Abstract
The fungus Fusarium oxysporum (Fo) is widely known for causing wilt disease in over 100 different plant species. Endophytic interactions of Fo with plants are much more common, and strains pathogenic on one plant species can even be beneficial endophytes on another species. However, endophytic and beneficial interactions have been much less investigated at the molecular level, and the genetic basis that underlies endophytic versus pathogenic behavior is unknown. To investigate this, 44 Fo strains from non-cultivated Australian soils, grass roots from Spain, and tomato stems from United States were characterized genotypically by whole genome sequencing, and phenotypically by examining their ability to symptomlessly colonize tomato plants and to confer resistance against Fusarium Wilt. Comparison of the genomes of the validated endophytic Fo strains with those of 102 pathogenic strains revealed that both groups have similar genomes sizes, with similar amount of accessory DNA. However, although endophytic strains can harbor homologs of known effector genes, they have typically fewer effector gene candidates and associated non-autonomous transposons (mimps) than pathogenic strains. A pathogenic ‘lifestyle’ is associated with extended effector gene catalogs and a set of “host specific” effectors. No candidate effector genes unique to endophytic strains isolated from the same plant species were found, implying little or no host-specific adaptation. As plant-beneficial interactions were observed to be common for the tested Fo isolates, the propensity for endophytism and the ability to confer biocontrol appears to be a predominant feature of this organism. These findings allow prediction of the lifestyle of a Fo strain based on its genome sequence as a potential pathogen or as a harmless or even beneficial endophyte by determining its effectorome and mimp number.
Highlights
Until the 19th century the interior of plants was generally considered to be practically sterile
To assess the endophytic potential of this set of strains, and to see whether this potential differs between strains isolated from the same plant species and those isolated from other plant species, we tested the 40-spore-producing Fusarium oxysporum (Fo) strains for their ability to colonize tomato seedlings
Endophytism is common among Fo, but it was unclear if this lifestyle is genetically determined or depends on the presence of a susceptible host
Summary
Until the 19th century the interior of plants was generally considered to be practically sterile. Plant–microbe interactions were thought to be limited to pathogenic microorganisms causing visible disease symptoms on the plant (Fernbach, 1888; Hardoim et al, 2015). Microorganisms inhabiting plant tissues can be broadly divided into pathogens and endophytes, based on their capability to cause disease, or not, to their host. Predicting the potential influence of plant-associated microorganisms on plant performance is an important step, especially since some endophytes can provide benefits to the colonized host plant in terms of growth and/or disease protection (Rodriguez et al, 2009; Busby et al, 2016), which makes their use in agriculture highly attractive. Whether a plant–microbe interaction culminates in disease depends – among other factors – on the host. Microbes may differ in their propensity to cause disease independent of host susceptibility and environmental factors
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