Isolation of bacterial dna from rhizophere of selected gesneriaceae plants

This study aimed to isolate and analyze bacterial DNA found in the rhizosphere of three plant species from the Gesneriaceae family which is Cytandra cupulata Ridl., Codonoboea rugosa, and Cytandra sp. in the Sungai Tiang area, Royal Belum, Perak. The rhizosphere refers to the soil layer inhabited by plant roots. This study aimed to determine the best method for extracting bacterial DNA from rhizosphere soil. To do this, the study used two distinct techniques to assess the quantity and quality of DNA extracted: the spin-column approach (MACHEREY-NAGEL NucleoSpin® Soil kit, Germany) and the traditional method (bead beating). Samples of rhizosphere soil were gathered from Sg. Papan, Sg. Kejar, and Sg. Kenarong, three distinct localities. The Faculty of Earth Science's Microbiology Laboratory served as the site for the DNA extraction procedure. The integrity of the collected DNA was also assessed using agarose gel electrophoresis, and a Nanodrop spectrophotometer was utilised at Biology Laboratory 1 of the Faculty of Agro-based Industry to determine the purity of the DNA. The results of the study showed that the spin-column (NucleoSpin® Soil kit MACHEREY-NAGEL, Germany), protocol kit method was more effective in producing high quality DNA, with A260/A280 values in the range of 1.8–2.0 and clearer DNA bands on agarose gel. Therefore, the conventional method showed inconsistent purity values and possible contamination or degradation of DNA, with negative DNA concentration and unrealistic A260/A280 purity ratio (up to 28.09), indicating contamination or interference of the reading. These results show that the spectrophotometer readings are being interfered with, most likely because of substantial contamination from substances like Tris-EDTA or partially removed organic soil components. This study shows that the bacterial community in the rhizosphere of Gesneriaceae plants can be studied metagenomically. Therefore, it is advisable to use the spin-column (NucleoSpin® Soil kit MACHEREY-NAGEL, Germany), protocol kit method to extract bacterial DNA for soil biodiversity studies. This is because a deeper understanding of the role of microbes in ensuring fertile soil and sustainable agriculture will increase.