Abstract
Rathayibacter toxicus is a gram-positive bacterium that infects the floral parts of several Poaceae species in Australia. Bacterial ooze is often produced on the surface of infected plants and bacterial galls are produced in place of seed. R. toxicus is a regulated plant pathogen in the U.S. yet reliable detection and diagnostic tools are lacking. To better understand this geographically-isolated plant pathogen, genetic variation as a function of geographic location, host species, and date of isolation was determined for isolates collected over a forty-year period. Discriminant analyses of recently collected and archived isolates using Multi-Locus Sequence Typing (MLST) and Inter-Simple Sequence Repeats (ISSR) identified three populations of R. toxicus; RT-I and RT-II from South Australia and RT-III from Western Australia. Population RT-I, detected in 2013 and 2014 from the Yorke Peninsula in South Australia, is a newly emerged population of R. toxicus not previously reported. Commonly used housekeeping genes failed to discriminate among the R. toxicus isolates. However, strategically selected and genome-dispersed MLST genes representing an array of cellular functions from chromosome replication, antibiotic resistance and biosynthetic pathways to bacterial acquired immunity were discriminative. Genetic variation among isolates within the RT-I population was less than the within-population variation for the previously reported RT-II and RT-III populations. The lower relative genetic variation within the RT-I population and its absence from sampling over the past 40 years suggest its recent emergence. RT-I was the dominant population on the Yorke Peninsula during the 2013–2014 sampling period perhaps indicating a competitive advantage over the previously detected RT-II population. The potential for introduction of this bacterial plant pathogen into new geographic areas provide a rationale for understanding the ecological and evolutionary trajectories of R. toxicus.
Highlights
Rathayibacter toxicus is a nematode-vectored, gram-positive bacterial plant pathogen with a narrow host range and a limited geographic distribution [1, 2, 3, 4, 5]
*Only DNA was available for this study **DNA sequences for these Rathayibacter species and Clavibacter michiganensis subsp. nebraskensis were retrieved from NCBI GenBank #This isolate was received from a culture collection as R. toxicus but we identified it as R. rathayi based on 16S ribosomal sequences; ABS-annual beard grass (Polypogon monspeliensis); ARG-annual ryegrass (Lolium rigidum); RG-ryegrass (Lolium sp.); LCG-lesser canary grass (Phalaris minor); PGparadoxa grass (Phalaris paradoxa); BO-black oat (Avena fatua); DG- Dactylis glomerata L
All generated sequences (R. toxicus, R. tritici, R. iranicus, R. rathayi, R. agropyri) and sequences retrieved from the NCBI GenBank nucleotide database (R. caricis, R. festucae and C. michiganensis subsp. nebraskensis) were aligned and two independent trees using NJ (Fig 2) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) methods were generated (S1 Fig; Table 1 and S1 Table)
Summary
Rathayibacter toxicus is a nematode-vectored, gram-positive bacterial plant pathogen with a narrow host range (certain species in the Poaceae, e.g., Lolium rigidum) and a limited geographic distribution (parts of Australia and South Africa) [1, 2, 3, 4, 5]. The bacterium causes a gummosis disease on L. rigidum Gaudin (annual ryegrass), Polypogon monspeliensis (L.) Desf. The decline in R. toxicus outbreaks in Australia in recent years may be due to better management of its invasive primary host, Lolium rigidum. The international trade of seed and hay of L. rigidum and other R. toxicus host species increases the risk of its movement to new geographic areas. R. toxicus was designated a U.S Select Agent in 2008 as a consequence of its ability to cause disease in plants and toxicities in animals [6]. The accuracy of molecular-based diagnostics is dependent upon the level of understanding of genetic variation in the target population
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