Development of rapid and efficient DNA extraction protocol for lowland rice paddy soils using powdered broken glass

Issue Date

7-2018

Abstract

Different farm practices of lowland rice production affect the soil microbial profile. Understanding the occurence and diversity of microbes which help in localization of atmospheric nitrogen provides an insight in the soil quality which greatly affects yield. Isolation of microbial DNA from paddy soil is difficult without the aid of commercial kits since cell lysis buffer cannot penetrate the micropores of clay where the anaerobes are found. In this study, a rapid and efficient extraction protocol. Using the GF-1 extraction kit (Vivantis TM, Malaysia), CTAB method and freeze-thawing protocols. Using the GF-1 kit yielded quality DNA but is not cost effective when dealing with large amount of samples. The CTAB method was not able to extract DNA while the freeze-thawing protocol has low contaminated yield. The developed method which use broken borosilicate-based laboratory glass and SDS was able to successfully isolate DNA. The optimized SDS concentration destabilized the cellular proteins which made cell lysis possible by grinding with the glass powder. To check the quality of the isolated DNA for downstream processing, the 16S ribosomal DNA region will be amplified. BLAST search of 16S amplicons shows the identities of the microbes present and reveals their biological interactions. With the help of associated bioinformatics pipelines and Canonical correspondence analysis (CCA) to ordinate the special compositions of the bacterial community to the measured soil parameters, this would contribute to the investigation of the functional capacity of the present microbial community in the paddy soil. Results may suggest how microorganisms affect crop productivity directly by modifications of their genetic material indirectly by enhancing the physico-chemical properties of the soil.

Source or Periodical Title

Philippine Journal of Crop Science

ISSN

0115-463X

Volume

43

Issue

Supplement no. 1

Page

67

Document Type

Article

Language

English

Subject

Soil composition; Soil chemistry; Rice

En – AGROVOC descriptors

SOIL MICROORGANISMS; SOIL CHEMICOPHYSICAL PROPERTIES; DNA; EXTRACTION; ISOLATION; ANALYTICAL METHODS; PADDY SOIL

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