Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
ISSN-L : 1342-6311
Volume 16 , Issue 3
Showing 1-9 articles out of 9 articles from the selected issue
Minireview
  • Philip Brookes
    Type: Regular Paper
    2001 Volume 16 Issue 3 Pages 131-140
    Published: 2001
    Released: October 12, 2001
    JOURNALS FREE ACCESS
    For many purposes the soil micro-organisms can be considered as a single pool of living soil organic matter (the soil microbial biomass). Current methods to measure the microbial biomass are described and their merits and demerits discussed. The concept of the microbial biomass as a living soil organic matter pool is illustrated by reference to it as a labile reservoir of potentially plant-available nutrients. An estimate of the turnover times of biomass carbon (C) of 0.94 years and of biomass phosphorus (P) of 0.39 years shows that the turnover rates of nutrients within the biomass may be quite different. An understanding of the dynamics of biomass P is important. The lack of P availability in many tropical agricultural soils has been described as `the bottle-neck of world hunger'. Even if P is supplied it may be rapidly and irreversibly fixed in these, usually, strongly P-fixing soils. By adding small rates of animal manures with the fertilizer, more biomass P is formed. During the process of biomass turnover, this P may be released slowly and taken up by the crop more efficiently. Thus, in a Kenyan P-fixing soil, crop yields were much larger when both manure and fertilizer P were given than when either were applied singly.
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Research Articles
  • Li Huixin, Kazuyuki Inubushi, Johji Miwa
    Type: Regular Paper
    2001 Volume 16 Issue 3 Pages 141-146
    Published: 2001
    Released: October 12, 2001
    JOURNALS FREE ACCESS
    Effects of temperature on the population growth of soil bacteria, P. fluorescens and B. subtilis, and a bacterial-feeding nematode, C. elegans, and their activities for N mineralization were studied in gnotobiotic microcosms at 15, 20 and 25°C. Nematode densities increased significantly with temperature. Inoculation of nematodes significantly increased bacterial densities of both P. fluorescens and B. subtilis at 20 and 25°C. Bacterial and nematode densities rose simultaneously. The amounts of NH4+-N were significantly greater in the microcosms with nematodes and bacteria than the microcosms with bacteria alone at 20 and 25°C. There were significant interactions between temperature, nematodes and bacterial populations. These results indicate that nitrogen mineralization was closely related to the population dynamics of the nematodes and bacteria.
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  • Keizo Nagasaki, Kenji Tarutani, Masami Hamaguchi, Mineo Yamaguchi
    Type: Regular Paper
    2001 Volume 16 Issue 3 Pages 147-154
    Published: 2001
    Released: October 12, 2001
    JOURNALS FREE ACCESS
    The partial DNA sequencing of a virus that infects an alga causing harmful blooms, Heterosigma akashiwo is reported. Approximately 2 kb of viral DNA was sequenced and 2 open reading frames (ORFs) were found. The deduced amino acid sequences of both ORFs showed high similarity to those of a typical microalgal virus, Paramecium bursaria Chlorella virus 1 (PBCV-1). To develop a simple PCR for detecting HaV, 3 primer sets were designed using the sequence data. They were reactive with 6 HaV isolates of different origins, and also applicable for detection of HaV particles suspended in natural seawater without extraction of the viral DNA.
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  • Kiyoshi Hirano, Masahito Hayatsu, Ichio Nioh, Hirokazu Nakai
    Type: Regular Paper
    2001 Volume 16 Issue 3 Pages 155-160
    Published: 2001
    Released: October 12, 2001
    JOURNALS FREE ACCESS
    Nitrogen-fixing bacteria isolated from the rhizospheres of rice grown in a field treated long-term with agrochemicals (conventional farming; CF) and in a field free of agrochemicals (nature farming; NF) were compared by 16S rDNA sequencing. All of the bacteria isolated from rice grown in the NF field belonged to Actinomyces, α-Proteobacteria and β-Proteobacteria, while those from rice grown in the CF field belonged mainly to Actinomyces and α-Proteobacteria. Several species of β-Proteobacteria were also present in rice grown in the CF field. A group of nitrogen-fixing bacteria that showed 99.3%-98.3% similarity with Agromonas oligotrophica was present in samples from both fields, while other bacteria isolated from rice grown in the two fields differed in 16S rDNA. The nitrogen-fixing bacterium N32 showed 99.2% similarity with Burkholderia vietnamiensis, which is known to promote the growth of rice.
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  • Mohammad Hasanuzzaman, Yoshio Araki
    Type: Regular Paper
    2001 Volume 16 Issue 3 Pages 161-168
    Published: 2001
    Released: October 12, 2001
    JOURNALS FREE ACCESS
    Microorganisms are reported to use siderophores as iron carriers in their high-affinity type iron-uptake systems. Since siderophores form rather stable complexes with ferric iron, the release of iron from internalized complexes is probably accomplished through reduction to ferrous forms, being catalyzed by ferric reductases. In the present study, one of the ferric reductases from the soluble fraction of Vibrio anguillarum E6-5 was partially purified and characterized. This was an NADH-dependent ferric reductase with ability to reduce different iron complexes such as ferric citrate, ferric-EDTA, and ferric chloride. Effects of flavin derivatives, metal ions, dithiothreitol (DTT), and β-mercaptoethanol were also studied. In gel filtration chromatography, the enzyme showed an apparent molecular mass of 26 kDa. Upon native-PAGE analysis, the partially purified preparation gave a single band with ferric reductase activity.
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  • In-gi Kim, Yasuhiro Kasahara, Kyung-Sook Whang
    Type: Regular Paper
    2001 Volume 16 Issue 3 Pages 169-176
    Published: 2001
    Released: October 12, 2001
    JOURNALS FREE ACCESS
    A phylogenetic analysis of heterotrophic bacterial populations inhabiting streams and groundwater contaminated by acid mine drainage (AMD) was conducted. The samples were collected from sites around an inactive underground Dae-Sung coal mine at Keumsan, Korea. The investigation showed pigment-forming bacteria to be the major strains inhabiting the pollutant, accounting for up to approximately 50% of all isolates. Twenty-six pigment-forming bacteria were isolated and their taxonomic characteristics determined by phenotypic, chemotaxonomic and phylogenetic analyses. Based on a phylogenetic analysis using 16S ribosomal RNA gene nucleotide sequences, these isolates were found to fall within four major phylogenetic groups: α, β, and γ subdivisions of Proteobacteria; and low-G+C gram-positive bacteria. The α-Proteobacteria were further separated into α-1, α-2 and α-4 subclasses. Many isolates from the polluted stream (site P5) and groundwater (site G) were identified as Sphingomonas of the Proteobacteria α-4 subclass. Because strains P5-21 and P5-11 appeared to be novel species within the genus Sphingomonas, the discussion was focused on their taxonomy as well as abundance in the polluted regions.
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  • Toshio Sakamoto, Donald A. Bryant
    Type: Regular Paper
    2001 Volume 16 Issue 3 Pages 177-184
    Published: 2001
    Released: October 12, 2001
    JOURNALS FREE ACCESS
    Synechococcus sp. PCC 7002 cells appeared to be nitrogen limited when grown on urea without nickel in the growth medium; the amounts of chlorophyll a and phycobiliproteins decreased and glycogen accumulated to high levels. When nickel was added to the urea medium, the diagnostics of nitrogen limitation was not observed. The activity of urease was dependent on the presence of nickel no matter what nitrogen source was used for cell growth. The ureC gene encoding the α-subunit of urease was constitutively transcribed in cells grown on all nitrogen sources tested. The addition of nickel to the growth medium rapidly led to a 15-fold increase in urease activity in 2 hours. These results indicate that cells of Synechococcus sp. PCC 7002 require a nickel supplement (5 μM NiSO4 in the growth medium) to utilize urea efficiently, and that Synechococcus sp. PCC 7002 cells are nickel-starved under the laboratory conditions regularly used for this strain. In two fresh water strains of cyanobacteria, Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, high levels of urease activity were detected without addition of nickel to the growth medium, suggesting that these fresh water strains have a high-affinity uptake system for nickel or that their nickel requirements are lower than Synechococcus sp. PCC 7002.
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  • Koji Satsuma, Hisanori Nakamura, Kiyoshi Sato, Yasuhiro Kato
    Type: Regular Paper
    2001 Volume 16 Issue 3 Pages 185-189
    Published: 2001
    Released: October 12, 2001
    JOURNALS FREE ACCESS
    A water-miscible solvent, such as acetone, acetonitrile or methanol, is often employed as a co-solvent to dissolve an organic test chemical of low water solubility in an environmental fate study using a laboratory model microcosm. These co-solvents, however, may disrupt the microflora in the water/sediment tested, and affect the biodegradation of the target compound. In the present study, a 0.1% concentration of acetonitrile as a co-solvent greatly suppressed the microbial degradation of herbicide atrazine [2-chloro-4-(ethylamino)-6-(isopropylamino)-s-triazine] throughout the experimental period (84 days). The rapid growth of specific microbes was considered to deprive atrazine-degrading microbes of their habitat (mainly the surface area of sediment particles) in the microcosm.
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  • Satoru Suzuki, Shin-ichi Kitamura, Hiroshi X. Chiura
    Type: Regular Paper
    2001 Volume 16 Issue 3 Pages 191-196
    Published: 2001
    Released: October 12, 2001
    JOURNALS FREE ACCESS
    Marine birnavirus (MABV) is a member of Aquabirnavirus and an opportunistic pathogenic virus in eukaryotic marine organisms. This virus has a broad host range in wild and cultured fish and shellfish. In this study, the distribution of MABV in seawater from different areas was examined by PCR of the VP2/Ns junction region of the MABV genome. We have detected the MABV genome in three marine water columns; off the coast of Japan, in the Pacific Ocean and in the Mediterranean Sea, suggesting that MABV is widely distributed. The MABV genome was also detected in samples of zooplankton from the Pacific Ocean. A high nucleotide sequence similarity (more than 98.5%) was observed among the PCR products from MABV genomes. Such a prevalent distribution of genetically similar MABV suggests that birnavirus is one of the components of the RNA pool in ocean environments.
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