Application of a colorimetric DNA-DNA hybridization method for identification ofAeromonas genomic species,isolated from diarrheal stools

The colorimetric DNA-DNA hybridization method for the identification of 18 strains ofAeromonas spp. isolated from human stools was used. Bacterial isolates were also examined by phenotypic characteristics. On the basis of biochemical tests 13 strains were included in phenogroupA. caviœ and 5 strains inA. sobria. Identification to the species level was obtained by colorimetric hybridization method. DNA-DNA similarity values showed that isolates ofA. caviœ group belong to hybridization group (HG) 4 whereas isolates ofA. sobria belong to HG 8/10. DNA relatedness results obtained by the colorimetric method showed good agreement with values detected by the spectrophotometric method. The background in the colorimetric method is lower than in the spectrophotometric one. Results of this study indicate the usefulness of the colorimetric DNA-DNA hybridization in microplates method for the identification ofAeromonas genomic species, isolated from human diarrheal stools.     

Phage specificity and lipopolysaccarides of stem- and root-nodulating bacteria (Azorhizobium caulinodans, Sinorhizobium spp., and Rhizobium spp.) of Sesbania spp

Phage susceptibility pattern and its correlation with lipopolysaccharide (LPS) and plasmid profiles may help in understanding the phenotypic and genotypic diversity among highly promiscuous group of rhizobia nodulating Sesbania spp.; 43 phages were from two stem-nodulating bacteria of S. rostrata and 16 phages were from root-nodulating bacteria of S. sesban, S. aegyptica and S. rostrata. Phage susceptibility pattern of 38 Sesbania nodulating bacteria was correlated with their LPS rather than plasmid profiles. Different species of bacteria (A. caulinodans- ORS571, SRS1-3 and Sinorhizobium saheli- SRR907, SRR912) showing distinct LPS subtypes were susceptible to different group of phages. Phages could also discriminate the strains of Si. saheli (SSR312, SAR610) possessing distinct LPS subtypes. Phages of Si. meliloti (SSR302) were strain-specific. All the strains of R. huautlense having incomplete LPS (insignificant O-chain) were phage-resistant. In in vitro assay, 100% of the phages were adsorbed to LPS of indicator bacterium or its closely related strain(s) only. These observations suggest the significance of LPS in phage specificity of Sesbania nodulating rhizobia. Highly specific phages may serve as biological marker for monitoring the susceptible bacterial strains in culture collections and environment.     

Phylogenetic relationship withinFusarium sambucinum Fuckel sensu lato,determined from ribosomal RNA sequences

Partial ribosomal RNA nucleotide sequences were determined for 11 strains ofFusarium sambucinum Fuckelsensu lato to assess by molecular genetic means, Nirenberg's recent morphotaxonomic interpretation which split the species into three distinct taxa:F. sambucinum sensu stricto, F. torulosum, and one other species, as yet unnamed (Fusarium species nova). Four sequence patterns were identified among the 11 strains. Two sequences that varied at one site were found among strains ofF. sambucinum, strains ofF. torulosum andFusarium sp. nov. showed no intraspecific variation. Interspecific comparisons revealed nucleotide sequence differences of 3–9 substitutions in the ca. 240 nucleotide rRNA segment examined. Although interspecific differences are not large in terms of percent nucleotide substitution, they are much larger than the observed intraspecific variation and support the morphological interpretation distinguishing three taxa. When the data were analysed using parsimony and bootstrapping, the three taxon tree was well supported. The phylogenetic arrangement of these strains is congruent with secondary metabolite profile similarities.     

Fusarium fractiflexum sp. nov. and two other species within theGibberella fujikuroi species complex recently discovered in Japan that form aerial conidia in false heads

Morphological and molecular phylogenetic analyses were conducted on 12 strains ofFusarium, deposited in MAFF asF. subglutinans (≡F. moniliforme var.subglutinans≡F. sacchari var.subglutinans) orFusarium sp. because they formed aerial conidia in false heads in the dark. These strains were resolved as three distinct species within theGibberella fujikuroi species complex. A new species,F. fractiflexum, and two species new to Japan,F. circinatum andF. concentricum, are described and illustrated and their morphological features are discussed.Fusarium fractiflexum, isolated from diseased yellow leaf spots ofCymbidium spp., is differentiated from other fusaria based on its yellowish colonies and aerial conidia formed in false heads in the dark and in zigzag-like conidial chains under black light. Japanese strains ofF. circinatum also formed elongate, coiled sterile hyphae. Phialidic aerial conidia with a pointed apex and a wedgeshaped base were found inF. concentricum cultured under black light and represent a new diagnostic character of the species, in addition to colonies with alternating concentric rings when cultured on PDA. Based on DNA sequences of the β-tubulin gene and two other loci, strains ofF. fractiflexum were resolved phylogenetically as members of the Asian clade of theG. fujikuroi species complex. In addition, Japanese strains ofF. circinatum andF. concentricum were phylogenetically identical to the ex-type strains.     

Genetic variation, real-time PCR, metabolites and mycotoxins ofFusarium avenaceum and related species

In this paper the latest studies dealing with genetic variation and mycotoxins ofF. avenaceum and related species are reviewed and compared to the data from chromatographic image analyses. Forty-three European strains ofFusarium avenaceum and related species were classified by chromatographic image analysis on full chromatographic matrices. The results were in most cases in agreement with those from morphological and molecular analyses and supported the separation betweenF. avenaceum, F. arthrosporioides andF. tricinctum and betweenF. avenaceum groups I and II. The mycotoxin profiles of the FinnishF. avenaceum, F. arthrosporioides andF tricinctum strains were very similar to each other. Moniliformin and enniatins were the main mycotoxins produced. A fluorogenic TaqMan PCR assay (qPCR) was used for the detection ofF. avenaceum/ F. arthrosporioides DNA in Finnish barley and wheat. The qPCR results obtained from grain samples were compared to mycotoxin levels. A correlation was found betweenF. avenaceum/F. arthrosporioides DNA and moniliformin (MON) and enniatin (ENNs) levels in barley. A correlation was also found between the combinedF. avenaceum/F. arthrosporioides/F. tricinctum contamination and MON and ENNs levels in barley in 2002, but not in 2003. This was probably due to the higher MON and ENNs levels in 2002 than in 2003. It was possible to use the DNA levels ofF. avenaceum/F. arthrosporioides to distinguish between most barley samples containing high amounts of MON and ENNs from those containing low levels of the mycotoxins. Presented at the EU-USA Bilateral Workshop on Toxigenic Fungi & Mycotoxins, New Orleans, USA, July 5–7, 2005 Financial support: Grants from the National Technology Agency of Finland (No. 40168/03) and the Academy of Finland (No. 52104); travel grants from NorFA and the European Commission to the Laboratory of Dr. Ulf Thrane     

Identification of QTLs related to cocoa resistance to three species of<Emphasis Type="Italic"> Phytophthora</Emphasis>

This study aimed to compare the genetic control of cacao resistance to three species of Phytophthora: Phytophthora palmivora, Phytophthora megakarya and Phytophthora capsici. The study was conducted on 151 hybrid progenies created in Côte d'Ivoire and grown in a green-house in Montpellier. Phytophthora resistance was screened by leaf-test inoculation with two different strains per species. Selection of the best individuals for resistance to P. palmivora at a 10% selection rate, would lead to a genetic progress of 47% in the disease evaluation for this species and a genetic progress of 42% and 21% for the two other species. A genetic map with a total length of 682 cM was built with 213 markers, 190 AFLPs and 23 microsatellites. QTLs were identified using composite interval mapping. QTLs were found located in six genomic regions. One of these was detected with five strains belonging to the three Phytophthora species. Two other regions were detected with two or three strains of two different species. Three additional QTLs were detected for only one species of Phytophthora. Each QTL explained between 8 to 12% of the phenotypic variation. For each strain, between 11.5% to 27.5% of the total phenotypic variation could be explained by the QTLs identified. The identification of multiple QTLs involved in resistance to Phytophthora offers the possibility to improve durability of resistance in cocoa by a possible cumulation of many different resistance genes located in different chromosome regions using marker-aided selection.Communicated by H.F. Linskens     

Differentiation between strains ofFlavobacterium breve and allied bacteria by comparisons of deoxyribonucleic acids

Chromosomal deoxyribonucleic acid was isolated and purified from 10 strains ofFlavobacterium breve, originating from human or other animal sources. The mean and standard deviation for the species in base content was 32.4±0.6% G+C, and in genome size was 3.21±0.37×10⁹ daltons. In vitro DNA reassociation showed that sevenF. breve strains (mainly from human sources) had high levels of intraspecific base sequence similarity (>70%) as derived from reassociations done at the optimum temperature of reassociation (TOR) or TOR—10°C (nonstringent conditions). The three otherF. breve strains contained a high degree of base sequence divergence. All 10 strains ofF. breve were readily distinguishable in their DNA characteristics fromF. meningosepticum, F. odoratum, and allied Gram-negative bacteria.     

Lack of genetic relatedness betweenYersinia philomiragia (the “philomiragia” bacterium) andYersinia species

Four strains ofYersinia philomiragia were studied biochemically and genetically. They showed a high degree of phenotypic similarity and formed a homogenous DNA relatedness group. We could not demonstrate any significant DNA relatedness between this group and otherYersinia species, other Enterobacteriaceae, orPasteurella multocida. Y. philomiragia is phenotypically quite different from other yersiniae and Enterobacteriaceae. These DNA and phenotypic data indicate thatY. philomiragia is not a member of the genusYersinia or a member of the family Enterobacteriaceae. It is suggested that, pending further study, this organism be referred to as the “Philomiragia” bacterium.     

Glucose utilization and growth response to protein hydrolysates byFusobacterium species

Glucose uptake was measured in the supernatants of 18 strains ofFusobacterium species cultured in BM medium. Some species, such asF. nucleatum andF. necrophorum, used between 25% and 48% of the glucose in the medium, but the terminal pH remained near neutral. By contrast, strains ofF. mortiferum andF. necrogenes used on average over 90% of the available glucose in the medium and produced a predictably low acidic pH. Strains ofF. varium used between 86% and 91% of the glucose present but produced a near neutral pH of between 5.8 and 5.9. The metabolic fate of glucose inF. varium was, therefore, examined in more detail. Glucose stimulated the growth of this species, and [¹⁴C]glucose was incorporated into the metabolic end products and various cellular components. Protein hydrolysates, tested for their growth-promoting effects onFusobacterium species, produced two general growth response patterns. Most species grew prolifically on trypticase, proteose peptone, and yeast extract, but poorly in casamino acids and vitamin-free casamino acids. Growth in bactocasitone was poor, but for three species,F. necrophorum, F. varium, andF. nucleatum, there was an approximately linear growth response up to 0.5%. These results suggest a major role for nitrogen metabolism but do not preclude glucose as an energy source in at least some species ofFusobacterium.     

Taxonomy of the marine,luminous bacteria

Summary One hundred and seventy-three strains of marine, luminous bacteria isolated from sea water, surfaces and intestines of fish, as well as from the luminous organs of fish and squid were submitted to an extensive phenotypic characterization. A numerical analysis of the results grouped these strains into four clusters which were formed on the basis of overall phenotypic similarity. One cluster, which was given the designationBeneckea harveyi, consisted of strains which had a moles% GC content in their DNAs of 46.5±1.3 and a single, sheathed, polar flagellum when grown in liquid medium. Most of these strains had unsheathed, peritrichous flagella in addition to the sheathed, polar flagellum when grown on solid medium. The two phenotypically similar clusters which were assigned the species designationsPhotobacterium phosphoreum andP. mandapamensis consisted of strains which had 1–3 unsheathed, polar flagella and moles % GC contents in their DNAs of 41.5±0.7 and 42.9±0.5, respectively. The cluster designatedP. fischeri contained strains having 2–8 sheathed, polar flagella and a moles % GC content of 39.8±1.1. These four species could be further distinguished on the basis of a number of nutritional properties as well as other phenotypic traits. The assignment of the luminous, marine bacteria to four species was supported by differences in the properties of the luminous system as well as differences in the pattern of regulation of spartokinase activity which are discussed. The speciesB. harveyi was found to be phenotypically similar to a number of previously characterized, non-luminous strains ofBeneckea which should probably be assigned to this species.Non-Standard Abbreviations ASW artificial sea water - ATCC American Type Culture Collection - BM basal medium - BMA basal medium agar - GC guanine plus cytosine - LA luminous medium agar - LB luminous medium broth - MA Difco Marine Agar - NCMB National Collection of Marine Bacteria - PHB poly--hydroxybutyrate - S similarity coefficient - YEB yeast extract broth This paper is part of a dissertation submitted by the senior author to the Graduate Division of the University of Hawaii in partial fulfillment of the requirements for the Ph.D. Degree in Microbiology     

A comparison of strains of King's group IIb of Flavobacterium with Flavobacterium meningosepticum

Twenty-two strains of Flavobacterium recently isolated from patients and other sources were compared with 6 strains of Flavobacterium meningosepticum and 3 strains of King's Flavobacterium group IIb. The field strains were found to resemble group IIb in their characteristics.All 31 strains of Flavobacterium gave similar results in 28 phenotypic tests; the DNA base compositions of 18 phenotypically representative strains ranged from 35 to 39% GC. Within this group, the 6 strains of F. meningosepticum were phenotypically homogeneous, had a % GC of 36.9, and differed consistently from the 25 strains of group IIb only in the pale colour of their pigment, slowness of pigment production, and inability to hydrolyse starch. All 25 strains of group IIb differed in at least 6 tests from the 6 strains of F. meningosepticum, although not the same 6 tests in each case. Antisera to F. meningosepticum agglutinated 10 strains of group IIb.     

Genetic relationships among clinical and environmental isolates ofVibrio cholerae from Australia

DNA-DNA homology among twenty-nine isolates having the phenotypic properties ofVibrio cholerae was studied using the S1 endonuclease method. Ten strains ofV. cholerae O1 isolated from patients and from the environment in Australia showed greater than 88% homology with the neotype strain ofV. cholerae NCTC 8021. Strains of the non-O1 serotype isolated from a variety of clinical and environmental sources also showed a high level of relatedness, including four luminescent strains and a reference strain of the biotypealbensis. A group of sucrose-negative strains showed a low level of homology (40 to 43%) withV. cholerae, but 75% and 82% homology within the group.     

Production of fumonisins byFusarium species of Taiwan

Twenty-nineFusarium species isolated from various sources in different districts of Taiwan were tested for their ability to produce fumonisins in corn cultures. OnlyFusarium moniliforme produced fumonisin B₁ (FB₁) and fumonisin B₂ (FB₂). The finding that the other 28Fusarium species produced neither FB₁ nor FB₂ is preliminary because only one strain per species was studied. The detection of FB₁ and FB₂ in cultures ofF. moniliforme was demonstrated by TLC and HPLC, and FB₁ was further confirmed by mass spectrometry. In a separate experiment, in which 38 strains ofF. moniliforme were tested for fumonisins, approximately 66% (25/38) produced FB₁ and/or FB₂. Of the 25 strains, 14 produced only FB₁ and 11 produced both FB₁ and FB₂, and the amounts of FB₁ and FB₂ produced by different strains varied greatly. This is the first report that fumonisins are found in corn cultures experimentally infected withF. moniliforme strains from Taiwan. It is safe to assume that fumonisin producing strains ofF. moniliforme are widely distributed among the economic crops such as corn, rice, sugarcane, and sorghum throughout the Island.Abbreviations FB₁ Fumonisin B₁ - FB₂ Fumonisin B₂ - OPA o-phthalidialdehyde     

Phenotypic characterization ofBeneckea anguillara biotypes I and II

Twenty-five strains of marine bacteria pathogenic for fish, which had been shown by means of in vitro DNA/DNA hybridization to comprise two biotypes of the speciesBeneckea anguillara, were subjected to a phenotypic characterization. A numerical analysis of the data segregated the strains into two phenotypically distinct clusters coincident with the biotypes established by DNA homology studies. The two biotypes were distinguishable fromPhotobacterium and other species ofBeneckea by a number of unrelated phenotypic properties.     

Molecular phylogeny of the domesticated silkworm,Bombyx mori, based on the sequences of mitochondrialcytochrome b genes

Pupae from the Chinese wild mulberry silkworm,Bombyx mandarina, and 11 representative strains of the domesticated silkworm,Bombyx mori were selected for preparation of mitochondrial DNA. The 5′-end fragments ofcytochrome b genes (Cytb) were generated by polymerase chain reaction products and sequenced directly. The homologous sequences of the JapaneseB. mandarina and three strains ofB. mori were from the GenBank database. The sequences of the 16 silkworm strains were analysed with DNASTAR software and a phylogenic tree was constructed using PHYLIP software. The result showed that: (i) The sequence divergence between the strains ofB. mori and the JapaneseB. mandarina was larger (5.4% ≈ 5.8%) compared with that between strains ofB. mori and the ChineseB. mandarina (0.8% ≈ 1.9%). Analysis of clustering also showed that the sequences ofB. mori strains and ChineseB. mandarina clustered into group (B group), while that of JapaneseB. mandarina (A group) was outside this cluster. This may be evidence for the hypothesis thatB. mori originated from ChineseB. mandarina. (ii) Among 14 strains ofB. mori, sequence divergence was small and the most divergence was seen between strains Yanhe-1 and Chuxiong, whose sequences branched off from those of the otherB. mori strains on the phylogenetic tree. From this and from historical records, we infer that the strains Yanhe-1 and Chuxiong originated independently from southwest China.     

Sexual fertility of fortyFusarium strains from the EuropeanFusarium sambucinum project

Fungus strains designated asFusarium sambucinum, F. torulosum, orFusarium sp. nov. were crossed withMAT1-1 andMAT1–2 tester strains ofGibberella pulicaris. Of the 40 field strains that were crossed with the tester strains, 13 strains produced fertile crosses and 27 strains did not produce fertile crosses. One strain designated asF. torulosum was fertile with a tester strain ofG. pulicaris, suggesting that this is an intraspecies cross and that the strain isG. pulicaris, and, consequently,F. sambucinum rather thanF. torulosum. The lack of fertile crosses between tester strains and 27 of the 40 field strains suggests that these strains are notG. pulicaris. Although the ability to form a fully fertile cross with a tester strain can determine the species of a fertile strain, it is more problematic to exclude a strain only because it is infertile.     

Reclassification of “Bacillus pulvifaciens” Group II as Brevibacillus agri

Organisms formerly identified as strains of Paenibacillus pulvifaciens group II were reclassified as members of the species Brevibacillus agri. The reclassification was based on phylogenetic analysis of 16S rRNA gene sequences from selected Bacillaceae. The analysis strongly supported placement of group II strains in the genus Brevibacillus. High DNA relatedness of 87–100% and close phenotypic similarity demonstrated that group II strains were members of the species Brevibacillus agri. Received: 10 September 1996 / Accepted: 2 October 1996     

Chemical and physiological characterization of taxa in theFusarium sambucinum complex

Forty-one isolates ofFusarium sambucinum sensu lato were screened for production of secondary metabolites in agar cultures. Of 16 strains ofF. sambucinum sensu stricto all but two strains produced diacetoxyscirpenol and two unidentified metabolites, TB1 and TB2 respectively. The two remainingF. sambucinum strains produced T-2 toxin, TB1 and TB2.Fusarium venenotum (6 strains) produced diacetoxyscirpenol and an unidentified metabolite BB.Fusarium torulosum (8 strains) produced wortmannin and antibiotic Y. The three species could be differentiated by their pattern of identified and unidentified metabolites detected by agar plug TLC combined with chemical data from HPLC-diode array detection of fungal extracts, and data on growth rates on potato sucrose agar and tannin sucrose agar.     

Discrimination of species and strains of basidiomycete genusCoprinus by random amplified polymorphic DNA (RAPD) analysis

All five examined strains ofCoprinus cinereus could be clearly discriminated from the strains of five otherCoprinus species by RAPD patterns with 12 of 13 primers. Also one specimen of unknownCoprinus strain was identified to beC. cinereus by this method. The RAPD patterns were similar among the strains in the same species; many common DNA fragments were recognized as well as some strain-specific DNA fragments. Thus all seven strains ofC. cinereus and all four strains ofC. angulatus examined could be distinguished individually. Diakryotic strains showed the combined RAPD patterns of the two monokaryotic strains constituting the dikaryon. The combined RAPD markers observed in the dikaryons were segregated in their basidiospore progeny. All 18 randomly picked progeny showed different combinations of RAPD markers from the parental strains.     

Distribution and evolution of mobile elements in the virilis species group of Drosophila

The distributions of Penelope and Ulysses, two transposable elements that can induce hybrid dysgenesis, were studied in several species groups of Drosophila. No significant hybridization to Penelope and Ulysses probes was detected by Southern blot analyses of species outside the virilis group. In contrast, both element families have had a long residence in all species of the virilis species group, as indicated by their strong presence in the heterochromatic chromocenter. Except for D. kanekoi, D. lummei, and some strains of D. virilis, species of the group carry full-sized, and at least potentially functional, copies of both element families. Consistent with the occurrence of recent transposition, Penelope and Ulysses elements are located at different chromosomal sites in different geographical strains of the same species. A total of 79 Penelope and 47 Ulysses euchromatic insertion sites were localized to chromosomal subsections in species of the virilis group. Highly significant deviations from independence of the distributions of Penelope and Ulysses and previously established inversion breakpoints were documented, suggesting that these transposable elements may have played an important role in genomic reorganization and evolution of the virilis species group, which is especially rich in karyotypic variation. Received: 13 April 1999; in revised form: 20 July 1999 / Accepted: 27 July 1999