The metabolic interactions between Paramecium bursaria Ehrbg. and Chlorella spec. in the Paramecium bursaria-symbiosis

In an organism (strain C 1/2 from Dr. P. R. Hayes, Leeds) regarded as a typical representative of the genus Flavobacterium, flexirubin-type pigments have been identified. The Flavobacterium pigments contain structural elements of both, the pigments of the genus Flexibacter and the pigments of the genus Cytophaga. As flexirubin-type pigments seem to have a rather restricted distribution among bacteria, and have formerly proved to be useful chemosystematic markers for the flexibacteria, this new observation may indicate that there is a relatively close phylogenetic relationship between this type of flavobacteria and the Cytophaga-Flexibacter group.     

Characteristics of bacterium GB-2, a presumptiveCytophaga species with novel immunoregulatory properties

A Gram-negative, psychrophilic bacterium, designated GB-2, was isolated from fetal calf serum and analyzed for its morphological, physiological, and biochemical characteristics. Gliding motility, sensitivity to actinomycin D, the presence of the pigment flexirubin and cytochrome c, growth on a variety of carbohydrates, the production of acid fermentation products, and a 34.9 mol% guanine+cytosine (G+C) content of bacterial DNA indicate GB-2 to be a member either of the generaCytophaga orFlexibacter. Growth of GB-2 was optimized in a simple defined medium to facilitate isolation and characterization of bacterial products. Liquid growth of GB-2 resulted in the release of significant quantities of a macromolecule free of both endotoxin and protein into the growth supernatant, which activated the proliferation of murine lymphocytes. The relationship between this bacterium and its end-products to other species of theCytophaga/Flexibacter group is discussed.     

Continuous observations of bacterial gliding motility in a dialysis microchamber: The effects of inhibitors

Use of a dialysis microchamber has allowed continuous observations on the same set of gliding bacteria during changes in the composition of the perfused medium. This procedure has revealed the presence of an adaptive, cyanide-insensitive metabolic pathway, which allows cyanide-treated Flexibacter BH3 to begin gliding again at a reduced rate when glucose is the substrate. In addition, it has revealed that individual flexibacter cells can maintain their gliding motility for up to 20 h in the absence of exogenous substrate.Gliding in Flexibacter BH3 was prevented by those inhibitors blocking the electron transport process. Inhibitors of glucose metabolism did not prevent motility, since the flexibacters obviously metabolize endogenous substrate under such circumstances. Proton ionophores, which induce membrane depolarization, rapidly inhibited gliding in Flexibacter BH3. This inhibition was irreversible in the case of gramicidin S. Gliding was not inhibited by cytochalasin B or antiactin antibody. High concentrations of Ca²⁺ were particularly inhibitory to the gliding process. The significance of these results is discussed in relation to a possible mechanism of gliding involving the generation of rhythmical contractions in the outer cell membrane of Flexibacter BH3.Abbreviations used CCCP carbonyl cyanide m-chlorophenyl hydrazone - DNP p-dinitrophenol - GMCS gramicidin S - HQNO 2-heptyl-4-hydroxyquinoline N-oxide - PCMB p-chloromercuribenzoate - CM complete Lewin's medium - BS Lewin's basal salts     

Substratum requirements for bacterial gliding motility

Flexibacter FS-1 filaments are unable to glide on agarose gels or on charge-neutralized glass unless those substrata are supplemented with the charged, cold water-soluble fraction of agar, or a variety of polyanionic polysaccharides derived from plants, yeasts and bacteria. Two graft polymers of xanthan gum also promote gliding motility under these conditions, as do an extracellular product of the bacteria themselves. A number of other polymers and small molecular species are ineffective as supplements. These results are considered in the context of the soil habitat of this Flexibacter. Among a variety of other gliding bacteria tested, several strains of the order Cytophagales also were unable to glide on agarose.Abbreviations CWSF Cold water-soluble fraction of agar - PMC 5 mM K phosphate buffer (pH 7)+0.1 mM MgCl₂+0.5 mM CaCl₂     

FspAI, a unique type II restriction endonuclease that recognizes the octanucleotide sequence 5′-RTGC↓GCAY-3′

A new type II restriction endonuclease designated FspAI has been partially purified from a Flexibacter species Tv-m21K. FspAI recognizes the octanucleotide sequence 5′-RTGC↓GCAY-3′ and cleaves it in the center generating blunt-ended DNA fragments.     

The phylogenetic position of the Thermococcus isolate AN1 based on 16S rRNA gene sequence analysis: a proposal that AN1 represents a new species, Thermococcus zilligii sp. nov.

The 16S rRNA gene from the Thermococcus New Zealand isolate AN1 was cloned and sequenced. Analysis of the gene revealed the presence of signature sequences, indicating that strain AN1 represents a new species of the genus Thermococcus. Since the isolate AN1 differed from other thermococci in both its lower optimal NaCl concentration and generally lower optimal temperature for growth, in its unusual lipid membrane composition, and in its sensitivity to antibiotics, we propose that strain AN1 represents a new species of Thermococcus. The proposed name is Thermococcus zilligii, and the type strain is DSM 2770. Received: 13 February 1997 / Accepted: 30 May 1997     

Physicochemical and in situ observations on the adhesion of gliding bacteria to surfaces

The ability of Flexibacter BH3 to adhere to solid surfaces and to overcome the horizontal drag involved in gliding across the surfaces was considered in terms of the Stefan adhesion principle. The extracellular slime produced by Flexibacter BH3 was suitable as a Stefan adhesive because it exhibited viscous properties characteristic of a linear colloid, increasing the adhesiveness of the bacterium but allowing translational motion across the surface. The water-soluble slime was a glycoprotein, containing glucose, fucose, galactose and some uronic acid. Vesicles and tubules on the outer surface of Flexibacter BH3 possessed trilaminar membranes, contained 2-keto-3-deoxyoctonate (KDO), and showed identity with phenol-extracted lipopolysaccharide (LPS) in gel-diffusion tests.Sections of Flexibacter BH3 gliding on a gold film overlaying an agar medium reveraled a highly convuluted cell envelope outer membrane, portions of which closely conformed to the microcontours of the gold surface. Possible mechanisms of gliding are discussed in relation to this close association with solid surface features, to the finding that flexibility and spiral motion are not essential for gliding, and to evidence revealing the extrusion of slime in advance of pathfinder bacteria.Abbreviations used KDO 2-keto-3-deoxyoctonate - LPS lipopolysaccharide     

Taxonomy Acanthamoeba royreba sp. n. from a Human Tumor Cell Culture*

SYNOPSIS. A new species of Acanthamoeba was isolated from a culture of an established line of human choriocarcinoma cells. The identification of this strain, originally called the Oak Ridge strain, and the establishment of a new species for it were based on morphologic, serologic, and immunochemical studies. In general, the structure of the trophozoite did not differ significantly from that of other species of Acanthamoeba, except that a body which more closely resembled a centriole than material described previously as centriolar satellites was observed in trophozoites examined with the electron microscope. The dimensions of the trophozoite were the smallest among the species of Acanthamoeba. The cyst was typical of the genus, but differed from those of other species by its smaller size and the presence of numerous ostioles. Studies of the Oak Ridge strain by immunofluorescence using antisera developed against the isolate and Acanthamoeba culbertsoni, A. castellanii, A. polyphaga, A. rhysodes, A. astronyxis, and A. palestinensis revealed the antigenic uniqueness of the Oak Ridge strain. It was demonstrated by immunoelectrophoretic analyses of the soluble proteins of the Oak Ridge strain that it shared ～ 1/2 of its antigenic structure with A. castellanii and A. culbertsoni. The antigenic differences of the isolate from other species of Acanthamoeba were deduced from comparison of the antigenic constitution of these species and the Oak Ridge strain with A. culbertsoni and A. castellanii. Although the strain was initially recognized by its cytopathogenicity for cultures, it did not produce acute infections in mice after intranasal inoculation of 1 × 10⁴ amebae/mouse. The foregoing results constituted the basis for the establishment of the Oak Ridge strain as a new species, A. royreba sp. n., in the genus Acanthamoeba.     

Ferroplasma cupricumulans sp. nov., a novel moderately thermophilic, acidophilic archaeon isolated from an industrial-scale chalcocite bioleach heap

A new species of Archaea was isolated from an industrial mineral sulphide bioleach heap. Strain BH2, a non-motile pleomorphic coccus, was capable of chemomixotrophic growth on ferrous sulphate and yeast extract. Growth was not supported in the absence of yeast extract. Phylogenetic analysis based on the 16S rRNA gene showed that strain BH2 was most closely related to the species Ferroplasma acidiphilum; however, it showed only 95% sequence similarity with this species. Strain BH2 had a temperature optimum of 53.6°C and a temperature range for growth between 22 and 63°C. Thus, it is the first moderately thermophilic member of the genus Ferroplasma. The optimum pH for the growth of the strain occurred between pH 1.0 and 1.2 and the lowest pH at which growth was observed was 0.4. Based on 16S rRNA gene sequence analysis and other physiological characteristics, strain BH2 constitutes a new species within the genus Ferroplasma. The name Ferroplasma cupricumulans is proposed for the new species and strain BH2 (DSM 16651) is proposed as the type strain.     

Gordonia sinesedis sp. nov., a novel soil isolate

The taxonomic position of an actinomycete isolated from soil was evaluated using a polyphasic approach. The organism, strain J72, was found to have chemical and morphological properties consistent with its assignment to the genus Gordonia. A nearly complete 16S rDNA sequence of the strain was determined by direct sequencing of the amplified gene. The tested strain formed a distinct phylogenetic line within the evolutionary radiation occupied by the genus Gordonia and was most closely related to G. polyisoprenivorans DSM 44302^T. The phenotypic profile of strain 372 readily distinguishes it from representatives of the validly described species of Gordonia. The combined genotypic and phenotypic data show that strain J72 merits recognition as a new species of Gordonia. The name proposed for the new species is Gordonia sinesedis; the type strain is J72^T (= DSM 44455^T = NCIMB 13802^T). This revised version was published online in June 2006 with corrections to the Cover Date.     

Nitrate reduction in a new strain ofRhodoferax fermentans

Using an enrichment technique avoiding the dominating fast-growing species Rhodobacter capsulatus and Rhodobacter sphaeroides, a new strain (designated B2c; DSM 10 139) of Rhodoferax fermentans, a facultatively phototrophic member of the β subclass of Proteobacteria, was isolated. In contrast to the type strain of this species, strain B2c was capable of reducing nitrate. Strain B2c contained a highly active nitrate reductase [0.3–0.4 μmol min^–1 (mg protein)^–1] which, in extracts from spheroplasts prepared by ultrasonic treatment, was associated with the membrane fraction. The physiological role of nitrate reductase depended on the growth conditions. The enzyme enabled the strain to grow with nitrate as a nitrogen source and to maintain redox balance in a culture medium with a highly reduced carbon compound. Received: 21 April 1995 / Accepted: 14 August 1995     

New exoelectrogen Citrobacter sp. SX-1 isolated from a microbial fuel cell

Aims: Isolation, identification and characterization of a new exoelectrogenic bacterium from a microbial fuel cell (MFC). Methods and Results: Exoelectrogenic bacterial strain SX‐1 was isolated from a mediator‐less MFC by conventional plating techniques with ferric citrate as electron acceptor under anaerobic condition. Phylogenetic analysis of the 16S rDNA sequence revealed that it was related to the members of Citrobacter genus with Citrobacter sp. sdy‐48 being the most closely related species. The bacterial strain SX‐1 produced electricity from citrate, acetate, glucose, sucrose, glycerol and lactose in MFCs with the highest current density of 205 mA m^?2 generated from citrate. Cyclic voltammetry analysis indicated that membrane‐associated proteins may play an important role in facilitating the electrons transferring from bacteria to electrode. Conclusions: This is the first study that demonstrates that Citrobacter species can transfer electrons to extracellular electron acceptors. Citrobacter strain SX‐1 is capable of generating electricity from a wide range of substrates in MFCs. Significance and Impact of the Study: This finding increases the known diversity of power generating exoelectrogens and provided a new strain to explore the mechanisms of extracellular electron transfer from bacteria to electrode. The wide range of substrate utilization by SX‐1 increases the application potential of MFCs in renewable energy generation and waste treatment.     

Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov.

Several barophilic Shewanella species have been isolated from deep-sea sediments at depths of 2,485– 6,499 m. From the results of taxonomic studies, all of these isolates have been identified as strains of Shewanella benthica except for strain DSS12. Strain DSS12 is a member of a novel, moderately barophilic Shewanella species isolated from the Ryukyu Trench at a depth of 5,110 m. On Marine Agar 2216 plates, this organism produced a violet pigment, whereas the colonies of other isolates (S. benthica) were rose-colored. Phylogenetic analysis based on 16 S ribosomal RNA gene sequences showed that strain DSS12 represents a separate lineage within the genus Shewanella that is closely related to S. benthica and particularly to the members of the Shewanella barophiles branch. The temperature range for growth and some of the biochemical characteristics indicate that strain DSS12 differs from other Shewanella species. Furthermore, strain DSS12 displayed a low level of DNA similarity to the Shewanella type strains. Based on these differences, it is proposed that strain DSS12 represents a new deep-sea Shewanella species. The name Shewanella violacea (JCM 10179) is proposed. Received: 15 May 1998 / Accepted: 15 July 1998     

Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China

A novel cold-resistant bacterium, designated YIM 016^T, was isolated from a peat bog sample collected from Mohe County, Heilongjiang Province, Northern China and its taxonomic position was investigated using a polyphasic approach. The strain was Gram-positive, aerobic, endospore-forming, motile and rod-shaped. Phylogenetic analyses based on the 16S rRNA gene sequence clearly revealed that strain YIM 016^T is a member of the genus Paenibacillus. The strain is closely related to Paenibacillus alginolyticus DSM 5050^T, Paenibacillus chondroitinus DSM 5051^T and Paenibacillus pocheonensis Gsoil 1138^T with similarities of 99.0 %, 97.0 % and 96.3 %, respectively. Meanwhile, the low DNA–DNA relatedness levels between strain YIM 016^T and its closely related phylogenetic neighbours demonstrated that this isolate represents a new genomic species in the genus Paenibacillus. Phenotypic and chemotaxonomic tests showed that growth of strain YIM 016^T occurred at 4–37 °C, pH 6.0–8.0 and with a NaCl tolerance up to 0.5 % (w/v). The peptidoglycan contained meso-diaminopimelic acid, alanine and glutamic acid. The whole-cell hydrolysates mainly contained glucose, galactose and ribose. The predominant menaquinone was MK-7 and the major fatty acids were anteiso-C_15:0 and iso-C_16:0. The DNA G+C content of strain YIM 016^T was 51.7 mol %. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain YIM 016^T could be clearly distinguished from other species of the genus Paenibacillus. It is therefore concluded that strain YIM 016^T represents a novel species in the genus Paenibacillus, for which the name Paenibacillus frigoriresistens sp. nov. is proposed. The type strain is YIM 016^T (= CCTCC AB 2011150^T = JCM 18141^T).     

Rhodotorula lamellibrachii sp. nov., a new yeast species from a tubeworm collected at the deep-sea floor in Sagami Bay and its phylogenetic analysis

A new species of the genus Rhodotorula was isolated from a tubeworm (Lamellibrachia sp.) collected at a depth of 1156 m in Sagami Bay, Japan. Strain SY-89 had physiological properties quite similar to R. aurantiaca. Two phylogenetic trees, one based on internal transcribed spacer (ITS) regions and 5.8S rDNA sequences and the other based on the D1/D2 region of the large subunit (26S) rDNA sequences, united strain SY-89 to the type strain of Sakaguchia dacryoides through a considerable evolutionary distance. Strain SY-89 was differentiated from S. dacryoides by the G+C content of the nuclear DNA and differences in the ability to utilize specific carbon and nitrogen compounds. The low complementarity of strain SY-89 DNA to that of the type strain of S. dacryoides confirmed that this strain was genetically unrelated to previously known species. The tubeworm isolates are described as R. lamellibrachii sp. nov. The type strain of R. lamellibrachii is strain SY-89 (= JCM 10907). R. lamellibrachii formed a cluster with Erythrobasidium hasegawianum, R. lactosa, S. dacryoides and Sporobolomyces elongatus on the ITS and 5.8S rDNA phylogenetic tree. These five species shared a signature sequence in 26S rDNA, although this relationship was not supported by phylogeny based on the D1/D2 region of 26S rDNA.     

Microbotryozyma collariae gen. nov., sp. nov., a basidiomycetous yeast isolated from a plant bug Collaria oleosa (Miridae)

Two strains of a basidiomycetous yeast were derived from an insect trypanosomatid culture isolated from the intestine of a plant bug, Collaria oleosa (Heteroptera: Miridae), collected in Costa Rica. The yeast did not form ballistoconidia but reproduced only by budding. Teliospores were not observed in individual and crossed cultures of each strain. Morphological and other taxonomic characteristics of the yeast were similar to those of the species in the polyphyletic genus Rhodotorula. However, molecular phylogeny inferred from the internal transcribed spacers and D1/D2 region of the large subunit rRNA gene showed that the strains represent a new species placed among the smut fungi in the family Ustilentylomataceae, which includes Aurantiosporium subnitens, Fulvisporium restifaciens, Ustilentyloma fluitans, and Rhodotorula hordea. Given the well distinguished phylogenetic position of this novel species within the Ustilentylomataceae, we propose Microbotryozyma collariae gen. nov., sp. nov. to accommodate the yeast isolated from C. oleosa, with strain American Type Culture Collection MYA-4666^T (= PRA303-1S = CBS 12537) designated as the type strain.     

Ruminococcus hydrogenotrophicus sp. nov., a new H2/CO2-utilizing acetogenic bacterium isolated from human feces

A new H₂/CO₂-utilizing acetogenic bacterium was isolated from the feces of a non-methane-excreting human subject. The two strains S5a33 and S5a36 were strictly anaerobic, gram-positive, non-sporulating coccobacilli. The isolates grew autotrophically by metabolizing H₂/CO₂ to form acetate as sole metabolite and were also able to grow heterotrophically on a variety of organic compounds. The major end product of glucose and fructose fermentation was acetate; the strains also formed ethanol, lactate and, to a lesser extent, isobutyrate and isovalerate. The G+C content of DNA of strain S5a33 was 45.2 mol%. 16S rRNA gene sequencing demonstrated that the two acetogenic isolates were phylogenetically identical and represent a new subline within Clostridium cluster XIVa. Based on phenotypic and phylogenetic considerations, a new species, Ruminococcus hydrogenotrophicus, is proposed. The type strain of R. hydrogenotrophicus is S5a33 (DSM 10507). Furthermore, H₂/CO₂ acetogenesis appeared to be a common property of most of the species phylogenetically closely related to strain S5a33 (Clostridium coccoides, Ruminococcus hansenii, and Ruminococcus productus). Received: 11 April 1996 / Accepted: 11 June 1996     

Halomonas sinaiensis sp. nov., a novel halophilic bacterium isolated from a salt lake inside Ras Muhammad Park, Egypt

An alkalitolerant and halotolerant bacterium, designated strain Sharm was isolated from a salt lake inside Ras Muhammad. The morphological, physiological and genetic characteristics were compared with those of related species of the genus Halomonas. The isolate grew optimally at pH 7.0, 5–15% NaCl at 35°C. The cells were Gram-negative rods, facultative anaerobes. They accumulated glycine-betaine, as a major osmolyte, and ectoine and glutamate as minor components. The strain Sharm^T biosynthetised α-glucosidase. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and a novel phosphoglycolipid as major components. Ubiquinone with nine repetitive unities (Q9) was the only quinone found and, nC16:0 and C19:0 with cyclopropane were the main cellular fatty acids, accounting for 87.3% of total fatty acids. The G + C content of the genomic DNA was 64.7 mol %. The 16S rRNA sequence analysis indicated that strain Sharm was a member of the genus Halomonas. The closest relatives of the strain Sharm were Halomonas elongata and Halomonas eurihalina. However, DNA–DNA hybridisation results clearly indicated that strain Sham was a distinct species of Halomonas. On the basis of the evidence, we propose to assign strain Sharm as a new species of the genus Halomonas, H. sinaiensis sp. nov, with strain Sharm^T as the type strain (DSM 18067^T; ATCC BAA-1308^T). The EMBL accession number for the 16S rRNA sequence of Halomonas sinaiensis strain Sharm^T is AM238662.