Current Classification of the Bacillus pumilus Group Species, the Rubber-Pathogenic Bacteria Causing Trunk Bulges Disease in Malaysia as Assessed by MLSA and Multi rep-PCR Approaches

Abstract

Bacillus pumilus is the causal agent of trunk bulges disease affecting rubber and rubberwood quality and yield production. In this study, B. pumilus and other closely related species were included in B. pumilus group, as they shared over 99.5% similarity from 16S rRNA analysis. Multilocus sequence analysis (MLSA) of five housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using REP, ERIC, and BOX primers conducted to analyze the diversity and systematic relationships of 20 isolates of B. pumilus group from four rubber tree plantations in Peninsular Malaysia (Serdang, Tanah Merah, Baling, and Rawang). Multi rep-PCR results revealed the genetic profiling among the B. pumilus group isolates, while MLSA results showed 98-100% similarity across the 20 isolates of B. pumilus group species. These 20 isolates, formerly established as B. pumilus , were found not to be grouped with B. pumilus . However, being distributed within distinctive groups of the B. pumilus group comprising of two clusters, A and B. Cluster A contained of 17 isolates close to B. altitudinis , whereas Cluster B consisted of three isolates attributed to B. safensis . This is the first MLSA and rep-PCR study on B. pumilus group, which provides an in-depth understanding of the diversity of these rubber-pathogenic isolates in Malaysia.

Genetic Divergence and Population Structure of Xanthomonas albilineans Strains Infecting Saccharum spp. Hybrid and Saccharum officinarum

“…Subsequently, rep-PCR fingerprinting was employed to amplify highly conserved repetitive sequences that are generally distributed in the bacterial genome to disclose diversity among the strain genomes [ 24 , 31 ]. The advantages of rep-PCR are a simple and fast operation, rich amplification bands, and an absence of strain-specific DNA probes [ 24 , 32 ]. Additionally, REP, ERIC, and BOX sequences for rep-PCR are frequently used in polymorphism analysis of bacteria to evaluate strain diversity [ 31 , 33 ].…”

“…For example, four strains from Group I (XaCN14 and XaCN17) and II (XaCN45 and XaCN55), identified by MLSA, were separated into four unique groups by rep-PCR fingerprinting. However, MLSA generates a discrete dataset based on the nucleotide sequences of known genes and allows for the accurate calculation of genetic distances compared to rep-PCR [ 32 ].…”

Short Communication: Genetic diversity of walnut blight-associated bacteria from China using rep-PCR

“…The polymorphisms of these conserved genetic elements can be used to differentiate sequences at a strain, species, or genus level, i.e. Bacillus pumilus group classification recently (Husni et al 2021). Species-specific REPs have been identified in many animal and plant-associated bacteria already (Hossain et al 2022;Mirzaei et al 2021).…”