Seiya Ogata

Microbial silica deposition in geothermal hot waters

Abstract. A combined use of molecular ecological techniques and geochemical surveys revealed that thermophilic or hyperthermophilic microorganisms living in geothermal environments are likely to be implicated in the formation of biogenic siliceous deposits. Electron microscopic observations indicated that numerous microorganism-like fabrics were preserved in naturally occurring siliceous deposits such as siliceous sinter, geyserite, and silica scale, which suggests microbial contribution to silica precipitation. Molecular phylogenetic analyses suggested that extreme thermophilic bacteria within the genera Thermus and Hydrogenobacter are predominant components among the indigenous microbial community in siliceous deposits formed in pipes and equipment of Japanese geothermal power plants. These bacteria seem to actively contribute to the rapid formation of huge siliceous deposits. Additionally, in vitro examination suggested that Thermus cells induced the precipitation of supersaturated amorphous silica during the exponential growth phase, concomitant with the production of a specific cell envelope protein. Dissolved silica in geothermal hot water may be a significant component in the maintenance of position and survival of microorganisms in limited niches.

Bio-deposition of Amorphous Silica by an Extremely Thermophilic Bacterium, Thermus spp.

The bio-deposition of amorphous silica, which occurred in vitro by exposure to the extremely thermophilic bacterium Thermus spp. began from the latter part of the exponential phase of growth of the bacteria. The concentration with which the deposition occurred exceeded the solubility of amorphous silica of neutral pH at the temperature 60~85°C. Our observations suggest that Thermus spp. promotes the formation of siliceous minerals in a geothermal environment.

Bacteriophages of the genus Clostridium.

Publisher Summary This chapter describes the properties and morphologies of phages that infect the industrially important clostridia, together with the nature of the damage and measures of control against phage contamination. The chapter also includes information about the well-known phages and phagelike particles of C. sporogenes, C. botulinum, and C. perfringens. One of the assays used for the phages of acetone-butanol-producing clostridia—is the modified double-layer method. In this method, a mixture of bacteria and phages is added to the bottom layer, covered with anaerobic agar medium containing sodium thioglycolate, and then incubated using the same procedure as for the cultivation of aerobes. The growth of phages is best under conditions which are good for the growth of the host organisms. In the case of C. botulinum and C. tetani, the plaque formation by phage infection is more difficult compared with C. sporogenes, C. perfringens, or C. saccharoperbutylacetonicum, because—the former species do not produce an even lawn on the agar plates.

A comparative study and phage typing of silage-making Lactobacillus bacteriophages.

To investigate basic characteristics of 10 virulent phages active on silage-making lactobacilli, morphological properties, host ranges, protein composition and genome characterization were separated into five groups based on host ranges and basic properties. The seven phages of groups I, II and V were active on Lactobacillus plantarum and Lactobacillus pentosus. Phage phiPY4 (group III) infected both L. casei and Lactobacillus rhamnosus. Phage phiPY5 (group IV) specifically infected Lactobacillus casei. Morphologically, three phages of groups I belonged to the Myoviridae family, while seven other phages of groups II, III and V belonged to the Siphoviridae family. SDS-PAGE profiles, restriction analysis, G + C contents of DNA and Dot blot hybridization revealed a high degree of homology in each group. Clustering derived from host range analysis was closely related to results of DNA and protein analyses. These phages may be applicable to phage typing for silage-making lactobacilli.

Pediococcus lolii sp. nov., isolated from ryegrass silage

A Gram-positive, coccus-shaped, lactic acid bacterium, strain NGRI 0510Q(T), was isolated from ryegrass silage produced in Okinawa Prefecture, Japan. The cell is non-spore-forming, non-motile, and occurs in pairs or tetrads. The strain is homofermentative and produces d- and l-lactic acid from glucose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NGRI 0510Q(T) belongs to the genus Pediococcus and clusters within the Pediococcus acidilactici and Pediococcus pentosaceus group, with 98.2 and 96.9 % sequence identity, respectively. DNA-DNA relatedness between strain NGRI 0510Q(T) and P. acidilactici JCM 8797(T) and P. pentosaceus JCM 5890(T) was 19.3 and 17.3 %, respectively. Based on its phenotypic characteristics, phylogenetic relationship and DNA-DNA relatedness, NGRI 0510Q(T) (=JCM 15055(T)=DSM 19927(T)) represents the type strain of a novel species, for which the name Pediococcus lolii sp. nov. is proposed.

The DNA sequence of γ-glutamyltranspeptidase gene of Bacillus subtilis (natto) plasmid pUH1

SummaryThe γ-glutamyltranspeptidase (γ-GTP) gene of Bacillus subtilis (natto) plasmid designated pUH1, which is responsible for polyglutamate production, has been cloned and the nucleotide sequence determined. The sequence contains a single open-reading frame stretching for 1260 bp with a relative molecular mass of 49356. Putative -35 and -10 sequences, TTCAAA and TATTAT, were observed as the consensus sequence for the promoter recognized by the σ43 RNA polymerase of B. subtilis, and the ribosome binding site, the sequence of which was AACGAG, was complementary to the binding sequence of B. subtilis 16S rRNA except for one base. The amino acid sequence of the gene with the segment of putative protein C403 of staphylococcal plasmid pE194 indicates homology, whereas that with Escherichia coli and mammalian γ-GTPs does not show any similarity at all.

Effects of bacitracin and excess Mg2+ on submerged mycelial growth of Streptomyces azureus

Effects of bacitracin (BC) and excess Mg2+ on pellet formation and mycelial growth of Streptomyces azureus were studied in a liquid culture using Bennett medium. The addition of Mg2+ at concentrations above 0.2 mM to the medium resulted in the promotion of pellet formation, a distinct inhibition of growth and decrease in cell mass. BC changed the growth type of mycelia from the compact pellet-type to the dispersed-type, and stimulated mycelial growth after a long lag period, accompanied by an increase in cell mass. In the presence of less than 0.2 mM Mg2+, BC completely inhibited mycelial growth. Ca2+ showed an effect similar to Mg2+. EDTA inhibited pellet formation, but never stimulated growth. Furthermore, EDTA suppressed the growth inhibitory and stimulatory actions of BC. From these results, we speculated that: (i) excess Mg2+ induced pellet formation; (ii) BC, similar to EDTA chelated with excess Mg2+ in the medium, leading to the inhibition of pellet formation; and (iii) BC-induced stimulation of growth might be due to its chelating and antimicrobial activities. It was also said that the growth inhibitory action of BC on S. azureus was antagonized by excess Mg2+ or Ca2+ and EDTA.

Stimulation of Expression of a Silica-Induced Protein (Sip) in Thermus thermophilus by Supersaturated Silicic Acid

ABSTRACT The effects of silicic acid on the growth of Thermus thermophilus TMY, an extreme thermophile isolated from a siliceous deposit formed from geothermal water at a geothermal power plant in Japan, were examined at 75°C. At concentrations higher than the solubility of amorphous silica (400 to 700 ppm SiO2), a silica-induced protein (Sip) was isolated from the cell envelope fraction of log-phase TMY cells grown in the presence of supersaturated silicic acid. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed the molecular mass and pI of Sip to be about 35 kDa and 9.5, respectively. Induction of Sip expression occurred within 1 h after the addition of a supersaturating concentration of silicic acid to TM broth. Expression of Sip-like proteins was also observed in other thermophiles, including T. thermophilus HB8 and Thermus aquaticus YT-1. The amino acid sequence of Sip was similar to that of the predicted solute-binding protein of the Fe3+ ABC transporter in T. thermophilus HB8 (locus tag, TTHA1628; GenBank accession no. NC_006461; GeneID, 3169376). The sip gene (987-bp) product showed 87% identity with the TTHA1628 product and the presumed Fe3+-binding protein of T. thermophilus HB27 (locus tag TTC1264; GenBank accession no. NC_005835; GeneID, 2774619). Within the genome, sip is situated as a component of the Fbp-type ABC transporter operon, which contains a palindromic structure immediately downstream of sip. This structure is conserved in other T. thermophilus genomes and may function as a terminator that causes definitive Sip expression in response to silica stress.

Thermus thermophilus TMY isolated from silica scale taken from a geothermal power plant

Aims:  To identify an extreme thermophile, strain TMY, isolated from silica scale from the geothermal electric power plant and to examine microdiversity of Thermus thermophilus strains.

Isolation of Enterocin SE-K4-Encoding Plasmid and a High Enterocin SE-K4 Producing Strain of Enterococcus faecalis K-4.

Enterococcus faecalis K-4, which produces a class IIa bacteriocin, enterocin SE-K4, carries two plasmids, pEK4S (approximately 60 kb) and pEK4L (approximately 75 kb). Plasmid-curing experiments showed that pEK4S was involved in the production of and immunity to enterocin SE-K4 in strain K-4. A derivative strain, M6, with pEK4S produced a higher amount of enterocin SE-K4 than the parental strain K-4, although its growth rate was lower than that of parental strain K-4. Phenotypic changes in strain M6 are attributed to an increase in plasmid copy number.