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ItemRoot and collar rot pathogens associated with yield decline of processing tomatoes in Victoria, AustraliaCallaghan, Sophia ( 2020)The processing tomato industry in Victoria, Australia, has experienced a yield decline over the last decade, resulting in losses estimated at 10% per annum. The decline was attributed to the necrosis of lateral and feeder rootlets and the collar region resulting in plant stunting and a reduction in fruit production. Therefore, the hypothesis underlying this study was that the decline is caused by the cumulative effects of damage by a complex of soil-borne root and collar rot pathogens. Surveys of processing tomato crops were undertaken over three consecutive growing seasons between 2016 and 2019 to investigate the pathogens, symptoms and diseases associated with yield decline. Soil-borne fungal and oomycete pathogens were the focus but bacterial pathogens, viruses, nematodes and phytoplasmas were also noted. Systematic isolation from diseased roots and the collar region of plants putatively infected by fungal and oomycete pathogens was undertaken. Identification of isolates was based on cultural morphology, ITS sequencing and in some cases commercial qPCR testing. Fusarium oxysporum and Pythium spp. were the most abundant putative pathogens associated with plants exhibiting poor growth. Other putative pathogenic fungi and oomycetes which were less commonly encountered included Alternaria spp., Colletotrichum coccodes, Fusarium solani, Phytophthora nictotianae, Phytophthora cajani, Plectosphaerella spp., Rhizoctonia solani, Sclerotinia minor and S. sclerotiorum. A novel Fusarium collar and root rot disease of processing tomatoes was discovered during the surveys. The disease was characterised by chocolate-brown streaking in the internal collar and tap root tissue, as well as lateral root rot of stunted tomato plants. Morphological characterisation and multi-loci phylogenetics (ITS, ef1a and Pgx4), were used to identify the causal pathogen as Fusarium oxysporum. The disease was initially thought to resemble Fusarium Crown and Root Rot (FCRR) caused by Fusarium oxysporum f. sp. radicis-lycopersici (Forl), a disease which has not been reported in Australia. However, subsequent pathogenicity and physiological assessments of isolates suggested the disease was caused by a novel Fusarium pathogen. Consequently, this disease was named chocolate streak disease (CSD) to differentiate it from FCRR. Pythium was the second most abundant organism isolated during the surveys. As Pythium is a large genus consisting of species beneficial, neutral and detrimental to plant growth, further investigation was required to understand the impact of Pythium spp. on processing tomato growth and yield. Eleven species of Pythium were identified based on cultural characteristics and phylogenetic analysis using ITS, Cox-1 and Cox-2 gene sequences. None of these Pythium species had been reported previously from processing or table tomatoes in Australia. In addition, this is the first report of P. carolinianum, P. heterothallicum, P. recalcitrans and a new Pythium sp. from field-grown tomato crops globally. Pythium dissotocum was the most abundant and widespread species. Pythium ultimum, P. aphanidermatum and P. irregulare were the most aggressive towards both seedlings and mature plants, causing pre- and post-germination damping-off, severe root rot and stunting. Collectively, the evidence provided by this study supports the hypothesis that a complex of root and collar rot pathogens, particularly F. oxypsporum and Pythium spp., are contributing to the 10% yield loss in Victorian processing tomatoes.