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

• Published in: Bioscience, biotechnology, and biochemistry Vol. 71; no. 2; pp. 343 - 351
• Main Authors: Hashidoko, Y.(Hokkaido Univ., Sapporo (Japan)), Kitagawa, E, Iwahashi, H, Purnomo, E, Hasegawa, T, Tahara, S
• Format: Journal Article
• Language: English
• Published: Tokyo Japan Society for Bioscience, Biotechnology, and Agrochemistry 01-02-2007; Japan Society for Bioscience Biotechnology and Agrochemistry; Oxford University Press
• Subjects: ACID SOILS; acid sulfate soil paddock; BACTERIA GRAM NEGATIVA; BACTERIE GRAM NEGATIF; Biological and medical sciences; Burkholderia cepacia - chemistry; Burkholderia cepacia - genetics; DNA Probes - chemistry; DNA, Bacterial - genetics; DNA, Bacterial - isolation & purification; Fundamental and applied biological sciences. Psychology; GRAM NEGATIVE BACTERIA; Hydrogen-Ion Concentration; Indonesia; Juncus; Juncus sp; KALIMANTAN; MICRO-ORGANISME DU SOL; MICROORGANISMOS DEL SUELO; Nucleic Acid Hybridization; NUCLEIC PROBES; Oligonucleotide Array Sequence Analysis; Oryza - microbiology; ORYZA SATIVA; RHIZOSPHERE; RIZOSFERA; RNA, Ribosomal, 16S - genetics; Soil - analysis; Soil Microbiology; SOIL MICROORGANISMS; SOL ACIDE; SONDAS NUCLEICAS; SONDE NUCLEIQUE; source of rhizospherous sphingomonads; Sphingomonas; Sphingomonas - genetics; Sphingomonas-detecting DNA array probes; SUELO ACIDO; Sulfates - chemistry; Kalimantan; Borneo; Asia; Indonesia; Monocotyledones; Sphingomonas; Juncus sp; Sulfates; Array; Soils; Juncaceae; Juncus; source of rhizospherous sphingomonads; acid sulfate soil paddock; Angiospermae; Bacteria; Spermatophyta; Molecular probe; Application; Sphingomonas-detecting DNA array probes
• ISSN: 0916-8451; 1347-6947
• DOI: 10.1271/bbb.60262

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.