Effects of calcium and magnesium ions and host viability on growth of bdellovibrios

Bdellovibrio spp. strains 6-5-S, 100, 109 (Davis), and A3.12 multiply in the presence of viable but non-proliferating or heat-killed (70 or 100 C, 10 min; 121 C, 5 min) cells ofSpirillum serpens strain VHL suspended in buffers supplemented with Ca⁺⁺ and/or Mg⁺⁺. Ca⁺⁺ (optimal, 2 × 10⁻³ m) and Mg⁺⁺ (optimal, 2 × 10⁻⁵ m) independently stimulate the groth of bdellovibrios: additive effects are noted. Multiplication ofBdellovibrio in the presence of Ca⁺⁺ and Mg⁺⁺ is associated with the release into the culture supernatant solution of UV-absorbing materials and of amino sugars (presumably by activating or stabilizing lytic enzymes). The growth rate ofBdellovibrio strain 6-5-S in suspensions of heat-killed host cells is lower than in living but non-proliferating host cells. Bdellovibrio spp. strains 100, 109 (Davis), 109 (Jerusalem), A3.12, and 6-5-S all require added Ca⁺⁺ for growth in cell suspensions of homologous or heterologous host bacteria which have been grown in minimal medium.Bdellovibrio sp. strain 109 (Jerusalem) is capable of growing in the presence of the low level of Ca⁺⁺ boundin situ to the cells of its host,E. coli B, when the host cells had been cultivated in a complex medium but not when the host cells had been grown in a Ca⁺⁺-depleted minimal medium (except when Ca⁺⁺ is added). Addition of ethylenediaminetetraacetic acid (0.01m) preventsBdellovibrio growth, which is restored by addition of Ca⁺⁺ and Mg⁺⁺. The nonparasitic growth ofBdellovibrio spp. strains 100, 109, A3.12, and 6-5-S in heat-killed cell suspensions only in the presence of added cations indicates that, in this system, the cations are essential for activity of bacteriolytic and other enzymes and that they might also directly affectBdellovibrio growth rather than — as may be the case in other systems of live host cells plusBdellovibrio — only indirectly by affecting attachment to the host cell, maintaining integrity of the host spheroplasts, and increasing the burst size.     

Phylogenetic affiliations ofRhodoferax fermentans and related species of phototrophic bacteria as determined by automated 16S rDNA sequencing

16S rDNA sequences of strains ofRhodoferax fermentans were analyzed and compared with those of species of the generaRubrivivax andRhodocyclus. Approximately 1.5-kb fragments of 16S rDNA from crude cell lysates were amplified by the polymerase chain reaction (PCR) and sequenced directly by usingTth DNA polymerase with the linear PCR sequencing protocol, followed by on-line detection with an automated laser fluorescent DNA sequencer. Pairwise sequence comparisons and distance matrix tree analysis showed thatRhodoferax fermentans, Rubrivivax gelatinosus, andRhodocyclus species belong to three separate lineages within the beta subclass of theProteobacteria, thereby confirming the phylogenetic validity of the genusRhodoferax, as well as of the generaRubrivivax andRhodocyclus.     

Inhibition of the predatory activity ofBdellovibrio by various environmental pollutants

The predatory activity of bdellovibrios is affected by various environmental pollutants such as detergents, heavy metals, and pesticides. This was shown in a two-membered system ofBdellovibrio andPhotobacterium, in which the effect of the predator on the bioluminescence of the prey indicated the activity of the former. The high sensitivity of the bdellovibrios toward certain chemicals (e.g., CdCl₂) indicates the possibility of using the system for biological monitoring of those chemicals.     

Physiological and phylogenetic diversity of thermophilic spore-forming hydrocarbon-oxidizing bacteria from oil fields

The distribution and population density of aerobic hydrocarbon-oxidizing bacteria in the high-temperature oil fields of Western Siberia, Kazakhstan, and China were studied. Seven strains of aerobic thermophilic spore-forming bacteria were isolated from the oil fields and studied by microbiological and molecular biological methods. Based on the 16S rRNA gene sequences, phenotypic characteristics, and the results of DNA-DNA hybridization, the taxonomic affiliation of the isolates was tentatively established. The strains were assigned to the first and fifth subgroups of the genusBacillus on the phylogenetic branch of the gram-positive bacteria. Strains B and 421 were classified asB. licheniformis. Strains X and U, located betweenB. stearothermophilus andB. thermocatenulatus on the phylogenetic tree, and strains K, Sam, and 34, related but not identical toB. thermodenitrificans andB. thermoleovorans, undoubtedly represent two new species. Phylogenetically and metabolically related representatives of thermophilic bacilli were found to occur in geographically distant oil fields     

Attempts to grow bdellovibrios micurgically-injected into animal cells

Incubation in buffer of Bdellovibrio bacteriovorus 109J, B. stolpii UKi2, or B. starrii A3.12 with washed eucaryotic animal cells (mouse liver, hamster kidney, or bovine mammary gland) resulted in neither attachment nor growth of the bdellovibrios. When cells of these bdellovibrio strains were incubated with erythrocyte suspensions (bovine or rabbit) a very low level of bdellovibrio attachment and penetration occurred, but no growth could be detected. Using micurgical procedures, bdellovibrios were injected into the perivetelline space or the cytoplasm of rabbit ova. After 18–24h incubation, neither a significant loss nor increase of injected, intracellular bdellovibrios was observed. Limited axenic growth of bdellovibrios (109J or UKi2) occurred in media containing rabbit ova extracts and dilute nutrient broth. It is concluded that eucaryotic rabbit ova do not provide a suitable environment for intracellular bdellovibrio growth.     

Confirmation of the specific status ofHapalemur aureus (Primates,Strepsirhini) by restriction genomic DNA banding patterns

This study confirms, on the basis of our molecular biology results and in accordance with cytogenetic, morphological and ethological data, the specific status ofHapalemur aureus. Furthermore, it appears clearly thatHapalemr simus began its differentiation fromHapalemur griseus griseus andHapalemur aureus (wich have a common branch) shortly after the separation ofLemur catta from the phylogenetic tree of theL. catta/ Hapalemur group.     

Evolution of flower shape inVeroniceae (Scrophulariaceae)

Floral evolution in the tribeVeroniceae was examined using phylogenetic analysis combining 24 adult morphology and chromosome number characters with 22 qualitative and quantitative floral development characters. Taxa sampled included nine species ofVeroniceae and as an outgroup one species each ofDigitaleae andVerbasceae. Veronica, Besseya, andSynthyris formed one clade, subtended byPseudolysimachion and then by theHebe group;Veronicastrum orWulfenia represent the basal-most branch of the tribe. The ancestral flowers of theVeroniceae may have been small with moderately short corolla tubes and lobes; long corolla tubes arose four times in the tribe and large corolla lobes twice.     

Prey Range Characterization, Ribotyping, and Diversity of Soil and Rhizosphere Bdellovibrio spp. Isolated on Phytopathogenic Bacteria

Thirty new Bdellovibrio strains were isolated from an agricultural soil and from the rhizosphere of plants grown in that soil. Using a combined molecular and culture-based approach, we found that the soil bdellovibrios included subpopulations of organisms that differed from rhizosphere bdellovibrios. Thirteen soil and seven common bean rhizosphere Bdellovibrio strains were isolated when Pseudomonas corrugata was used as prey; seven and two soil strains were isolated when Erwinia carotovora subsp. carotovora and Agrobacterium tumefaciens, respectively, were used as prey; and one tomato rhizosphere strain was isolated when A. tumefaciens was used as prey. In soil and in the rhizosphere, depending on the prey cells used, the concentrations of bdellovibrios were between 3 × 10² to 6 × 10³ and 2.8 × 10² to 2.3 × 10⁴ PFU g⁻¹. A prey range analysis of five soil and rhizosphere Bdellovibrio isolates performed with 22 substrate species, most of which were plant-pathogenic and plant growth-enhancing bacteria, revealed unique utilization patterns and differences between closely related prey cells. An approximately 830-bp fragment of the 16S rRNA genes of all of the Bdellovibrio strains used was obtained by PCR amplification by using a Bdellovibrio-specific primer combination. Soil and common bean rhizosphere strains produced two and one restriction patterns for this PCR product, respectively. The 16S rRNA genes of three soil isolates and three root-associated isolates were sequenced. One soil isolate belonged to the Bdellovibrio stolpii-Bdellovibrio starrii clade, while all of the other isolates clustered with Bdellovibrio bacteriovorus and formed two distantly related, heterogeneous groups.     

Growth Cycle of Predacious Bdellovibrios in a Host-Free Extract System and Some Properties of the Host Extract

Host-free growth and reproduction of a host-dependent strain of Bdellovibrio bacteriovorus incubated with an extract from host cells were studied. The morphological changes occurring in the cells were correlated with deoxyribonucleic acid (DNA) synthesis as measured by labeled nucleotide or orthophosphate incorporation. The host-free developmental cycle of Bdellovibrio is similar to that of the two-membered system; the early loss of flagella, the elongation into filaments, and multiple fission into flagellated progeny are typical for both host-free and intraperiplasmic development of bdellovibrios. Filament length and time of division appear to depend on the concentration of the host extract. Host extract was found to be heat stable and DNase stable, and Pronase sensitive and RNase sensitive. Addition of ribonucleic acid to the extract medium at various times during the Bdellovibrio growth cycle demonstrated that host extract is required continuously during the cycle for growth. The observations reported give a unified picture of Bdellovibrio development and allow for the suggestion that wild-type bdellovibrios depend upon the presence of some host factor for induction of DNA synthesis, whereas depletion of host factor triggers division. The ecological implications of such host dependence are discussed.     

Phylogenetic relationship of medicinally importantCnidium officinale and Japanese Apiaceae based onrbcL sequences

Cnidium officinale Makino is important medicinally and economically, but its origin is uncertain. The phylogenetic relationship ofC. officinale is provided from the analyses based on the ribulose-1,5-bisphosphate carboxylase/oxgenase gene (rbcL) sequences of 41 species which represent the 34 genera of Aplaceae, the four genera of Araliaceae, and one genus each of Pittosporaceae, Cornaceae, and Caprifoliaceae. The strict consensus tree obtained supports a close relationship ofC. officinale to the Chinese members ofLigusticum, especially toL. chuanxiong. Additionally, the tree shows (1) polyphyly of the genusLigusticum and (2) monophyly of the subfamily Apioideae. Within Apioideae, we recognized some groups in our phylogenetic tree. The grouping is discordant in several respects with the traditional tribal divisions based mainly on fruit morphology.     

A Comparative Study of the Effect of Certain Pollutants on Free-living and Immobilized Bdellovibrio

The paper deals with a comparative study of the growth of free-living and immobilized predatory bacteria of the genus Bdellovibrio in the presence of toxic concentrations of urea and phenol. It was found that the cell wall of bdelloplasts plays a protective role in the adaptation of bdellovibrios to xenobiotics. The attachment of bdellovibrios to solid surfaces allows them to survive under unfavorable environmental conditions.     

Molecular reexamination of korean umbelliferae based on internal transcribed spacer sequences of rDNA:Ligusticum tenuissimum (Nakai) Kitagawa andLibanotis coreana (Wolff) kitagawa

The taxonomic status ofLigusticum tenuissimum (Nakai) Kitagawa andLibanotis coreana (Wolff) Kitagawa has been controversial in Korea. We examined their phylogenetic relationships by comparing the internal transcribed spacer (=ITS) sequences of the nuclear ribosomal RNA gene (=rDNA) with another seven species in the Korean Umbelliferae. Our results support the legitimacy of the nomenclatural combination withL. tenuissimum Kitagawa rather than withAngelica tenuissima Nakai. We also suggest usingL coreana (Wolff) Kitagawa instead ofSeseli coreanum Wolff becauseL. coreana has been completely separated from most taxa of the genusSeseli. In addition, we have confirmed at least three phylogenetic lines in the genusLigusticum. One is the core group ofLigusticum that comprisesL tenuissimum and four other species. This clade includes theLigusticum hultenii line andLigusticum scothicum, known as an anomaly ofLigusticum. The second clade is composed ofLigusticum physospermifolium withSeseli monatum, which indicates the polyphyly ofLigusticum. The third line isLigusticum acutilobum, clustered as a sister grade ofDystaenia.     

Interaction ofBdellovibrio with Its prey in mixed microbial populations

The interaction ofBdellovibrio with its prey can be affected by the presence of other microorganisms regardless of whether they serve as a prey for the bdellovibrios. This was shown in a system in which the fate of one prey could be followed in mixed bacterial populations thanks to a specific trait, bioluminescence. The attacking bdellovibrio causes decay of bioluminescence, and the rate of light decay of the population indicates the rate at which the luminous bacteria are attacked. Using this system it was found that different bacteria affected the predatorprey interaction in different ways: some competed with the original prey for the predator; others enhanced the activity of the predator toward the original prey, and others inhibited it. The significance of these findings in relation to the distribution and activity ofBdellovibrio in the natural ecosystem is discussed.     

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.     

A phylogenetic dissection of the family micrococcaceae

A comparative analysis of 16S ribosomal RNA sequences in the Micrococcaceae shows the family not to be a phylogenetically coherent unit. In fact, at least two of its three genera are themselves not valid phylogenetic units. Species, of the genusMicrococcus are phylogenetically inseparable from those ofArthrobacter. The genusPlanococcus groups specifically with certain members ofBacillus, andStaphylococcus is also related to the genusBacillus, though more peripherally. These findings question the validity of spherical shape as a valid indicator of phylogenetic relationships on all but the lowest levels.     

Bdellovibrio possesses a prey-derived OmpF protein in its outer membrane

Bdellovibrio bacteriovorus 109D andBdellovibrio stolpii derive one of their major outer membrane proteins from the outer membrane of their prey. This prey-derived protein corresponds to the OmpF protein ofEscherichia coli. Bdellovibrios cultivated onSalmonella typhimurium prey acquire theSalmonella OmpF protein; this protein is distinguishable electrophoretically from the OmpF protein ofE. coli. Bdellovibrios containing the prey-derived OmpF protein are sensitive to killing by colicin A but not colicin E1, whereas bdellovibrios without this protein are completely resistant to colicin killing.     

Nitrite utilization byBrettanomyces

The utilization of nitrite was tested in a number ofBrettanomyces strains which fail to utilize nitrate as sole source of nitrogen. It was established that some of these strains utilize nitrite. The taxonomical implications of this phenomenon are discussed and it is concluded that neither nitrate nor nitrite utilization serves any purpose for the delimitation of species within the genusBrettanomyces. The possibility of a phylogenetic relationship betweenBrettanomyces andHanseniaspora is discussed.     

Deoxyribonucleic acid reassociation and interspecies relationships of the genusChlorella (Chlorophyceae)

Phylogenetic relationships within the genusChlorella were studied by means of DNA/DNA hybridization under both optimal and relaxed reassociation conditions as well as by determination of the thermal stability of hybrid DNA duplexes. The results indicate a relationship betweenC. fusca var.fusca, C. fusca var.rubescens, C. fusca var.vacuolata, and the genusScenedesmus. In addition, the strains endosymbiotic withParamecium bursaria seem to be related with theC. vulgaris/sorokiniana group. The relations between most other species, however, could not be sufficiently resolved by the above methods. This implies considerable phylogenetic divergency within the genusChlorella.     

Cloning and sequencing of mutantpsbB genes of the cyanobacteriumSynechocystis PCC 6803

Ten strains from a collection of mutants ofSynechocystis 6803 defective in Photosystem II (PS II) function were transformed with chromosomal DNA of wild-type and mutant cells. Cross hybridization data allowed to identify four groups of PS II-mutants. Highly efficient transformation was observed between different mutant groups, but not within the groups. Restoration of photosynthetic activity of the mutant cells was also achieved by transformation with different parts of a 5.6 kbBam HI fragment of wild typeSynechocystis DNA containing thepsbB gene. Each group of mutants was transformed to photoautotrophic growth by specific subfragments of thepsbB gene. DNA fragments of four selected mutant strains hybridizing with thepsbB gene were isolated and sequenced. The mutations were identified as a single nucleotide insertion or substitution leading to stop codon formation in two of the mutants, as a deletion of 12 nucleotides, or as a nucleotide substitution resulting in an amino acid substitution in the other two mutants. Deletion of 12 nucleotides in mutant strain PMB1 and stop codon formation in strain NF16 affect membrane-spanning regions of the gene product, the CP 47 protein.     

Phylogeny of the GenusAgaricusInferred from Restriction Analysis of Enzymatically Amplified Ribosomal DNA

Bunyard, B. A., Nicholson, M. S., and Royse, D. J. 1996. Phylogeny of the genusAgaricusinferred from restriction analysis of enzymatically amplified ribosomal DNA.Fungal Genetics and Biology20,243–253. The 26S and 5S ribosomal RNA genes and the intergenic region between the 26S and the 5S rRNA genes of the ribosomal DNA repeat of 21 species ofAgaricuswere amplified using PCR and then digested with 10 restriction enzymes. Restriction fragment length polymorphisms were found among the 21 putative species ofAgaricusinvestigated and used to develop a phylogenetic tree of the evolutionary history ofA. bisporus.The 5′ end of the 26S gene showed more variability than the 3′ end.A. excellens, A. chionodermus,andA. carolirepresented the species most distantly related toA. bisporus.We present here the first comprehensive attempt at systematically resolving the entire genusAgaricususing modern techniques for molecular genetic analysis. Our data indicate that previous taxonomic schemes, based on morphological characters, are in need of revision.