Phosphorus is one of three macronutrients limiting plant growth in natural soils. For efficient phosphate uptake from soil, plants get help from root-associated fungi such as arbuscular mycorrhizal fungi and the root endophyte Colletotrichum tofieldiae. Plants have also developed a phosphate starvation response (PSR) system that senses phosphate starvation and increases phosphate uptake. In this review, we discuss how these two root-associated beneficial fungi contribute to plant growth in phosphate-starvation conditions. We also discuss how the plant PSR system regulates beneficial fungi via the regulation of tryptophan-derived secondary metabolites of the plant.

To understand the diversity of nonfluorescent isolates of the tomato pith necrosis pathogens distributed in Japan, we used a polyphasic approach to analyze 21 isolates, obtained from eight prefectures (Iwate, Miyagi, Tochigi, Saitama, Chiba, Shizuoka, Ishikawa, and Oita) between 1980 and 2002. All isolates were demonstrated to reproduce the typical pith necrosis symptoms on tomato after inoculation of stems, and no significant differences in symptoms and virulence were found among the isolates. They were gram-negative, aerobic rods with one to three polar flagella, and did not produce fluorescent pigments on King’s B medium. On the other hand, in the phylogenetic tree based on the concatenated sequences of the 16S rRNA gene and rpoD and in the dendrogram based on a MALDI-TOF MS analysis using the Bruker MALDI Biotyper system, these isolates and reference strains were classified into the following three groups: Group 1 (six isolates and the type strain of Pseudomonas corrugata [Pc]), Group 2 (seven isolates and the type strain of P. mediterranea [Pm]), and Group 3 (eight isolates). Group 1 and Group 2 were identified as Pc and Pm, respectively, based on biochemical and physiological characterizations and PCR assays using species-specific primer sets designed in this study. To our knowledge, this report is the first in Japan of domestic isolates identified as Pm. On the other hand, Group 3 formed a monophyletic clade separated from Pc and Pm in the phylogenetic analysis, utilized 2-ketogluconate and d-aspartic acid, did not utilize meso-tartrate and histamine, and gave different PCR results from Pc and Pm, suggesting that it might represent a novel taxon (new species, or new subspecies of Pc or Pm). Therefore, we propose the tentative treatment of Group 3 as “Pseudomonas sp.” and to add Pm and Pseudomonas sp. as new causal agents of tomato pith necrosis disease in Japan. Pm and Pseudomonas sp. (Group 3), together with Pc, may have been involved in the outbreak of this disease in Japan from the outset, but there is no information on their origins or the history of their invasion in Japan. Thus, we need to establish reliable detection methods based on the results obtained in this study to clarify the origins, ecology and distribution of these three pathogens responsible for this disease.

Recently, a heavy outbreak of Japanese pear rust caused by Gymnosporangium asiaticum developed in Fukuoka Prefecture, Japan. We carried out a retrospective cohort study of commercial orchards in Yame region to analyze the reason. Among the factors investigated, the use of non-sterol-demethylation-inhibitor (non-DMI) fungicides was only related to extent of disease severity in 2013 and disease incidence in 2014. However, DMI fungicides did not control rust well. These results suggested the possibility that DMI fungicide resistance developed in G. asiaticum populations there. Furthermore, our results indicated that retrospective cohort study is useful for the analysis of occurrence factors on plant diseases.