Cropping systems and cultural practices determine the Rhizoctonia anastomosis groups associated with Brassica spp. in Vietnam

Versatile role of Pseudomonas fuscovaginae cyclic lipopeptides in plant and microbial interactions

Pseudomonas fuscovaginae is the most prominent bacterial sheath rot pathogen, causing sheath brown rot disease in rice. This disease occurs worldwide and it is characterized by typical necrotic lesions on the sheath, as well as a reduction in the number of emitted panicles and filled grains. P. fuscovaginae has been shown to produce syringotoxin and fuscopeptin cyclic lipopeptides (CLPs), which have been linked to pathogenicity. In this study, we investigated the role of P. fuscovaginae UPB0736 CLPs in plant pathogenicity, antifungal activity and swarming motility. To do so, we sequenced the strain to obtain a single-contig genome and we constructed deletion mutants in the biosynthetic gene clusters responsible for the synthesis of CLPs. We show that UPB0736 produces a third CLP of 13 amino acids, now named asplenin, and we link this CLP with the swarming activity of the strain. We could then show that syringotoxin is particularly active against Rhizoctonia solani in vitro. By testing the mutants in planta we investigated the role of both fuscopeptin and syringotoxin in causing sheath rot lesions. We proved that the presence of these two CLPs considerably affected the number of emitted panicles, although their number was still significantly affected in the mutants deficient in both fuscopeptin and syringotoxin. These results reveal the importance of CLPs in P. fuscovaginae pathogenicity, but also suggest that other pathogenicity factors may be involved.

Diversity and Aggressiveness of Rhizoctonia spp. from Nebraska on Soybean and Cross-Pathogenicity to Corn and Wheat

Rhizoctonia and Rhizoctonia-like species of fungi that cause disease are known to have varying host ranges and aggressiveness. Accurate identification of these species causing disease is important for soybean disease management that relies upon crop rotation. The anamorphic genus Rhizoctonia contains several diverse species and anastomosis groups (AGs) including some known soybean pathogens, such as Rhizoctonia solani, whereas for others the ability to cause disease on soybean has not been well described. The present study was conducted to identify the predominant species and AG of Rhizoctonia from soybean, corn, and wheat fields that are pathogenic on soybean and characterize cross-pathogenicity to common rotational crops, corn and wheat. We surveyed for Rhizoctonia spp. in Nebraska; isolates were identified to species and AG, and aggressiveness was assessed. A total of 59 R. zeae isolates, 49 R. solani, nine binucleate Rhizoctonia, three R. circinata, and two R. oryzae isolates were collected in 2016 and 2017 from a total of 29 fields in 15 counties. The most abundant R. solani AGs were AG-4, AG-1 IB, AG-2-1, AG-3, and AG-5. R. solani AG-4 and R. zeae were found in all three regions of the state (west, central, and eastern). Some isolates that were most aggressive to soybean seedlings were cross-pathogenic on both wheat and corn. In addition, R. zeae was pathogenic on soybean when evaluated at 25°C, which is warmer than temperatures used previously, and isolates were identified that were aggressive on soybean and cross-pathogenic on both corn and wheat.

Surveillance of Pathogenicity of Rhizoctonia solani Japanese Isolates with Varied Anastomosis Groups and Subgroups on Arabidopsis thaliana

Rhizoctonia solani is a necrotrophic plant pathogen with a wide host range. R. solani is a species complex consisting of thirteen anastomosis groups (AGs) defined by compatibility of hyphal fusion reaction and subgroups based on cultural morphology. The relationship between such classifications and host specificity remains elusive. Here, we investigated the pathogenicity of seventeen R. solani isolates (AG-1 to 7) in Japan towards Arabidopsis thaliana using leaf and soil inoculations. The tested AGs, except AG-3 and AG-6, induced symptoms in both methods with variations in pathogenicity. The virulence levels differed even within the same AG and subgroup. Some isolates showed tissue-specific infection behavior. Thus, the AGs and their subgroups are suggested to be not enough to define the virulence (host and tissue specificity) of R. solani. We also evaluated the virulence of the isolates on Arabidopsis plants pretreated with salicylic acid, jasmonic acid, and ethylene. No obvious effects were detected on the symptom formation by the virulence isolates, but ethylene and salicylic acid slightly enhanced the susceptibility to the weak and nonvirulent isolates. R. solani seems to be able to overcome the induced defense by these phytohormones in the infection to Arabidopsis.

First Report of Soybean Seedling Disease caused by Rhizoctonia solani AG-7 in Taiwan

From August to November 2020, reduced emergence and damping-off of soybean seedlings were observed in two fields (Benzhou and Wandan) in Taiwan. Disease incidence was approximately 40% in Benzhou by field scouting. The roots of damping-off seedlings were brown. Affected seedlings could be easily pulled out from the soil and the lesions on the roots/stem were generally dry and sunken. These symptoms suggested the possibility of Rhizoctonia infection. Soil surrounding symptomatic seedlings were collected to bait the potential pathogen and symptomatic plants were used for pathogen isolation. The diseased tissues were washed with tap water and surface-disinfected with 1% bleach before placing on the Dexon selection medium at 26°C for 2 days (Ko and Hora 1971). Hyphae were transferred to potato dextrose agar (PDA), and a brown colony with brown and irregular-shaped sclerotia grew from 90 out of 99 isolates. The hyphae exhibited typical characteristics of Rhizoctonia solani, including a constriction and a septum near the end of branching hyphae (Ajayi-Oyetunde and Bradely, 2018). Two isolates from Benzhou and two isolates from Wandan were tested for their pathogenicity, and eight surface-disinfected seeds were distributed evenly on the water agar plates covered by 2-day-old mycelia at 25°C in dark for 7 days. All isolates caused cotyledon rot and reduced germination. To verify their pathogenicity in pots, double-sterilized sorghum seeds were inoculated with two strains and incubated at 25°C for 2 weeks to be used as fungal inoculum (Ajayi-Oyetunde and Bradely, 2017). A layer of 15 ml of fungal inoculum was placed 5 cm beneath the soil surface in pots. Four soybean seeds were planted approximately 3 cm above the inoculum in each pot. After two weeks, reddish lesions on the hypocotyls or taproots of all seedlings in the inoculated pots were observed, while seedlings in the control pots inoculated with sterile sorghum seeds remained healthy. The pathogen was re-isolated from lesions and had identical morphology to the original isolates. To characterize the fungal identity, the internal transcribed spacer (ITS) was sequenced using the primers ITS1/ITS4 (Sharon et al., 2006). Using BLASTN in the NCBI database, the sequence (GenBank no. MW410857 and MW410858) showed 100% (639/639 bp) similarity to KF907734 and 99.83% (635/636 bp) similarity to AF354099, both belong to R. solani anastomosis group 7 (AG-7) (Hua et al. 2014; Gonzalez et al. 2001). Phylogenetic analysis comparing sequences with different AGs (Ajayi-Oyetunde and Bradely, 2017) grouped our isolates within the AG-7 clade with a 100% bootstrap confidence. In the anastomosis test, an incompatible zonation and unequal mycelial growth rates were observed when AG-7 isolates were paired with an AG-1 IA isolate. On the other hand, the compatible tuft reaction was observed when two AG-7 isolates were paired, and the compatible merge reaction was observed in the self-pairing tests (Macnish et al. 1997). Accordingly, the molecular and morphological characterizations confirmed the causal pathogen as R. solani AG-7. R. solani AG-7 was first reported on radishes in Japan (Homma et al., 1983), first found on carnation in Taiwan (Lo et al., 1990), and in field soils of various crops but not soybean (Chuang, 1997). It was suggested that Rhizoctonia diseases of soybean may be present in Taiwan, but molecular confirmation was lacking (Anonymus, 1979). As R. solani AG-7 causes diseases of soybean in the US and Japan (Baird et al., 1996), the importance of AG-7 as an endemic pathogen of soybean in Taiwan should be recognized and its prevalence determined as a first step to managing this disease.

Waitea circinata var. zeae Causing Root Rot of Cabbage and Oilseed Rape

Cabbage, a widely used and popular vegetable, and oilseed rape, the second most valuable oilseed crop in the world, are two important species from the Brassicaceae family. Two geographically separated outbreaks of cabbage and oilseed rape root rot with estimated incidence of 15 and 20%, respectively, were recorded during 2017 in the Vojvodina region, Serbia. Twelve hyphal-tip isolates were obtained from symptomatic cabbage and oilseed rape plants and identified as Waitea circinata var. zeae based on morphological and molecular features. This indicates that W. circinata var. zeae has expanded its host range to the Brassicaceae family. Sequence analyses of internal transcribed spacer (ITS) and large subunit of the ribosomal DNA, RPB2, and β-tubulin genes revealed the highest similarity with multiple W. circinata var. zeae. Neighbor-joining analyses of ITS sequences resulted in a phylogenetic tree with one well-defined branch of W. circinata var. zeae, with two separate groups. All Serbian isolates and the majority of isolates originating from natural infection of dicotyledonous plants grouped together in group I. Following artificial inoculation, W. circinata var. zeae isolates caused mild to medium root necrosis of seedlings of 2 monocotyledonous and 12 dicotyledonous plant species, implying a wider host range than was known for W. circinata var. zeae. Additionally, this is the first occurrence of W. circinata var. zeae on dicotyledonous host plants in Europe. Because cabbage and oilseed rape are important crops grown worldwide, the occurrence of this new soilborne pathogen with a broad host range imposes the necessity for changes in routine disease control practices, particularly crop rotation.

Genetic Diversity and Pathogenicity of Rhizoctonia spp. Isolates Associated with Red Cabbage in Samsun (Turkey)

A total of 132 Rhizoctonia isolates were recovered from red cabbage plants with root rot and wirestem symptoms in the province of Samsun (Turkey) between 2018 and 2019. Based on the sequence analysis of the internal transcribed spacer (ITS) region located between the 18S and 28S ribosomal RNA genes and including nuclear staining, these 124 isolates were assigned to multinucleate Rhizoctonia solani, and eight were binucleate Rhizoctonia. The most prevalent anastomosis group (AG) was AG 4 (84%), which was subdivided into AG 4 HG-I (81%) and AG 4 HG-III (3%), followed by AG 5 (10%) and AG-A (6%), respectively. The unweighted pair group method phylogenetic tree resulting from the data of 68 isolates with the inter-PBS amplification DNA profiling method based on interspersed retrotransposon element sequences confirmed the differentiation of AGs with a higher resolution. In the greenhouse experiment with representative isolates (n = 24) from AGs on red cabbage (cv. Rondale), the disease severity index was between 3.33 and 4.0 for multinucleate AG isolates and ranged from 2.5 to 3.17 for AG-A isolates. In the pathogenicity assay of six red cabbage cultivars, one isolate for each AG was tested using a similar method, and all cultivars were susceptible to AG 4 HG-I and AG 4 HG-III isolates. Redriver and Remale were moderately susceptible, while Rescue, Travero, Integro, and Rondale were susceptible to the AG 5 isolate. The results indicate that the most prevalent and aggressive AGs of Rhizoctonia are devastating pathogens to red cabbage, which means that rotation with nonhost-crops for these AGs may be the most effective control strategy. This is the first comprehensive study of Rhizoctonia isolates in red cabbage using a molecular approach to assess genetic diversity using iPBS-amplified DNA profiling.

Detection and Quantification of Rhizoctonia solani and Rhizoctonia solani AG1-IB Causing the Bottom Rot of Lettuce in Tissues and Soils by Multiplex qPCR

In the muck soil region of southwestern Quebec, vegetable growers are threatened by several soilborne diseases, particularly the bottom rot of lettuce caused by the fungus Rhizoctonia solani. The particularly warm temperature of the few last seasons was marked by an increase in disease severity, and the associated yield losses were significant for Quebec lettuce growers. In the absence of registered fungicides and resistant cultivars, the management of Rhizoctonia solani-induced diseases in lettuce is based on good agricultural practices, which require detailed knowledge of the pathogen. In this study, Rhizoctonia solani fungal strains were isolated from infected field-grown lettuce plants presenting bottom rot symptoms to determine the anastomotic groups (AGs) of these isolates by internal transcribed spacer region (ITS) sequencing. Rhizoctonia solani AG 1-IB was identified as the main anastomotic group causing bottom rot lettuce in field-grown lettuce in organic soils in the Montérégie region. Two specific and sensitive quantitative PCR assays were then developed for R. solani AG1-IB and R. solani. The AG 1-IB qPCR assay amplified all strains of R. solani AG 1-IB tested, and no PCR product was obtained for any non-target strains. The R. solani qPCR assay amplified all strains of R. solani and did not amplify non-target strains, except for two strains of binucleate Rhizoctonia AG-E. In artificially inoculated soils, the sensitivity of both qPCR assays was set to 1 μg of sclerotia g^-1 of dry soil. In the growth chamber experiment, a minimum concentration between 14 and 42 μg sclerotia g^-1 of dry soil was required to induce the development of symptoms on the lettuce. Indeed, the AG 1-IB qPCR assay was sensitive enough to detect the lowest soil concentration of AG1-IB capable of inducing symptoms in head lettuce. In addition, the qPCR assays successfully detected R. solani and R. solani AG 1-IB from infected plant tissue samples and soil samples from lettuce fields. The qPCR assays developed in this study will be useful tools in lettuce bottom rot management.

Viruses Infecting the Plant Pathogenic Fungus Rhizoctonia solani

The cosmopolitan fungus Rhizoctonia solani has a wide host range and is the causal agent of numerous crop diseases, leading to significant economic losses. To date, no cultivars showing complete resistance to R. solani have been identified and it is imperative to develop a strategy to control the spread of the disease. Fungal viruses, or mycoviruses, are widespread in all major groups of fungi and next-generation sequencing (NGS) is currently the most efficient approach for their identification. An increasing number of novel mycoviruses are being reported, including double-stranded (ds) RNA, circular single-stranded (ss) DNA, negative sense (−)ssRNA, and positive sense (+)ssRNA viruses. The majority of mycovirus infections are cryptic with no obvious symptoms on the hosts; however, some mycoviruses may alter fungal host pathogenicity resulting in hypervirulence or hypovirulence and are therefore potential biological control agents that could be used to combat fungal diseases. R. solani harbors a range of dsRNA and ssRNA viruses, either belonging to established families, such as Endornaviridae, Tymoviridae, Partitiviridae, and Narnaviridae, or unclassified, and some of them have been associated with hypervirulence or hypovirulence. Here we discuss in depth the molecular features of known viruses infecting R. solani and their potential as biological control agents.

Diversity and Pathogenicity of Rhizoctonia Species from the Brazilian Cerrado

Eighty-one Rhizoctonia-like isolates were identified based on morphology and nuclei-staining methods from natural and agricultural soils of the Cerrado (Brazilian savanna). The nucleotide similarity analysis of ITS1-5.8S-ITS2 regions identified 14 different taxa, with 39.5% of isolates assigned to Waitea circinata (zeae, oryzae, and circinata varieties), while 37.0% belonged to Thanatephorus cucumeris anastomosis groups (AGs) AG1-IB, AG1-ID, AG1-IE, AG4-HGI, and AG4-HGIII. Ceratobasidium spp. AG-A, AG-F, AG-Fa, AG-P, and AG-R comprised 23.5%. Rhizoctonia zeae (19.8%), R. solani AG1-IE (18.6%), and binucleate Rhizoctonia AG-A (8.6%) were the most frequent anamorphic states found. Root rot severity caused by the different taxa varied from low to high on common beans, and tended to be low to average in maize. Twenty-two isolates were pathogenic to both hosts, suggesting difficulties in managing Rhizoctonia root rots with crop rotation. These results suggest that cropping history affects the geographical arrangement of AGs, with a prevalence of AG1 in the tropical zone from central to north Brazil while the AG4 group was most prevalent from central to subtropical south. W. circinata var. zeae was predominant in soils under maize production. To our knowledge, this is the first report on the occurrence of W. circinata var. circinata in Brazil.

Identification and Characterization of Rhizoctonia Species Associated with Soybean Seedling Disease

In an effort to identify the Rhizoctonia spp. associated with seedling diseases of soybean, Rhizoctonia isolates were recovered from soybean seedlings with damping off and root and hypocotyl rot symptoms from Arkansas, Illinois, Kansas, Michigan, Minnesota, and the Canadian province of Ontario between 2012 and 2014. Based on cultural morphology, polymerase chain reaction restriction fragment length polymorphism, and phylogenetic analysis of the internal transcribed spacer (ITS) region of the ribosomal RNA genes, 80 isolates were confirmed to be Rhizoctonia solani, 24 were binucleate Rhizoctonia spp., and 10 were R. zeae. Of the 80 R. solani isolates, one belonged to anastomosis group (AG) 2-1, 52 belonged to AG-2-2IIIB, five belonged to AG-3 PT, three belonged to AG-4 HGI, two belonged to AG-4 HGIII, nine belonged to AG-7, and eight belonged to AG-11. Bayesian inference of phylogeny using the ITS region revealed two clades of R. solani AG-7 that possibly correspond to different AG-7 subgroups. Phylogenetic analysis also provided evidence for genetic relatedness between certain binucleate Rhizoctonia and some R. solani isolates. On 'Williams 82' soybean, isolates of AG-2-2IIIB were the most aggressive, followed by isolates of AG-7, AG-4, and AG-11. On 'Jubilee', a sweet corn cultivar, AG-2-2IIIB and AG-4 isolates caused significant stunting and root damage, whereas the damage caused by the AG-11 isolates was mostly restricted to the mesocotyl. Isolates of R. zeae and the binucleate Rhizoctonia spp. were not pathogenic on soybean or corn. Our results indicate that soybean and corn are hosts to the predominant and aggressive AG of R. solani, implying that rotation between these two crops may not be an effective management practice.

Characterization of Rhizoctonia solani Associated with Black Scurf in Cyprus

During 2011, 96 sclerotial isolates of Rhizoctonia solani were collected from potato tubers from all main potato-cultivating regions of Cyprus. All isolates were found to be multinucleate. Characterization of anastomosis groups (AG) based on hyphal anastomosis reactions showed that 91 isolates belonged to AG3 and 5 to AG4. Sequence analysis of the internal transcribed spacer (ITS) regions (ITS1 and ITS2) of ribosomal DNA (rDNA) of 68 isolates confirmed the prevalence of AG3. In addition, phylogenetic analysis found that AG3 isolates were of the potato type, distinctly separated from the AG3 tobacco type, while AG4 isolates were separated into two different subgroups (HGI and HGII). Temperature studies showed that isolates belonging to both AG4 subgroups had significantly higher optimum growth temperatures compared with AG3. In vitro sensitivities to the fungicide pencycuron, in terms of concentrations where 50% growth inhibition was observed, ranged from 0.012 to 0.222 μg/ml. Pathogenicity and aggressiveness of the isolates was determined on 'Annabelle' potato sprouts and seedlings of a number of selected hosts, based on crop rotations followed in Cyprus. The majority of the isolates were pathogenic to potato sprouts, with disease severity (DS) values ranging from 0 to 88%. Mean DS values were statistically different among AG and subgroups, with AG4-HGI (69.25%) and AG4-HGII (3.12%) being the most and least aggressive, respectively. However, AG4-HGII isolates were the most aggressive in all rotational hosts tested, while AG3 isolates were the least aggressive. More specifically, the highest DS levels by AG4-HGI were recorded to barley, by AG4-HGII to lettuce and melon, and by AG3 isolates to vetch. This is the first comprehensive study to elucidate the AG composition, pathogenicity and other biological aspects of R. solani isolates associated with potato black scurf in Cyprus.