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Rhizoctonia solani is a soil-borne fungal species with worldwide distribution and poses serious threats to a wide range of economically important crops such as grain and forage crops. This pathogen has survival capabilities within plants and soil, giving rise to sclerotia and persisting for several months or years. Alfalfa (Medicago sativa) is the most widely grown and important forage crop in China and worldwide. The unique characteristics of alfalfa, such as excellent forage quality, ruminant desirability, and substantial biomass output, distinguish it from other fodder crops, and it is also known as the “Queen of Forages”. However, the production of alfalfa is seriously affected by R. solani, with yield losses of 20% to 60% globally. This review firstly summarizes diseases such as seedling damping-off, root rot, crown rot, root cankers, stem cankers, blight, and stem rot caused by R. solani in alfalfa and the survival mechanism of this pathogen. The techniques for R. solani detection and quantification from plants and soils, as well as management through host resistance, cultural practices, fungicides, and biological control, were then overviewed. This review provides scientific knowledge to enable researchers to efficiently manage R. solani in alfalfa production.

Fusarium tricinctum is a globally devastating fungal pathogen associated with root rot disease in alfalfa. The absence of a complete genome sequence has hindered molecular investigations into its pathogenic mechanisms. This study reports the first chromosome-level genome assembly of the virulent F. tricinctum strain MsR-QD66, generated using a combined sequencing strategy integrating Illumina, PacBio HiFi, and Hi-C technologies. The 46.2 Mb assembly (scaffold N50 = 5.1 Mb) comprises 10 chromosomes with Merqury-validated abase accuracy (QV = 34.8, error rate <0.01%). The genome achieved 95.6% completeness according to CEGMA and complete BUSCO scores. This assembly comprises 13,594 protein-coding genes, 336 non-coding RNAs, and a comprehensive repertoire of repetitive elements. Functional annotation identified 1,871 transcription factors and 1,241 secreted proteins. Comparative genomics and virulence factor analyses revealed 527 genes linked to 36 key diseases across diverse hosts. This chromosome-level genome assembly provides a valuable resource for studying molecular mechanisms of F. tricinctum pathogenicity to alfalfa and will facilitate the development of sustainable strategies for managing root rot in alfalfa.

Background The production of secondary metabolites with antibiotic properties is a common characteristic to entomopathogenic bacteria Xenorhabdus spp. These metabolites not only have diverse chemical structures but also have a wide range of bioactivities with medicinal and agricultural interests such as antibiotic, antimycotic and insecticidal, nematicidal and antiulcer, antineoplastic and antiviral. It has been known that cultivation parameters are critical to the secondary metabolites produced by microorganisms. Even small changes in the culture medium may not only impact the quantity of certain compounds but also the general metabolic profile of microorganisms. Manipulating nutritional or environmental factors can promote the biosynthesis of secondary metabolites and thus facilitate the discovery of new natural products. This work was conducted to evaluate the influence of nutrition on the antibiotic production of X. bovienii YL002 and to optimize the medium to maximize its antibiotic production. Results Nutrition has high influence on the antibiotic production of X. bovienii YL002. Glycerol and soytone were identified as the best carbon and nitrogen sources that significantly affected the antibiotic production using one-factor-at-a-time approach. Response surface methodology (RSM) was applied to optimize the medium constituents (glycerol, soytone and minerals) for the antibiotic production of X. bovienii YL002. Higher antibiotic activity (337.5 U/mL) was obtained after optimization. The optimal levels of medium components were (g/L): glycerol 6.90, soytone 25.17, MgSO 4 ·7H 2 O 1.57, (NH 4 ) 2 SO 4 2.55, KH 2 PO 4 0.87, K 2 HPO 4 1.11 and Na 2 SO 4 1.81. An overall of 37.8% increase in the antibiotic activity of X. bovienii YL002 was obtained compared with that of the original medium. Conclusions To the best of our knowledge, there are no reports on antibiotic production of X. boviebii by medium optimization using RSM. The results strongly support the use of RSM for medium optimization. The optimized medium not only resulted in a 37.8% increase of antibiotic activity, but also reduced the numbers of experiments. The chosen method of medium optimization was efficient, simple and less time consuming. This work will be useful for the development of X. bovienii cultivation process for efficient antibiotic production on a large scale, and for the development of more advanced control strategies on plant diseases.

Rhizoctonia solani is one of the major fungal pathogens associated with root rot in alfalfa that severely limits commercial alfalfa production worldwide. Host resistance is considered the most cost-effective and sustainable way to manage diseases caused by this pathogen. This study aimed to determine whether any host resistances to R. solani exist among a wide-ranging alfalfa collection and whether host resistances were associated with a specific geographic origin. We found a large variation in disease responses among the 68 alfalfa varieties, with the range of disease indices of shoots from 23 to 94% and roots from 31 to 98% as well as reductions in dry weight of shoots from 35 to 96% and roots from 2 to 99%. Among these, three varieties (Gannong 9, Trifecta and Common), originating from three different countries, displayed a high level of resistance, with disease indices of shoots and roots as well as reductions in dry weight of shoots and roots being all ≤40%. Hierarchical clustering and principal component analysis revealed three main groups of disease responses existed among varieties, with five varieties (7%) showing resistance, 15 varieties (22%) being moderately resistant and the remaining ones exhibiting susceptibility. Besides, varieties with a similar disease response were associated with various geographic origins. This study provides valuable resistance sources for breeding programs to develop alfalfa varieties with improved resistance to R. solani, and for facilitating the identification of molecular mechanisms underlying the resistant varieties to this pathogen.

Strawberry (Fragaria × ananassa) is one of the most important berry crops worldwide. Fusarium wilt poses a serious threat to commercial strawberry production worldwide and causes severe economic losses. Our previous surveys suggested that soil pH, soil amendment with organic matter and/or crop rotation could offer opportunities for improved management of strawberry disease. Studies were conducted for the first time to determine the effects of soil pH, soil amendments with manure compost and crop residue, and crop rotation on the severity and impact of Fusarium wilt on strawberry. At soil pH 6.7, plants showed the least severe disease and the lowest reductions in shoot and root dry weight (DW) of plants from disease, significantly lower than those of plants in acidic soil at pH 5.2 or 5.8. In soil amendment with manure compost at 5.0 %, plants showed the least severe disease and the lowest reductions in shoot and root DW of plants from disease, significantly lower than those of plants in the other three levels of manure compost. In soil amendment with crop residue at 2.5 % or 5.0 %, shoot and root disease of plants and reductions in shoot and root DW of plants from disease were significantly lower than those of plants in soil without crop residue or excessive crop residue amendment at 10.0 %. Plants in soil rotated with tomato not only showed the least severe disease but also showed the lowest reductions in shoot and root DW of plants from disease, significantly lower than those of plants in soil continuously planted with strawberry without rotation or rotated with capsicum. Soil pH, soil amendment with manure compost or crop residue, and crop rotation, all significantly reduced the severity and impact of Fusarium wilt on strawberry. There is great potential for manipulating soil pH, adding soil organic amendments and utilizing crop rotation, not only to successfully manage Fusarium wilt on strawberry, but to do so in a sustainable way without current reliance upon chemical fumigants.

Neuroimaging studies have shown that autism spectrum disorders (ASDs) may be associated with abnormalities in brain structures and functions at rest as well as during cognitive tasks. However, it remains unclear if functional connectivity (FC) of all brain neural networks is also changed in these subjects. In this study, we acquired functional magnetic resonance imaging scans from 93 children with ASD and 79 matched healthy subjects. Group independent component analysis was executed for all of the participants to estimate FC. One-sample -tests were then performed to obtain the networks for each group. Group differences in the different brain networks were tested using two-sample -tests. Finally, relationships between abnormal FC and clinical variables were investigated with Pearson's correlation analysis. The results from one-sample -tests revealed nine networks with similar spatial patterns in these two groups. When compared with the controls, children with ASD showed increased connectivity in the right dorsolateral superior frontal gyrus and left middle frontal gyrus (MFG) within the occipital pole network. Children with ASD also showed decreased connectivity in the left gyrus rectus, left middle occipital gyrus, right angular gyrus, right MFG and right inferior frontal gyrus (IFG), orbital part within the lateral visual network (LVN), the left IFG, right precuneus, and right angular gyrus within the left frontoparietal (cognition) network. Furthermore, the mean FC values within the LVN showed significant positive correlations with total score of the Childhood Autism Rating Scale. Our findings indicate that abnormal FC extensively exists within some networks in children with ASD. This abnormal FC may constitute a biomarker of ASD. Our results are an important contribution to the study of neuropathophysiological mechanisms in children with ASD.

Strawberry (Fragaria×ananassa) is one of the most important berry crops in the world. Root rot of strawberry caused by Rhizoctonia spp. is a serious threat to commercial strawberry production worldwide. However, there is no information on the genetic diversity and phylogenetic status of Rhizoctonia spp. associated with root rot of strawberry in Australia. To address this, a total of 96 Rhizoctonia spp. isolates recovered from diseased strawberry plants in Western Australia were characterized for their nuclear condition, virulence, genetic diversity and phylogenetic status. All the isolates were found to be binucleate Rhizoctonia (BNR). Sixty-five of the 96 BNR isolates were pathogenic on strawberry, but with wide variation in virulence, with 25 isolates having high virulence. Sequence analysis of the internal transcribed spacers of the ribosomal DNA separated the 65 pathogenic BNR isolates into six distinct clades. The sequence analysis also separated reference BNR isolates from strawberry or other crops across the world into clades that correspond to their respective anastomosis group (AG). Some of the pathogenic BNR isolates from this study were embedded in the clades for AG-A, AG-K and AG-I, while other isolates formed clades that were sister to the clades specific for AG-G, AG-B, AG-I and AG-C. There was no significant association between genetic diversity and virulence of these BNR isolates. This study demonstrates that pathogenic BNR isolates associated with root rot of strawberry in Western Australia have wide genetic diversity, and highlights new genetic groups not previously found to be associated with root rot of strawberry in the world (e.g., AG-B) or in Australia (e.g., AG-G). The wide variation in virulence and genetic diversity identified in this study will be of high value for strawberry breeding programs in selecting, developing and deploying new cultivars with resistance to these multi-genetic groups of BNR.

Fusarium oxysporum f. sp. lycopersici (Fol) causes vascular wilt disease in tomato. Upon colonization of the host, Fol secretes many small effector proteins into the xylem sap to facilitate infection. Besides known SIX (secreted in xylem) proteins, the identity of additional effectors that contribute to Fol pathogenicity remains largely unexplored. We performed a deep RNA-sequencing analysis of Fol race 2-infected tomato, used the sequence data to annotate a published genome assembly generated via PacBio SMRT sequencing of the Fol race 2 reference strain Fol4287, and analysed the resulting transcriptome to identify Fol effector candidates among the newly annotated genes. We examined the Fol-infection expression profiles of all 13 SIX genes present in Fol race 2 and identified 27 new candidate effector genes that were likewise significantly upregulated upon Fol infection. Using Agrobacterium-mediated transformation, we tested the ability of 22 of the new candidate effector genes to suppress or induce cell death in leaves of Nicotiana benthamiana. One effector candidate designated Fol-EC19, encoding a secreted guanyl-specific ribonuclease, was found to trigger cell death and two effector candidates designated Fol-EC14 and Fol-EC20, encoding a glucanase and a secreted trypsin, respectively, were identified that can suppress Bax-mediated cell death. Remarkably, Fol-EC14 and Fol-EC20 were also found to suppress I-2/Avr2- and I/Avr1-mediated cell death. Using the yeast secretion trap screening system, we showed that these three biologically-active effector candidates each contain a functional signal peptide for protein secretion. Our findings provide a basis for further understanding the virulence functions of Fol effectors.

Background Xenocoumacin 1 (Xcn1) and Xenocoumacin 2 (Xcn2) are the main antimicrobial compounds produced by Xenorhabdus nematophila . Culture conditions, including pH, had remarkably distinct effects on the antimicrobial activity of X. nematophila . However, the regulatory mechanism of pH on the antimicrobial activity and antibiotic production of this bacterium is still lacking. Results With the increase of initial pH, the antimicrobial activity of X. nematophila YL001 was improved. The levels of Xcn1 and nematophin at pH 8.5 were significantly ( P  <  0.05 ) higher than that at pH 5.5 and 7.0. In addition, the expression of xcnA - L , which are responsible for the production of Xcn1 was increased and the expression of xcnMN , which are required for the conversion of Xcn1 to Xcn2 was reduced at pH 8.5. Also, the expression of ompR and cpxR were decreased at pH 8.5. Conclusion The alkaline pH environment was found to be beneficial for the production of Xcn1 and nematophin, which in turn led to high antimicrobial activity of X. nematophila at pH 8.5.

Summary CpxR is a global response regulator that negatively influences the antimicrobial activities of Xenorhabdus nematophila. Herein, the wildtype and ΔcpxR mutant of X. nematophila were cultured in a 5‐l and 70‐l bioreactor. The kinetic analysis showed that ΔcpxR significantly increased the cell biomass and antibiotic activity. The maximum dry cell weight (DCW) and antibiotic activity of ΔcpxR were 20.77 ± 1.56 g L−1 and 492.0 ± 31.2 U ml−1 and increased by 17.28 and 97.33% compared to the wildtype respectively. Xenocoumacin 1 (Xcn1), a major antimicrobial compound, was increased 3.07‐fold, but nematophin was decreased by 48.7%. In 70‐l bioreactor, DCW was increased by 18.97%, while antibiotic activity and Xcn1 were decreased by 27.71% and 11.0% compared to that in 5‐l bioreactor respectively. Notably, pH had remarkable effects on the cell biomass and antibiotic activity of ΔcpxR, where ΔcpxR was sensitive to alkaline pH conditions. The optimal cell growth and antibiotic activity of ΔcpxR occurred at pH 7.0, while Xcn1 was increased 5.45‐ and 3.87‐fold relative to that at pH 5.5 and 8.5 respectively. These findings confirmed that ΔcpxR considerably increased the biomass of X. nematophila at a late stage of fermentation. In addition, ΔcpxR significantly promoted the biosynthesis of Xcns but decreased the production of nematophin. ·Deleting cpxR of X. nematophila results in a prolonged lag phase, and lower biomass at early‐ and mid‐stage of fermentation, but significantly increased the biomass at a late stage in contrast to the wildtype. Deleting cpxR of X. nematophila promoted the production of Xcns, but decreased the production of nematophin. ΔcpxR mutant was hypersensitive to alkaline condition and exhibited lower biomass under pH 8.5.