First report of Sclerotinia minor causing soft rot of Scabiosa atropurpurea in California.

In May of 2019, Scabiosa atropurpurea samples with brown discoloration, soft rot of the crown and lower stem, with presence of white mycelium and black sclerotia (Supp. Fig. 1A, B) were collected from a 0.10 ha open field diversified cut flower production in San Luis Obispo County, CA. Approximately 30 to 40% of the scabiosa crop planted in a quarter of the field, exhibited symptoms. Symptomatic crowns and lower stems from five plants were surface disinfested by rinsing in 0.1% Tween 20, soaking in 70% ethanol for 30 s, 1% sodium hypochlorite for 2 min and sterile water. Disinfested tissue was placed in 1/10 potato dextrose agar (PDA) and incubated at 20°C (12 h photoperiod). Resulting colonies (n = 5) formed abundant white mycelia, with black sclerotia formed on the outer edge of the plates after two weeks (Suppl. Fig. 1C). Sclerotia (n = 50) had an average size of 1.6 (± 0.19) mm in diameter. Morphological identification resulted in Sclerotinia sp. (Hao et al., 2003). The pathogen was further identified by DNA extraction of two hyphal tipped isolates, followed by amplification and sequencing of the rDNA internal transcribed spacer (ITS) region, ITS1/ITS4 (White et al. 1990), calmodulin (CaM), CAL-228F/CAL-737R (Carbone and Kohn, 1999), and DNA replication licensing factor Mcm7 Mcm7-709for/Mcm7-1348rev (Schmitt et al., 2009). NCBI BLAST searches with consensus sequences for each maker revealed 99 to 100% identity with S. minor ex-types for all loci (Supp. Table 1). A maximum parsimony multilocus phylogenetic analysis clustered Californian isolates with reference strains of S. minor (Supp. Fig. 1F). Sequences were deposited in GenBank (Supp. Table 1). Pathogenicity tests were conducted with isolate CS435, which was transferred onto PDA plates and incubated at 20°C for one week. Inoculum consisted of CS435 infested PDA plugs (1 cm3). In the greenhouse, the experiment was set as a complete randomized design and observed for six weeks. Fourteen-week-old scabiosa 'Merlot Red' grown in 3.78 L pots (n = 6), were inoculated by wounding plants at 0.5 cm above the crowns with a 1 mm probe. Inoculum was placed directly on top of the wound and was secured with parafilm. Negative control plants (n = 6) were wounded as above and inoculated with PDA plugs. In experiment 1(19.4 (± 3) °C, RH 46.9), 83% of plants exhibited yellowing of the lower leaves and wilting at one week post inoculation (wpi). Symptoms progressed over time until wilting, major leaf and stem necrosis, was observed in all inoculated plants (Supp. Fig 1E, D). Plant mortality incidence at five wpi was 83%. Pathogen signs including white mycelia and black sclerotia were also observed. In experiment 2 (20.0 (± 10) °C, RH 39.6), 66% of the total plants were symptomatic at five wpi: 33% exhibited yellowing of the lower leaves and wilting, and 33% of plants died. Disease did not develop in non-inoculated plants in either experiment. S. minor was successfully reisolated from surface disinfested tissue of at least 50% (Exp. 1) and 100% (Exp. 2) of inoculated plants, yielding identical sequences to those of the inoculated isolate. S. minor is a soil-borne pathogen that infects tomato, lettuce, brassica, and sunflower crops in California. This study stablishes S. minor as a new soil-borne pathogen of Scabiosa in California. Soil-borne pathogens are a recurrent issue in the cut flower industry, characterizing new pathogens in these crops can inform crop advisors and disease diagnostician to improve disease management in the ornamental industry.

Nutrients and sediments in surface runoff water from direct-seeded rice fields: implications for nutrient budgets and water quality.

Nutrient losses from rice fields can have economic and environmental consequences. Little is known about nutrient losses in surface runoff waters from direct-seeded rice systems, which are common in the United States and increasingly more so in Asia. The objectives of this research were to quantify nutrient losses from California rice fields in surface runoff waters and to determine when and under what conditions losses are greatest. Research was conducted in 10 rice fields varying in residue (burned or incorporated) and water management over a 2-yr period. Concentrations of NH-N and NO-N in runoff water across sites, seasons, and management practices averaged <0.1 mg N L. Runoff water PO-P concentration averaged 0.14 mg L and was not affected by season or straw management practices. However, P fluxes were higher in the winter when rice straw was burned (2.59 kg ha) as opposed to incorporated (0.44 kg ha). Average seasonal runoff water K concentrations did not vary with season and straw management, although they were highest at the onset of the winter season. Average total suspended solids (TSS) concentrations did not vary by season but were highest during the winter in the straw-incorporated fields (46 mg L). Rice fields were sinks for K (4.9 kg K ha) during the growing season. Fields were not significant sources of nutrients or TSS during the growing season; however, during the winter fallow they could be sources of NH-N, P, K, and TSS, especially as water fluxes from fields increased.

Increased fitness of rice plants to abiotic stress via habitat adapted symbiosis: a strategy for mitigating impacts of climate change.

Climate change and catastrophic events have contributed to rice shortages in several regions due to decreased water availability and soil salinization. Although not adapted to salt or drought stress, two commercial rice varieties achieved tolerance to these stresses by colonizing them with Class 2 fungal endophytes isolated from plants growing across moisture and salinity gradients.Plant growth and development, water usage, ROS sensitivity and osmolytes were measured with and without stress under controlled conditions.The endophytes conferred salt, drought and cold tolerance to growth chamber and greenhouse grown plants. Endophytes reduced water consumption by 20-30% and increased growth rate, reproductive yield, and biomass of greenhouse grown plants. In the absence of stress, there was no apparent cost of the endophytes to plants, however, endophyte colonization decreased from 100% at planting to 65% compared to greenhouse plants grown under continual stress (maintained 100% colonization).These findings indicate that rice plants can exhibit enhanced stress tolerance via symbiosis with Class 2 endophytes, and suggest that symbiotic technology may be useful in mitigating impacts of climate change on other crops and expanding agricultural production onto marginal lands.

Seasonal losses of dissolved organic carbon and total dissolved solids from rice production systems in northern California.

Water quality concerns have arisen related to rice (Oryza sativa L.) field drain water, which has the potential to contribute large amounts of dissolved organic carbon (DOC) and total dissolved solids (TDS) to the Sacramento River. Field-scale losses of DOC or TDS have yet to be quantified. The objectives of this study were to evaluate the seasonal concentrations of DOC and TDS in rice field drain water and irrigation canals, quantify seasonal fluxes and flow-weighted (FW) concentrations of DOC and TDS, and determine the main drivers of DOC and TDS fluxes. Two rice fields with different straw management practices (incorporation vs. burning) were monitored at each of four locations in the Sacramento Valley. Fluxes of DOC ranged from 3.7 to 34.6 kg ha(-1) during the growing season (GS) and from 0 to 202 kg ha(-1) during the winter season (WS). Straw management had a significant interaction effect with season, as the greatest DOC concentrations were observed during winter flooding of straw incorporated fields. Fluxes and concentrations of TDS were not significantly affected by either straw management or season. Total seasonal water flux accounted for 90 and 88% of the variability in DOC flux during the GS and WS, respectively. Peak DOC concentrations occurred at the onset of drainflow; therefore, changes in irrigation management may reduce peak DOC concentrations and thereby DOC losses. However, the timing of peak DOC concentrations from rice fields suggest that rice field drainage water is not the cause of peak DOC concentrations in the Sacramento River.

Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast.

Maturation of the large subunit rRNAs includes a series of cleavages that result in removal of the internal transcribed spacer (ITS2) that separates mature 5.8S and 25/28S rRNAs. Previous work demonstrated that formation of higher order secondary structure within the assembling pre-ribosomal particle is a prerequisite for accurate and efficient pre-rRNA processing. To date, it is not clear which specific sequences or secondary structures are required for processing. Two alternative secondary structure models exist for Saccharomyces cerevisiae ITS2. Chemical and enzymatic structure probing and phylogenetic comparisons resulted in one structure (Yeh & Lee, J Mol Biol, 1990, 211:699-712) referred to here as the "hairpin model." More recently, an alternate folded structure was proposed (Joseph et al., Nucleic Acids Res, 1999, 27:4533-4540), called here the "ring model." We have used a functional genetic assay to examine the potential significance of these predicted structures in processing. Our data indicate that elements of both structural models are important in efficient processing. Mutations that prevent formation of ring-specific structures completely blocked production of mature 25S rRNA, whereas those that primarily disrupt hairpin elements resulted in reduced levels of mature product. Based on these results, we propose a dynamic conformational model for the role of ITS2 in processing: Initial formation of the ring structure may be required for essential, early events in processing complex assembly and may be followed by an induced transition to the hairpin structure that facilitates subsequent processing events. In this model, yeast ITS2 elements may provide in cis certain of the functions proposed for vertebrate U8 snoRNA acting in trans.