| Design of sphingomonad-detecting probes for a DNA array, and its application to investigate the behavior, distribution, and source of Rhizospherous sphingomonas and other sphingomonads inhabiting an acid sulfate soil paddock in Kalimantan, Indonesia. | |
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MedLine Citation:
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PMID: 17284854 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Throughout Central and South Kalimantan, Indonesia, strongly acidic soil (pH 2.1-3.7) is widely distributed, and the local acidic soil-tolerant plants, including local rice varieties, often possess sphingomonads in their rhizosphere and rhizoplane. To investigate the behavior of sphingomonads inhabiting the rhizosphere of such acid-tolerant plants, we designed 13 different DNA array probes (each of 72 mer) specific to a group of sphingomonads, using a hypervariable V6 region of the 16S rRNA gene. This DNA array system was used preliminarily for an analysis of microfloral dynamisms, particularly of sphingomonads, in acidic paddock ecosystems, and the results suggest that the acid-tolerant local rice shares rhizospherous sphingomonads with wild Juncus sp., a predominant weed that thrives in acidic paddocks during the off-season for rice farming. This tentative conclusion supports the bio-rationality of the traditional rice farming system with respect to functional rhizobacteria. |
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Authors:
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Yasuyuki Hashidoko; Emiko Kitagawa; Hitoshi Iwahashi; Erry Purnomo; Toshihiro Hasegawa; Satoshi Tahara |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2007-02-07 |
Journal Detail:
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Title: Bioscience, biotechnology, and biochemistry Volume: 71 ISSN: 0916-8451 ISO Abbreviation: Biosci. Biotechnol. Biochem. Publication Date: 2007 Feb |
Date Detail:
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Created Date: 2007-02-23 Completed Date: 2007-05-09 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9205717 Medline TA: Biosci Biotechnol Biochem Country: Japan |
Other Details:
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Languages: eng Pagination: 343-51 Citation Subset: IM |
Affiliation:
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Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan. yasu-h@abs.agr.hokudai.ac.jp |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Burkholderia cepacia
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chemistry,
genetics DNA Probes / chemistry* DNA, Bacterial / genetics, isolation & purification Hydrogen-Ion Concentration Indonesia Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Oryza sativa / microbiology RNA, Ribosomal, 16S / genetics Soil / analysis Soil Microbiology* Sphingomonas / genetics* Sulfates / chemistry |
| Chemical | |
Reg. No./Substance:
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0/DNA Probes; 0/DNA, Bacterial; 0/RNA, Ribosomal, 16S; 0/Soil; 0/Sulfates |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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