Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
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Volume 26 , Issue 1
Showing 1-15 articles out of 15 articles from the selected issue
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Regular Papers
  • Teruki Amano, Ikuo Yoshinaga, Takao Yamagishi, Chu Van Thuoc, Pham The ...
    Volume 26 (2011) Issue 1 Pages 1-6
    Released: March 05, 2011
    [Advance publication] Released: November 06, 2010
    JOURNALS FREE ACCESS
    Mangrove forests are common in subtropical regions, and have received considerable attention as vegetative buffers against anthropogenic N-loading. In this study, we investigated anaerobic ammonium oxidation (anammox) as one of potentially important microbial N-removing pathways in mangrove and shrimp pond sediment in Haiphong, Vietnam. Measurements with 15N-labeled compounds demonstrated the occurrence of anammox in sediment of mangrove forest and a water channel connecting shrimp ponds to the sea in both 2005 and 2007, and of a semi-intensive shrimp pond in 2005. The rate of potential anammox activity reached to 0.7 nmol-N2 cm-3 h-1, although the contribution of anammox was less significant than denitrification. Anammox-type 16S rRNA gene fragments phylogenetically related to ‘Scalindua’ species were predominantly recovered from mangrove forest and water channel sediment in a PCR-clone library analysis targeting anammox bacteria. ‘Kuenenia’-like gene fragments were also recovered from shrimp pond sediment as the major component. We demonstrated the occurrence of potential anammox activity, and suggested the possibility that diverse species of uncultured anammox bacteria contribute to the nitrogen cycle in subtropical mangrove-aquaculture ecosystems. Furthermore, this study provides new insight into the biogeography of anammox bacteria: ‘Scalindua’ and ‘Kuenenia’-like species coexisted in the blackish sediment as in some temperate estuarine sediment.
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  • Nobutaka Someya, Seishi Ikeda, Tomohiro Morohoshi, Masako Noguchi Tsuj ...
    Volume 26 (2011) Issue 1 Pages 7-14
    Released: March 05, 2011
    [Advance publication] Released: November 06, 2010
    JOURNALS FREE ACCESS
    A total of 100 isolates of chitinolytic bacteria were obtained from the rhizospheres of various agronomic plants, and the 16S rRNA gene sequences of these isolates were determined. Phylogenetic analyses revealed that 81 isolates belonged to the classes Betaproteobacteria (39 isolates) and Gammaproteobacteria (42 isolates). Of the remaining 19 isolates, 16 belonged to the phylum Firmicutes. Clustering analysis identified 6 and 3 operational taxonomic units (OTUs) in Gammaproteobacteria and Betaproteobacteria, respectively, at the genus level. The majority of chitinolytic bacteria in Gammaproteobacteria belonged to the genera Serratia, Stenotrophomonas, and Lysobacter (14, 15, and 7 isolates, respectively) while those in Betaproteobacteria belonged to the genus Mitsuaria (37 isolates). The 16 isolates placed in Firmicutes belonged to 2 genera, Paenibacillus and Bacillus (8 isolates each). The isolates in the remaining OTUs belonged to the genera Erwinia, Aeromonas, Pseudomonas, Achromobacter, Flavobacterium, and Microbacterium, in less abundance. These results showed a wide distribution of culturable chitinolytic bacteria in the rhizospheres of various agronomic plants. Considering the potential antagonistic activity of chitinolytic enzymes against phytopathogenic fungi, which is exhibited by fungal cell wall degradation, the above-mentioned native chitinolytic bacteria in rhizospheres could potentially be utilized for the biological control of soil-borne phytopathogenic fungi.
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  • Meng Li, Huiluo Cao, Yi-Guo Hong, Ji-Dong Gu
    Volume 26 (2011) Issue 1 Pages 15-22
    Released: March 05, 2011
    [Advance publication] Released: December 04, 2010
    JOURNALS FREE ACCESS
    The community and population dynamics of anammox bacteria in summer (wet) and winter (dry) seasons in estuarial mudflat sediment of the Mai Po Nature Reserve were investigated by 16S rRNA and hydrazine oxidoreductase (hzo) genes. 16S rRNA phylogenetic diversity showed that sequences related to ‘Kuenenia’ anammox bacteria were presented in summer but not winter while ‘Scalindua’ anammox bacteria occurred in both seasons and could be divided into six different clusters. Compared to the 16S rRNA genes, the hzo genes revealed a relatively uniform seasonal diversity, with sequences relating to ‘Scalindua’, ‘Anammoxoglobus’, and planctomycete KSU-1 found in both seasons. The seasonal specific bacterial groups and diversity based on the 16S rRNA and hzo genes indicated strong seasonal community structures in estuary sediment of this site. Furthermore, the higher abundance of hzo genes in summer than winter indicates clear seasonal population dynamics. Combining the physicochemical characteristics of estuary sediment in the two seasons and their correlations with anammox bacteria community structure, we proposed the strong seasonal dynamics in estuary sediment of Mai Po to be due to the anthropogenic and terrestrial inputs, especially in summer, which brings in freshwater anammox bacteria, such as ‘Kuenenia’, interacting with the coastal marine anammox bacteria ‘Scalindua’.
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  • Naoki Matsutani, Tatsunori Nakagawa, Kyoko Nakamura, Reiji Takahashi, ...
    Volume 26 (2011) Issue 1 Pages 23-29
    Released: March 05, 2011
    [Advance publication] Released: November 30, 2010
    JOURNALS FREE ACCESS
    Ammonia-oxidizing archaea (AOA) are generally cultivated at ammonium concentrations of less than 2 mM. The physiology and abundance in the environment of AOA suggest an important role in the nitrogen cycle. We report here a novel marine ammonia-oxidizing crenarchaeote, strain NM25 belonged to ‘Candidatus Nitrosopumilus’, that was enriched from coastal sand of an eelgrass zone and grew in a medium containing 15 mM ammonium at 30°C. A phylogenetic analysis based on the 16S rRNA gene revealed this crenarchaeote was related to the ammonia-oxidizing archaeon ‘Candidatus Nitrosopumilus maritimus’ strain SCM1, with 98.5% identity. The ammonia monooxygenase subunit A (amoA) gene of strain NM25 was less closely related to that of known cultivable AOA (>95%) and environmental clones (>97%). This finding suggests the existence of AOA adapted to high ammonium-containing environments.
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  • Kanako Tago, Satoshi Ishii, Tomoyasu Nishizawa, Shigeto Otsuka, Keishi ...
    Volume 26 (2011) Issue 1 Pages 30-35
    Released: March 05, 2011
    [Advance publication] Released: November 11, 2010
    JOURNALS FREE ACCESS
    Denitrifiers can produce and consume nitrous oxide (N2O). While little N2O is emitted from rice paddy soil, the same soil produces N2O when the land is drained and used for upland crop cultivation. In this study, we collected soils from two types of fields each at three locations in Japan; one type of field had been used for continuous cultivation of rice and the other for rotational cultivation of rice and soybean. Active denitrifiers were isolated from these soils using a functional single-cell isolation method, and their taxonomy and denitrifying properties were examined. A total of 110 denitrifiers were obtained, including those previously detected by a culture-independent analysis. Strains belonging to the genus Pseudogulbenkiania were dominant at all locations, suggesting that Pseudogulbenkiania denitrifiers are ubiquitous in various rice paddy soils. Potential denitrifying activity was similar among the strains, regardless of the differences in taxonomic position and soil of origin. However, relative amounts of N2 in denitrification end products varied among strains isolated from different locations. Our results also showed that crop rotation had minimal impact on the functional diversity of the denitrifying strains. These results indicate that soil and other environmental factors, excluding cropping systems, could select for N2-producing denitrifiers.
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  • Salem Djedidi, Tadashi Yokoyama, Naoko Ohkama-Ohtsu, Chandra Prasad Ri ...
    Volume 26 (2011) Issue 1 Pages 36-45
    Released: March 05, 2011
    [Advance publication] Released: December 04, 2010
    JOURNALS FREE ACCESS
    Thirty two rhizobial isolates were obtained from different bioclimatic regions of Tunisia using as trap plants, Medicago sativa, Medicago ciliaris, Medicago polymorpha and Medicago minima. To study their diversity and characterize them in relation to Mediterranean conditions, abiotic stress resistance, symbiotic properties and genetic diversity in terms of 16S rRNA and nodA sequences were assessed. Five isolates from M. sativa, three from M. ciliaris and three from M. minima could grow at 45°C. Only two isolates from M. sativa grew at 4% NaCl. The most stress tolerant isolates were obtained from arid soils. A phylogenetic analysis of 16S rRNA genes revealed 29 isolates to be closely related to Ensifer including one (Pl.3-9) that showed a 16S rRNA sequence similar to that of Ensifer meliloti and nodA sequence similar to that of Ensifer medicae. However, three isolates were categorized into Agrobacterium containing the nodA of Ensifer. Furthermore, these isolates developed nodules on original hosts. The results for the four isolates suggest horizontal gene transfer between the species.
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  • Kazuo Isobe, Yuichi Suwa, Junko Ikutani, Megumi Kuroiwa, Tomoko Makita ...
    Volume 26 (2011) Issue 1 Pages 46-53
    Released: March 05, 2011
    [Advance publication] Released: November 30, 2010
    JOURNALS FREE ACCESS
    The measurement of 15N concentrations in environmental samples requires sophisticated pretreatment devices and expensive isotope-ratio mass spectrometry (IRMS). This report describes the use of a gas chromatograph equipped with a quadrupole-type mass spectrometer (GC/MS) to measure 15N concentrations of ammonium, nitrate, nitrite, and total dissolved nitrogen (TDN) in distilled water, a 2 M KCl solution and a 0.5 M K2SO4 solution. The system measures nitrous oxide (N2O) that is ultimately converted from the target N compound, requiring no special apparatus such as a purge-and-trap pretreatment device. It uses a denitrifier lacking N2O reductase, which produces N2O from nitrate. Persulfate oxidation was applied to convert TDN to nitrate, while additional pretreatment with ammonia diffusion was required for ammonium prior to the persulfate oxidation. Up to 100 samples can be measured daily using the system. We can generally run 15N measurements with only 1-10 mL of sample for each chemical species of N, a volume 1/10-1/100 times smaller than the amount necessary for conventional methods. Our method is useful for measuring 15N with GC/MS, offering greater convenience than IRMS.
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  • Gab-Joo Chee, Hideto Takami
    Volume 26 (2011) Issue 1 Pages 54-60
    Released: March 05, 2011
    [Advance publication] Released: December 17, 2010
    JOURNALS FREE ACCESS
    Group II introns inserted into genes often undergo splicing at unexpected sites, and participate in the transcription of host genes. We identified five copies of a group II intron, designated Oi.Int, in the genome of an extremely halotolerant and alkaliphilic bacillus, Oceanobacillus iheyensis. The Oi.Int4 differs from the Oi.Int3 at four bases. The ligated exons of the Oi.Int4 could not be detected by RT-PCR assays in vivo or in vitro although group II introns can generally self-splice in vitro without the involvement of an intron-encoded open reading frame (ORF). In the Oi.Int4 mutants with base substitutions within the ORF, ligated exons were detected by in vitro self-splicing. It was clear that the ligation of exons during splicing is affected by the sequence of the intron-encoded ORF since the splice sites corresponded to the joining sites of the intron. In addition, the mutant introns showed unexpected multiple products with alternative 5' splice sites. These findings imply that alternative 5' splicing which causes a functional change of ligated exons presumably has influenced past adaptations of O. iheyensis to various environmental changes.
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  • Fabiano L. Thompson, Antonio Alves Neto, Eidy de O. Santos, Kaori Izut ...
    Volume 26 (2011) Issue 1 Pages 61-66
    Released: March 05, 2011
    [Advance publication] Released: December 14, 2010
    JOURNALS FREE ACCESS
    We analyzed the effect of N-acetyl-D-glucosamine (GlcNAc) on gene expression in the marine bacterium Vibrio parahaemolyticus. The total number of genes whose expression was induced and repressed genes in the presence of GlcNAc was 81 and 55, respectively. The induced genes encoded a variety of products, including proteins related to energy metabolism (e.g. GlcNAc and chitin utilization), transport, central metabolism and chemotaxis, hypothetical proteins, mannose-sensitive hemagglutinin pilus (MSHA), and a PilA protein, whereas the repressed genes encoded mainly hypothetical proteins. GlcNAc appears to influence directly or indirectly a variety of cellular processes, including energy metabolism, chitin utilization, competence, biofilm formation and pathogenicity. GlcNAc, one of the most abundant aminosugars in the oceans, is used by V. parahaemolyticus as an energy source and affects the cellular functioning of this marine bacterium.
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  • Tomonori Kindaichi, Takanori Awata, Yuji Suzuki, Katsuichiro Tanabe, M ...
    Volume 26 (2011) Issue 1 Pages 67-73
    Released: March 05, 2011
    [Advance publication] Released: December 11, 2010
    JOURNALS FREE ACCESS
    We established an enrichment culture of marine anaerobic ammonium oxidation (anammox) bacteria using an up-flow column reactor fed with artificial sea water supplemented with nitrogen and minerals and inoculated with coastal surface sediment collected from Hiroshima Bay. After 2 months of reactor operation, simultaneous removal of NH4+ and NO2- was observed, suggesting that an anammox reaction was proceeding. A total nitrogen removal rate of 2.17 g-N L-1 day-1 was attained on day 594 while the nitrogen loading rate was 3.33 g-N L-1 day-1. Phylogenetic analysis revealed that at least two dominant “Candidatus Scalindua” species were present in this reactor. Moreover, many uncultured bacteria and archaea, including candidate division or ammonia-oxidizing archaea, were present. Fluorescence in situ hybridization (FISH) revealed that anammox bacteria accounted for 85.5 ± 4.5% of the total bacteria at day 393. We also designed two oligonucleotide probes specific to each dominant “Candidatus Scalindua” species. A simultaneous FISH analysis using both probes showed that two different “Candidatus Scalindua” species were clearly recognizable and coexisted during reactor operation, although there was some variation in their abundance. The marine anammox bacteria enriched in this study have potential applications to the treatment of industrial wastewater containing high levels of ammonium and salt.
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  • Noriko Ryuda, Tomoyoshi Hashimoto, Daisuke Ueno, Koichi Inoue, Takashi ...
    Volume 26 (2011) Issue 1 Pages 74-80
    Released: March 05, 2011
    [Advance publication] Released: January 14, 2011
    JOURNALS FREE ACCESS
    The abundance of denitrifying bacteria in soil has been determined primarily by the conventional most probable number (MPN) method. We have developed a single-cell identification technique that is culture-independent, direct in situ PCR, to enumerate denitrifying bacteria in soils. The specificity of this method was evaluated with six species of denitrifying bacteria using nirK as the target gene; Escherichia coli was used as a negative control. Almost all (97.3%-100%) of the nirK-type denitrifying bacteria (Agromonas oligotrophica, Alcaligenes faecalis, Achromobacter denitrificans, Bradyrhizobium japonicum, and Pseudomonas chlororaphis) were detected by direct in situ PCR, whereas no E. coli cells and only a few cells (2.4%) of nirS-type denitrifying bacteria (Pseudomonas aeruginosa) were detected. Numbers of denitrifying bacteria in upland and paddy soil samples quantified by this method were 3.3 × 108 to 2.6 × 109 cells g-1 dry soil. These values are approximately 1,000 to 300,000 times higher than those estimated by the MPN method. These results suggest that direct in situ PCR is a better tool for quantifying denitrifying bacteria in soil than the conventional MPN method.
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