IDENTIFIKASI MOLEKULER DAN REKONSTRUKSI HUBUNGAN FILOGENETIK ISOLAT ACTINOMYCETES ASAL RIZOSFER BAWANG MERAH

Abstract

Actinomycetes are filamentous bacteria with high taxonomic and genetic diversity and are widely distributed in soil ecosystems, including plant rhizospheres. Phenotypic characterization alone may not provide sufficient taxonomic resolution; therefore, molecular approaches are required. This study aimed to molecularly identify and analyze the phylogenetic relationships of six Actinomycetes isolates obtained from shallot rhizosphere, namely E3S1, R1L3, R2L5, E5S5, R2S2, and E1M1. The analysis involved genomic DNA extraction, 16S rRNA gene amplification, sequencing, BLASTn analysis, sequence alignment, and phylogenetic reconstruction using the Maximum Likelihood method. DNA concentrations ranged from 57.6 to 82.5 ng/µL, with A260/A280 ratios of 1.76–1.88. PCR products ranged from 1,405 to 1,438 bp, whereas cleaned sequences ranged from 1,348 to 1,384 bp. BLASTn analysis showed 98.91–99.64% sequence similarity with reference Actinomycetes sequences. Phylogenetic reconstruction indicated that the six isolates were distributed among several related groups. These findings provide an initial molecular overview of Actinomycetes diversity associated with shallot rhizosphere and establish a basis for further multilocus or genome-based analyses.