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Contrasting genetic diversity of listeria pathogenicity islands 3 and 4 harbored by non-pathogenic listeria spp.
Full text linkListeria monocytogenes causes the severe foodborne disease listeriosis. Several clonal groups of L. monocytogenes possess the pathogenicity islands Listeria pathogenicity island 3 (LIPI-3) and LIPI-4. Here, we investigated the prevalence and genetic diversity of LIPI-3 and LIPI-4 among 63 strains of seven non-pathogenic Listeria species from the natural environment (i.e., wildlife and surface waters). Analysis of the whole genome sequence data suggested that both islands were horizontally acquired but differed considerably in their incidence and genetic diversity. LIPI-3 was identified among half of the Listeria innocua strains in the same genomic location as Listeria monocytogenes (guaA hotspot) in a truncated form with only three strains harboring full-length LIPI-3, and a highly divergent partial LIPI-3 was observed in three Listeria seeligeri strains, outside the guaA hotspot. Premature stop codons (PMSCs) and frameshifts were frequently noted in the LIPI-3 gene encoding listeriolysin S. On the other hand, full-length LIPI-4 without any PMSCs was found in all Listeria innocua strains, in the same genomic location as L. monocytogenes and with ~85% similarity to the L. monocytogenes counterpart. Our study provides intriguing examples of genetic changes that pathogenicity islands may undergo in non-pathogenic bacterial species, potentially in response to environmental pressures that promote either maintenance or degeneration of the islands. Investigations of the roles that LIPI-3 and LIPI-4 play in non-pathogenic Listeria species are warranted to further understand the differential evolution of genetic elements in pathogenic versus non-pathogenic hosts of the same genus
Beet leafhopper and BCTV strain survey 2022 progress report
Full text linkAt the request of a sugar beet industry stakeholder, beet leafhopper (BLH) populations in southern Idaho were tracked during the 2020 (4 counties) and 2021 (5 counties) growing seasons in desert areas and sugar beet and dry bean fields in southern Idaho. Samples were collected on a weekly basis from mid-April through mid-September to assess all leafhoppers for population levels and the presence of Beet curly top virus (BCTV) strains. Crop plants from monitored fields were also assessed for the presence of BCTV strains. Once BLH populations in Elmore Co. began increasing in May, they were present in at least double-digit numbers through most of the summer at all sites both years. Thus, BLH numbers at desert sites in other areas were at or near zero, except for Owyhee Co. in 2021 late in the summer. Local weed populations appeared to be the primary source of BLH in crop fields and not desert sites. Two haplotypes (based on cytochrome oxidase gene) dominated the BLH population both years and were present in all areas of southern Idaho. Over the 22-week collection period, the horizontal card averaged 45 to 75% fewer BLH than the vertical card indicating vertical card placement is preferable. In 2020, 42% of the BLH samples were positive for the BCTV coat protein gene and in 2021 67% of the samples were positive. The Worland strain of BCTV was dominant both years in the BLH population, but the BCTV strains found in the plant samples were more of a mix. Phytoplasma has been detected in a few BLH samples, but all plant samples tested to date have been negative. Once all data are collected, the project will establish the BCTV strains for which host plant resistance is needed and the best time for when control of BLH is necessary
Beet curly top resistance in USDA-ARS Plant Introduction lines, 2022.
Full text linkCurly top symptom development was uniform and no other disease problems were evident in the plot area. The resistant and susceptible checks performed as expected for the visual ratings. Statistically, 12 of the entries contain at least some minor resistance since their visual ratings were significantly lower than those for both susceptible checks. Nine entries from the USDA-ARS Utah sugar beet program that were donated to the NPGS in 1983 (3, 4, 5, 6, 7, 8, 9, 10, and 14) were not significantly different from the resistant check. All nine of these entries were statistically more resistant than both susceptible check lines. An additional two entries from the USDA-ARS Utah sugar beet program (NSL 183366 and NSL 183511) and one Beta vulgaris spp. maritima accession collected by USDA-ARS researchers in Morocco (W6 44508) were statistically more resistant than the susceptible sugar beet check SV2012RR, but had statistically higher curly top ratings than the resistant check. These entries along with entries with similar levels of resistance from prior years evaluations will be retested and, if resistance is confirmed, these lines will be considered for incorporation into the USDA-ARS germplasm improvement program as a source of resistance to BCTV
Kimberly sugar beet germplasm evaluated for rhizomania and storage rot resistance in Idaho, 2022
Full text linkRhizomania caused by Beet necrotic yellow vein virus (BNYVV) and storage losses are serious sugar beet production problems. To identify sugar beet germplasm lines with resistance to BNYVV and storage rots, seven Beta vulgaris lines and five check cultivars were screened. The lines were grown in a sugar beet field infested with BNYVV during the 2022 growing season in a randomized complete block design with 6 replications. At harvest on 12 October, roots were dug and evaluated for rhizomania symptoms and then placed in an indoor commercial sugar beet storage building. After 152 days in storage, samples were evaluated for the percentage of root surface area covered by fungal growth or rot. Rhizomania symptom development in the field was uniform and other disease problems were not evident in the plot area. The BNYVV susceptible sugar and red beet checks both had 100% foliar symptoms and a high root disease severity ratings. The resistant check with two resistance genes, Rz1 + Rz2 (check 3), had no foliar symptoms and low root rating. The resistant checks with only one resistance gene had foliar symptoms ranging from 0 to 8%, but their root ratings were still within an acceptable range. Foliar symptoms indicate single gene resistance for BNYVV is becoming marginal. Based on the root ratings, all entries had some level of BNYVV resistance since they were all better than the susceptible checks. Entry 3 (KEMS12; PI672570) had a level of BNYVV resistance similar to resistant checks based on both foliar and root ratings. Although entries 1, 2, 6, and 7 all had poor foliar ratings, their root ratings were better than those for the susceptible checks. Both entries 1 (KEMS09) and 3 were described as containing some rhizomania resistance in their release notes, but entry 1 appears to have lost some of its resistance, while entry 3 remains resistant. All the entries had some resistance to fungal rots in storage, but only entry 3 performed well for all three variables. Thus, some entries will serve as genetic sources for identifying additional resistance to BNYVV and storage rots, which will aid the sugar beet industry in improving sucrose yield and retention in commercial sugar beet cultivars
Growing and non-growing season nitrous oxide emissions from manured soil under irrigation
Full text linkDairy manure is used in semiarid southern Idaho to improve soil fertility, but campaigns to measure resulting nitrous oxide (N2O) emissions over the complete year have not been conducted to date. The objective of this study was to measure N2O fluxes throughout the growing and non-growing seasons in 2020 (sugar beet) and 2021 (corn silage) in a field that received inorganic N fertilizer or was previously treated with dairy manure solids on an annual and biennial basis for 8 years. Gas fluxes were measured daily using automated chambers that were connected to a gas chromatograph for in situ analysis of N2O. The N2O emissions were found to be highly episodic and major pulses were associated with freeze-thaw events in the winter, irrigation events during the growing season, and soil disturbance at harvest. Emissions were greatest from soil that had received manure at the highest annual application rate of 52 Mg/ha (dry wt.), with cumulative totals of 3.6 and 3.0 kg N2O-N/ha in 2020 and 2021, respectively. These cumulative totals were about 3-fold greater than emissions from plots treated with inorganic fertilizer or manure at 17 Mg/ha annually or 35 Mg/ha biennially. This outcome can be attributed to high concentrations of nitrate produced through mineralization of organic N in manure. Emission factors indicated that 0.6 to 0.9% of the total N applied was lost as N2O-N over the two years. When breaking down the emissions by season, anywhere from 49 to 63% (2020) and 37 to 58% (2021) of the N2O-N emissions occurred during the non-growing season. Cumulative growing and non-growing season N2O emissions were found to be statistically equivalent in the inorganic fertilizer and manure treatments. This finding stresses the need to also measure N2O emissions during the non-growing season as a way to improve the accuracy of annual emission estimates
A crop water stress index based internet of things decision support system for precision irrigation of wine grape
Full text linkThe goal of irrigation for wine grape grown in arid or semiarid regions is to sustain vine survival and to optimize berry attributes for quality wine production. Precision irrigation of wine grape is hindered by the lack of a smart, decision support system (DSS) to remotely monitor vine water status. The objectives of this study were to: develop and field test an Internet of Things (IoT) DSS system for precision irrigation of wine grape. The IoT system was comprised of a suite of insitu sensors used to monitor real-time weather conditions, grapevine canopy temperature, soil moisture, and irrigation amount. Sensor data were collected and stored on a field deployed data logger that calculated a daily thermal Crop Water Stress Index (CWSI) for grapevine using a neural network model with real-time sensor data model inputs. The data logger also hosted, via a cellular modem, webpages showing a running, 12-day history of daily CWSI, fraction of available soil moisture (fASW), irrigation amount, and other sensor data. The webpages were accessible to vineyard managers via cell phone or computer. The CWSI based IoT DDS system was installed at two small acreage, commercial estate vineyards in southwestern Idaho USA over four growing seasons. At each vineyard site, the DSS was used daily by the vineyard irrigation manager to schedule irrigation events. Neither vineyard manager used any other quantitative vine water status monitoring tool for irrigation management decisions. The midday leaf water potential (LWP) of grapevines was routinely measured by research project personnel. Data collected over the study period at each vineyard showed a significant (p < 0.001) correlation with LWP and fASW, providing evidence that, under the conditions of this study, the daily CWSI based IoT provided automated, remote monitoring of vine water status. Both vineyard managers reported daily use of the DSS for irrigation scheduling decisions. Over the four-year study, each vineyard manager was able to maintain consistent seasonal average CWSI daily values and irrigation application amounts, despite yearly differences in climatic conditions. The results of this study demonstrate that a CWSI based IoT DSS can be used for precision irrigation of wine grape in a commercial vineyard under semiarid growing conditions
Regulatory roles of small non-coding RNAs in sugar beet resistance against beet curly top virus
Full text linkBeet curly top virus (BCTV) mediated yield loss in sugar beets is a major problem worldwide. The circular single-stranded DNA virus is transmitted by the beet leafhopper. Genetic sources of BCTV resistance in sugar beet are limited and commercial cultivars rely on chemical treatments versus durable genetic resistance. Phenotypic selection and double haploid production have resulted in sugar beet germplasm (KDH13-13 and KDH4-9-4) that are highly resistant to BCTV. The molecular mechanism of resistance to the virus is unknown, especially the role of small noncoding RNAs (sncRNAs) during early plant-viral interaction. Using the resistant lines along with a susceptible line (KDH19-17; 19), we demonstrate the role of sugar beet miRNAs in BCTV resistance during early infection stages when symptoms are not yet visible. The differentially expressed miRNAs altered the expression of their corresponding target genes such as pyruvate dehydrogenase (EL10Ac1g02046), carboxylesterase (EL10Ac1g01087), serine/threonine protein phosphatase (EL10Ac1g01374), and LRR receptor-like (EL10Ac7g17778), that were highly expressed in the resistant lines versus susceptible lines. Pathway enrichment analysis of the miRNA target genes showed an enrichment of genes involved in glycolysis/gluconeogenesis, galactose metabolism, starch, and sucrose metabolism to name a few. Carbohydrate analysis revealed altered glucose, galactose, fructose, and sucrose concentration in the infected leaves of resistant versus susceptible lines. We also demonstrate differential regulation of BCTV derived sncRNAs in the resistant versus susceptible lines that target sugar beet genes such as LRR (EL10Ac1g01206), 7-deoxyloganetic acid glucosyltransferase (EL10Ac5g12605), and transmembrane emp24 domain containing (EL10Ac6g14074) and altered their expression. In response to viral infection, we found that plant derived miRNAs targeted BCTV capsid protein/replication related genes and showed differences in expression among resistant and susceptible lines. The data presented here demonstrate the contribution of miRNA mediated regulation of metabolic pathways and cross-kingdom RNAi in sugar beet BCTV resistance
Foliar insecticides for the control of curly top in Idaho sugar beet, 2021
Full text linkCurly top caused by Beet curly top virus (BCTV) is a widespread disease problem vectored by the beet leafhopper in semiarid sugar beet production areas. Host resistance is the primary defense against this problem, but resistance in commercial cultivars is only low to intermediate. The neonicotionoid seed treatments currently supplement this resistance to provide early season control. In order to identify other management options seven foliar insecticides were screened in 2021 on a commercial sugar beet cultivar approved for production. The plots were arranged in a randomized complete block design with eight replications. A curly top epiphytotic was created by releasing six viruliferous beet leafhoppers per plant at the eight-leaf growth stage on 22 June. Foliar symptoms were evaluated on 10 August and 10 September using a scale of 0-9 (0 = healthy and 9 = dead). Curly top symptom development was uniform and no other disease problems were evident in the plot area. The disease pressure in the test was severe with good symptom development in the non-treated check. Two treatments (Poncho Beta seed treatment and the Scorpion foliar treatment) provided a similar level of control on the second rating and had similar root yield and ERS. The Applaud foliar treatment provided less control based on ratings, but ERS was not significantly different from the Poncho Beta and Scorpion treatments. The foliar insecticide treatments containing Asana or Spear T provided marginal control of BCTV, but these treatments were better than the non-treated check in foliar ratings, root yield, and ERS. The Venom and Ninja + Asana treatments also showed higher root yield and ERS relative to the non-treated check. The remaining treatments were similar to or worse than the non-treated check with respect to sucrose, root yield, and ERS. These data show that sugar beet production in areas with curly top would likely suffer considerably without the neonicotinoid seed treatments and the supplemental foliar treatments
Beet leafhopper and BCTV strain survey 2021 progress report
Full text linkAt the request of a sugar beet industry stakeholder, beet leafhopper (BLH) populations in southern Idaho were tracked during the 2020 (4 counties) and 2021 (5 counties) growing seasons in desert areas and sugar beet and dry bean fields in southern Idaho. Samples were collected on a weekly basis from mid-April through mid-September to assess all leafhoppers for population levels and the presence of Beet curly top virus (BCTV) strains. Crop plants from monitored fields were also assessed for the presence of BCTV strains. Elmore Co. had green plants in the desert coming out of the winter and through the summer the past two years. Once BLH populations in Elmore Co. began increasing in May, they were present in at least double-digit numbers through most of the summer at all sites both years. Coming out of the winter, the desert sites in Minidoka Co. both years, Twin Falls Co. in 2020, and Owyhee Co. in 2021 were dry and had no green plants. At the 2021 Twin Falls desert site, the only live vegetation was sagebrush. Thus, BLH numbers at these desert sites were at or near zero. Local weed populations appeared to be the primary source of BLH in crop fields in these counties. Preliminary data suggest two haplotypes (based on cytochrome oxidase gene) dominate the BLH population. Over the 22-week collection period, the horizontal card averaged 45 to 75% fewer BLH than the vertical card indicating vertical card placement is preferrable. In 2020, 42% of the BLH samples were positive for the BCTV coat protein and Worland was found to be the dominant strain of BCTV. The phytoplasma, morphotyping, and 2021 BCTV strain identifications are currently a work in progress. Once all data are collected, the project will establish the BCTV strains for which host plant resistance is needed and the best time for when control of BLH is necessary
Model for calculating ammonia emission from stored animal liquid manure
Full text linkNational inventories calculate ammonia emission from livestock manure using static emission factors. These do not account for local environmental condition, management practice or variation in manure composition. We present a model that estimates emission from liquid manure per area and time as related to slurry composition, temperature and surface covers. Data was extracted from articles and used to parameterize and validate the model, and the scenario calculations demonstrate the usefulness of the model