Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
ISSN-L : 1342-6311
Volume 16 , Issue 2
Showing 1-9 articles out of 9 articles from the selected issue
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  • Branko Velimirov
    Type: Regular Paper
    2001 Volume 16 Issue 2 Pages 67-77
    Published: 2001
    Released: July 16, 2001
    JOURNALS FREE ACCESS
    Very small forms of bacteria have been reported from marine and freshwater systems as well as from soils, subsurface terrestrial environments' and more recently from samples of kidney stones. Also, such small cells could be obtained in the laboratory during starvation experiments, indicating that bacteria which survive periods of nutrient deprivation manifest a decrease of cell size. Even though the various reports brought about poorly defined designations for small bacteria, they have stimulated the discussion on how small a living bacterium could be. The information derived from the literature concerning starvation forms, ultramicrobacteria and nanobacteria is analysed in the light of own field and laboratory observations. It could be shown that despite conceptual shortcomings and problems with definitions of what is meant by "small", starvation forms and ultramicrobacteria are clearly distinguishable according to physiological characteristics, which could not be achieved for nanobacteria or nanobes. Furthermore, it is documented that ultramicrobacteria are not the smallest procaryotes and that the size of bacterial starvation forms are much closer to the calculated minimal sizes required to ensure independent viable life. A bacterial cell which is growing and dividing needs to be large enough to accommodate DNA and RNA, enzymes for replication transcription and translation, solvent for ubstances as well as a minimum set of proteins and plasamtic space to run the operations. Many authors assume that this requires a cell with a diameter not smaller than 200 nm and with a volume between 0.014 and 0.06 μm3. Most cells with diameters equal or below 0.2 μm are rods while cocci are numerically of minor importance in natural aquatic systems. It seems that the rod morphotype has more potential to produce viable cells with minimal volumes than spherical morhotypes. This supports the assumption that not only size but also cell shape is important to achieve functional minimum cell volumes. Many cell parameters can be estimated with relatively high precision, but one should remember that absolute calibration is still not possible. Even if we assume that there are errors involved in most biometric measurements, there is still a trend which indicates that rod shaped cells can function with diameters below 0.2 μm and cell volumes well below 0.02 μm3. Such dimensions could be an indication that the lower size limit of a viable bacterium may be close to the size of the smallest hypothetical living cell, indicating that there is still more to know about the minimal required cell components allowing a bacterium the remain viable.
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Research Articles
  • Abdul Hadi, Muhammad Haridi, Kazuyuki Inubushi, Erry Purnomo, Fadly Ra ...
    Type: Regular Paper
    2001 Volume 16 Issue 2 Pages 79-86
    Published: 2001
    Released: July 16, 2001
    JOURNALS FREE ACCESS
    Effects of land-use change in tropical peatlands on the microbial population and emissions of nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) were studied in the field and laboratory. The study area covered secondary forest, paddy field and paddy-soybean rotation field in Indonesia. ATP content, and numbers of viable bacteria and fungi, cellulolytic bacteria and fungi, NH4+ oxidizers and denitrifiers in a paddy-soybean rotation field and paddy field were reduced to 1-30% and 3-90% of those in secondary forest, respectively. The field measurements of greenhouse gas emissions showed that significantly more CH4 was emitted from paddy field than secondary forest, but no significant difference in the emission of either N2O or CO2. The laboratory incubation experiment showed that the soil moisture level and land-use change significantly affected the emission of N2O, CH4 and CO2. These results suggested that land-use change significantly affected the microbial population and emissions of greenhouse gases.
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  • Midori Nakazawa, Sumito Hatta, Takao Kamura, Takamitsu Konno
    Type: Regular Paper
    2001 Volume 16 Issue 2 Pages 87-90
    Published: 2001
    Released: July 16, 2001
    JOURNALS FREE ACCESS
    Atmospheric precipitation samples (rainwater and dry deposits) were added to thiosulfate media to measure sulfur-oxidizing activities. The dry deposits collected outdoors showed sulfur-oxidizing activity, while those collected indoors showed little each activity. Although sulfur-oxidizing activity was observed in all atmospheric samples, it was greater in the neutral culture medium (pH 6) inoculated with rainwater than the acidic medium (pH 3.5). In addition, the sulfur-oxidizing activity found in those samples was markedly suppressed by various methods of sterilization. It was suggested that biological oxidation of sulfur occurred in these samples. Therefore, atmospheric biological sulfur oxidation should be considered in the global sulfur cycle.
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  • Kazunori Yamamoto, Ritsuko Murakami, Yoshichika Takamura
    Type: Regular Paper
    2001 Volume 16 Issue 2 Pages 91-99
    Published: 2001
    Released: July 16, 2001
    JOURNALS FREE ACCESS
    Random amplified polymorphic DNA (RAPD) analysis was applied to the differentiation of 11 thermophilic clostridia species, 11 type strains and 14 reference strains, at the species level. The 6 primers used in amplification generated 2 to 11 bands with 170-3,300 bp that were different depending on each of the strains and the primers used. From a comparison of RAPD fingerprints: sizes, numbers, and intensities of bands, it was demonstrated that (Clostridium) thermocellum, (Clostridium) thermolacticum, Moorella thermoacetica, and Thermoanaerobacterium thermosaccharolyticum were genotypically homogeneous at each species level. Each species showed species-specific and -common bands in RAPD profiles that were most pertinent for the discrimination of strains at the species level. In contrast, it was shown that each species of Thermoanaerobacter thermohydrosulfuricus, Thermoanaerobacter thermocopriae and Thermoanaerobacterium thermosulfurigenes was genotypically heterogeneous because none of the 6 primers produced species-common band patterns. However, each type strain of thermophilic clostridia species gave different RAPD fingerprints with each primer. Results obtained by the RAPD analysis therefore complement and support the current classification of these species and this study also shows that RAPD has the potential to differentiate between these species.
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  • Hirofumi Tomiyama, Mifuyu Ohshima, Satoko Ishii, Kazuo Satoh, Reiji Ta ...
    Type: Regular Paper
    2001 Volume 16 Issue 2 Pages 101-108
    Published: 2001
    Released: July 16, 2001
    JOURNALS FREE ACCESS
    An ammonia-oxidizing bacterium, strain NRS527 and nitrite-oxidizing bacterium, strain NRB 5220 were newly isolated from rhizoplane of paddy rice. The cells of strain NRS527 are spiral (0.2-0.3 μm wide, with 3-6 turns), gram negative, obligately aerobic, and chemolithotrophic. Intracytoplasmic membranes, a characteristic of ammmonia-oxidizing bacteria are absent. The optimum concentration of ammonium sulfate (substrate) in the medium is 38 mM. The G+C content of the total DNA is 59.18 mol%. The similarity of 16S rRNA (%) to Nitrosospira briensis C-128 is 94.71. The supplemental effect of organic compounds could not be recognized. The cells of strain NRB5220 are rod shaped (0.5-0.8 ×1.0-2.0 μm), gram negative, and obligately aerobic. The G+C content is 60.37 mol%. The similarity of 16S rRNA (%) to Nitrobacter agilis ATCC14123 is 97.38. The optimum concentration of sodium nitrite (substrate) in the medium is 22 mM. Growth of strain NRB5220 is hastened when peptone and yeast extract are added to the medium as nutrients. Both strains were resistant to tetracycline at 33 μg/ml. The new nitrifying bacteria isolated from rhizoplane of paddy rice were identified as Nitrosospira sp. NRS527 and Nitrobacter sp. NRB5220.
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  • Akiko Hashimoto, Kazuhiro Iwasaki, Mutsuyasu Nakajima, Osami Yagi
    Type: Regular Paper
    2001 Volume 16 Issue 2 Pages 109-116
    Published: 2001
    Released: July 16, 2001
    JOURNALS FREE ACCESS
    We developed a method for enumerating trichloroethylene (TCE) degrading Mycobacterium sp. TA27 by means of PCR. The PCR primers and probe were designed based on the 16S rRNA sequences of Mycobacterium sp. TA27, compared with corresponding regions of 8 phylogenetically related strains. The total DNAs of strain TA27 and the other 8 mycobacteria were extracted and used for PCR amplification by a 5'-nuclease real-time PCR assay. The highest specificity for strain TA27 was observed at an annealing temperature of 62°C and at forward and reverse primer concentrations of 0.2 μM each. The other 8 mycobacteria were not detected under these conditions. The detection limits for the DNA and cells of strain TA27 were 0.05 pg/tube and 25 cells/tube, respectively. The utility of the PCR assay for the quantification of strain TA27 cells was demonstrated in TCE-polluted groundwater.
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  • Tsuneo Shiba, Makoto Sasaki, Bok You, Ikuo Yoshinaga, Toshimichi Maeda
    Type: Regular Paper
    2001 Volume 16 Issue 2 Pages 117-120
    Published: 2001
    Released: July 16, 2001
    JOURNALS FREE ACCESS
    In a PCR-based 5' nuclease assay with a fluorogenic 16S rDNA probe, we found an increase in fluorescence that was not caused by the digestion of the DNA probe in the PCR. The fluorescence diminished to a base line level by ethanol precipitation of the 5' nuclease PCR product. Boiling the PCR product also decreased the fluorescence to the level of a control containing no template DNA. Hence, the increase in fluorescence in the assay did not seem to be caused by hybridization to the complementary structure of the template DNA, but seemed to be dependent on the intact probe remaining in the PCR reaction mixture. The increase in fluorescence appeared to be the result of a probe/template association other than the hybridization.
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  • Haruo Mimura, Shinichi Nagata
    Type: Regular Paper
    2001 Volume 16 Issue 2 Pages 121-123
    Published: 2001
    Released: July 16, 2001
    JOURNALS FREE ACCESS
    We used Brevibacterium sp. JCM 6894, which was isolated from seawater, to degrade the water-soluble fraction of jellyfish. After 27 h of incubation, the protein content in the supernatant was reduced from 1.97 to 1.31 mg/ml with an increase in cell yield of 0.40 mg cell protein/ml. The missing protein content in the fraction was 0.26 mg/ml. By the cell growth, the content of NH3 was increased from 0.38 to 4.57 μmol/ml. The value of chemical oxygen demand, which is a marker of remaining organic compounds in the fraction, was reduced from 890 to 431 mg O2/liter.
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  • Fumio Inagaki, Yoshinobu Motomura, Katsumi Doi, Sachihiro Taguchi, Eij ...
    Type: Regular Paper
    2001 Volume 16 Issue 2 Pages 125-130
    Published: 2001
    Released: July 16, 2001
    JOURNALS FREE ACCESS
    At Steep Cone hot spring, Lower Geyser Basin, Yellowstone National Park, a mound of siliceous deposits called "siliceous sinter" forms from discharged boiling geothermal water that is supersaturated with amorphous silica. Electron-probe microanalyzer (EPMA) observations suggested that silica is deposited on the surface of the cells and that microorganisms affect the formation of the siliceous sinter. EPMA signals and backscattered electron images of sinter samples taken at the inner wall of the boiling pool revealed framboidal pyrite structures associated with a network of silicified microbial structures. The structure of bacterial community in a beige-colored sinter sediment (75.8°C, pH 8.6) was studied by molecular clone type phylogenetic analysis of PCR-mediated 16S rDNA fragments. The bacterial rDNA clones found indicated the presence of a complex community in the sinter sediment. Sequences closely related to the genera Thermus and Saccharomonospora were dominated; evidence of indigenous microbial components.
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