Re-Speciation of the Original Reference Strains of Serovars in the Citrobacter freundii (Bethesda-Ballerup Group) Antigenic Scheme of West and Edwards

The antigenic scheme for the Bethesda-Ballerup group of bacteria established by West and Edwards in 1954 has continued to be applied as a serotyping scheme for Citrobacter freundii. In 1993, however, the classification of the Citrobacter was drastically revised and the species C. freundii redefined by Brenner et al. Accordingly, to judge the propriety to continuously use a single antigenic scheme for the C. freundii complex, the 90 reference strains listed in the antigenic scheme for C. freundii by West and Edwards were characterized phenotypically and specified based on the revised classification. Of these 90 strains, two strains of Hafnia alvei and one of Escherichia coli were found. Among the remaining 87 reference strains, Citrobacter youngae was the predominant species (40 strains), followed by Citrobacter braakii (25 strains), Citrobacter werkmanii (13 strains), and the unnamed Citrobacter genospecies 10 of Brenner et al (six strains). Citrobacter freundii, as redefined, accounted for only three strains and ranked behind the other four species. No overlapping with most of the 42 O-groups and 82 H-antigens was recognized between species with few exceptions. O-groups 1–9 inclusive, which were estimated to represent more than 90% of the former C. freundii strains, occurred in strains of C. youngae and C. braakii; and all nine strains of O-group 29, formerly known as the Ballerup group, were identified as C. braakii. These findings suggest that further study of the serotyping system is needed for all H₂S-producing Citrobacter species.     

Ornibactin production and transport properties in strains of Burkholderia vietnamiensis and Burkholderia cepacia (formerly Pseudomonas cepacia)

Several strains of Burkholderia vietnamiensis, isolated from the rhizosphere of rice plants, and four strains formerly known as Pseudomonas cepacia including two collection strains and two clinical isolates were compared for siderophore production and iron uptake. The B. vietnamiensis (TVV strains) as well as the B. cepacia strains (ATCC 25416 and ATCC 17759) and the clinical isolates K132 and LMG 6999 were all found to produce ornibactins under iron starvation. The two ATCC strains of B. cepacia additionally produced the previously described siderophores, pyochelin and cepabactin. Analysis of the ratio of isolated ornibactins (C4, C6 and C8) by HPLC revealed nearly identical profiles. Supplementation of the production medium with ornithine (20 mm) resulted in a 2.5-fold increase in ornibactin synthesis. Ornibactin-mediated iron uptake was independent of the length of the acyl side chain and was observed with all strains of B. vietnamiensis and B. cepacia, but was absent with strains of Pseudomonas aeruginosa, Pseudomonas fluorescens and Pseudomonas stutzeri, known to produce pyoverdines or desferriferrioxamines as siderophores. These results suggest that ornibactin production is a common feature of all Burkholderia strains and that these strains develop an ornibactin-specific iron transport system which is distinct from the pyoverdine-specific transport in Pseudomonas strains.     

Physiological and biochemical contributions to the taxonomy of the genus Prototheca

Prototheca zopfii (12 strains) is able to use glucose, fructose, propanol, glycerol, and acetate as sources of carbon for growth. One of the strains is biochemically (utilization also of galactose and mannose), and two strains are morphologically slightly different.Two strains can be identified as P. wikerhamii. They exhibit good growth with glucose, fructose, galactose, trehalose, propanol, glycerol, acetate, and glutamate as sources of carbon. P. spec. 263-2 grows only with glucose and acatate. P. zopfii and P. wickerhamii are able to use urea, glycine, and glutamate as sources of nitrogen. P. spec. 263-2, on the other hand, cannot utilize these organic nitrogen compounds for growth.Four strains of Chlorella protothecoides are able to use glucose, fructose, galactose, and acetate as sources of carbon for growth in the dark. Three of them utilize also mannose, trehalose, and glutamate. Two strains can grow with glycerol, and one is able to use lactose. — Urea and glycine can serve as sources of nitrogen for the four strains of C. protothecoides. Glutamate supports growth of three strains, and one strain is able to use nicotinamide.     

Updating the Taxonomy of Dermatophytes of the BCCM/IHEM Collection According to the New Standard: A Phylogenetic Approach

Recent taxonomical revisions based on multilocus gene sequencing have provided some clarifications to dermatophyte (Arthrodermataceae) family tree. These changes promoted us to investigate the impact of the changed nomenclature of the dermatophyte strains in the BCCM/IHEM fungal collection, which contains strains of all dermatophyte genera except for Ctenomyces. For 688 strains from this collection, both internal transcribed spacer region (ITS) and partial β-tubulin (BT) sequences were aligned and a multilocus phylogenetic tree was constructed. The ITS?+?BT phylogentic tree was able to distinguish the genera Arthroderma, Lophophyton, Microsporum, Paraphyton, Nannizzia and Trichophyton with high certainty. Epidermophyton, which is widely considered as a well-defined genus with E. floccosum as the only representative, fell within the Nannizzia clade, whereas the phylogenetic analysis, based on the ITS region alone, differentiates Epidermophyton from Nannizzia as a separate genus. Re-identification and reclassification of many strains in the collection have had a profound impact on the composition of the BCCM/IHEM dermatophyte collection. The biggest change is the decline of prevalence of Arthroderma strains; starting with 103 strains, only 22 strains remain in the genus after reassessment. Most Arthroderma strains were reclassified into Trichophyton, with A. benhamiae and A. vanbreuseghemii leaving the genus. The amount of Microsporum strains also dropped significantly with most of these strains being reclassified into the genera Paraphyton and Nannizzia.

     

辣椒镰孢根腐病防病促生细菌的筛选及其效应

【目的】筛选辣椒(Capsicum annuum L.)根腐病防病促生细菌并明确其防病促生效应。【方法】采集健康辣椒根围土壤样品,以辣椒根腐病病原真菌茄镰孢(Fusarium solani)和尖镰孢(Fusarium oxysporum)为指示菌,采用平板对峙法筛选生防细菌,采用选择性培养基筛选溶无机磷、溶有机磷、固氮菌和解钾菌等促生菌,钼锑抗比色法测定溶磷量,凯氏定氮法测定固氮量,火焰原子吸收光谱法测定解钾量。对特性良好组合的菌株进行16S rDNA序列分析鉴定并制作菌剂,最后采用盆栽法测定菌剂防病促生效果。【结果】共筛选得到323株特性良好的功能菌株,拮抗菌78株,溶有机磷菌87株,溶无机磷菌107株,固氮菌128株,解钾菌123株,部分菌株同时具有多个功能特性。互作组合得到6个特性良好的菌株组合,包括8株功能菌株,鉴定发现XP271和XP181为枯草芽胞杆菌(Bacillus subtilis),XP125为特基拉芽胞杆菌(Bacillus tequilensis),XP236为耐盐芽胞杆菌(Bacillus halotolerans),XP79为巨大芽胞杆菌(Bacillus ...     

Numerical taxonomy of fluorescent Pseudomonas associated with tomato roots

The phenetic taxonomy of 110 fluorescent bacterial strains, isolated from the roots of tomatoes and other plants was numerically studied through 97 features including 69 assimilation tests. Thirty-two reference strains of various Pseudomonas spp. were additionally included. The strains clustered into 16 clusters at the 74% similarity level when using Jaccard similarity coefficients. Almost all field strains belonged to the P. fluorescens/P. putida-complex while none clustered with P. syringae and allied bacteria. The biovar II branch, as well as the newly described biovar VI of P. fluorescens, made up 55% and 20% respectively, of the field strains; two % were allocated to P. fluorescens biovar I and three % to biovar IV. Eleven % of the root associated strains were designated P. putida; six strains were biovar A, three strains biovar B while four strains could not be referred to any known biovar. The continuum within the P. fluorescens/P. putida-complex as well as the taxonomic status of the six biovars of P. fluorescens and the three biovars of P. putida are discussed.     

Bioactivity,Chemical Profiling,and 16S rRNA-Based Phylogeny of <Emphasis Type="BoldItalic">Pseudoalteromonas</Emphasis> Strains Collected on a Global Research Cruise

One hundred one antibacterial Pseudoalteromonas strains that inhibited growth of a Vibrio anguillarum test strain were collected on a global research cruise (Galathea 3), and 51 of the strains repeatedly demonstrated antibacterial activity. Here, we profile secondary metabolites of these strains to determine if particular compounds serve as strain or species markers and to determine if the secondary metabolite profile of one strain represents the bioactivity of the entire species. 16S rRNA gene similarity divided the strains into two primary groups: One group (51 strains) consisted of bacteria which retained antibacterial activity, 48 of which were pigmented, and another group (50 strains) of bacteria which lost antibacterial activity upon sub-culturing, two of which were pigmented. The group that retained antibacterial activity consisted of six clusters in which strains were identified as Pseudoalteromonas luteoviolacea, Pseudoalteromonas aurantia, Pseudoalteromonas phenolica, Pseudoalteromonas ruthenica, Pseudoalteromonas rubra, and Pseudoalteromonas piscicida. HPLC-UV/VIS analyses identified key peaks, such as violacein in P. luteoviolacea. Some compounds, such as a novel bromoalterochromide, were detected in several species. HPLC-UV/VIS detected systematic intra-species differences for some groups, and testing several strains of a species was required to determine these differences. The majority of non-antibacterial, non-pigmented strains were identified as Pseudoalteromonas agarivorans, and HPLC-UV/VIS did not further differentiate this group. Pseudoalteromonas retaining antibacterial were more likely to originate from biotic or abiotic surfaces in contrast to planktonic strains. Hence, the pigmented, antibacterial Pseudoalteromonas have a niche specificity, and sampling from marine biofilm environments is a strategy for isolating novel marine bacteria that produce antibacterial compounds.     

块菌(松露)宿主可培养内生菌群落结构与多样性研究

探究四川凉山彝族自治州块菌主产区华山松内生菌群的结构及多样性。在会东县选取4个点(新田乡、新云乡、淌塘镇、雪山乡)的块菌宿主华山松的根、茎、叶为实验材料,通过不同培养基分离样品根、茎、叶的内生细菌、真菌、放线菌,DNA分子鉴定分离菌株的种属,最终分离得到细菌46株,其中欧文氏菌属(Erwinia)5株,沙门氏菌属(Salmonell)1株,杆菌属(Bacillus)22株,葡萄球菌属(Staphylococcus)2株,假单胞菌属(Pseudomonas)2株,类芽胞杆菌属(Paenibacillus)2株,布丘氏菌属(Buttiauxella)2株,肠杆菌属(Enterobacte)3株,爱文氏菌属(Ewingella)1株,泛菌属(Rahnella)1株,拉恩氏菌属(Rahnella Izard)2株,其他属3株;真菌19株,均为子囊菌门(Ascomycota),其中青霉属(Penicillium)4株,疱霉属(Phoma)1株,子囊菌门未知菌1株,篮状菌属(Cladosporium)1株,分枝孢子菌属(Sydowia)1株,曲霉属(Aspergillus)1株,其他属10株;放线菌33株,为链霉菌属(Streptomyces)22株,短小杆菌属(Curtobacterium)2株,短杆菌属(Brevibacterium)1株,其他属8株。研究结果表明,来自不同地点、不同植株部位、不同培养基分离得到的块菌宿主华山松内生菌有差异,证实微生物在土壤、块菌、宿主植物之间有着复杂的相互作用,为块菌的人工栽培提供参考。     

Genetic variability of plant-associated proteobacteria isolated from Slovak (Central European) territory

Genetic variability of 17 wild strains of γ-proteobacteria isolated from different host plants, locations and seasons, identified via routine diagnostics as Erwinia amylovora, was analysed. The ERIC-PCR confirmed the genetic homogeneity among 15 virulent strains while 2 avirulent strains were genetically distinct. These two avirulent strains differed in their antibiotic susceptibility from all virulent strains. The only avirulent Ra1051/98 strain showed significant ampicillin resistance. All 15 virulent strains were confirmed via the ERIC-PCR and MALDI-TOF MS, as closely related to the reference strain NCPPB 683 of E. amylovora. Avirulent strains were identified as Rahnella aquatilis and L. quercina subsp. britannica (formerly Brenneria quercina), by MALDI-TOF MS and the identification was confirmed by 16S rRNA gene sequence analysis. For the first time, L. quercina subsp britannica was identified in the fire blight-symptomatic samples in Central Europe, and for the first time this bacterium was isolated from the host different than oak.     

Epidemiological investigation of <Emphasis Type="Italic">eaeA</Emphasis>-positive <Emphasis Type="Italic">Escherichia coli</Emphasis> and <Emphasis Type="Italic">Escherichia albertii</Emphasis> strains isolated from healthy wild birds

Escherichia coli has commonly been associated with diarrheal illness in humans and animals. Recently, E. albertii has been reported to be a potential pathogen of humans and animals and to be carried by wild birds. In the present study, the prevalence and genetic characteristics of intimin-producing E. coli and E. albertii strains were evaluated in wild birds in Korea. Thirty one of 790 Enterobacteriaceae strains from healthy wild birds were positive for the intimin gene (eaeA) and twenty two of the 31 strains were identified as atypical enteropathogenic E. coli (aEPEC) that did not possess both EAF and bfpA genes. A total of nine lactose non-fermenting coliform bacterial strains were identified as E. albertii by PCR and sequence analysis of housekeeping genes. A total of 28 (90.3%) eaeA-positive strains were isolated from waterfowl. Fifteen aEPEC (68.2%) and two E. albertii (22.2%) strains had a β-intimin subtype and 14 aEPEC strains harboring β-intimin belonged to phylogenetic group B2. AU eaeA-positive E. albertii and 3 aEPEC strains possessed the cytolethal distending toxin gene (cdtB). The eaeA-positive E. coli and E. albertii strains isolated from healthy wild birds need to be recognized as a potential pathogroup that may pose a potential threat to human and animal health. These findings indicate that eaeA-positive E. coli as well as E. albertii can be carried by wild birds, posing a potential threat to human and animal health.     

Studies of Pseudomonas aeruginosa Infections Among Hospitalized Patients

A rapid identification method of glucose nonfermentative gram-negative rods was established and 320 strains isolated were divided into five groups according to their characteristics in pigmentation, acid from glucose, cytochrome oxidase activity and motility. Further characterization of the strains in each group resulted in the identification that the strains in group I were Pseudomonas aeruginosa, strains in group II, P. aeruginosa and Pseudomonas putida. Achromogenic strains of P. aeruginosa were classified into group III, Pseudomonas maltophilia, Pseudomonas alcaligenes and Alcaligenes faecalis into group IV and Acinetobacter calcoaceticus (Acinetobacter anitratus and Achromobacter lwoffii) in group V. When fluorescent pigment production was taken as a standard, 259 out of 263 chromogenic strains were identified as P. aeruginosa and the remaining four were P. putida. Whereas forty-five achromogenic strains included twenty-four A. calcoaceticus, eight P. aeruginosa, six A. faecalis, five P. maltophilia and two P. alcaligenes. From May 1970 to June 1971, 368 strains of glucose nonfermentative rods were isolated from clinical specimens sent to the Central Laboratories of Tohoku University Hospital and three fourth (286/368) of the isolates were P. aeruginosa     

Identification of Actinomycetes Producing Phospholipase D with High Transphosphatidylation Activity

Previously we isolated six actinomycetes strains, 9-4, 10-1, 10-2, 10-3, 10-6, and 21-4, that produce phospholipase D (PLD) with high transphosphatidylation activity. In this study, we identified these strains, and the PLD activities were compared with those of reference strains. 16S rDNA sequences and DNA–DNA hybridization tests indicated taxonomic affiliations of strain 9-6 with Streptomyces senoensis, strains 10-1 and 10-6 with S. vinaceus, and strains 10-2 and 10-3 with S. racemochromogenes. Strain 21-4, though identified as a Streptomyces sp., could not be identified with any known species. Meanwhile, most of the culture supernatants of reference strains demonstrated no or very weak PLD activity, while those of our strains exhibited significantly higher activity. All of the strains in this study were identified as Streptomyces species. The PLD activity of our strains exceeded most of the reference Streptomyces strains. The findings in this study imply that the Streptomyces strains, although they are members of the same species, can produce different quantities of PLD enzyme.     

Mutations in the rfbT Gene Are Responsible for the Ogawa to Inaba Serotype Conversion in Vibrio cholerae O1

In cultures of Vibrio cholerae strains of Ogawa serotype, variant strains which had undergone serotype conversion from Ogawa to Inaba were identified. The rfbT genes cloned from the parent strains were found to produce a 31-kDa protein in the maxicell system, and to cause serotype conversion when introduced into E. coli cells expressing Inaba serotype specificity. On the other hand, rfbT genes cloned from the variant strains neither produced the 31-kDa protein nor caused serotype conversion. Nucleotide sequence of these rfbT genes as well as those of two clinical Vibrio cholerae strains of Inaba serotype revealed that mutations causing premature termination of their rfbT genes were invariably present in strains expressing Inaba serotype specificity. The result strongly suggested that genetic alteration of the rfbT gene is responsible for serotype conversion of Vibrio cholerae O1.     

Killer yeasts of Kluyveromyces and Hansenula genera with potential application in fermentation and therapy

The killing/immunity interactions among killer strains of the genera Kluyveromyces, Hansenula and Saccharomyces from the Czechoslovak Collection of Yeasts were studied with the aim to find the strains with broad specificity and killer activity targeted against a range of undesirable wild yeasts causing stuck fermentations. Among 49 tested Kluyveromyces strains, five strains were found, and among 55 Hansenula strains, ten yeast strains were found with activity against a sensitive strain of Saccharomyces. Hansenula mrakii CCY 38-7-1 and Hansenula saturnus var. subsufficiens CCY 38-4-2 showed exceptional activity against the wine contaminants, Zygosaccharomyces bailii, as well as against pathogenic Candida species within a broad range of pH 2.9–5.1. Their potential biotechnological application is discussed.     

Characterization of Two Novel Biovar of <Emphasis Type="Italic">Agrobacterium tumefaciens</Emphasis> Isolated from Root Nodules of <Emphasis Type="Italic">Vicia faba</Emphasis>

A total of eight strains of bacteria were isolated from the root nodule of Vicia faba on the selective media of Rhizobium. Two of these strains produced phenotypically distinct mucoid colonies (one slow growing and the other fast growing) and were examined using a polyphasic approach for taxonomic identification. The two strains (MTCC 7405 and MTCC 7406) turned out to be new strains of biovar 1 Agrobacterium rather than Rhizobium, as they showed growth on alkaline medium as well as on 2% NaCl and neither catabolized lactose as the carbon source nor oxidized Tween-80. The distinctness between the two strains was marked with respect to their growth on dextrose and the production of lysine dihydrolase, ornithine decarboxylase and DNA G + C content. 16S rDNA sequencing and their comparison with the 16S rDNA sequences of previously described agrobacteria as well as rhizobia strains confirmed the novelty of the two strains. Both of the strains clustered with strains of Agrobacterium tumefaciens in the 16S rDNA-based phylogenetic tree. The phenotypic and biochemical properties of the two strains differed from those of the recognized biovar of A. tumefaciens. It is proposed that the strains MTCC 7405 and MTCC 7406 be classified as novel biovar of the species A. tumefaciens (Type strains MTCC 7405 = DQ383275 and MTCC 7406 = DQ383276).

Properties of a High Malic Acid-Producing Strains of Saccharomyces cerevisiae Isolated from Sake Mash

We characterized high malic acid-producing strains of Saccharomyces cerevisiae isolated from sake mash. We compared the gene expression of these strains with those of the parental strain by DNA microarray, and found that stress response genes, such as HSP12, were commonly upregulated in the high malate-producing strains, whereas thiamine synthesis genes, such as THI4 and SNZ2, were downregulated in these strains.     

Detection of type III secretion gene as an indicator for pathogenic Edwardsiella tarda

Aims: To differentiate pathogenic and nonpathogenic Edwardsiella tarda strains based on the detection of type III secretion system (T3SS) gene using polymerase chain reaction (PCR). Methods and Results: Primers were designed to amplify Edw. tarda T3SS component gene esaV, catalase gene katB, haemolysin gene hlyA and 16S rRNA gene as an internal positive control. Genomic DNAs were extracted using a commercial isolation kit from 36 Edw. tarda strains consisting of 18 pathogenic and 18 nonpathogenic strains, and 50 ng of each DNA was used as the template for PCR amplification. PCR was performed with a thermocycler (TaKaRa TP600) in a 25‐μl volume. Products of esaV were detected in all pathogenic strains, but not in nonpathogenic strains; katB was detected in all pathogenic strains and one of nonpathogenic strains; hlyA was not detected in any strains. Conclusions: The detection of esaV gene can be used for the assessment of pathogenic Edw. tarda strains. Significance and Impact of the Study: The strategy using T3SS gene as the virulence indicator provides a useful tool for the clinical assessment of pathogenic Edw. tarda strains and prediction of edwardsiellosis risk in fish culture environments.     

Characterization of Clinical Isolates of <Emphasis Type="Italic">Gordonia</Emphasis> Species in Japanese Clinical Samples During 1998–2008

During 1998–2008, there were 31 strains of Gordonia species isolated from clinical specimens in our laboratory. Our identification of the 31 strains of Gordonia species showed that major pathogenic Gordonia species in Japan were classifiable, respectively into 14 and 13 strains of Gordonia sputi and Gordonia bronchialis. The four remaining strains were identified as three Gordonia species: G. aichiensis (2 strains), and G. terrae (1 strain), and G. otitidis (1 strain). Results of drug susceptibility tests for these 31 strains of Gordonia isolates are reported herein.     

Re-identification of <Emphasis Type="Italic">Aspergillus fumigatus</Emphasis> sensu lato based on a new concept of species delimitation

The species concept of Aspergillus fumigatus sensu stricto has recently been defined by polyphasic taxonomy. Based on the new concept of species delimitations, 146 worldwide strains of Aspergillus fumigatus sensu lato were re-identified. Of those 146 strains, 140 (95.8%) could be identified as A. fumigatus sensu stricto, 3 (2.1%) as A. lentulus, and the remaining 3 strains as A. viridinutans complex, Neosartorya udagawae, and N. cf. nishimurae. Of 98 clinical strains, only 1 from dolphin nostril was identified as A. lentulus and not A. fumigatus sensu stricto. Random amplification of polymorphic DNA-polymerase chain reaction (RAPD-PCR) with primers PELF and URP1F produced nearly the same band patterns among 136 strains of A. fumigatus sensu stricto while discriminated the species from its related species. We also discussed about identification of several atypical A. fumigatus strains from clinical environments.     

Biological control of rice root-knot nematode,Meloidogyne graminicola through mixture of Pseudomonas fluorescens strains

The plant growth promoting rhizobacterium, Pseudomonas fluorescens strains PF1, TDK1, and PY15 were evaluated individually and in combinations for their efficacy against root-knot nematode, Meloidogyne graminicola, in rice plants under in vitro, glass house and field conditions. Culture filtrates of these strains either individually or as mixture inhibited egg hatching and caused mortality of juveniles of M. graminicola in vitro. The efficacy was more pronounced when filtrates of the strain were used as mixtures than as individual strains. Mixtures of P. fluorescens strains signficantly reduced M. graminicola infestation when applied as bacterial suspensions through seed treatment. The higher activity of peroxidase and chitinase enzymes was observed in plants treated with P. fluorescens mixtures than the plants treated with individual strains, two strain mixtures and untreated control. In field trials on rice, talc formulations of the P. fluorescens strains individually as well as mixtures were evaluated as seed treatment, soil treatment and combination of both. A mixture of the three strains was the most effective when applied either as seed + soil treatment or as seed treatment alone. The introduced P. fluorescens strains survived endophytically on rice roots. The application of the P. fluorescens mixture PF1 + TDK1 + PY15 in seed + soil treatment resulted in higher grain yield which provided a 27.3% increase over the control followed by P. fluorescens mixture PF1 + TDK1 + PY15 in seed treatment alone, which increased the grain yield of rice by 24.7% compared to the control.