Shifts in the microbial community composition of Gulf Coast beaches following beach oiling

Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand population structures. Among sequences classified to genus, Alcanivorax, Alteromonas, Marinobacter, Winogradskyella, and Zeaxanthinibacter exhibited the largest relative abundance increases in oiled sands.

Falsochrobactrum ovis gen. nov., sp. nov., isolated from a sheep

A Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (B1315(T)) was isolated from the placenta of a sheep with abortion. On the basis of 16S rRNA gene sequence analyses the strain was assigned to the Brucella-Ochrobactrum-Paenochrobactrum-Pseudochrobactrum group with 94.5-94.8 %, 94.3-96.1 %, 95.0-95.1 %, and 95.9-96.1 % sequence similarities to type strains of species of the four genera, respectively. Phylogenetic trees indicated a close relationship to the type strains of Ochrobactrum gallinifaecis and Ochrobactrum oryzae (95.9 and 96.1 % sequence similarity, respectively). Chemotaxonomic data confirmed the allocation of strain B1315(T) to the family Brucellaceae (quinone system: ubiquinone Q-10 and major fatty acids: C18 : 1ω7c and C19 : 0 cyclo ω8c). The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and the unidentified but unique phospholipid PL7. The polyamine pattern of strain B1315(T) contained the major polyamines spermidine and putrescine. On the basis of the 16S rRNA gene and recA sequence phylogeny and chemotaxonomic data strain B1315(T) was clearly different from the genera Brucella, Ochrobactrum, Paenochrobactrum and Pseudochrobactrum. On the basis of these data we propose the novel genus Falsochrobactrum gen. nov. with the type species Falsochrobactrum ovis sp. nov. with the type strain B1315(T) ( = CCM 8460(T) = LMG 27356(T.)) The taxonomic allocation of O. gallinifaecis, which grouped inconsistently together with strain B1315(T) on the basis of 16S rRNA gene sequence data, but shows the chemotaxonomic features of the genus Ochrobactrum, remains to be clarified.

Rubritalea sabuli sp. nov., a carotenoid- and squalene-producing member of the family Verrucomicrobiaceae, isolated from marine sediment

The taxonomic status of a verrucomicrobial strain isolated from marine sediment was established based on a polyphasic examination. The novel isolate, strain YM29-052T, was obligately aerobic, Gram-negative, non-motile, coccoid or rod-shaped and chemoheterotrophic. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that the new isolate shared approximately 94-99 % sequence similarity with members of genus Rubritalea of the family Verrucomicrobiaceae within the phylum 'Verrucomicrobia'. Genomic DNA-DNA hybridization between strain YM29-052T and Rubritalea squalenifaciens HOact23T showed relatedness of <70 %, the value commonly accepted as the threshold for the phylogenetic definition of a species. Strain YM29-052T produces carotenoid compounds that render the cell biomass a pink colour; the strain also contains squalene. The cell-wall peptidoglycan of the novel strain contains muramic acid and meso-diaminopimelic acid. The DNA G+C content of strain YM29-052T was 47.7 mol%; MK-8 and MK-9 were the major menaquinones. The presence of iso-C14 : 0, iso-C16 : 0 and C16 : 1 omega 7c as major cellular fatty acids supported the identification of the novel isolate as a member of the genus Rubritalea. On the basis of polyphasic taxonomic evidence, it was concluded that strain YM29-052T should be classified within a novel species of the genus Rubritalea, for which the name Rubritalea sabuli sp. nov. is proposed. The type strain is YM29-052T (=MBIC08323T =KCTC 22127T).

Isolation of urease-positive Ochrobactrum intermedium in the stomach of a non-ulcer dyspeptic patient from north India

Ochrobactrum intermedium is an opportunistic human pathogen found in immunocompromised individuals. We report the case of a north Indian patient with non-ulcer dyspepsia whose gastric biopsy revealed the presence of O. intermedium, along with Helicobacter pylori. Further description of O. intermedium was performed with 16S rRNA (1500 nucleotides) and RecA (1065 nucleotides) gene sequencing, and the identity and phylogenetic affiliation of the isolate was confirmed by 100% nucleotide similarity with O. intermedium LMG3301. Further investigation is required in order to evaluate the link between H. pylori and O. intermedium in the gastric niche.

Pink-pigmented non-fermentative gram-negative rods associated with human infections: a clinical and diagnostic challenge

Over the past several decades, the appearance of pink-pigmented bacteria in clinical specimens has gone from being a microbiologic curiosity in the clinical laboratory to the recognition of these aerobic microorganisms as etiologic agents of human disease, most notably bloodstream infections. Advances in the fields of molecular taxonomy and phylogenetics indicate that at least four distinct genera and eight different species are associated with clinical infections in susceptible patient populations. However, these bacteria are slow growing and present multiple diagnostic challenges to the microbiology laboratory including culture, isolation, and identification to species rank. This article provides a current review of these unusual non-fermentative chromogenic bacteria including their disease spectrum, taxonomy, and laboratory identification. The review also highlights the pitfalls or shortcomings we currently have in our knowledge of these microbes and their disease-producing capabilities.

Thermobacillus composti sp. nov., a moderately thermophilic bacterium isolated from a composting reactor

A Gram-negative, rod-shaped, spore-forming and moderately thermophilic bacterium, strain KWC4(T), was isolated from a composting reactor. Cells of strain KWC4(T) were 2.0-5.0 microm long and 0.5-0.7 microm in diameter. Strain KWC4(T) grew aerobically at 32-61 degrees C, with optimal growth occurring at 50 degrees C. It grew at pH 5.6-10.1, with optimal growth at around pH 9.0. The optimum NaCl concentration for growth was almost 0 % (w/v), but strain KWC4(T) was moderately halotolerant and was able to grow at NaCl concentrations up to 4.4 % (w/v). The DNA G+C content of strain KWC4(T) was 60.0 mol%. The major fatty acids were iso-16 : 0 (39.0 %) and anteiso-15 : 0 (33.3 %). Based on 16S rRNA gene sequence similarity data, strain KWC4(T) belonged to the genus Thermobacillus and was related to Thermobacillus xylanilyticus. However, strain KWC4(T) had a 38 bp insertion sequence located near the 3' end of its 16S rRNA gene that was not present in T. xylanilyticus. The 16S rRNA gene sequence similarity value between strain KWC4(T) and T. xylanilyticus was 95.7 %. The DNA-DNA hybridization value between strain KWC4(T) and T. xylanilyticus strain XE(T) was 66 %. On the basis of phenotypic and genotypic evidence, strain KWC4(T) (=DSM 18247(T)=JCM 13945(T)) is the type strain of a novel species, for which the name Thermobacillus composti sp. nov. is proposed.

Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria

Bacteria in the phylum Acidobacteria are widely distributed and abundant in soils, but their ecological roles are poorly understood, owing in part to a paucity of cultured representatives. In a molecular survey of acidobacterial diversity at the Michigan State University Kellogg Biological Station Long-Term Ecological Research site, 27% of acidobacterial 16S rRNA gene clones in a never-tilled, successional plant community belonged to subdivision 1, whose relative abundance varied inversely with soil pH. Strains of subdivision 1 were isolated from these never-tilled soils using low-nutrient medium incubated for 3 to 4 weeks under elevated levels of carbon dioxide, which resulted in a slightly acidified medium that matched the pH optima of the strains (between 5 and 6). Colonies were approximately 1 mm in diameter and either white or pink, the latter due to a carotenoid(s) that was synthesized preferentially under 20% instead of 2% oxygen. Strains were gram-negative, aerobic, chemo-organotrophic, nonmotile rods that produced an extracellular matrix. All strains contained either one or two copies of the 16S rRNA encoding gene, which along with a relatively slow doubling time (10 to 15 h at ca. 23 degrees C) is suggestive of an oligotrophic lifestyle. Six of the strains are sufficiently similar to one another, but distinct from previously named Acidobacteria, to warrant creation of a new genus, Terriglobus, with Terriglobus roseus defined as the type species. The physiological and nutritional characteristics of Terriglobus are consistent with its potential widespread distribution in soil.

Characterization of Dialister species in infected root canals

Members of the Dialister genus are asaccharolytic obligately anaerobic gram-negative coccobacilli that are culture-difficult or remain uncultivated. Their participation in endodontic infections has been only consistently demonstrated after advent of molecular biology approaches. This study was undertaken to characterize Dialister species in samples from primary endodontic infections using a devised 16S rRNA gene-based group-specific heminested PCR assay followed by sequencing of PCR products. Genomic DNA was isolated directly from clinical samples and used as template for PCR. Amplicons from positive specimens were sequenced and phylogenetically analyzed to determine species identity. Ten of 21 clinical samples yielded sequences with the highest percent similarities to oral Dialister species/phylotypes. Seven sequences were from Dialister invisus, and the other three sequences belonged to Dialister pneumosintes, Dialister oral clone BS095 and Dialister sp. clone IS013B24. Findings demonstrated that different Dialister species can take part in the microbiota associated with apical periodontitis lesions.

A new bacterial strain mediating As oxidation in the Fe-rich biofilm naturally growing in a groundwater Fe treatment pilot unit

A bacterial strain B2 that oxidizes arsenite into arsenate was isolated from the biofilm growing in a biological groundwater treatment process used for Fe removal. This strain is phylogenetically and morphologically different from the genus Leptothrix commonly encountered in biological iron oxidation processes. T-RFLP fingerprint of the biofilm revealed that this isolated strain B2 corresponds to the major population of the bacterial community in the biofilm. Therefore, it is probably one of the major contributors to arsenic removal in the treatment process.

Analysis of fae and fhcD genes in Mono Lake, California

Genes for two enzymes of the tetrahydromethanopterin-linked C(1) transfer pathway (fae and fhcD) were detected in hypersaline, hyperalkaline Mono Lake (California), via PCR amplification and analysis. Low diversity for fae and fhcD was noted, in contrast to the diversity previously detected in a freshwater lake, Lake Washington (Washington).

Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum ‘Bacteroidetes’

An aerobic, Gram-negative, non-fermentative, rod-shaped, motile, orange-pigmented bacterium, UST20020801T, was isolated from sea-water samples collected from Port Shelter, Hong Kong, S.A.R., China, in August 2002. The full 16S rRNA gene sequence of this strain shared only 87·5 % similarity with its nearest relative, Crocinitomix catalasitica, a species of the family Cryomorphaceae. However, strain UST20020801T possessed menaquinone-6, a major respiratory quinone of members of the family Flavobacteriaceae. This strain contains unique fatty acids such as i15 : 1G, i17 : 1ω9c, 2-OH 15 : 0, 15 : 1ω6c and three unknown fatty acids of equivalent chain-length of 11·543, 13·565 and 16·582. Further analysis of its ecophysiology and biochemistry suggests that this strain represents a new genus in the phylum ‘Bacteroidetes’. The name Owenweeksia hongkongensis gen. nov., sp. nov. is proposed. The type strain is UST20020801T (=NRRL B-23963T=JCM 12287T).

[Evolution and phylogeny of rhizobia]

Nitrogen fixation an ancient process that may is have originated in the archaean Eon under the primitive atmosphere anoxygenic conditions. Diazotrophy is an exclusive process of prokaryotes, only Euryarchaeota and 6 of 54 Bacteria phyla have diazotrophs lineages. Some of them coevolved with flowering plants for the establishment of molecular bases of a mutualistic symbiosis relationship. In rhizobia, the nitrogen fixation occurs inside the nodules, special structures on the roots or stems of legumes. Nodule organogenesis starts with the bacterial nodulation factors (Nod factors) codified in large plasmids or symbiotic islands in the bacterial genomes. Nodulation genes had more recent origin than the nitrogen fixation ones because the origin of the nod gene is associated with the origin of the hosts. The 16S rRNA phylogeny groups rhizobia in 7 genuses of the alpha-Proteobacteria: Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium, Methylobacterium and Devosia, and two genuses recently described in f-Proteobacteria: Burkholderia and Wautersia. The phylogenies obtained with other chromosomal genes are similar at the genus level, but it is incongruent with the symbiotic gene (nif & nod) phylogeny, because horizontal gene transfer has allowed their evolution in function to the legume host fitness.

The microbial content of non-sterile pharmaceuticals distributed in Norway

Seventy-seven registered trademark pharmaceuticals and allied products, not required by the relevant monographs to comply with the test for sterility, were investigated for their microbial content. All the products examined complied with current regulations with respect to the numbers and types of microbes isolated, indicating the effectiveness of existing production practices in meeting existing standards. Gram-positive endospore-forming rods accounted for the majority of the bacteria isolated. Gram-negative rods were present for the most part in incidental numbers. However, some of these were of species that have been previously indicated as opportunistic pathogens and which should be considered as objectionable in pharmaceuticals. A number of the isolates showed antibiotic resistances unusual for the species in question.

Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge

A thermophilic, marine, anaerobic, chemolithoautotrophic, sulfate-reducing bacterium, strain CIR29812T, was isolated from a deep-sea hydrothermal vent site at the Kairei vent field on the Central Indian Ridge. Cells were Gram-negative motile rods that did not form spores. The temperature range for growth was 55-80 degrees C, with an optimum at 70 degrees C. The NaCl concentration range for growth was 10-35 g l(-1), with an optimum at 25 g l(-1). The pH range for growth was 6-6.7, with an optimum at approximately pH 6.25. H2 and CO2 were the only electron donor and carbon source found to support growth of the strain. However, several organic compounds were stimulatory for growth. Sulfate was used as electron acceptor, whereas elemental sulfur, thiosulfate, sulfite, cystine, nitrate and fumarate were not. No fermentative growth was observed with malate, pyruvate or lactate. The phenotypic characteristics of strain CIR29812T were similar to those of Thermodesulfobacterium hydrogeniphilum, a recently described thermophilic, chemolithoautotrophic sulfate-reducer. However, phylogenetic analyses of the 16S rRNA gene sequences showed that the new isolate was distantly related to members of the family Thermodesulfobacteriaceae (similarity values of less than 90%). The chemotaxonomic data (fatty acids and polar lipids composition) also indicated that strain CIR29812T could be distinguished from Thermodesulfobacterium commune, the type species of the type genus of the family Thermodesulfobacteriaceae. Finally, the G+C content of the genomic DNA of strain CIR29812T (46.0 mol%) was not in the range of values obtained for members of this family. On the basis of phenotypic, chemotaxonomic and genomic features, it is proposed that strain CIR29812T represents a novel species of a new genus, Thermodesulfatator, of which Thermodesulfatator indicus is the type species. The type strain is CIR29812T (=DSM 15286T=JCM 11887T).

Pseudoalteromonas sagamiensis sp. nov., a marine bacterium that produces protease inhibitors

A marine bacterium producing protease inhibitors was isolated from neritic sea water and was studied phenotypically, genotypically and phylogenetically. This bacterium (strain B-10-31(T)) produced three types of protease inhibitor, namely, marinostatin, monastatin and leupeptin, which were considerably different in terms of their chemical structure and properties. Strain B-10-31(T) was a rod-shaped, non-spore-forming, Gram-negative, strictly aerobic bacterium that was motile by means of one polar flagellum. The strain required Na(+) for growth and exhibited optimal growth at 27 degrees C, pH 8.0 and 2 % (w/v) NaCl. It utilized various substrates, such as D-glucose, maltose, maltotriose, N-acetylglucosamine, L-threonine, L-serine, L-arginine, L-proline, L-alpha-alanine and L-glutamate, as the sole energy source. Ubiquinone-8 was the major respiratory quinone. The major fatty acids were C(16 : 0), C(16 : 1) omega7c, C(16 : 1) omega9c and C(18 : 1) omega7c. The G+C content of the DNA of strain B-10-31(T) was 42.0 mol%. Phylogenetic analysis, based on 16S rDNA sequences, showed that the strain clustered in the gamma-Proteobacteria. The aerobic marine bacterium Pseudoalteromonas bacteriolytica was the species most closely related to the new isolate (90.4 % 16S rDNA sequence similarity); other described species in the gamma-Proteobacteria cluster showed low levels of sequence similarity with strain B-10-31(T) (<90 %). Based on the above results, it is proposed that the novel marine bacterium should be classified as a new species, for which the name Pseudoalteromonas sagamiensis (type strain B-10-31(T)=JCM 11461(T)=DSM 14643(T)) is proposed.

Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent

A novel thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium designated strain TR(T) was isolated from a sample of a deep-sea hydrothermal chimney collected at the Rainbow vent field on the Mid-Atlantic Ridge (36 degrees 14'N). Gram-negative, non-spore-forming, non-motile rods occurred singly or in pairs. The organism grew in the temperature range 37-80 degrees C with an optimum at 70 degrees C and at pH 5.5-8.4 with an optimum around 6.7. The NaCl range for growth was 10-50 g l(-1) with an optimum of 30 g l(-1). Strain TR(T) grew chemoorganoheterotrophically with carbohydrates, proteinaceous substrates, organic acids and alcohols using oxygen or nitrate as electron acceptors. The isolate was able to grow at oxygen concentrations from 0.5 to 21%. Oxygen concentrations that promoted fastest growth ranged from 4 to 8% under agitation. The novel isolate was able to grow lithoheterotrophically with molecular hydrogen as the energy source. The G + C content of the genomic DNA was 68.4 mol%. Phylogenetic analysis of the 16S rDNA sequence placed strain TR(T) within the phylum Deinococcus-Thermus of the Bacteria. On the basis of phenotypic and phylogenetic data, it is proposed that this isolate should be described as a member of a novel species of a new genus as Vulcanithermus mediatlanticus gen. nov., sp. nov. The type strain is TR(T) (= DSM 14978T = VKM B-2292T = JCM 11956T).

Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov

A phylogenetically novel aerobic bacterium was isolated from an anaerobic-aerobic sequential batch reactor operated under enhanced biological phosphorus removal conditions for wastewater treatment. The isolation strategy used targeted slowly growing polyphosphate-accumulating bacteria by combining low-speed centrifugations and prolonged incubation on a low-nutrient medium. The isolate, designated strain T-27T, was a gram-negative, rod-shaped aerobe. Cells often appeared to divide by budding replication. Strain T-27T grew at 25-35 degrees C with an optimum growth temperature of 30 degrees C, whilst no growth was observed below 20 degrees C or above 37 degrees C within 20 days incubation. The pH range for growth was 6.5-9.5, with an optimum at pH 7.0. Strain T-27T was able to utilize a limited range of substrates, such as yeast extract, polypepton, succinate, acetate, gelatin and benzoate. Neisser staining was positive and 4,6-diamidino-2-phenylindole-stained cells displayed a yellow fluorescence, indicative of polyphosphate inclusions. Menaquinone 9 was the major respiratory quinone. The cellular fatty acids of the strain were mainly composed of iso-C15:0, C16:1 and C14:0. The G + C content of the genomic DNA was 66 mol%. Comparative analyses of 16S rRNA gene sequences indicated that strain T-27T belongs to candidate division BD (also called KS-B), a phylum-level lineage in the bacterial domain, to date comprised exclusively of environmental 16S rDNA clone sequences. Here, a new genus and species are proposed, Gemmatimonas aurantiaca (type strain T-27T=JCM 11422T=DSM 14586T) gen. nov., sp. nov., the first cultivated representative of the Gemmatimonadetes phyl. nov. Environmental sequence data indicate that this phylum is widespread in nature and has a phylogenetic breadth (19% 16S rDNA sequence divergence) that is greater than well-known phyla such as the Actinobacteria (18% divergence).

Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. nov

Thirteen Ralstonia pickettii-like isolates from the environment (water, soil and activated sludge) and human clinical samples (including respiratory secretions of cystic fibrosis patients) were investigated in a polyphasic taxonomic study that employed 16S rDNA sequence analysis, DNA-DNA hybridization, determination of DNA base composition, whole-cell protein analysis, biochemical characterization and PCR-based assays. All isolates were classified as a novel Ralstonia species, for which the name Ralstonia insidiosa sp. nov. is proposed. The type strain, LMG 21421T (= CCUG 46789T), was isolated from the sputum of a patient with acute lymphoblastic leukaemia. R. insidiosa can be differentiated from other species of the genus Ralstonia and phenotypically similar species (including the Burkholderia cepacia complex and Achromobacter xylosoxidans) by a variety of biochemical tests, whole-cell protein analysis and several PCR-based assays. Some outstanding issues in the taxonomy of the genus Ralstonia are also discussed.

Cetobacterium somerae sp. nov. from human feces and emended description of the genus Cetobacterium

Phenorypic and phylogenetic studies were performed on four isolates of an unidentified gram-negative, microaerotolerant, non-spore-forming, rod-shaped bacterium isolated from the feces of children. The unknown organism was bile resistant and produced acetic acid as the major end product of metabolism of peptides and carbohydrates. It possessed a low DNA G + C content of 31 mol %. Comparative 16S rRNA gene sequencing demonstrated that the four isolates were phylogenetically identical (100% 16S rRNA sequence similarity) and represent a hitherto unknown sub-line within the genus Cetobacterium. The novel bacterium displayed approximately 5% sequence divergence with Cetobacterium ceti, and can be readily distinguished from the latter by physiological and biochemical criteria. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown fecal bacterium be classified in the genus Cetobacterium, as Cetobacterium somerae sp. nov. The proposed type strain of Cetobacterium somerae is WAL 14325(T) (ATCC BAA-474(T) = CCUG 46254T).

Marine acidophilic sulfur-oxidizing bacterium requiring salts for the oxidation of reduced inorganic sulfur compounds

An acidophilic sulfur-oxidizing bacterium was isolated from seawater, and designated as strain SH. Strain SH was a Gram-negative, rod-shaped and motile bacterium, which had an optimum temperature and pH value for growth of 30 degrees C and 4.0, respectively. The mol% guanine plus cytosine of the DNA was 46.0. Chemolithotrophic growth was observed with elemental sulfur and tetrathionate at pH 4.0, and was not observed with ferrous ion. The isolate was able to utilize carbon dioxide as a carbon source, and was unable to grow heterotrophically with yeast extract or glucose. The growth of strain SH was activated in medium supplemented with NaCl. However, LiCl and KCl did not sustain the growth of strain SH. The results indicate that strain SH was an acidophilic, halophilic, and obligately chemolithotrophic sulfur-oxidizing bacterium. Phylogenetic analysis based on 16S rDNA sequences indicated that strain SH had a close relationship to Acidithiobacillus thiooxidans. The oxidizing activities of sulfur and sulfite with resting cells were stimulated not only by the addition of NaCl, but also by KCl and LiCl. The oxidation of sulfite was inhibited by ionophores, carbonyl cyanide- m-chlorophenylhydrazone (CCCP), and monensin, and respiratory inhibitors, KCN and 2-heptyl-4-hydroxy-quinoline-N-oxode (HQNO).

Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae

A bright, saffron-colored marine bacterium HTCC2559T was isolated from the Bermuda Atlantic Time Series station in the western Sargasso Sea, Atlantic Ocean by high throughput culturing methods and characterized by polyphasic approaches. Phenotypic data and phylogenetic analyses showed that the strain is a member of the family Flavobacteriaceae. The strain was gram-negative, non-motile, chemoheterotrophic, strictly aerobic, NaCl-requiring, rod-shaped cells that contain carotenoid pigments but not flexirubin. Several kinds of macromolecules (gelatin, DNA, starch, casein, and elastin) were degraded and carbohydrates, sugar alcohols, organic acids, and amino acids were utilized as sole carbon sources. The dominant fatty acids were branched or hydroxy acids, and 3-OH i17:0, i15:0, i15:1, and i17:1 omega9c were abundant. The DNA G+C content of the strain is 34.8 mol%. Phylogenetic analyses using three treeing algorithms based on 16S rRNA gene sequences revealed that the strain formed a very distinct lineage that is allied closely with several seawater environmental clones in the family Flavobacteriaceae. Therefore, it is proposed from the polyphasic studies that strain HTCC2559T (=ATCC BAA-628T = KCTC 12090T) belongs to a new genus and species named Croceibacter atlanticus gen. nov., sp. nov.

[Species identification and molecular epidemiology of bacteria belonging to Ochrobactrum genus]

Two species of medical interest belong to the genus Ochrobactrum, Ochrobactrum anthropi and Ochrobactrum intermedium. They are members of the microbiota of soil and an increasing number of works report the isolation of O. anthropi from clinical specimen, especially from immunocompromised patients and nosocomial infection. Involving of each species in human infection is poorly estimated due to unclear differential phenotypic characters. We performed 16S rDNA sequencing for identification of 20 clinical isolates of Ochrobactrum sp. to the species level. Then, we studied the phenotype of each isolate especially, morphology, culture onto different media and at different temperatures, biochemical characters and antibiotics resistance pattern. Colony morphology after growth onto Trypticase-Soy and McConkey agar, culture at 45 degrees C onto Trypticase-Soja agar, presence of urease, and netilmycin, tobramycin and colistin resistance allowed identification of species. Ribotyping using HindIII and EcoRI gave a supplementary criterion for species determination but did not allow typing at the infra-species level. In contrast, Pulsed-Field Gel Electrophoresis showed high degree of polymorphism between strains and proved the clonality of certain isolates. Thus, this method could be a useful tool for molecular epidemiology of Ochrobactrum infections.

Marinithermus hydrothermalis gen. nov., sp. nov., a strictly aerobic, thermophilic bacterium from a deep-sea hydrothermal vent chimney

A novel thermophilic marine bacterium, designated strain T1T, was isolated from a deep-sea hydrothermal vent chimney sample collected from the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1,385 m. Cells of strain T1T were rod-shaped, occurring in pairs or filamentous, and stained Gram-negative. Growth was observed between 50.0 and 72.5 degrees C (optimum 67.5 degrees C; 30 min doubling time) and at pH 6.25-7.75 (optimum pH 7.00). The isolate absolutely required NaCl, at a concentration of 0.5-4.5% (optimum 30%). It was a strictly aerobic heterotroph capable of growing solely on complex organic substrates such as yeast extract, tryptone and Casamino acids, utilizing glutamate, proline, serine, cellobiose, trehalose, sucrose, acetate and pyruvate as complementary substrates. The G+C content of the genomic DNA was 68.6 mol%. The 16S rRNA gene sequence of the isolate was most similar to those from members of the genus Thermus, but the isolate was distantly related to them at the genus level (<90%). In addition, phylogenetic analysis indicated that the isolate was on a novel lineage, deeply branched prior to divergence of the genus Thermus. On the basis of phylogenetic analysis and physiological traits of the isolate, it should be described as a member of a novel genus distinct from the previously described genus Thermus. The name Marinithermus gen. nov. is proposed, with Marinithermus hydrothermalis gen. nov., sp. nov. as the type species. The type strain of M. hydrothermalis gen. nov., sp. nov. is strain T1T (=JCM 11576T =DSM 14884T).

Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats

Several strains isolated from Antarctic winter sea water, sea-ice algal assemblages and quartz stone subliths were found to belong to a novel 16S rDNA sequence cluster within the family Flavobacteriaceae (Cytophaga-Flavobacterium-Bacteroides division). The strains were gram-negative, non-motile, psychrotolerant, strictly aerobic, chemoheterotrophic rod-shaped cells that contained orange or yellow carotenoid pigments and required yeast extract when grown in defined mineral-salts media. The requirement for sodium ions varied between strains. Results of DNA-DNA hybridization analysis were used to divide the strains into four distinct genospecies, which were differentiated by physiological and nutritional characteristics. The DNA G+C content of the strains was 33-39 mol%. The fatty acid profiles of representative strains were very similar, with major constituents including i15:1omega10c, a15:1omega10c, i15:0, a15:0, i16:1omega6c, i17:1omega5c and 3-OH i16:0. The novel genus Aequorivita gen. nov., which has widespread distribution in the Antarctic region, is proposed. The genus comprises four species: the type species Aequorivita antarctica sp. nov. (type strain SW49T = ACAM 640T = DSM 14231T), Aequorivita lipolytica sp. nov. (type strain Y10-2T = ACAM 641T = DSM 14236T), Aequorivita crocea sp. nov. (type strain Y12-2T = ACAM 642T = DSM 14239T) and Aequorivita sublithincola sp. nov. (type strain 9-3T= ACAM 643T = DSM 14238T).

Identification of bacteria in drinking and purified water during the monitoring of a typical water purification system

BACKGROUND

A typical purification system that provides purified water which meets ionic and organic chemical standards, must be protected from microbial proliferation to minimize cross-contamination for use in cleaning and preparations in pharmaceutical industries and in health environments.

METHODOLOGY

Samples of water were taken directly from the public distribution water tank at twelve different stages of a typical purification system were analyzed for the identification of isolated bacteria. Two miniature kits were used: (i) identification system (api 20 NE, Bio-Mérieux) for non-enteric and non-fermenting gram-negative rods; and (ii) identification system (BBL crystal, Becton and Dickson) for enteric and non-fermenting gram-negative rods. The efficiency of the chemical sanitizers used in the stages of the system, over the isolated and identified bacteria in the sampling water, was evaluated by the minimum inhibitory concentration (MIC) method.

RESULTS

The 78 isolated colonies were identified as the following bacteria genera: Pseudomonas, Flavobacterium and Acinetobacter. According to the miniature kits used in the identification, there was a prevalence of isolation of P. aeruginosa 32.05%, P. picketti (Ralstonia picketti) 23.08%, P. vesiculares 12.82%,P. diminuta 11.54%, F. aureum 6.42%, P. fluorescens 5.13%, A. lwoffi 2.56%, P. putida 2.56%, P. alcaligenes 1.28%, P. paucimobilis 1.28%, and F. multivorum 1.28%.

CONCLUSIONS

We found that research was required for the identification of gram-negative non-fermenting bacteria, which were isolated from drinking water and water purification systems, since Pseudomonas genera represents opportunistic pathogens which disperse and adhere easily to surfaces, forming a biofilm which interferes with the cleaning and disinfection procedures in hospital and industrial environments.

Survival and nutritional requirements of three bacteria isolated from ultrapure water

Bacteria isolated previously from ultrapure water (UPW) systems were examined for their ability to survive in UPW, with the ultimate goal of elucidating potential carbon and energy sources for the bacteria. Two strains of Ralstonia pickettii isolated from different areas within the UPW system (pretreatment and polishing loop, and referred to as strains 3A1 and MF254A, respectively) and a strain of Bradyrhizobium sp. were compared to increase our understanding of the fundamental behavior of bacteria contaminating UPW. R. pickettii (3A1) grew significantly slower in R2A medium, with a final cell yield much lower than the isolate from the polishing loop. In addition, R. pickettii MF254A showed a broader substrate range than either strain 3A1 or Bradyrhizobium sp. In UPW, there appears to be a threshold cell concentration (approximately 10(6) colony-forming units/ml), whereby the cell numbers remain constant for a prolonged period of 6 months or more. Below this concentration, rapid proliferation is observed until the threshold concentration is attained. Preliminary experiments suggested that nitrogen gas (frequently added to UPW storage tanks) may contribute to growth of Bradyrhizobium sp. Above the threshold concentration, the strain of Ralstonia sp. isolated from the polishing loop was capable of cryptic growth with heat-killed cells in UPW. However, cryptic growth was not observed when the cells supplied as nutrients were killed using UV254 light. Furthermore, cryptic growth did not appear to contribute significantly to proliferation of Bradyrhizobium sp. or Ralstonia sp. 3A1 (isolated from the pretreatment loop). We believe that cryptic growth may aid survival of the bacteria in UPW, but further experiments are warranted to prove this phenomenon conclusively.

Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov

Three aerobic, gram-negative, rod-shaped, non-spore-forming, red-pigmented, airborne bacteria (I/26-Cor1T, I/32A-Cor1 and I/74-Cor2) collected in the Museo Correr (Venice, Italy) were investigated to determine their taxonomic status by analysing their biochemical, physiological and chemotaxonomic features and the G+C content of genomic DNA and by comparing their genomic fingerprints. Additionally, the almost complete 16S rRNA gene sequence of strain I/26-Cor1T was analysed. The three strains were nearly identical in their morphological, physiological, biochemical and chemotaxonomic properties. The strains contained a menaquinone system with the predominant menaquinone MK-7 and a fatty acid profile with C15:0 anteiso, C15:0 iso and C16:1 predominant. Phosphatidylethanolamine and several unidentified lipids were detected in the polar lipid profiles. The polyamine pattern consisted of sym-homospermidine as the major compound. meso-Diaminopimelic acid was found as the characteristic cell-wall diamino acid. The DNA base composition of the three strains ranged from 60 to 63 mol% G+C. Phylogenetically, strain I/26-Cor1T was most closely related to Hymenobacter actinosclerus (95.8% 16S rRNA gene sequence similarity). Physiological and genomic characteristics indicated that the two strains I/26-Cor1T and I/32A-Cor1 are representatives of the same species. The phylogenetic distance to any validly described taxon as indicated by 16S rRNA gene sequence similarities demonstrates that I/26-Cor1T and I/32A-Cor1 represent a novel species, for which the name Hymenobacter aerophilus sp. nov. is proposed, with the type strain I/26-Cor1T (= DSM 13606T = LMG 19657T). I/32A-Cor1 (= DSM 13607 = LMG 19658) is another strain of the species Hymenobacter aerophilus. Since the taxonomic status of strain I/74-Cor2 within the genus Hymenobacter was not determined unambiguously, it is designated Hymenobacter sp. I/74-Cor2 (= DSM 13611 = LMG 19659).

Ilyobacter insuetus sp. nov., a fermentative bacterium specialized in the degradation of hydroaromatic compounds

The mesophilic, anaerobic bacterium strain VenChi2T was isolated with quinic acid (1,3,4,5-tetrahydroxy-cyclohexane-1-carboxylic acid) as the sole source of carbon and energy. Of more than 30 substrates tested, only quinic acid and shikimic acid (3,4,5-trihydroxy-1-cyclohexene-1-carboxylic acid) were utilized, yielding acetate, propionate, butyrate, H2 and CO2 as fermentation products. Sugars, alcohols, (di-)carboxylic acids, amino acids and aromatic compounds were not fermented and no external electron acceptors were used. Strain VenChi2T is a gram-negative, strictly anaerobic, coccoid rod; it does not employ the classical hydroaromatic pathway of aerobic bacteria for the degradation of hydroaromatic compounds (no aromatic intermediates involved). Comparative 16S and 23S rDNA sequence analyses placed strain VenChi2T in the fusobacteria phylum, with the closest relatives among species of the genera Ilyobacter and Propionigenium. The results indicate that, disregarding the taxonomically misplaced Ilyobacter delafieldii, which is a member of the clostridia, the validly described Ilyobacter and Propionigenium species are phylogenetically intermixed. Based on its phenotypic properties, strain VenChi2T (= DSM 6831T = ATCC BAA-291T) is assigned to the genus Ilyobacter as the type strain of a novel species, Ilyobacter insuetus sp. nov.

Propionivibrio limicola sp. nov., a fermentative bacterium specialized in the degradation of hydroaromatic compounds, reclassification of Propionibacter pelophilus as Propionivibrio pelophilus comb. nov. and amended description of the genus Propionivibrio

Strain GolChi1T, a mesophilic, anaerobic bacterium, was isolated with quinic acid (1,3,4,5-tetrahydroxy-cyclohexane-1-carboxylic acid) as the sole source of carbon and energy. Of more than 30 substrates tested, only the hydroaromatic compounds quinic acid and shikimic acid (3,4,5-trihydroxy-1-cyclohexene-1-carboxylic acid) were utilized, yielding acetate and propionate as the only fermentation products. Sugars, alcohols, (di-)carboxylic acids, amino acids and aromatic compounds were not fermented and no external electron acceptors were used. Strain GolChi1T is a gram-negative, rod-shaped, aerotolerant anaerobe that possesses superoxide dismutase; it does not employ the classical hydroaromatic pathway of aerobic bacteria for the degradation of hydroaromatic compounds (no aromatic intermediates involved). 16S-rRNA-based phylogenetic analyses revealed a common origin of this isolate and Rhodocyclus, Propionibacter and Propionivibrio species. High sequence similarity (> 96%) and phenotypic traits indicated a closer relationship between strain GolChi1T and the type species of the monospecific genera Propionivibrio and Propionibacter but, due to its phenotypic properties, strain GolChi1T could not be assigned conclusively to either of these taxa. We propose (i) the amended description of the genus Propionivibrio, (ii) the reclassification of Propionibacter pelophilus Meijer et al. 1999 as Propionivibrio pelophilus comb. nov. and (iii) designation of Propionivibrio limicola sp. nov., with the type strain GolChi1T (= DSM 6832T = ATCC BAA-290T).

[Occurrence of beta-lactamase types ESBL and AmpC among gram-negative rods isolated from food]

The aim of the study was to isolate extended spectrum beta-laktamases (ESBL) and chromosomal beta-laktamases AmpC producing strains from food products. A total of 739 Gram-negative bacteria were tested with double disc diffusion method using cefotaxim, ceftasidim and amoxycillin with clavulanic acid. One strain producing ESBL and belonging to Stenotrophomonas maltophilia was detected from the ice cream (0.14% of all strains). From different food products a total of 14 microorganisms (1.9%) having AmpC enzymes have been isolated. They belonged to Enterobacter spp, Hafnia spp, Morganella spp, Citrobacter, Acinetobacter, and Cedecea. Appearance of strains producing beta-laktamases ESBL and AmpC among microorganism isolated from food make it necessary to monitor enzymes activity during routine microbiological control of foods.

[Chemical characterisation and serological activity of lipopolysaccharides of Ralstonia solanacearum]

Lipopolysaccharides (LPS) of 8 strains of Ralstonia solanacearum (767, 4157, 5712, 7944, 7945, 7955, 8089 and 8110) characterized by different types of the structures of O-specific polysaccharide chains have been investigated. The ELISA and ELISA-inhibition methods were used to investigate the extent of antigenic activity of the presented LPS with respect to the obtained polyclonal O-antisera to the above strains. When analyzing the results obtained the strains were divided into five serogroups as the result of biochemical and serological investigations. The first serogroup included the strains 5712, 7945, 7955 and 8110, whose LPS and O-antisera were characterized by the high level of serological affinity. The second and the third serogroups included the strains 767 and 7944, respectively. Their LPS demonstrated antigenic specificity in the homologous systems only, as well as to O-serum to the strain 5712. The fourth and the fifth serogroups included strains 4157 and 8089, respectively, whose LPS did not manifest the antigenic specificity with respect to O-antisera of the other strains, besides their own ones, and which were characterized by different in principle types of the O-PS structures O-PS.

Development, characterization, and preliminary evaluation of a temperature-sensitive mutant of Ornithobacterium rhinotracheale for potential use as a live vaccine in turkeys

A temperature-sensitive (Ts) mutant strain of Ornithobacterium rhinotracheale (ORT) was developed after exposure of the wild-type organism to N-methyl-N'-nitro-N-nitrosoguanidine. The Ts mutant strain grew at 31 C but had its growth inhibited at 41 C unlike wild-type parent strain. The Ts mutant and parent strains were characterized. Morphologic and biochemical properties of wild-type and mutant strains did not show any differences. The strains were also characterized by polymerase chain reaction (PCR)-based fingerprinting methods. Results showed similar patterns in repetitive sequences by repetitive PCR (enterobacterial repetitive intergenic consensus, highly conserved repeated DNA elements present in Streptococcus pneumoniae (BOX), repetitive extragenic palindromic, and Salmonella enteritidis repetitive element primers); however, random amplified polymorphic DNA fingerprinting was able to differentiate mutant and parent strains showing a unique pattern for each of the ORT strains. The rationale for the use of a Ts strain as a vaccine is based on the ability of the mutant to colonize the upper respiratory tract but not the lower respiratory tract and systemic system of the birds, where the wild-type strain causes severe lesions. In a preliminary evaluation, Ts strain of ORT was recovered from tracheas and choanae of Ts-treated turkeys for 13 days postadministration of the strain either in drinking water or by oculonasal instillation. Humoral immune response was detected in Ts-vaccinated but not in control group birds after 3 wk postadministration. Results suggest that Ts strain of ORT has promising potential use as a live vaccine for ORT.

Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge

An extremely halotolerant and alkaliphilic bacterium was isolated previously from deep-sea sediment collected at a depth of 1050 m on the Iheya Ridge. The strain, designated HTE831 (JCM 11309, DSM 14371), was Gram-positive, strictly aerobic, rod-shaped, motile by peritrichous flagella, and spore-forming. Strain HTE831 grew at salinities of 0-21% (w/v) NaCl at pH 7.5 and 0-18% at pH 9.5. The optimum concentration of NaCl for growth was 3% at both pH 7.5 and 9.5. The G+C content of its DNA was 35.8%. Low level (12-30%) of DNA-DNA relatedness between strain HTE831 and the species of these genera was found, indicating that HTE831 could not be classified as a member of a new species belonging to known genera. Based on phylogenetic analysis using 16S rDNA sequencing, chemotaxonomy, and the physiology of strain HTE831, it is proposed that this organism is a member of a new species in a new genus, for which the name Oceanobacillus iheyensis is proposed.

[Identification and cloning of partial mbh2 gene cluster of hyperthermophile Aquifex pyrophilus]

A 0.8 kb fragment of mbhS2 gene of Aquifex pyrophilus was obtained by PCR with designed primers basing mbhS2 gene of A. aeolicus. It showed 85% homology with the corresponding region of A. aeolicus. Using it as probe, a 5.0 kb Nco I fragment was fished out from the partial genomic library of A. pyrophilus. Then this fragment was cloned, subcloned and sequenced. The result revealed that the fragment contains the full length gene for the mbhS2, the gene orf1 and the first 366 bp of orf2. Comparison with mbhS2 and orf963 of A. aeolicus shows 81% and 60% homologies in amino acid sequence, respectively.

Arenibacter gen. nov., new genus of the family flavobacteriaceae and description of a new species, Arenibacter latericius sp. nov

Five dark-orange-pigmented, Gram-negative, rod-shaped, non-motile, aerobic bacterial strains were isolated from sandy sediment samples collected in the South China Sea in the Indian Ocean, from a holothurian, Apostichopus japonicus, in the Sea of Japan and from a brown alga, Chorda filum, from the Sea of Okhotsk in the Pacific Ocean. Phenotypic data were collected, demonstrating that the bacteria are chemo-organotrophic and require seawater-based media for growth. Polar lipids were analysed and 27% of the total extract comprised phosphatidylethanolamine as the major component. The predominant cellular fatty acids were branched-chain saturated and unsaturated [i-C15:0, i-C15:1, a-C15:0, C15:0, C16:1(n-7)]. The DNA base composition was 37.5-38.2 mol % G+C. The level of DNA homology of the five isolates was 83-94%, indicating that these isolates belong to the same species. A 16S rDNA sequence of the type strain KMM 426T was determined and phylogenetic analysis, based on neighbour-joining and Fitch-Margoliash methods, revealed that the type strain formed a distinct phyletic line in a clade corresponding to the family Flavobacteriaceae and represented a new genus. From the results of this polyphasic taxonomic analysis, it is proposed that the bacterial strains be classified in a new genus, Arenibacter gen. nov., and species, Arenibacter latericius sp. nov. The type strain is KMM 426T (VKM B 2137DT = LMG 19694T = CIP 106861T).

Phenotypic and molecular characterization of isolates of Ornithobacterium rhinotracheale from Peru

Twenty-five isolates of Ornithobacterium rhinotracheale were examined by agar gel precipitation, immunoperoxidase assay, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, western blot analysis, and a polymerase chain reaction. All of the isolates were identified as serotype A. Protein profiles of whole cell extracts were similar for all the isolates, and a polypeptide with a molecular weight of 33 kD was a major component, being present in all the isolates. In the main, proteins of 33, 42, 52, and 66 kD were recognized in immunoblots with sera from chickens naturally exposed to O. rhinotracheale. A modified polymerase chain reaction assay identified O. rhinotracheale DNA from all the isolates and tracheal swabs, producing amplicons of 784 bp, and distinguished O. rhinotracheale from bacterial agents causing similar clinical signs.

Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov

Bacterial strains were isolated from sponge and green algae which were collected on the coast of Japan and Palau. The phylogenetic relationships of these isolates among marine species of the Cytophaga-Flavobacterium-Bacteroides complex were analysed by using their gyrB nucleotide sequences and translated peptide sequences (GyrB) in addition to 16S rDNA sequences. These isolates were closely related to the previously characterized marine Flexibacter species, [Flexibacter] maritimus and [Flexibacter] ovolyticus. These Flexibacter species are distantly related to Flexibacter flexilis, the type species of the genus Flexibacter, and phylogenetically belong to the family Flavobacteriaceae (according to analysis using both 16S rDNA and GyrB sequences). Their phylogenetic, chemotaxonomic and phenotypic characteristics prompted the proposal that these two species should be transferred to the new genus Tenacibaculum, as Tenacibaculum maritimum and Tenacibaculum ovolyticum, respectively. Two additional new species of the genus Tenacibaculum, Tenacibaculum mesophilum gen. nov., sp. nov. (= MBIC 1140T = IFO 16307T) and Tenacibaculum amylolyticum gen. nov., sp. nov. (= MBIC 4355T = IFO 16310T), which were isolated from sponges and macroalgae, are also reported. For taxonomic considerations at the species level, the resolution of gyrB sequences was superior to that of 16S rDNA sequences, and the grouping based on the gyrB phylogram was consistent with DNA-DNA hybridization results.

Evaluation of the VITEK 2 system for the identification and susceptibility testing of three species of nonfermenting gram-negative rods frequently isolated from clinical samples

VITEK 2 is a new automatic system for the identification and susceptibility testing of the most clinically important bacteria. In the present study 198 clinical isolates, including Pseudomonas aeruginosa (n = 146), Acinetobacter baumannii (n = 25), and Stenotrophomonas maltophilia (n = 27) were evaluated. Reference susceptibility testing of cefepime, cefotaxime, ceftazidime, ciprofloxacin, gentamicin, imipenem, meropenem, piperacillin, tobramycin, levofloxacin (only for P. aeruginosa), co-trimoxazole (only for S. maltophilia), and ampicillin-sulbactam and tetracycline (only for A. baumannii) was performed by microdilution (NCCLS guidelines). The VITEK 2 system correctly identified 91.6, 100, and 76% of P. aeruginosa, S. maltophilia, and A. baumannii isolates, respectively, within 3 h. The respective percentages of essential agreement (to within 1 twofold dilution) for P. aeruginosa and A. baumannii were 89.0 and 88.0% (cefepime), 91.1 and 100% (cefotaxime), 95.2 and 96.0% (ceftazidime), 98.6 and 100% (ciprofloxacin), 88.4 and 100% (gentamicin), 87.0 and 92.0% (imipenem), 85.0 and 88.0% (meropenem), 84.2 and 96.0% (piperacillin), and 97.3 and 80% (tobramycin). The essential agreement for levofloxacin against P. aeruginosa was 86.3%. The percentages of essential agreement for ampicillin-sulbactam and tetracycline against A. baumannii were 88.0 and 100%, respectively. Very major errors for P. aeruginosa (resistant by the reference method, susceptible with the VITEK 2 system [resistant to susceptible]) were noted for cefepime (0.7%), cefotaxime (0.7%), gentamicin (0.7%), imipenem (1.4%), levofloxacin (2.7%), and piperacillin (2.7%) and, for one strain of A. baumannii, for imipenem. Major errors (susceptible to resistant) were noted only for P. aeruginosa and cefepime (2.0%), ceftazidime (0.7%), and piperacillin (3.4%). Minor errors ranged from 0.0% for piperacillin to 22.6% for cefotaxime against P. aeruginosa and from 0.0% for piperacillin and ciprofloxacin to 20.0% for cefepime against A. baumannii. The VITEK 2 system provided co-trimoxazole MICs only for S. maltophilia; no very major or major errors were obtained for co-trimoxazole against this species. It is concluded that the VITEK 2 system allows the rapid identification of S. maltophilia and most P. aeruginosa and A. baumannii isolates. The VITEK 2 system can perform reliable susceptibility testing of many of the antimicrobial agents used against P. aeruginosa and A. baumannii. It would be desirable if new versions of the VITEK 2 software were able to determine MICs and the corresponding clinical categories of agents active against S. maltophilia.

Group-specific 16S rRNA targeted probes for the detection of type I and type II methanotrophs by fluorescence in situ hybridisation

The study of methane-oxidising bacteria (methanotrophs) is of special interest, because of their role in the natural reduction of methane emissions from many different sources. Therefore new probes were developed to detect specifically either type I (Methylococcaceae) or type II methanotrophs (Methylocystaceae). The probes have shown high specificity in fluorescence in situ hybridisations (FISH), as demonstrated by parallel hybridisation of target and reference strains as well as sequence data analysis. With these probes, methanotrophs were detected in soil and root samples from rice microcosms, demonstrating their applicability even in a complex environmental matrix.

Oral colonization of aerobic and facultatively anaerobic gram-negative rods and cocci in irradiated, dentate, xerostomic individuals

This study aimed at investigating the oral colonization of aerobic and facultatively anaerobic gram-negative rods and cocci in head- and neck-irradiated, dentate, xerostomic individuals. Subjects were recruited from a nasopharyngeal carcinoma clinic and were segregated into group A: <60 years (n=25, 48+/-6 years, 5+/-5 years post-irradiation) and group B: >or=60 years (n=8, 67+/-4 years, 2+/-2 years post-irradiation) and were compared with age- and sex-matched normal individuals, group C: <60 years (n=20, 44+/-12 years) and group D: >or=60 years (n=10, 70+/-3 years). Selective culture of the oral rinse samples was carried out to isolate, quantify and speciate (using API 20E kit) aerobic and facultatively anaerobic gram-negative rods and cocci recovery. All test subjects were put under comprehensive oral and preventive care for 3 months, and 12 group A and 5 group B subjects were recalled for reassessment of aerobic and facultatively anaerobic gram-negative rods and cocci colonization. All identical isolates, pre- and post-hygienic care, were phenotypically (Vitek, Hazelwood, MA and antibiogram profile) and genotypically (pulsed-field gel electrophoresis) evaluated. The aerobic and facultatively anaerobic gram-negative rods and cocci isolated from the first round oral rinse samples included: Acinetobacter, Neisseria, Chryseomonas, Flavimonas, Pseudomonas, Citrobacter, Enterobacter, Escherichia, Klebsiella, Flavobacterium and Weeksella species. The aerobic and facultatively anaerobic gram-negative rods and cocci isolation rate was high for irradiated individuals, and they were 64/25% and 100/80% for groups A/C and B/D, respectively. Recovery of aerobic and facultatively anaerobic gram-negative rods and cocci and Klebsiella pneumoniae subsp. pneumoniae in oral rinse samples were found to be significantly more prevalent in the irradiated subjects (groups A and B). Enterobacteriaceae were more frequently isolated from oral rinse samples of aged irradiated subjects (group B vs D, P<0.05), where the quantity of Citrobacter freundii (colony-forming units/ml oral rinse) was also significantly elevated. The isolation rate of aerobic and facultatively anaerobic gram-negative rods and cocci after hygienic care remained unchanged; 3 of 12 and 3 of 5 of the recalled subjects from groups A and B, respectively, harbored same aerobic and facultatively anaerobic gram-negative rods and cocci species. However, only two pairs of K. pneumoniae subsp. pneumoniae, sequentially isolated from same patients in group B, were found to be identical by pulsed-field gel electrophoresis. This may be due to reinfection of the microbes from the same source or permanent colonization. In conclusion, irradiation-induced xerostomia seems to favor frequent, repeated, transient intraoral colonization of aerobic and facultatively anaerobic gram-negative rods and cocci.

Molecular typing demonstrating transmission of gram-negative rods in a neonatal intensive care unit in the absence of a recognized epidemic

Molecular typing techniques have been used in outbreak investigations. In this study, molecular typing techniques were used to track the spread of gram-negative rods (GNRs) in a neonatal intensive care unit (NICU) in the absence of an outbreak. Stool or rectal swab cultures for GNRs were obtained from all infants on admission, weekly, and on discharge. GNRs were tested for gentamicin susceptibility and were typed by contour-clamped homogeneous electric field electrophoresis. Transmission of identical strains of GNRs among infants was noted. Shared strains were more gentamicin resistant compared with unique strains (53% vs. 10%; P=.0001). Infants first colonized when they were >1 week of age had more total days of antibiotic treatment and had a higher rate of acquiring a shared and gentamicin-resistant strain, compared with infants colonized earlier. Antibiotic use increases colonization of infants in the NICU with resistant and shared strains of GNRs.

Distribution of catabolic pathways in some hydrocarbon-degrading bacteria from a subsurface polluted soil

Enrichment cultures on naphtha solvent were used to select aromatic hydrocarbon-degrading bacteria from a BTEX (benzene, toluene, ethylbenzene, xylene)-contaminated subsoil obtained from beneath a paint factory located in Milan, Italy. Fifteen isolated strains were studied for their different biodegradative capacities. Among these, 13 were able to grow on naphtha solvent. Ten were identified as Pseudomonas putida and three as Pseudomonas aureofaciens. Two other degraders were identified as Pseudomonas aeruginosa and Alcaligenes xylosoxidans subsp. denitrificans. Further molecular characterization of the isolates was carried out by randomly amplified polymorphic DNA analysis to ascertain that all the studied strains belonged to different haplotypes. The isolates were characterized for the presence of genes encoding for toluene dioxygenase, xylene monooxygenase and catechol 2,3-dioxygenase by polymerase chain reaction analysis and by Southern analysis. P. putida strain CM23, which showed homology with xylA,M, xylE and todC1C2BA genes, possessed multiple pathways which enabled the strain to grow on benzene, toluene and m-xylene.

Polyphasic characterization of poly-3-hydroxybutyrate-co-3-hydroxyvalerate (p(HB-co-HV)) metabolizing and denitrifying Acidovorax sp. strains

For the purpose of denitrification in small drinking water plants, a bacterial mixed population was isolated from a packed bed column bioreactor with poly-3-hydroxybutyrate-co-3-hydroxyvalerate (P(HB-co-HV)) as a substrate for the denitrification of ground water (10 degrees C). Isolates 2nIII from the mixed culture, with the ability to denitrify and metabolize P(HB-co-HV), were used as starter cultures for the elimination of nitrate in ground water. The strains were characterized by diverse techniques. Classical phenotypic studies lead to rRNA group III of the genus Pseudomonas. Results obtained by molecular techniques demonstrated that the 2nIII strains are members of the Comamonadaceae and shows similarities to the genus Acidovorax. However, an integration of the 2nIII isolates within one of the known Acidovorax species is not possible for the moment. The 2nIII starter cultures clustered close to Av. temperans according to their whole cell proteins and fatty acids, whereas in DNA/DNA hybridization no significant DNA binding (< 25%) was found. In contrast a significant but low degree of DNA/DNA hybridization was found between the 2nIII strains and Av. facilis and Av. delafieldii. Our polyphasic results lead to the conclusion that the 2nIII strains may constitute a separate Acicdovorax species.

Oral health status, oral microflora, and non-surgical periodontal treatment of renal transplant patients receiving cyclosporin A and FK506

OBJECTIVES

To determine the oral health status, oral microflora and the effect of non-surgical periodontal treatment on gingival overgrowth of renal allograft recipients receiving either cyclosporin A (CsA) or FK506 (Tacrolimus) as an immunosuppressant.

MATERIALS AND METHODS

A total of 47 patients receiving CsA (mean age 43.1 years) and 10 receiving FK506 (mean age 40.1 years) were included in the study. Stone casts were taken for measurement of gingival overgrowth. An oral rinse technique was used to investigate the prevalence of yeasts, and aerobic and facultatively anaerobic Gram-negative rods (AGNR).

RESULTS

The CsA and FK506 patients exhibited a Gingival Overgrowth Index (GOI) of 45.2%, and 25.1%, respectively (p < 0.05). The CsA patients had a GOI of 15.2% after one year of non-surgical periodontal treatment. The difference between pre- and postoperative gingival overgrowth indices was significant (p < 0.0001). Candida albicans and Klebsiella pneumoniae were the most notable yeast and AGRN found.

CONCLUSIONS

Renal transplant patients, being immunocompromised, constitute a high-risk group for gingival overgrowth. However, the FK506 regime appeared to ameliorate this effect, compared with CsA. Non-surgical periodontal treatment was effective in reducing established gingival overgrowth in both CsA and FK506 patients (p < 0.05). Adequate pre- and post-transplant oral health care is recommended, for these patients, irrespective of the drug regime.

Properties of a bacterium which degrades solid poly(tetramethylene succinate)-co-adipate, a biodegradable plastic

Various microorganisms were screened for their ability to degrade poly(tetramethylene succinate)-co-(tetramethylene adipate) (PBSA). Strain BS-3, which was newly isolated from a soil sample, was selected as the best strain. From taxonomical studies, the strain was tentatively ascribed to belong to the genus Acidovorax, most probably to the species A. delafieldii. Strain BS-3 could degrade both solid and emulsified PBSA, and also emulsified poly(tetramethylene succinate). During the degradation, a lipase activity was observed in the culture broth. This lipase activity was induced more strongly by PBSA than by tributyrin or triolein which are typical substrates of lipase. These observations strongly suggest that this lipase was involved in the PBSA biodegradation in strain BS-3.

[Bacterial infections of skin and soft tissues in filariasis]

Adenolymphangitis is a common occurrence in filarial lymphedema. Damage to the lymphatics and lymph nodes by F. bancrofti is followed by obliteration of lymph vessels and lymph stasis. Obstruction of lymphatics prevents the bacteria penetrating skin to be evacuated with lymph stream to regional lymph nodes. Colonization of dermis, subcutis and lymphatics evokes clinical symptoms of adenolymphangitis. The question arises which strains of bacteria are responsible for the acute and chronic types of adenolymphangitis. The most probable strains responsible for this condition belong to the cocci and probably the bacillus strains.

Symbiosis of Astragalus cicer with its microsymbionts: partial nodC gene sequence, host plant specificity, and root nodule structure

Astragalus cicer (cicer milkvetch) nodule bacteria were investigated for host plant specificity and partial nodC gene sequences, whilst their native host was studied for the microscopic structure of root nodules. The strains under investigation formed nodules not only on the original host but also on Astragalus glycyphyllos, Astragalus sinicus, Lotus corniculatus, and Phaseolus vulgaris. The nodules induced on the cicer milkvetch were classified as indeterminate and characterized by apical, persistent meristem, a large bacteroid region with infected and uninfected cells, and elongated bacteroids singly located inside peribacteroid membranes. By comparison of the partial nodC gene sequences of a representative strain of astragali rhizobia to those contained in the GenBank database, a close symbiotic relationship of A. cicer microsymbionts to Rhizobium sp. (Oxytropis) was found.

Degradation of various chlorophenols under alkaline conditions by gram-negative bacteria closely related to Ochrobactrum anthropi

From concrete debris of a demolished herbicide production plant several Gram-negative bacterial strains were isolated, which exhibit metabolic capabilities for the degradation of 2,4-dichlorophenol (DCP)l), 4-chloro-2-methylphenol (MCP) and 4-chlorophenol (4-CP), while 2-chlorophenol (2-CP) was degraded at a slower rate. Degradative activity was inducible and was impeded by adding of 100 mg/l of chloramphenicol to growing cultures. The strains displayed alkaliphilic properties with optimum DCP/MCP degradation at pH values around 8.5-9.5; activity was observed up to pH values of 11. Degradation was most likely complete according to chlorine balances; formation of intermediary products was observed with MCP some time. Specific activity of up to 380 mumol/h.g dry mass was found within the concentration range of 10-20 mg/l DCP; higher concentrations retarded the activity with complete inhibition at 200-400 mg/l. Some of the strains carry plasmids whose presence was not unambiguously correlated to the degradative properties. Ribotyping revealed a high degree of relationship between the strains. Preliminary taxonomic investigations showed close relationship to Ochrobactrum anthropi.