Revised 02/2015; Originally published: 2000. / The most important disease of woody dicotyledonous plants in Arizona is Phymatotrichopsis root rot (Cotton or Texas root rot) caused by a unique and widely distributed soil-borne fungus, Phymatotrichopsis omnivora. The fungus is indigenous to the alkaline, low-organic matter soils of the southwestern United States and central and northern Mexico.

The overall goal of this research is to develop ground-based technologies for disease detection and mapping which can maximize the effectiveness and efficiency of cotton root rot (CRR) treatments. Accurately mapping CRR could facilitate a much more economical solution than treating entire fields. Three cotton fields around CRR-prone areas of Texas have been the sites for three years of data collection. A complete soil apparent electrical conductivity (ECa) survey was conducted for each field with an EM38DD sensor. Multiple linear regression was used to relate physical and chemical soil properties to the ECa values obtained from the EM38DD. The variability in soil ECa measurements can be best accounted for using calcium carbonate levels as well as clay and sand contents in the soil. T-tests were used to determine that soil pH, clay, sand, and inorganic carbon content were significantly related to CRR incidence as determined by aerial images of each location. Spectral data were obtained for freshly picked cotton leaves from healthy, disease-stressed, and dying or dead plants using an ASD VisNIR spectroradiometer. The leaf spectra were evaluated using linear discriminant analysis (LDA), the receiver operator characteristic, and wavelet analysis to relate them to classifications of infection level. It was determined that healthy and infected leaves can be correctly classified 85% of the time based on the spectral data. The results from this study suggest that differences in soil characteristics may not be pronounced enough to accurately map CRR in the soil; however, the precision treatment of CRR may possible using an optoelectronic sensor to diagnose infected plants based on leaf reflectance.

The meals from many oilseed crops contain biocidal chemicals that are known to inhibit the growth and activity of several soil pathogens, though little is known concerning impacts on whole soil microbial communities. We investigated the effect of oilseed meals (SMs) from both brassicaceous plants, including mustard and camelina, as well as non-brassicaceous plants, including jatropha and flax, on P. omnivora (the casual agent of cotton root rot) in Branyon clay soil (at 1 and 5% application rates). We also investigated the effect of SMs from camelina, jatropha, flax, and wheat straw on microbial communities in Weswood loam soil. We also used four types of isothiocyanates (ITCs) including allyl, butyl, phenyl, and benzyl ITC to test their effects on P. omnivora growth on potato dextrose agar (PDA), as well as on soil microbial communities in a microcosm study. Community qPCR assays were used to evaluate relative abundances of soil microbial populations. Soil microbial community composition was determined through tag-pyrosequencing using 454 GS FLX titanium technology, targeting ITS and 16S rRNA gene regions for fungal and bacterial communities, respectively. The results showed that all tested brassicaceous and jatropha SMs were able to inhibit P. omnivora sclerotial germination and hyphal growth, with mustard SM being the most effective. Flax didn't show any inhibitory effects on sclerotial germination. All tested ITCs inhibited P. omnivora OKAlf8 hyphal growth, and the level of inhibition varied with concentration and ITC type. Total soil fungal populations were reduced by ITC addition, and microbial community compositions were changed following SM and ITC application. These changes varied according to the type of SM or ITC added. Our results indicated that SMs of several brassicaceous species as well as jatropha may have potential for reducing cotton root rot as well as some other pathogens. Different SMs releasing varied ITCs may result in differential impacts on soil microorganisms including some pathogens.