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Alternaria brassicicola is a successful saprophyte and necrotrophic plant pathogen. Several A. brassicicola genes have been characterized as affecting pathogenesis of Brassica species. To study regulatory mechanisms of pathogenesis, we mined 421 genes in silico encoding putative transcription factors in a machine-annotated, draft genome sequence of A. brassicicola. In this study, targeted gene disruption mutants for 117 of the transcription factor genes were produced and screened. Three of these genes were associated with pathogenesis. Disruption mutants of one gene (AbPacC) were nonpathogenic and another gene (AbVf8) caused lesions less than half the diameter of wild-type lesions. Unexpectedly, mutants of the third gene, Amr1, caused lesions with a two-fold larger diameter than the wild type and complementation mutants. Amr1 is a homolog of Cmr1, a transcription factor that regulates melanin biosynthesis in several fungi. We created gene deletion mutants of Δamr1 and characterized their phenotypes. The Δamr1 mutants used pectin as a carbon source more efficiently than the wild type, were melanin-deficient, and more sensitive to UV light and glucanase digestion. The AMR1 protein was localized in the nuclei of hyphae and in highly melanized conidia during the late stage of plant pathogenesis. RNA-seq analysis revealed that three genes in the melanin biosynthesis pathway, along with the deleted Amr1 gene, were expressed at low levels in the mutants. In contrast, many hydrolytic enzyme-coding genes were expressed at higher levels in the mutants than in the wild type during pathogenesis. The results of this study suggested that a gene important for survival in nature negatively affected virulence, probably by a less efficient use of plant cell-wall materials. We speculate that the functions of the Amr1 gene are important to the success of A. brassicicola as a competitive saprophyte and plant parasite.

Traditional cover cropping systems for nematode management seldom consider weed and soil nutrient management concurrently. Integrating cover crops suppressive to plant-parasitic nematodes with a cover crop mulching system could improve traditional approaches. Two field experiments were conducted in 2003 and 2004 to evaluate 'Tropic Sun' sunn hemp (Crotalaria juncea) and 'Iron Clay' cowpea (Vigna unguiculata) as summer cover crops and as organic mulches. Both experiments were in a 3 × 3 split-plot design in which the main plots were summer planting of sunn hemp, cowpea or fallow, and the subplots were organic mulch of sunn hemp, cowpea or no mulch. The summer cover crop was followed by turnip (Brassica rapa) and lima bean (Phaseolus lunatus) in the autumn. Using sunn hemp as organic mulch suppressed root-knot nematodes more effectively than using it as a cover crop, but only on a less susceptible host such as turnip, and not on a very susceptible host such as lima bean. While sunn hemp as a cover crop failed to enhance beneficial free-living nematodes, sunn hemp as an organic mulch enhanced bacterial-feeding nematode population densities. Sunn hemp mulch also suppressed broadleaf weeds but not grasses or nutsedges. Although sunn hemp and cowpea cover crops did not increase lima bean N and K content, their mulches increased N and K content. Similar results were observed for turnip and lima bean yields. Population density of root-knot nematodes was positively related to abundance of omnivorous nematode in 2003. The abundance of plant-parasitic nematodes was negatively related to the infestation levels of Pasteuria penetrans, and the abundance of predatory nematodes in 2004. Factors that might have affected the performance of sunn hemp on nematode communities are discussed.

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In 2013 and 2014, different mulching systems were investigated for their potential to suppress above and below ground pests, and enhance beneficial arthropods and soil health in green onion (Allium cepa) plantings. Three types of mulch systems (organic, living and solarization mulch) were evaluated and compared. Green onions were grown in four pre-plant treatments: 1) organic mulch generated by flail mowing a sunn hemp (Crotalaria juncea) cover crop (SH) followed by a no-till cropping system, 2) soil solarization (Sol), 3) sunn hemp-solarization mulch in which the sunn hemp was incorporated into the soil followed by soil solarization (SHSol), and 4) bare ground with insecticides (BG). Sol, SHSol and BG were practiced in conventional tilled system. SH (in 2013 and 2014) and SHSol (in 2014) treatments included strips of buckwheat and cowpea along the crop border to serve as living mulch or insectary plants. Green onion plants in SH had lower thrips and leaf miners damage than other treatments in both study years. When insectary borders were added to SHSol in 2014, thrips and leaf miners damages were also reduced in SHSol compared to Sol and BG. Incidence of purple blotch was reduced in SH and SHSol treatments in 2014. The SH treatment contained an increased abundance and richness of detritivores, predatory arthropods, parasitoids and beneficial free-living nematodes (particularly bacterivores and fungivores). Although weeds and initial populations of plant-parasitic nematodes were lower in solarization (Sol, SHSol) than other treatments, green onion yield was greatest in SH organic mulch systems in both study years. Overall, the integration of surface organic, living and solarization mulches into a green onion agroecosystem provided multiple ecosystem services including suppression of above and below ground pest organisms.

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