The Role of Chitinase Production by Stenotrophomonas maltophilia Strain C3 in Biological Control of Bipolaris sorokiniana

The role of chitinase production by Stenotrophomonas maltophilia strain C3 in biological control of leaf spot on tall fescue (Festuca arundinacea), caused by Bipolaris sorokiniana, was investigated in vitro and in vivo. The filtrate of a broth culture of C3, with chitin as the carbon source, was separated into fractions. A high molecular-weight fraction (\u3e8 kDa) was chitinolytic and more inhibitory than a low-molecularweight, nonchitinolytic fraction to conidial germination and hyphal growth by B. sorokiniana and to leaf spot development. A protein fraction derived by ammonium sulfate precipitation and a chitinase fraction purified by chitin affinity chromatography also were chitinolytic and highly antifungal. The chitinolytic fractions caused swelling and vacuolation of conidia and discoloration, malformation, and degradation of germ tubes. When boiled, the chitinolytic fractions lost chitinase activity along with most of the antifungal properties. Two chitinase-deficient and two chitinase- reduced mutants of C3 were compared with the wild-type strain for inhibition of germination of B. sorokiniana conidia on tall fescue leaves and for suppression of leaf spot development in vivo. The mutants exhibited reduced antifungal activity and biocontrol efficacy, but did not lose all biocontrol activity. An aqueous extract of leaves colonized by wild-type C3 had higher chitinase activity than that of noncolonized leaves and was inhibitory to conidial germination. The addition of chitin to leaves along with the wild-type strain increased both chitinase and antifungal activity. The chitinase activity level of extracts from leaves colonized by a chitinase-deficient mutant of C3, with and without added chitin, was no higher than the background, and the extracts lacked antifungal activity. Chitinolysis appears to be one mechanism of biological control by strain C3, and it functions in concert with other mechanisms

Origin of agricultural plant pathogens: Diversity and pathogenicity of \u3ci\u3eRhizoctonia\u3c/i\u3e fungi associated with native prairie grasses in the Sandhills of Nebraska

The Sandhills of Nebraska is a complex ecosystem, covering 50,000 km2 in central and western Nebraska and predominantly of virgin grassland. Grasslands are the most widespread vegetation in the U.S. and once dominated regions are currently cultivated croplands, so it stands to reason that some of the current plant pathogens of cultivated crops originated from grasslands, particularly soilborne plant pathogens. The anamorphic genus Rhizoctonia includes genetically diverse organisms that are known to be necrotrophic fungal pathogens, saprophytes, mycorrhiza of orchids, and biocontrol agents. This study aimed to evaluate the diversity of Rhizoctonia spp. on four native grasses in the Sandhills of Nebraska and determine pathogenicity to native grasses and soybean. In 2016 and 2017, a total of 84 samples were collected from 11 sites in the Sandhills, located in eight counties of Nebraska. The samples included soil and symptomatic roots from the four dominant native grasses: sand bluestem, little bluestem, prairie sandreed, and needle-and-thread. Obtained were 17 Rhizoctonia-like isolates identified, including five isolates of binucleate Rhizoctonia AG-F; two isolates each from binucleate Rhizoctonia AG-B, AG-C, and AG-K, Rhizoctonia solani AGs: AG-3, and AG-4; one isolate of binucleate Rhizoctonia AG-L, and one isolate of R. zeae. Disease severity was assessed for representative isolates of each AG in a greenhouse assay using sand bluestem, needle-and-thread, and soybean; prairie sandreed and little bluestem were unable to germinate under artificial conditions. On native grasses, all but two isolates were either mildly aggressive (causing 5–21% disease severity) or aggressive (21–35% disease severity). Among those, three isolates were cross-pathogenic on soybean, with R. solani AG-4 shown to be highly aggressive (86% disease severity). Thus, it is presumed that Rhizoctonia spp. are native to the sandhills grasslands and an emerging pathogen of crops cultivated may have survived in the soil and originate from grasslands

Genetic (co)variation and accuracy of selection for resistance to viral mosaic disease and production traits in an inter-ecotypic switchgrass breeding population

Obtaining good accuracy and reliability of estimated breeding values is essential to increase the efficiency of a plant breeding program. Genetic variation was assessed for categorical (Virc) and binary (Virb) mosaic (caused by Panicum mosaic virus), dry matter (DMY) and predicted ethanol (Etoh) yields, and lignin content (Klason or KL, and acid-detergent or ADL) in a Summer–Kanlow switchgrass (Panicum virgatum L.) population. Breeding values were predicted with the restricted maximum likelihood–best linear unbiased prediction (REML-BLUP) approaches using a multivariate phenotypic (PBLUP) and animal (ABLUP) models, integrating a three-generation pedigree (1,622 half-sibs) in ABLUP and not in PBLUP. Models were compared in their precision (accuracy and reliability) in assessing genetic parameters and estimating breeding values. The models were similar in most aspects, allocating the highest heritability (ℎ2i) values to DMY (.38 ± .035 vs. .41 ± .035), Etoh (.46 ± .031 vs. .42 ± .033), and Virc (.43 ± .046 vs. .37 ± .047) and the lowest (.17 ± .032 to .30 ± .044) to KL, ADL, and Virb. Genetic correlations were always larger than residual and phenotypic correlations. Intermediate or strong additive genetic control suggest that selecting for high-biomass genotypes will slightly increase lignin content and simultaneously impart mosaic tolerance. Mitigating an increase in lignin content will require including Etoh in a selection index based on its much stronger negative correlation (rG = −.63) with lignin. In this population, accuracy values ranged from .06 to .94 (PBLUP) and from .26 to .92 (ABLUP) and corresponding reliability ranged from .004 to .89 and from .07 to .87. However, ABLUP improved average reliability of DMY and Etoh by 11% and of other traits by 4–5% over the PBLUP model. The ABLUP was a better model over PBLUP, which is a valid analysis in the absence of a pedigree

A Two-Amino Acid Difference in the Coat Protein of \u3ci\u3eSatellite panicum mosaic virus\u3c/i\u3e Isolates Is Responsible for Differential Synergistic Interactions with \u3ci\u3ePanicum mosaic virus\u3c/i\u3e

Panicum mosaic virus (PMV) (genus Panicovirus, family Tombusviridae) and its molecular parasite, Satellite panicum mosaic virus (SPMV), synergistically interact in coinfected proso and pearl millet (Panicum miliaceum L.) plants resulting in a severe symptom phenotype. In this study, we examined synergistic interactions between the isolates of PMV and SPMV by using PMV-NE, PMV85, SPMV-KS, and SPMV-Type as interacting partner viruses in different combinations. Coinfection of proso millet plants by PMV-NE and SPMV-KS elicited severe mosaic, chlorosis, stunting, and eventual plant death compared with moderate mosaic, chlorotic streaks, and stunting by PMV85 and SPMV-Type. In reciprocal combinations, coinfection of proso millet by either isolate of PMV with SPMV-KS but not with SPMV-Type elicited severe disease synergism, suggesting that SPMV-KS was the main contributor for efficient synergistic interaction with PMVisolates. Coinfection of proso millet plants by either isolate of PMV and SPMV-KS or SPMV-Type caused increased accumulation of coat protein (CP) and genomic RNA copies of PMV, compared with infections by individual PMV isolates. Additionally, CP and genomic RNA copies of SPMV-KS accumulated at substantially higher levels, compared with SMPV-Type in coinfected proso millet plants with either isolate of PMV. Hybrid viruses between SPMV-KS and SPMV-Type revealed that SPMV isolates harboring a CP fragment with four differing amino acids at positions 18, 35, 59, and 98 were responsible for differential synergistic interactions with PMV in proso millet plants. Mutation of amino acid residues at these positions in different combinations in SPMV-KS, similar to those as in SPMV-Type or vice-versa, revealed that A35 and R98 in SPMV-KS CP play critical roles in enhanced synergistic interactions with PMVisolates. Taken together, these data suggest that the two distinct amino acids at positions 35 and 98 in the CP of SPMV-KS and SPMV-Type are involved in the differential synergistic interactions with the helper viruses

Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars

The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar ‘Kanlow’ and upland cultivar Summer are distinct and can be exploited for trait improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown ‘Kanlow’, and ‘Summer’ plants. Three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/ senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes of Summer plants. It is plausible that cultivar (ecotype)-specific genes and gene-networks could be one of the drivers for the documented differences in responses to leaf-borne pathogens between these two cultivars. Incorporating broad resistance to plant pathogens in elite switchgrass germplasm could improve sustainability of biomass production under low-input conditions

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Induced Resistance as a Mechanism of Biological Control by \u3ci\u3eLysobacter enzymogenes\u3c/i\u3e Strain C3

Induced resistance was found to be a mechanism for biological control of leaf spot, caused by Bipolaris sorokiniana, in tall fescue (Festuca arundinacea) using the bacterium Lysobacter enzymogenes strain C3. Resistance elicited by C3 suppressed germination of B. sorokiniana conidia on the phylloplane in addition to reducing the severity of leaf spot. The pathogen-inhibitory effect could be separated from antibiosis by using heat-inactivated cells of C3 that retained no antifungal activity. Application of live or heat-killed cells to tall fescue leaves resulted only in localized resistance confined to the treated leaf, whereas treatment of roots resulted in systemic resistance expressed in the foliage. The effects of foliar and root applications of C3 were long lasting, as evidenced by suppression of conidial germination and leaf spot development even when pathogen inoculation was delayed 15 days after bacterial treatment. When C3 population levels and germination of pathogen conidia was examined on leaf segments, germination percentage was reduced on all segments from C3-treated leaves compared with segments from nontreated leaves, but no dose–response relationship typical of antagonism was found. Induced resistance by C3 was not host or pathogen specific; foliar application of heat-killed C3 cells controlled B. sorokiniana on wheat and also was effective in reducing the severity of brown patch, caused by Rhizoctonia solani, on tall fescue. Treatments of tall fescue foliage or roots with C3 resulted in significantly elevated peroxidase activity compared with the control

Virulence of \u3ci\u3eMetarhizium anisopliae\u3c/i\u3e (Deuteromycotina: Hyphomycetes) Strain ESC-1 to the German Cockroach (Dictyoptera: Blattellidae) and Its Compatibility with Insecticides

Virulence of Metarhizium anisopliae (Metschnikoff) Sorokin strain ESC-1 against the German cockroach, Blattella germanica (L.), was determined using 5 concentrations ranging from 83107 to 23109 spores per milliliter. The calculated LD50 value was 4.18 by 108 spores per milliliter (4.18 3 105 spores per cockroach). In vitro study was conducted to determine the compatibility of M. anisopliae strain ESC-1 with chlorpyrifos, propetamphos, and cyfluthrin. Insecticides did not affect conidial germination but did adversely affect the growth and sporulation of M. anisopliae strain ESC-1. The growth of M. anisopliae colonies on media amended only with 50 and 500 ppm of chlorpyrifos and 500 ppm of propetamphos treatments at 3, 6, and 9 d was significantly inhibited compared with the control. Similarly, sporulation was significantly reduced in treated colonies exhibiting partial colony growth. The colonies cultured on SDAY media amended with 50 ppm of chlorpyrifos had significantly reduced sporulation compared with the control and no sporulation was observed in colonies cultured on media amended with 500 ppm of chlorpyrifos and propetamphos

Mutagenesis of β-1,3-Glucanase Genes in \u3ci\u3eLysobacter enzymogenes\u3c/i\u3e Strain C3 Results in Reduced Biological Control Activity Toward Bipolaris Leaf Spot of Tall Fescue and Pythium Damping-Off of Sugar Beet

Lysobacter enzymogenes produces extracellular lytic enzymes capable of degrading the cell walls of fungi and oomycetes. Many of these enzymes, including β-1,3-glucanases, are thought to contribute to the biological control activity expressed by several strains of the species. L. enzymogenes strain C3 produces multiple extracellular β-1,3-glucanases encoded by the gluA, gluB, and gluC genes. Analysis of the genes indicates they are homologous to previously characterized genes in the related strain N4-7, each sharing \u3e95% amino acid sequence identity to their respective counterparts. The gluA and gluC gene products encode enzymes belonging to family 16 glycosyl hydrolases, whereas gluB encodes an enzyme belonging to family 64. Mutational analysis indicated that the three genes accounted for the total β-1,3-glucanase activity detected in culture. Strain G123, mutated in all three glucanase genes, was reduced in its ability to grow in a minimal medium containing laminarin as a sole carbon source. Although strain G123 was not affected in antimicrobial activity toward Bipolaris sorokiniana or Pythium ultimum var. ultimum using in vitro assays, it was significantly reduced in biological control activity against Bipolaris leaf spot of tall fescue and Pythium damping-off of sugar beet. These results provide direct supportive evidence for the role of β-1,3-glucanases in biocontrol activity of L. enzymogenes strain C3