First report of Fusarium proliferatum causing necrotic leaf lesions and bulb rot on storage onion (Allium cepa) in southwestern Idaho.

In September 2014, a high rate of bulb rot (5-15% depending on producer) was reported across all cultivars developing early in the storage season in the onion producing region of southwestern Idaho. Spanish yellow onion bulbs cv. Vaquero displaying tan to light brown necrotic rot were obtained. The bulb rot originated in the neck and spread to successive scales (Figure 1). In August 2015, onion cv. Redwing and Vaquero were observed to have wet necrotic lesions developing on leaves in the field (Figure 2). Margins of necrotic tissue, 1-2 cm3, were excised, surface sterilized, plated on water agar medium and incubated at 24°C. Hyphal growth was sub-cultured from eight strains (A- D in 2014; E-H in 2015) to fresh potato dextrose agar to obtain pure cultures. Cultures were characteristic of Fusarium species as described by Nelson et al. (1983) with the presence of microconidia formed on polyphialides with macroconidia present. Primers ITS4-A1 and ITS5 primers (White et al. 1990); EF-1 and EF-2 (O'Donnell et al. 1998); and fRPB2-5F and fRPB2-7cR (Liu et al. 1999) were used to amplify regions of the ITS, elongation factor 1-α and the second largest subunit of DNA-directed RNA polymerase II. Amplicons were sequenced and analyzed using BLAST (https://www.ncbi.nlm.nih.gov/) and in combination using Pairwise DNA Alignment and Polyphasic Identification (http://www.westerdijkinstitute.nl/Fusarium/DefaultInfo.aspx?Page=Home) as described by O'Donnell et al. 2015. Analysis indicated that these strains are Fusarium proliferatum, which is part of the F. fujikuroi species complex (O'Donnell et al. 1998). Similarity (99.5%) was observed in pairwise analyses and the polyphasic identification clustering to representative F. proliferatum strain NRRL 22944 and others. Sequences were submitted to Genbank and registered accession numbers are found in Table 1. To complete Koch's postulates, cv. Vaquero onion bulbs were surface sterilized and injected with 3 × 105 microconidia into the shoulder of each bulb. Five bulbs were inoculated for each isolate, placed in a mesh bag, and incubated at 30°C in the dark. Five bulbs injected with sterile water and five non-inoculated bulbs served as controls. After 14 days, each bulb was sliced vertically down the center and inspected for rot. All eight strains induced tan to light brown necrotic rot symptoms in each inoculated bulb. No symptoms were observed for the water inoculated and the non-inoculated onion bulbs. A fungus was isolated from the necrotic tissue and confirmed to be F. proliferatum as described above. Ten µl aliquots containing 1 × 105 microconidia of F. proliferatum strains (C, E-H) were applied to leaves in triplicate of 12-week-old onion plants (cv. Vaquero) wounded with a 21-gauge needle. Water controls were included. Within three days lesions, with light chlorosis, began to form and quickly spread on the leaves. A fungus was isolated and confirmed to be F. proliferatum as described above. This is the first extensive description and identification of F. proliferatum causing bulb rot in storage in Idaho (Mohan et al. 1997). In addition, this is the first report of the fungus causing leaf infection in the field. These findings confirm F. proliferatum as the causal agent of the high incidence of bulb rot observed in 2014 and 2015. This bulb rot continues to occur in southwestern Idaho and since the pathogen can cause leaf infections growers are encouraged to be vigilant for both leaf lesions during the growing season and bulb rot in storage.

Feasibility of Volatile Biomarker-Based Detection of Pythium Leak in Postharvest Stored Potato Tubers Using Field Asymmetric Ion Mobility Spectrometry.

The study evaluates the suitability of a field asymmetric ion mobility spectrometry (FAIMS) system for early detection of the Pythium leak disease in potato tubers simulating bulk storage conditions. Tubers of Ranger Russet (RR) and Russet Burbank (RB) cultivars were inoculated with Pythium ultimum, the causal agent of Pythium leak (with negative control samples as well) and placed in glass jars. The headspace in sampling jars was scanned using the FAIMS system at regular intervals (in days up to 14 and 31 days for the tubers stored at 25 °C and 4 °C, respectively) to acquire ion mobility current profiles representing the volatile organic compounds (VOCs). Principal component analysis plots revealed that VOCs ion peak profiles specific to Pythium ultimum were detected for the cultivars as early as one day after inoculation (DAI) at room temperature storage condition, while delayed detection was observed for tubers stored at 4 °C (RR: 5th DAI and RB: 10th DAI), possibly due to a slower disease progression at a lower temperature. There was also some overlap between control and inoculated samples at a lower temperature, which could be because of the limited volatile release. Additionally, data suggested that the RB cultivar might be less susceptible to Pythium ultimum under reduced temperature storage conditions. Disease symptom-specific critical compensation voltage (CV) and dispersion field (DF) from FAIMS responses were in the ranges of -0.58 to -2.97 V and 30-84% for the tubers stored at room temperature, and -0.31 to -2.97 V and 28-90% for reduced temperature, respectively. The ion current intensities at -1.31 V CV and 74% DF showed distinctive temporal progression associated with healthy control and infected tuber samples.

Identification of volatile biomarkers for high-throughput sensing of soft rot and Pythium leak diseases in stored potatoes.

Soft rot and Pythium leak are postharvest storage diseases of potato tubers that can cause substantial crop losses in the US. This study focused on detecting volatile organic compounds (VOCs) associated with rot inoculated tubers during storage (up to 21 days) using headspace solid-phase microextraction (SPME) coupled to gas chromatography (GC) with mass spectrometry (MS) and flame ionization detector (FID) analysis. Russet Burbank and Ranger Russet tubers were inoculated with the rot pathogens. Static sampling with 50 min trapping time followed by GC-MS and GC-FID analysis identified 23 and 30 common VOCs from the pathogen inoculated tubers. Overall, n,n-dimethylmethylamine, acetone, 1-undecene, and styrene, occurred frequently and repeatability in inoculated samples based on GC-MS analysis, with the latter two found using GC-FID analysis as well. Identification of such biomarkers can be useful in developing high-throughput VOC sensing systems for early disease detection in potato storage facilities.

Complete genome of the switchgrass endophyte Enterobacter clocace P101.

The Enterobacter cloacae complex is genetically very diverse. The increasing number of complete genomic sequences of E. cloacae is helping to determine the exact relationship among members of the complex. E. cloacae P101 is an endophyte of switchgrass (Panicum virgatum) and is closely related to other E. cloacae strains isolated from plants. The P101 genome consists of a 5,369,929 bp chromosome. The chromosome has 5,164 protein-coding regions, 100 tRNA sequences, and 8 rRNA operons.