Identification of Pectobacterium species isolated from the soft rot of tetecho (Neobuxbaumia tetetzo), a columnar cactus, and associated metagenomics

Neobuxbaumia tetetzo, commonly known as tetecho, is a columnar cactus endemic to Mexico. In the last 15 years, damage has been observed in young and adult plants of N. tetetzo, ranging from chlorotic spots with a wet appearance in early stages to tissue necrosis in advanced stages and finally the death of the plant; Pectobacterium brasiliense is the causal agent of the damages. Disease progression may be delayed or accelerated by the involvement of other bacteria, either pathogenic or endophytic, at the site of infection. Our goal was to confirm the presence of Pectobacterium brasiliense, in the soft rot of N. tetetzo and to determine the presence of other bacteria associated with the rot. We isolated three bacterial strains (A1, A3 and A8) from diseased tissue from three separate N. tetetzo plants, and compare them using biochemical and molecular techniques, such as whole-genome sequencing of strains A1 and A3. Phylogenetic analyzes confirmed that A1 corresponded to P. brasiliense, whereas A3 was more misimlar to P. polaris. Additionally, sequencing of 16S rRNA gene from metagenomic DNA isolated from healthy and diseased tissue of N. tetetzo indicated the presence of four operational taxonomic units (OTUs) at the order level, unique to the diseased tissue: Actinomycetales, Burkholderiales, Caulobacterales, and Sphingomonadales, with probable participation in the soft rot process.