Design of Sphingomonad-Detecting Probes for a DNA Array, and Its Application to Investigate the Behavior, Distribution, and Source of Rhizospherous<i>Sphingomonas</i>and Other Sphingomonads Inhabiting an Acid Sulfate Soil Paddock in Kalimantan, Indonesia

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  • HASHIDOKO Yasuyuki
    Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University
  • KITAGAWA Emiko
    National Institute of Advanced Industrial Science and Technology (AIST)
  • IWAHASHI Hitoshi
    National Institute of Advanced Industrial Science and Technology (AIST)
  • PURNOMO Erry
    Department of Soil Science, Faculty of Agriculture, Lambung Makrad University
  • HASEGAWA Toshihiro
    National Institute of Agro-Environmental Sciences
  • TAHARA Satoshi
    Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University

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  • 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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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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