Elisabeth Ageron

Azospirillum irakense sp. nov., a nitrogen-fixing bacterium associated with rice roots and rhizosphere soil.

A new species of nitrogen-fixing bacteria, Azospirillum irakense, was found associated with roots and the rhizosphere of rice in the region of Diwaniyah (Qadisya), Iraq. The seven isolates, on which the species description is based, have vibrioid to S-shaped cells with one polar flagellum in liquid medium. Additional lateral flagella are seen on cells grown on nutrient agar. Poly-beta-hydroxybutyrate granules are present in cells. Nitrogen fixation occurs in microaerobic conditions. The phenotypic characters were found to be very close to those of A. amazonense with the following differences: growth occurred in the presence of 3% NaCl, and at pH 5.5 and 8.5, myo-inositol was not utilized as sole source of carbon and energy and pectin was slowly (6 to 9 days) hydrolysed. The seven studied strains formed a DNA-relatedness group distinct from other Azospirillum and Herbaspirillum species. The G + C content of the DNA was 64 to 67 mol %. The type strain is KBC1 (CIP 103311).

Classification of citrobacteria by DNA hybridization: designation of Citrobacter farmeri sp. nov., Citrobacter youngae sp. nov., Citrobacter braakii sp. nov., Citrobacter werkmanii sp. nov., Citrobacter sedlakii sp. nov., and three unnamed Citrobacter genomospecies.

DNA relatedness studies (hydroxyapatite method) were done on 112 strains of citrobacteria. By using the recommended definition of a genomospecies 11 genomospecies were identified in the genus Citrobacter. These genomospecies were separable by their biochemical profiles. Citrobacter koseri (Citrobacter diversus) and Citrobacter amalonaticus proved to be homogeneous species, as previously described. C. amalonaticus biogroup 1, as described by Farmer et al. (J. Clin. Microbiol. 21:46-76, 1985), was shown to be a separate homogeneous species, which was named Citrobacter farmeri sp. nov. The Citrobacter freundii complex was quite heterogeneous. C. freundii sensu stricto, as represented by the type strain, contained only 9 of 66 strains in this complex. The remaining 57 strains were members of seven genomospecies. Genomospecies 5, containing 21 strains, was named Citrobacter youngae sp. nov. Genomospecies 6, containing 15 strains, was named Citrobacter braakii sp. nov. Genomospecies 7 and 8, each containing six strains, were named Citrobacter werkmanii sp. nov. and Citrobacter sedlakii sp. nov., respectively. Genomospecies 9, 10, and 11, each containing three strains, were not named.

A secreted anti-activator, OspD1, and its chaperone, Spa15, are involved in the control of transcription by the type III secretion apparatus activity in Shigella flexneri.

Bacteria of Shigella spp. are responsible for shigellosis in humans and use a type III secretion (TTS) system to enter epithelial cells and trigger apoptosis in macrophages. Transit of translocator and effector proteins through the TTS apparatus is activated upon contact of bacteria with host cells. Transcription of ≈15 genes encoding effectors is regulated by the TTS apparatus activity and controlled by MxiE, an AraC family activator, and its coactivator IpgC, the chaperone of IpaB and IpaC translocators. Using a genetic screen, we identified ospD1 as a gene whose product negatively controls expression of genes regulated by secretion activity. OspD1 associates with the chaperone Spa15 and the activator MxiE and acts as an anti‐activator until it is secreted. The mechanism regulating transcription in response to secretion activity involves an activator (MxiE), an anti‐activator (OspD1), a co‐anti‐activator (Spa15), a coactivator (IpgC) and two anti‐coactivators (IpaB and IpaC) whose alternative and mutually exclusive interactions are controlled by the duration of the TTS apparatus activity.

Serratia entomophila sp. nov. Associated with Amber Disease in the New Zealand Grass Grub Costelytra zealandica

Serratia entomophila sp. nov. is a homogeneous deoxyribonucleic acid relatedness group most closely related to Serratia ficaria and Serratia marcescens. All 19 strains studied resembled S. marcescens (the phenotypically closest species) by their inability to ferment or utilize l-rhamnose, l-rhamnose, d-melibiose, dulcitol, and d-raffinose but differed from S. marcescens by their inability to ferment or utilize sorbitol and their lack of lysine and ornithine decarboxylases. All strains utilized itaconate, a unique characteristic among Serratia species. Two biotypes could be distinguished. Strains of biotype 1 utilized d-arabitol but not l-arabitol or d-xylose. Strains of biotype 2 utilized l-arabitol and d-xylose but not d-arabitol. S. entomophila has been isolated from insect larvae and water. Most strains were isolated in New Zealand from the grass grub Costelytra zealandica infected with amber disease. None of the strains were isolated from infected humans, animals (other than insects), or plants. The type strain is strain A1T (ATCC 43705T).

rRNA gene restriction patterns of Legionella species: A molecular identification system

A total of 28 species of Legionella could be differentiated by rRNA gene restriction patterns generated after cleavage of total DNA with either EcoRV or HindIII restriction endonucleases, and hybridization of fragments with 32P-labelled Escherichia coli 16 + 23S rRNA. Different species gave different fragment patterns. When several isolates of a species were tested, the patterns obtained were often identical. However, more than one pattern was often observed when more than one serotype was considered. The method should be useful for the identification of all species of Legionella including those exhibiting immunological cross-reactions.

Taxonomic diversity of anaerobic glycerol dissimilation in the Enterobacteriaceae

A total of 1,123 strains representing 128 taxa in the Enterobacteriaceae (named species or subspecies and genomic species) were screened for the presence of glycerol dehydrogenases and 1,3-propanediol dehydrogenase. Only eight taxa, Citrobacter freundii sensu stricto, C. youngae, C. braakii, C. werkmanii, Citrobacter genomospecies 10 and 11, Enterobacter gergoviae and Klebsiella pneumoniae subsp. pneumoniae could grow fermentatively on glycerol and possessed both glycerol dehydrogenase type I (induced by glycerol and dihydroxyacetone) and 1,3-propanediol dehydrogenase which are typical enzymes of the anaerobic glycerol dissimilation pathway. Six other species, C. koseri, E. aerogenes, E. intermedium, K. oxytoca, K. planticola and K. terrigena could not grow fermentatively on glycerol and possessed a glycerol dehydrogenase type I but no 1,3-propanediol dehydrogenase. Other glycerol dehydrogenases types were found: type II (induced by glycerol and hydroxyacetone), type III (induced by glycerol only) and type IV (induced by hydroxyacetone only). They were widely distributed among the Enterobacteriaceae. Classification and identification may take advantage of tests exploring the dissimilation of glycerol.

Erwinia carotovora subsp. odorifera subsp. nov., associated with odorous soft rot of chicory (Cichorium intybus L.).

Eleven strains of Erwinia carotovora that were isolated mainly, but not exclusively, from slimy rot of witloof chicory and were previously designated “atypical” E. carotovora subsp. atroseptica strains were characterized and compared with strains of E. carotovora subsp. carotovora, E. carotovora subsp. atroseptica, and Erwinia chrysanthemi (including the type strains). The 11 atypical E. carotovora subsp. atroseptica strains produced a typical bananalike odor when they were inoculated onto witloof chicory leaves. DNA-DNA homology experiments, biochemical tests, tests to determine carbon utilization patterns, and tests to identify the volatile metabolites produced from rotting witloofs were performed. The volatile end products of witloof decay were analyzed by gas chromatography. Alcohols, methylketones, and ethylacetate were produced by all of the Erwinia strains which we studied, whereas propyl acetate, isobutyl acetate, isoamyl acetate, and 2-actamyl acetate were produced only by the flavoring witloof soft-rot strains. A DNA relatedness study was performed by hybridizing DNAs with a tritium-labeled DNA and estimating the δTm values (δTm is the difference between the thermal denaturation midpoint of a homoduplex and the thermal denaturation midpoint of a heteroduplex). The 11 flavoring strains constituted a tight DNA hybridization group (79 to 91% related to type strain CFBP 1878 isolated from witloof). Strains of E. carotovora subsp. carotovora were 59 to 88% related to strain CFBP 1878T (T = type strain) (δTm range, 3 to 4.5°C), indicating that they belonged to the same species but another subspecies. E. carotovora subsp. atroseptica and E. carotovora subsp. betavasculorum appeared to be less closely related to strain CFBP 1878T than E. carotovora subsp. carotovora was, exhibiting 53% homology (δTm, 7°C) and 48 to 51% homology (δTm, 8.5°C), respectively, with strain CFBP 1878T. Therefore, we propose that the 11 flavoring strains are members of a new subspecies, Erwinia carotovora subsp. odorifera. We examined 95 biochemical characteristics, API strip tests, and assimilation tests in Biotype galleries and identified nine tests which can be used for phenotypic differentiation of the new subspecies.

Capping of actin filaments by vinculin activated by the Shigella IpaA carboxyl-terminal domain.

Shigella, the causative agent of bacillary dysentery, invades epithelial cells. Upon bacterial–cell contact, the type III bacterial effector IpaA binds to the cytoskeletal protein vinculin to promote actin reorganization required for efficient bacterial uptake. We show that the last 74 C‐terminal residues of IpaA (A559) bind to human vinculin (HV) and promotes its association with actin filaments. Polymerisation experiments demonstrated that A559 was sufficient to induce HV‐dependent partial capping of the barbed ends of actin filaments. These results suggest that IpaA regulates actin polymerisation/depolymerisation at sites of Shigella invasion by modulating the barbed end capping activity of vinculin.

Classification of Brucella strains isolated from marine mammals using DNA-DNA hybridization and ribotyping

DNA-DNA hybridization showed that the Brucella strains recently isolated from marine mammals belong to the monospecific genus Brucella (more than 77% DNA relatedness). Ribotyping (HindIII rDNA restriction patterns) showed that they may represent a separate subgroup (marine type) specifically associated with marine mammals.

Vibrio navarrensis sp. nov., a species from sewage.

A group of 11 strains, mostly isolated from sewage water in the Province of Navarra, Spain, were found to constitute a DNA relatedness group which is 2 to 39% related to 23 species of the genus Vibrio and 2 to 3% related to two Aeromonas species. Phenotypically, these strains have all of the properties that define the genus Vibrio. However, they differ from the previously described species by three or more properties. The strains are negative for arginine, ornithine, and lysine decarboxylase activities and the Voges-Proskauer test and are unable to utilize putrescine, gluconate, glucuronate, and histidine. They utilize and produce acid from sucrose and grow at 40 degrees C. All strains grow in the presence of 0.5% (wt/vol) NaCl, and seven strains grow weakly in peptone water lacking NaCl. The group of strains which we studied can also be differentiated from other Vibrio species by fatty acid content. The G+C ratio of the DNA is 45 to 47 mol%. The name Vibrio navarrensis sp. nov. is proposed for these strains; strain 1397-6 (= CIP 103381) is the type strain.