Damage to roots of Trifolium subterraneum L. (subterranean clover), failure of seedlings to establish and the presence of root pathogens during autumn-winter

Field‐based plant bioassays were employed to assess the potential for pre‐ and post‐emergence loss of seedlings and for root damage affecting Trifolium subterraneum L. (subterranean clover) during autumn–winter at 17 pasture sites across a broad agricultural area of temperate southern Australia. Between 9 and 93% (median 21%) of T. subterranean seedlings failed to emerge at the 14 locations where soil moisture was considered adequate for germination. Post‐emergence losses were lower (range 0–32%; median 7%). Moderate damage (lateral roots) to severe damage (taproots) was recorded on surviving test plants at all of the sites. Sublethal damage to pasture roots constitutes a potentially large, but underestimated cost to production because it was so widespread and because the damage occurs during autumn–winter when pasture yield limits stocking rate. Potential for the loss of Lolium rigidum × multiflorum (annual ryegrass) seedlings was also demonstrated at some of the sites. DNA assays for common root rot disease pathogens (Pythium irregulare, Phytopthora clandestina and Rhizoctonia) were used for the first time to construct cost‐effective profiles of fungal and oomycete pathogens at each site. These assays may be useful for indicating disease risks and guiding plant cultivar selection and appropriate use of pesticides. DNA assays for arbuscular mycorrhizal fungi were also used and have the potential to provide novel insights into the soil biology of farming systems.