Assessment of genetic diversity of latent bacteria in coconut leaves associated with lethal yellowing disease symptoms in Kenya

Abstract

Coconut (Cocos nucifera) is an economically important palm tree with diverse applications. However, limited scientific research exists on coconut diseases in the Kenyan coastal region. This cross‐sectional study aimed to investigate the genetic diversity of latent bacteria associated with yellowing symptoms in coconut plants along the Kenyan coast. Sixty‐two samples with symptoms were collected and their bacterial diversity assessed using culture‐independent methods. DNA was extracted from controls and symptomatic samples using the cetyl trimethyl ammonium bromide (CTAB) method. Next‐generation sequencing with Illumina MiSeq was used to profile the bacterial communities using amplicons of 16S ribosomal RNA sequences (V4 region). Sequence data were analysed using the Quantitative Insights Into Microbial Ecology 2 (QIIME 2) pipeline. A total of 113,330 reads were obtained, which clustered into 285 Operational Taxonomic Units. Bacterial diversity was highest in Kilifi, followed by Kwale and Lamu, while control samples exhibited low bacterial diversity. Actinobacteria was the predominant phylum across all counties, and Streptomyces was the most abundant genus. Kilifi and Kwale counties were more affected than Lamu. This is a pioneer study that provides insight into the bacterial diversity associated with yellowing disease symptoms in coconut plants in Kenya and will help with future elucidation of the agents causing or exacerbating coconut disease symptoms.