon in the Gram-positive bacterial cluster. Here, we describe the 3.57 Mb genome sequence of S.thermophilum. The genome consists of 3338 protein-coding sequences, out of which 2082 have functional assignments. Despite the high G + C content (68.7%), the genome is closest to that of Firmicutes, a phylum consisting of low G + C Gram-positive bacteria. This provides evidence for the presence of an undefined category in the Gram-positive bacterial group. The presence of both spo and related genes and microscopic observation indicate that S.thermophilum is the first high G + C organism that forms endospores. The S.thermophilum genome is also characterized by the widespread insertion of class C group II introns, which are oriented in the same direction as chromosomal replication. The genome has many membrane transporters, a number of which are involved in the uptake of peptides and amino acids. The genes involved in primary metabolism are largely identified, except those that code several biosynthetic enzymes and carbonic anhydrase. The organism also has a variety of respiratory systems including Nap nitrate reductase, which has been found only in Gram-negative bacteria. Overall, these features suggest that S.thermophilum is adaptable to and thus lives in various environments, such that its growth requirement could be a substance or a physiological condition that is generally available in the natural environment rather than a highly specific substance that is present only in a limited niche. The genomic information from S.thermophilum offers new insights into microbial diversity and evolutionary sciences, and provides a framework for characterizing the molecular basis underlying microbial commensalism.

Actinobacteria↗
PubMed2002

Isolation and characterization of the dcw cluster from the piezophilic deep-sea bacterium Shewanella violacea.

The dcw cluster of genes involved in cell division and cell wall synthesis from the piezophilic deep-sea bacterium Shewanella violacea was isolated and characterized. It comprises 15 open reading frames, of which the organization is mraZ-mraW-ftsL-ftsI-murE-murF-mraY-murD-ftsW-murG-murC-ftsQ-ftsA-ftsZ-envA, in that order. To analyze transcription upstream from the ftsZ gene, Northern blot and primer extension analyses were performed. The results showed that gene expression is not pressure dependent. Western blot analysis showed that the FtsZ protein is equally expressed under several pressure conditions in the range of atmospheric (0.1 MPa) to high (50 MPa) pressures. Using immunofluorescence microscopy, the FtsZ ring was observed in the center of cells at pressure conditions of 0.1 to 50 MPa. These results imply that the FtsZ protein function is not affected by elevated pressure in this piezophilic bacterium.

Amino Acid Sequence↗
PubMed1992

Purification and properties of trimethylamine N-oxide reductase from aerobic photosynthetic bacterium Roseobacter denitrificans.

Trimethylamine N-oxide (TMAO) reductase was purified from an aerobic photosynthetic bacterium Roseobacter denitrificans. The enzyme was purified from cell-free extract by ammonium sulfate fractionation, DEAE ion exchange chromatography, hydrophobic chromatography, and gel filtration. The purified enzyme was composed of two identical subunits with molecular weight of 90,000, as identified by SDS-polyacrylamide gel electrophoresis, containing heme c and a molybdenum cofactor. The molecular weight of the native enzyme determined by gel filtration was 172,000. The midpoint redox potential of heme c was +200 mV at pH 7.5. Absorption maxima appeared at 418,524, and 554 nm in the reduced state and 410 nm in the oxidized state. The enzyme reduced TMAO, nicotine acid N-oxide, picoline N-oxide, hydroxylamine, and bromate, but not dimethyl sulfoxide, methionine sulfoxide, chlorate, nitrate, or thiosulfate. Cytochrome c2 served as a direct electron donor. It probably catalyzes the electron transfer from cytochrome b-c1 complex to TMAO reductase. Cytochrome c552, another soluble low-molecular-weight cytochrome of this bacterium, also donated electrons directly to TMAO reductase.

Bacteria↗
PubMed1976

Metabolism of threo-beta-methylmalate by a soil bacterium.

Studies on threo-beta-methylmalate metabolism in a soil bacterium of the genus Bacillus which can utilize threo-beta-methylmalate as a sole carbon source were carried out. When DL-threo-beta-methylmalate was incubated with a cell-free extract of the bacterium, citramalate was found to be formed. Similarly, formation of threo-beta-methylmalate from DL-citramalate was confirmed. These dicarbosylic acids were identified by gas chromatography-mass spectrometry. Examination of inducibility, substrate specificity, and cofactor requirement of the enzymes involved in the reactions showed the existence of two interconversion reactions between the threo-beta-methylmalate and citramalate. One was an interconversion reaction between L-threo-beta-methylmalate and L-citramalate via mesaconate and the other was an interconversion reaction between D-threo-beta-methylmalate and D-citramalate via citraconate. These reactions were both reversible and were catalyzed by distinct and inducible enzymes. It is suggested that the two reactions participate in the catabolism of threo-beta-methylmalate.

Bacillus↗
PubMed1977

Determination of molecular species of phospholipids from thermophilic bacterium PS3 by mass chromatography.

The molecular species of phosphatidylethanolamine, phosphatidyglycerol and cardiolipin of thermophilic bacterium PS3 were determined by a new and simple mass chromatographic technique. The fatty acyl groups of these compounds, unlike those of usual phospholipids, were all saturated and were mixtures of even and odd numbered carbon chains; their [M-CnH2n+1-COOCH2]+ and [M-Cn+1H2n+3COO]+ peaks overlapped. Thus, the acetyldiglycerides derived from these phospholipids were subjected to a combination of mass chromatography using chemical ionization with NH3 and treatment of the phospholipids with phospholipase A2 [EC 3.1.1.4]. These three phospholipids had similar patterns of diglycerides. Expressed as R1 : R2, %, they were found to be 14:14,0-1%, 15:14,0-4%, 15:15, 22-23%, 16:15, 16-20%, 17:15, 28-32%, 17:16, 6-9%, 18:15, 7-13%, 17:17, 3-6%, and 18:16, 0-1%. These results should be of significance in connection with the high stability of the biomembranes of this bacterium.

Bacteria↗
PubMed1980

ESR studies on the membrane properties of a moderately halophilic bacterium. II. Effect of extreme growth conditions on liposome properties.

Lipid preparations from the cells of a moderately halophilic bacterium, Pseudomonas halosaccharolytica grown under the two extreme conditions of high temperature-high NaCl concentration and low temperature-low NaCl concentration showed distinctively different profiles in phospholipid and fatty acid composition. Cells grown at 40 degrees C in medium containing 3.5 M NaCl had high concentrations of saturated and C19 cyclopropanoic fatty acids (about 50 per cent of the total), whereas cells grown at 20 degrees C in medium containing 0.5 M NaCl had decreased concentrations of these fatty acids with increased concentrations of the corresponding unsaturated fatty acids. The phospholipid composition was also affected ty the culture conditions; cells grown at 40 degrees C in 3.5 M NaCl had large amounts of acidic phospholipids, whereas those grown at 20 degrees C in 0.5 M NaCl had small amounts. ESR studies on liposomes prepared from lipids of cells grown under the two conditions showed characteristic profiles for correlation times and order parameters of three spin labels of stearic acid derivatives similar to those of membranes of whole cells of this bacterium. ESR studies showed that the physical properties of the liposomes from the total extractable lipids and isolated phosphatidylglycerol from the cells were completely different from those of synthetic dioleoylphosphatidylglycerol. Liposomes of the lipids extracted from cells grown at 40 degrees C in 3.5 M NaCl showed change in rotational viscosity on altering the NaCl concentration to 0.5M, whereas liposomes of lipids extracted from cells grown at 20 degrees C in 0.5 M NaCl did not show change in rotational viscosity on increasing the NaCl concentration to 3.5 M.

Electron Spin Resonance Spectroscopy↗
PubMed1984

Chemotaxis in thermophilic bacterium PS-3.

Depositing the thermophilic bacterium PS-3 on semi-solid agar plate containing rich medium, several chemotactic rings were formed as in the cases of Escherichia coli and Salmonella typhimurium, indicating that the bacterium is chemotactic. The cells were attracted to L-amino acids: L-alanine, tryptophan, L-aspartate, and glutamate; and to sugars: D-glucose, maltose, D-fructose, and sucrose. In order to find out some sort of methylatable proteins were present, which has been proven to be important in the case of Escherichia coli, the PS-3 cells were labeled with radioactive methionine under conditions in which the protein synthesis had been inhibited. The results showed that the cells contained methylatable proteins of 60,000 to 88,000 daltons. The banding pattern of these methylated proteins was very similar to that of Escherichia coli when the proteins were analyzed by SDS-polyacrylamide gel electrophoresis. In addition, the methyl groups attached onto the proteins were alkaline labile, indicating that the site of methylation was on carboxyl group. The methylation and demethylation reactions of these proteins were affected by the presence of attractants.

Amino Acids↗
PubMed2001

Phytoene desaturase, CrtI, of the purple photosynthetic bacterium, Rubrivivax gelatinosus, produces both neurosporene and lycopene.

Biosynthetic pathways for carotenoids in the purple photosynthetic bacterium, Rubrivivax gelatinosus, which synthesizes spirilloxanthin in addition to spheroidene and OH-spheroidene, were investigated by means of genetic manipulation. A phytoene desaturase gene (crtI) found in the photosynthesis gene cluster of this bacterium was expressed in an Escherichia coli strain that can produce phytoene. Both neurosporene and lycopene were synthesized in the recombinant, probably by three- and four-step desaturation reactions of CrtI. A mutant of RVI: gelatinosus lacking the crtI gene produced only phytoene, indicating that this organism had no other phytoene desaturases. When the crtI deletion mutant was complemented by the three-step phytoene desaturase of Rhodobacter capsulatus, spirilloxanthin and its precursors were not synthesized, although spheroidene and OH-spheroidene were accumulated. It was concluded that neurosporene and lycopene are produced by a single phytoene desaturase in RVI: gelatinosus resulting in the synthesis of spheroidene and spirilloxanthin, and that there are no pathways for spirilloxanthin synthesis via spheroidene.

Bacteria↗
PubMed2005

Current status and future directions for Laribacter hongkongensis, a novel bacterium associated with gastroenteritis and traveller's diarrhoea.

PURPOSE OF REVIEW: Despite extensive investigations, a microbiological cause cannot be found in about half of the patients with infectious disease. Throughout the years, scientists have spent tremendous efforts in looking for microorganisms associated with these "unexplained infectious disease syndromes". Recently, a novel bacterium, Laribacter hongkongensis, was discovered and shown to be associated with gastroenteritis and traveller's diarrhoea. This review summarizes the current status, and shares with the readers the authors' experience in the microbiology, classification, epidemiology, clinical disease, laboratory diagnosis, antibiotic resistance and treatment of L. hongkongensis. It also discusses the importance and perspective of describing novel pathogenic bacterial species. RECENT FINDINGS: L. hongkongensis was shown to be associated with gastroenteritis and traveller's diarrhoea. Consumption of fish was associated with recovery of L. hongkongensis. Freshwater fish was a reservoir of L. hongkongensis. Genotypic typing revealed the possibility of virulent clones of L. hongkongensis. The class C beta-lactamase of L. hongkongensis has been cloned and characterized. SUMMARY: In 2001, L. hongkongensis, a novel genus and species, was first discovered in Hong Kong from the blood and empyema pus of a patient with alcoholic cirrhosis. Subsequently, it was isolated from patients in other parts of the world. Recently, this bacterium was found to be associated with community-acquired gastroenteritis and traveller's diarrhoea using cefoperazone MacConkey agar as the selective medium. Further studies, including setting up of animal and tissue culture models and characterization of virulence factors, should be performed. For pathogenic microbes, even one strain of a novel species should be described, so that global concerted efforts can be drawn to look for more cases associated with such a pathogen.

Diarrhea↗
PubMed1991

Helicobacter nemestrinae sp. nov., a spiral bacterium found in the stomach of a pigtailed macaque (Macaca nemestrina)

A new microaerophilic, spirally curved, rod-shaped bacterium was isolated from the gastric mucosa of a pigtailed macaque (Macaca nemestrina). The gram-negative cells of this bacterium are oxidase, catalase, and urease positive and strongly resemble Helicobacter pylori (Campylobacter pylori) cells. Like H. pylori, this organism does not metabolize glucose, does not reduce nitrate or produce indole, does not produce H2S from triple sugar iron agar, does not hydrolyze hippurate or esculin, and does not grow in the presence of 1% glycine, 1.5% salt, or 1% bile. Also like H. pylori, it is resistant to nalidixic acid and susceptible to cephalothin. However, unlike H. pylori, the colorless colonies are flat and have irregular edges. This organism has a unique cellular fatty acid composition, forming a new gas-liquid chromatography group, group K, and a distinctive DNA content (24 mol% guanine plus cytosine). It exhibits less than 10% DNA-DNA homology (as determined by the nylon filter blot method at 65 degrees C) with other members of the genus Helicobacter. Although the levels of DNA relatedness between previously described Helicobacter species and the new organism are low (less than 10%) and the difference in guanine-plus-cytosine content is large (24 versus 36 to 41 mol%), the genus Helicobacter is the only genus in which it is logical to include the organism at this time. We propose that our single strain represents a new species, Helicobacter nemestrinae, and we designate strain T81213-NTB (= ATCC 49396) as the type strain.

Animals↗
PubMed1992

Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium.

On the basis of phenotypical characteristics and analysis of 16S rRNA sequence, a new species belonging to a new genus is described, and the name Marinobacter hydrocarbonoclasticus is proposed. This organism, isolated from Mediterranean seawater near a petroleum refinery, is a gram-negative, aerobic, rod-shaped bacterium. It grows at NaCl concentrations of 0.08 to 3.5 M and uses various hydrocarbons as the sole source of carbon and energy. Its DNA has a guanine-plus-cytosine content of 52.7 mol%. The 16S rRNA analysis shows a clear affiliation between M. hydrocarbonoclasticus and the gamma group of the phylum Proteobacteria. A close phylogenetic relationship appears among the species Marinomonas vaga, Oceanospirillum linum, Halomonas elongata, and Pseudomonas aeruginosa. Because of the impossibility of finding a single most closely related species, we suggest that this bacterium be assigned to a new genus, at least temporarily. The possibility of a revision of this status when new data appear is, however, not excluded. The type strain is M. hydrocarbonoclasticus SP.17 (= ATCC 49840).

Bacteriolysis↗
PubMed1994

Phylogenetic analysis of a new LL-diaminopimelic acid-containing coryneform bacterium from herbage, Nocardioides plantarum sp. nov.

The 16S rRNA gene sequence of a previously undescribed LL-diaminopimelic acid-containing coryneform bacterium isolated from herbage was determined in order to clarify the taxonomic position of this organism. A comparative sequence analysis revealed that the bacterium represents a new line of descent within the genus Nocardioides. On the basis of the results of a phylogenetic analysis and the phenotypic distinctiveness of the organism, a new species, Nocardioides plantarum, is proposed. The type strain is NCIMB 12834.

Actinomycetales↗