Beta vulgaris lines from USDA-ARS Kimberly evaluated for resistance to Cercospora beticola, 2016

In 2016, six sugar beet (Beta vulgaris L.) germplasm lines from the USDA-ARS Kimberly program and 2 check lines [EL50/2 (resistant) and F1042 (susceptible)] were screened for resistance to Cercospora beticola. The Cercospora leaf spot (CLS) evaluation was conducted at the Michigan State University Saginaw Valley Research and Extension Center (SVREC) near Frankenmuth, MI in a field that had been planted in wheat with clover underseeded in 2015. The germplasm was planted on 6 May and thinned by hand as necessary. Single-row plots 4.5 m long with 51 cm between row spacing were planted with the treatments arranged in a randomized complete block design with four replications. Quadris 2.08SC (azoxystrobin) was applied at 0.0091 kg/100 m row in a 14 cm band in-furrow at planting to control Rhizoctonia damping-off. Weeds were controlled by a preplant application of ethofumesate 9 May, four times with mixtures of phenmedipham, desmedipham, triflusulfuron methyl, and clopyralid (18 and 23 May, 10 Jun., and 21 Jun), and once with S-metolachlor (29 Jun). The herbicide spray treatments had to also be supplemented with hand weeding. The nursery was spray inoculated on 5 Jul. with a liquid spore suspension (1 x 103 spores/ml) of C. beticola. The inoculum was produced from a mixture of leaves collected from the 2015 CLS nursery at SVREC and from naturally infected sugar beets grown at SVREC and on the Michigan State University campus farms in East Lansing, MI. The plots were rated for foliar symptom development on 6 Sep. using a scale of 0 to 10 (0 = healthy and 10 = all leaves dead; J. Am. Soc. Sugar Technol. 16:284). Data were rank transformed prior to analysis in SAS (Ver. 9.4) with mixed linear models (Proc MIXED), but the non-transformed means have been presented in the table. Mean separation was based on a PDIFF comparison with a probability cutoff of 0.05. Cercospora leaf spot development was uniform and moderate and other disease and pest problems were evident in the plot area. The checks performed as expected for the visual rating. Statistically, five of the entries contain at least moderate resistance since their visual ratings were at least as good as the moderate and resistant checks. However, entry 3 was better than the resistant check and entries 4, 5, and 6 were equal to the resistant check. These data confirm what had been determined the previous year, so these lines will be incorporated into the USDA-ARS germplasm improvement program as a source of resistance to CLS

Beta vulgaris lines from USDA-ARS Kimberly evaluated for resistance to Cercospora beticola, 2015.

In 2015, six sugar beet (Beta vulgaris L.) germplasm lines from the USDA-ARS Kimberly program and 2 check lines [EL50/2 (resistant) and F1042 (susceptible)] were screened for resistance to Cercospora beticola. The Cercospora leaf spot (CLS) evaluation was conducted at the Michigan State University Saginaw Valley Research and Extension Center (SVREC) near Frankenmuth, MI in a field that had been planted in wheat with clover underseeded in 2014. The germplasm was planted on 30 Apr. and thinned by hand as necessary. Single-row plots 4.5 m long with 51 cm between row spacing were planted with the treatments arranged in a randomized complete block design with three replications. Quadris 2.08SC (azoxystrobin) was applied at 0.0091 kg/100 m row in a 14 cm band in-furrow at planting to control Rhizoctonia damping-off. Weeds were controlled by a preplant application of ethofumesate (7 May), three times with mixtures of phenmedipham, desmedipham, triflusulfuron methyl, and clopyralid (23 May, 11 Jun., and 24 Jun), and once with S-metolachlor (17 Jun.). The herbicide spray treatments had to also be supplemented with hand weeding. The nursery was spray inoculated on 2 Jul with a liquid spore suspension (1 x 103 spores/ml) of C. beticola. The inoculum was produced from a mixture of leaves collected from the 2014 CLS nursery at SVREC and from naturally infected sugar beets grown at SVREC and on the Michigan State University campus farms in East Lansing, MI. The plots were rated for foliar symptom development on 9 Sep. using a scale of 0 to 10 (0 = healthy and 10 = all leaves dead; J. Am. Soc. Sugar Technol. 16:284). Data were rank transformed prior to analysis in SAS (Ver. 9.4) with mixed linear models (Proc MIXED), but the non-transformed means have been presented in the table. Mean separation was based on a PDIFF comparison with a probability cutoff of 0.05. Cercospora leaf spot development was uniform and moderate and other disease and pest problems were evident in the plot area. The checks performed as expected for the visual rating. Statistically, five of the entries contain at least moderate resistance since their visual ratings were at least as good as the moderate and resistant checks. However, 3 entries (4, 5, and 6) were better than the resistant check and entry 3 was equal to the resistant check. If the resistance in these four entries can be confirmed, these lines will be considered for incorporation into the USDA-ARS germplasm improvement program as a source of resistance to CLS

Virulence, Distribution and Diversity of Rhizoctonia Solani from Sugar Beet in Idaho and Oregon

Rhizoctonia root rot causes serious losses on sugar beet worldwide. In order to help explain why Rhizoctonia root rot management practices have not performed well in some areas of the Intermountain West (IMW), a survey was conducted. In the IMW from 2004 to 2006, 94 Rhizoctonia solani field isolates were collected from sugar beet roots. These field isolates were compared with 19 reference strains and 46 accessions from GenBank for genetic diversity based on sequencing of the ITS-5.8S rDNA region. Greenhouse pathogenicity tests on sugar beet and silage corn were conducted and plant damage was assessed using a randomized complete block design with at least four replications. The majority (92%) of the isolates had identity with the AG-2-2 IIIB (48%) or AG-4 subgroups (44%). Isolates from AG-2-2 IIIB were the most virulent on sugar beet and had the most diversity in phylogenetic analysis. Seven (all AG-2-2 IIIB) of 18 isolates tested could attack both sugar beet and corn, with two of the isolates causing less root rot than the others. To reduce Rhizoctonia root rot on sugar beet and corn, crop rotations and the isolates utilized for selecting host resistance could be given further consideration

Integrated Analysis of Clinical and Microbiome Risk Factors Associated with the Development of Oral Candidiasis during Cancer Chemotherapy.

Oral candidiasis is a common side effect of cancer chemotherapy. To better understand predisposing factors, we followed forty-five subjects who received 5-fluorouracil- or doxorubicin-based treatment, during one chemotherapy cycle. Subjects were evaluated at baseline, prior to the first infusion, and at three additional visits within a two-week window. We assessed the demographic, medical and oral health parameters, neutrophil surveillance, and characterized the salivary bacteriome and mycobiome communities through amplicon high throughput sequencing. Twenty percent of all subjects developed oral candidiasis. Using multivariate statistics, we identified smoking, amount of dental plaque, low bacteriome and mycobiome alpha-diversity, and the proportions of specific bacterial and fungal taxa as baseline predictors of oral candidiasis development during the treatment cycle. All subjects who developed oral candidiasis had baseline microbiome communities dominated by Candida and enriched in aciduric bacteria. Longitudinally, oral candidiasis was associated with a decrease in salivary flow prior to lesion development, and occurred simultaneously or before oral mucositis. Candidiasis was also longitudinally associated with a decrease in peripheral neutrophils but increased the neutrophil killing capacity of Candida albicans. Oral candidiasis was not found to be associated with mycobiome structure shifts during the cycle but was the result of an increase in Candida load, with C. albicans and Candida dubliniensis being the most abundant species comprising the salivary mycobiome of the affected subjects. In conclusion, we identified a set of clinical and microbiome baseline factors associated with susceptibility to oral candidiasis, which might be useful tools in identifying at risk individuals, prior to chemotherapy

Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis.

BACKGROUND: Gastrointestinal mucosal injury (mucositis), commonly affecting the oral cavity, is a clinically significant yet incompletely understood complication of cancer chemotherapy. Although antineoplastic cytotoxicity constitutes the primary injury trigger, the interaction of oral microbial commensals with mucosal tissues could modify the response. It is not clear, however, whether chemotherapy and its associated treatments affect oral microbial communities disrupting the homeostatic balance between resident microorganisms and the adjacent mucosa and if such alterations are associated with mucositis. To gain knowledge on the pathophysiology of oral mucositis, 49 subjects receiving 5-fluorouracil (5-FU) or doxorubicin-based chemotherapy were evaluated longitudinally during one cycle, assessing clinical outcomes, bacterial and fungal oral microbiome changes, and epithelial transcriptome responses. As a control for microbiome stability, 30 non-cancer subjects were longitudinally assessed. Through complementary in vitro assays, we also evaluated the antibacterial potential of 5-FU on oral microorganisms and the interaction of commensals with oral epithelial tissues. RESULTS: Oral mucositis severity was associated with 5-FU, increased salivary flow, and higher oral granulocyte counts. The oral bacteriome was disrupted during chemotherapy and while antibiotic and acid inhibitor intake contributed to these changes, bacteriome disruptions were also correlated with antineoplastics and independently and strongly associated with oral mucositis severity. Mucositis-associated bacteriome shifts included depletion of common health-associated commensals from the genera Streptococcus, Actinomyces, Gemella, Granulicatella, and Veillonella and enrichment of Gram-negative bacteria such as Fusobacterium nucleatum and Prevotella oris. Shifts could not be explained by a direct antibacterial effect of 5-FU, but rather resembled the inflammation-associated dysbiotic shifts seen in other oral conditions. Epithelial transcriptional responses during chemotherapy included upregulation of genes involved in innate immunity and apoptosis. Using a multilayer epithelial construct, we show mucositis-associated dysbiotic shifts may contribute to aggravate mucosal damage since the mucositis-depleted Streptococcus salivarius was tolerated as a commensal, while the mucositis-enriched F. nucleatum displayed pro-inflammatory and pro-apoptotic capacity. CONCLUSIONS: Altogether, our work reveals that chemotherapy-induced oral mucositis is associated with bacterial dysbiosis and demonstrates the potential for dysbiotic shifts to aggravate antineoplastic-induced epithelial injury. These findings suggest that control of oral bacterial dysbiosis could represent a novel preventive approach to ameliorate oral mucositis

Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing

Background and objective: The advent of next-generation sequencing has significantly facilitated characterization of the oral microbiome. Despite great efforts in streamlining the processes of sequencing and data curation, upstream steps required for amplicon library generation could still influence 16S rRNA gene-based microbial profiles. Among upstream processes, DNA extraction is a critical step that could represent a great source of bias. Accounting for bias introduced by extraction procedures is important when comparing studies that use different methods. Identifying the method that best portrays communities is also desirable. Accordingly, the aim of this study was to evaluate bias introduced by different DNA extraction procedures on oral microbiome profiles. Design: Four DNA extraction methods were tested on mock communities consisting of seven representative oral bacteria. Additionally, supragingival plaque samples were collected from seven individuals and divided equally to test two commonly used DNA extraction procedures. Amplicon libraries of the 16S rRNA gene were generated and sequenced via 454-pyrosequencing. Results: Evaluation of mock communities revealed that DNA yield and bacterial species representation varied with DNA extraction methods. Despite producing the lowest yield of DNA, a method that included bead beating was the only protocol capable of detecting all seven species in the mock community. Comparison of the performance of two commonly used methods (crude lysis and a chemical/enzymatic lysiscolumn-based DNA isolation) on plaque samples showed no effect of extraction protocols on taxa prevalence but global community structure and relative abundance of individual taxa were affected. At the phylum level, the latter method improved the recovery of Actinobacteria, Bacteroidetes, and Spirochaetes over crude lysis. Conclusion: DNA extraction distorts microbial profiles in simulated and clinical oral samples, reinforcing the importance of careful selection of a DNA extraction protocol to improve species recovery and facilitate data comparison across oral microbiology studies

Virulence, Distribution and Diversity of Rhizoctonia Solani from Sugar Beet in Idaho and Oregon

Rhizoctonia root rot causes serious losses on sugar beet worldwide. In order to help explain why Rhizoctonia root rot management practices have not performed well in some areas of the Intermountain West (IMW), a survey was conducted. In the IMW from 2004 to 2006, 94 Rhizoctonia solani field isolates were collected from sugar beet roots. These field isolates were compared with 19 reference strains and 46 accessions from GenBank for genetic diversity based on sequencing of the ITS-5.8S rDNA region. Greenhouse pathogenicity tests on sugar beet and silage corn were conducted and plant damage was assessed using a randomized complete block design with at least four replications. The majority (92%) of the isolates had identity with the AG-2-2 IIIB (48%) or AG-4 subgroups (44%). Isolates from AG-2-2 IIIB were the most virulent on sugar beet and had the most diversity in phylogenetic analysis. Seven (all AG-2-2 IIIB) of 18 isolates tested could attack both sugar beet and corn, with two of the isolates causing less root rot than the others. To reduce Rhizoctonia root rot on sugar beet and corn, crop rotations and the isolates utilized for selecting host resistance could be given further consideration