Solani Anastomosis Group Research Articles

Occurrence and Anastomosis Grouping of Rhizoctonia spp. Inducing Black Scurf and Greyish-White Felt-Like Mycelium on Carrot in Sweden.

Carrots with different Rhizoctonia-like symptoms were found in the main Swedish carrot production areas from 2001–2020. The most commonly observed symptoms were a greyish-white felt-like mycelium and black scurf, the latter often associated with Rhizoctonia solani anastomosis group (AG) 3-PT on potato. An overall increase in disease incidence in all studied fields over time was observed for both symptoms. The majority of Rhizoctonia isolates sampled from carrot in the period 2015–2020 were identified as AG 3 (45%) and AG 5 (24%), followed by AG 1-IB (13%), AG 11 (5%), AG-E (5%), AG BI (3%), AG-K (3%) and AG 4-HGII (2%). To our knowledge, this is the first report describing AG 5 in Sweden as well as AG 3, AG 11 and AG-E inducing Rhizoctonia-like symptoms on carrot. Secondly, we report for the first time that R. solani AG 3, and the less observed AGs: AG 1-IB and AG 5 can induce black scurf symptoms on the taproot of carrots. Due to a widely used carrot-potato crop rotation in Swedish areas, a possible cross-over from potato to carrot is suggested. This information is of high importance to reduce Rhizoctonia inoculum in soils, since avoiding carrot-potato crop rotations needs to be considered.

First report of leaf blight and petiole rot of carrot caused by Rhizoctonia solani AG-1 IB

Carrot plants with leaf blight and petiole rot were found in Hokkaido, Japan, in September 2016. The causal fungus, identified as Rhizoctonia solani anastomosis group (AG)-1 IB, caused leaf blight and petiole rot on carrot but not root rot in inoculation tests. We also confirmed that it can be discriminated on the basis of symptoms and pathogenicity from the pathogen R. solani AG-2-2 IV, which causes carrot root rot. This is the first report of leaf blight and petiole rot of carrot caused by R. solani AG-1 IB.

First Report of Damping-off on Sedum plumbizincicola Caused by Rhizoctonia solani AG 2-1 in China.

Sedum plumbizincicola X.H. Guo et S.B. Zhou sp. nov. is a plant species of the family Crassulaceae that has the ability to hyperaccumulate cadmium and zinc in high concentrations (Liu et al. 2017). In April of 2018 and 2019, a disease of damping-off was observed on S. plumbizincicola seedlings in a nursery in Changsha (28°13'N; 112°56'E), the Hunan Province of China, in which nearly 1 million seedlings were planted. Approximately 40% of the surveyed plants were infected. The affected plants displayed water-soaking on the shoots and stems, and chlorosis on the leaves. As the disease spread upward, leaf stalks or the whole plants became wilted and collapsed. Five diseased stem and leaf samples were collected. Symptomatic tissues were excised and surface sterilized with 70% ethanol for 10 s, and 0.1% HgCl2 for 2 min, washed with sterile distilled water for three times, and then cultured on potato dextrose agar (PDA) at 26°C in darkness. Fungal colonies were similar in morphology: white, light gray to brown, with hyphae branched at nearly right angles, septa near the branching point and constrictions at the base of hyphal branches. After 10 days, white-gray to brown sclerotia were produced. The morphological characteristics were consistent with those of Rhizoctonia solani J.G. Kühn (Sneh et al. 1991). Genomic DNA of a representative isolate was extracted using the cetyltrimethylammonium bromide method. The internal transcribed spacer (ITS) region of rDNA was amplified and sequenced with the primer pairs ITS4/ITS5 (White et al. 1990). When analyzed by the BLASTn program, the ITS sequence (GenBank Accession No. MN961664) had 100% identity to the corresponding gene sequence of R. solani anastomosis group (AG) 2-1(Accession Nos: LC202869.1 and MH862641.1). In addition, primers Rhsp1/ITS4B and Rhsp2/ITS1F specific for R. solani, and AG21sp/ITS4B specific for R. solani AG 2-1 were also used (Salazar et al. 2000). Results revealed that our isolate was R. solani AG 2-1. Pathogenicity was confirmed via in vivo inoculation of one-month-old S. plumbizincicola seedlings in sterilized nursery soil with four representative isolates. For each pot, five 5-mm-diameter mycelial plugs from 7-days old colonies on PDA were placed in the soil near the base of the stems. Plants inoculated with agar plugs without mycelium served as controls. The inoculated plants were kept in a growth chamber at 25°C with a 12/12 h light/dark cycle. Pathogenicity tests were performed twice, with three replicative potted plants for each isolate in each test. Approximately 25 days after inoculation, the damping-off symptoms resembling those observed in the field were displayed on the inoculated plants, while no obvious symptoms were observed on the control plants. R. solani was re-isolated from all infected plants and molecularly characterized, thus confirming Koch's postulates. R. solani has been previously reported as the pathogen of damping-off disease in many plants, such as canola (Paulitz et al. 2006) and oat (Zhang et al. 2016). However, to the best of our knowledge, this is the first report of R. solani causing damping-off of S. plumbizincicola in China. S. plumbizincicola is widely planted for heavy metal pollution treatment in China. The occurrence of this disease could seriously affect the production of the seedlings, and management strategies should be developed.

First Report of Rhizoctonia solani AG 11 Causing Stem Rot of Phaseolus vulgaris in Idaho

In July 2018, bean plants (cv. Viva pink) at one location in south central Idaho were observed to have reduced growth with approximately 20% of the plants affected over 1 ha. Visual assessment showed that the below-ground parts of stems consistently displayed brown lesions up to 2 cm in length, which sometimes girdled the entire plant. To determine the causal agent, affected material (approximately 5 mm³) was surface disinfested in sodium hypochlorite (2%) for 30 s, rinsed twice in sterile water, and plated onto water agar medium amended with penicillin G (0.2 g/liter) and streptomycin sulfate (0.8 g/liter). After 3 days, colonies of Rhizoctonia solani were identified based on the presence of relatively broad (8 to 12 μm), septate hyphae with right-angle branching. Hyphal tips of R. solani colonies were transferred to potato dextrose agar (PDA) and grown for 2 weeks at 21°C. DNA was then extracted from hyphae taken from a single representative isolate (DB23). Anastomosis group (AG) was identified by ribosomal DNA ITS sequencing of isolate DB23. DNA was extracted and sequenced as previously described (Woodhall et al. 2013). The resulting sequence (GenBank no. MT256181) was over 99% identical with isolates previously identified as R. solani AG 11 (LC215403). To confirm pathogenicity, 2-week-old pinto bean plants (cv. Windbreaker) were each inoculated by placing a fully colonized 10-mm² plug taken from a 2-week-old PDA culture of isolate DB23 next to the stem 10 mm below the soil surface. Sterile PDA plugs were placed next to the stems of control plants. Each treatment was replicated five times. Plants were grown in a greenhouse at 21°C in potting compost (Scotts, Marysville, OH) under light for 16 h a day. After 5 weeks, each plant was assessed for disease using a previously described stem disease severity scale (Carling and Leiner 1990). No symptoms were present in the control plants. Plants inoculated with isolate DB23 had an average stem disease severity score of 2.6 (from a maximum of 4), and R. solani was consistently reisolated, thereby confirming Koch’s postulates. To our knowledge, this is the first report of R. solani AG 11 in Idaho on any host. Previously, R. solani AG 11 has been reported on Phaseolus vulgaris in Turkey (Eken and Demirci 2004) and on lily in Japan (Misawa et al. 2017). AG 11 has also been associated with soybeans in Arkansas (Ajayi-Oyetunde and Bradley 2017; Carling et al. 1994) and Illinois (Ajayi-Oyetunde and Bradley 2017). AG 11 has also been reported on rice in Arkansas (Carling et al. 1994; Spurlock et al. 2016) and sweet corn in New York (Ohkura et al. 2009). In western Australia, it was found on wheat and lupin, and these isolates were pathogenic to potatoes in controlled environment studies (Carling et al. 1994). Idaho is a major producer of wheat, potatoes, and dry beans; the presence of soilborne R. solani AG 11 also needs to be considered when diagnosing and managing Rhizoctonia diseases of these crops.

Enhanced resistance to fungal and bacterial diseases in tomato and Arabidopsis expressing BSR2 from rice.

The overexpression of rice BSR2 would offer a simple and effective strategy to protect plants from multiple devastating diseases in tomato and Arabidopsis. Many devastating plant diseases are caused by pathogens possessing a wide host range. Fungal Botrytis cinerea and Rhizoctonia solani, as well as bacterial Pseudomonas syringae and Ralstonia pseudosolanacearum are four such pathogens that infect hundreds of plant species, including agronomically important crops, and cause serious diseases, leading to severe economic losses. However, reports of genes that can confer resistance to broad host-range pathogens via traditional breeding methods are currently limited. We previously reported that Arabidopsis plants overexpressing rice BROAD-SPECTRUM RESISTANCE2 (BSR2/CYP78A15) showed tolerance not only to bacterial P. syringae pv. tomato DC3000 but also to fungal Colletotrichum higginsianum and R. solani. Rice plants overexpressing BSR2 displayed tolerance to two R. solani anastomosis groups. In the present study, first, BSR2-overexpressing (OX) Arabidopsis plants were shown to be additionally tolerant to B. cinerea, R. solani, and R. pseudosolanacearum. Next, tomato 'Micro-Tom' was used as a model to determine whether such tolerance by BSR2 can be introduced into dicot crops to prevent infection from pathogens possessing wide host range. BSR2-OX tomato displayed broad-spectrum disease tolerance to fungal B. cinerea and R. solani, as well as to bacterial P. syringae and R. pseudosolanacearum. Additionally, undesirable traits such as morphological changes were not detected. Thus, BSR2 overexpression can offer a simple and effective strategy to protect crops from multiple destructive diseases.

Full genome sequence of a new mitovirus from the phytopathogenic fungus Rhizoctonia solani.

A double-stranded RNA (dsRNA) segment was identified in Rhizoctonia solani anastomosis group (AG)-2-2IIIB, the primary causal agent of Rhizoctonia crown and root rot of sugar beet. The dsRNA segment represented the genome replication intermediate of a new mitovirus that was tentatively designated as "Rhizoctonia solani mitovirus 39" (RsMV-39). The complete sequence of the dsRNA was 2805bp in length with 61.9% A+U content. Using either the fungal mitochondrial or universal genetic code, a protein of 840 amino acids containing an RNA-dependent RNA polymerase (RdRp) domain was predicted with a molecular mass of 94.46kDa. BLASTp analysis revealed that the RdRp domain of RsMV-39 had 43.55% to 72.96% sequence identity to viruses in the genus Mitovirus, and was the most similar (72.96% identical) to that of Ceratobasidium mitovirus A (CbMV-A). Phylogenetic analysis based on RdRp domains clearly showed that RsMV-39 is a member of a distinct species in the genus Mitovirus of the family Mitoviridae. This is the first full genome sequence of a mycovirus associated with R. solani AG-2-2IIIB.

Real-time PCR quantification of Rhizoctonia solani AG-3 from soil samples

Rhizoctonia solani anastomosis group 3 (AG-3) causes several diseases of potato, including black scurf and stem canker, affecting potato production in the Skagit Valley, Washington, and around the world. Primers for a SYBR-Green II-based real-time polymerase chain reaction (qPCR) assay were designed from sequences of the nuclear internal transcribed spacer (ITS) regions of fungal isolates of potato and onion from the Pacific Northwest, USA. The primers preferentially amplified R. solani AG-3 DNA, compared to DNA from R. solani AG-4, AG-5 and AG-8. In silico analysis of primer-template duplex stability indicated that the assay also will detect R. solani AG-3 isolates from pea and onion in Washington State and from diverse crop species around the world, but not R. solani AG-9 and AG-2-1. The assay was used to quantify R. solani AG-3 populations in pathogen-infested field soils after temporary flooding rotation, a practice found to be effective for reducing Sclerotinia sclerotiorum and R. solani AG-3 in potatoes in growth chamber studies. Population densities of the pathogen were not significantly reduced in saturated (flooded) soils relative to fallow. However, the qPCR approach was more sensitive and quantitative than the toothpick baiting method for diagnosis of these soil samples. Accurate detection and quantification of R. solani AG-3 in soil will facilitate the development of integrated management plans for Rhizoctonia diseases of potato.

First report of stem and root rot of monkshood caused by Rhizoctonia spp. in Japan

Japanese monkshood (Aconitum japonicum subsp. subcuneatum) with stem rot and root rot were found in two fields in Hokkaido and Toyama, Japan, in 2015. The isolate obtained from Hokkaido was identified as Rhizoctonia solani anastomosis group (AG)-5, and the isolate from Toyama was binucleate Rhizoctonia AG-U based on the number of nuclei, hyphal fusion reactions, and sequences of the rDNA-ITS region. The symptoms were reproduced in inoculation tests. This is the first report of stem and root rot of monkshood caused by Rhizoctonia spp. in Japan.

Interaction of Rhizoctonia solani and Leuconostoc spp. causing sugar beet root rot and tissue pH changes in Idaho

Late season Rhizoctonia root rot in sugar beet is a serious yield limiting disease problem caused by an interaction between Rhizoctonia solani and Leuconostoc spp. in Idaho. To better understand this interaction, the two most common Leuconostoc haplotypes were co-inoculated with 17 R. solani strains representing the range of genetic diversity established previously. The study was conducted twice by inoculating sugar beet roots in the field using a plug assay and measuring root rot and tissue pH. L. mesenteroides strain L12311 (17 mm of rot) had significantly (P < 0.0001) more rot than L. pseudomesenteroides strain L12487 (13 mm) when combined with the fungal strains. The R. solani anastomosis group (AG) 2–2 IIIB strains (16 mm of rot) led to significantly (P < 0.0001–0.0073) more rot than strains associated with other AGs: 2–2 IV (11 mm), 4 HG-I (5 mm) and 4 HG-II (3 mm). When R. solani AG-2-2 IIIB strains from three phylogenetic groups were compared, rot ranged from 15 to 17 mm and did not differ (P = 0.1275–0.5565). The pH for root tissue with at least 30 mm of rot was lower (4.0–4.2 ± 0.2–0.4) than tissue with < 2 mm of rot and water checks (6.2–6.4 ± 0.1–0.2). Both isolations and tissue pH suggest late season sugar beet root rot is primarily associated with Leuconostoc and secondary organisms. However, damage was minor without both R. solani AG-2-2 and Leuconostoc strains present when internal rot initiates.

Glasshouse-specific occurrence of basal rot pathogens and the seasonal shift of Rhizoctonia solani anastomosis groups in lettuce

Basal rot is a common disease in Belgian lettuce, which is mainly controlled by fungicides and chemical soil disinfestation. A seasonal appearance of the basal rot pathogens: Rhizoctonia solani, Sclerotinia spp., Botrytis cinerea and Pythium spp. has been reported, but lettuce growers use standard spraying schemes, irrespective of the occurrence of the pathogen. Due to stricter regulations and environmental concerns the superfluous use of fungicides should be omitted. We investigated if the use of fungicides could be reduced by only controlling the active pathogens. Therefore, lettuce was continuously grown in three glasshouses without any fungal disease control and the active pathogens causing basal rot were identified. The occurrence of basal rot pathogens appeared to be glasshouse specific and the different basal rot pathogens were active throughout the year. However, a seasonal appearance of R. solani anastomosis groups and Pythium spp. was observed with AG4-HGI and Pythium ultimum active at higher temperatures and AG2–1, AG-BI, AG1-IB and Pythium sylvaticum at lower temperatures. We report for the first time the isolation of AG-BI from infected plants. Each R. solani anastomosis group had its own optimal growth rate in vitro. Differences in pathogenicity between R. solani anastomosis groups were observed on detached leaves. AG1-IB and AG4-HGI were most pathogenic, followed by AG2–1 and AG-BI. These results show that the fungicide spraying scheme should be adapted to the occurring pathogens in the glasshouse. This information is of high importance in developing a sustainable control strategy for basal rot pathogens.

Genotypes and Genomic Regions Associated With Rhizoctonia solani Resistance in Common Bean.

Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris) is an important root rot pathogen of common bean (Phaseolus vulgaris L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; n = 273) and Middle American (MDP; n = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using R. solani anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP (n = 28) and ∼6% of the MDP (n = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to R. solani in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume.

First Report of Rhizoctonia solani AG 2-2IIIB Causing Elephant Hide on Potato Tubers in South Africa

Rhizoctonia solani is a common pathogen that affects the yield and quality of potato (Solanum tuberosum) tubers. R. solani produces sclerotia on the progeny tubers (black scurf) as well as brown sunken lesions (cankers) on the stolons, stems, and roots of the plant (Banville 1989). In addition, Rhizoctonia is associated with atypical symptoms on potato tubers such as deformation, cracking, elephant hide, and pitting (Campion et al. 2003; Muzhinji et al. 2014). R. solani is taxonomically complex, consisting of 13 anastomosis groups (AGs) that differ in morphology, ecology, and host range (Sneh et al. 1998). R. solani AG 3-PT is the predominant AG associated with potato diseases globally (Woodhall et al. 2007). In February 2017, potato tuber samples (cv. Mondial) displaying dark brown scab lesions (elephant hide) (Muzhinji et al. 2014) were collected from the Limpopo, Eastern and Western Free State, potato growing regions in South Africa. The symptoms were similar to those of elephant hide and corky crack symptoms reported by Muzhinji et al. (2014) in South Africa. Small sections of infected tissue were excised, sterilized in 70% ethanol for 30 s and then in 1% NaOCl for 1 min, rinsed in sterile water, plated onto potato dextrose agar (PDA), and incubated at 25°C for 5 days. Hyphal tips of an isolate (R1A) with Rhizoctonia-like colonies were subcultured on PDA and examined for morphological characteristics microscopically. The hyphae were branched at right angles, with constriction at the point of origin, and the mycelium was aerial, brown, and fluffy, characteristics consistent with the Rhizoctonia genus (Sneh et al. 1998). The identity of the fungus was confirmed by sequencing the partial internal transcribed spacer (ITS) region of ribosomal DNA (rDNA) using ITS1-F and ITS4 primers (Gardes and Bruns 1993; White et al.1990). The resulting sequence (MK024251) showed 99% homology with other AG2-2IIIB sequences found in the NCBI GenBank database (GU811673 and FJ492113). Therefore, based on morphological and molecular methods, the isolate was identified as R. solani AG2-2IIIB. The isolate was deposited in the National Collection of Fungi, hosted at the Agricultural Research Council–Plant Health and Protection. Pathogenicity tests were conducted in the greenhouse to fulfill Koch’s postulates. Five PDA plugs of an actively growing culture were mixed with 10 g of sterile barley grains in a 250-ml Erlenmeyer flask and incubated for 14 days until fully colonized. One disease-free mini-tuber (cv. Mondial) was planted in each of 24 5-liter pots and inoculated with 10 g of colonized barley grains. Control plants were inoculated with sterile barley grains only. After inoculation, plants were placed in the greenhouse with a 12-h photoperiod at 25 ± 2°C. Progeny tubers were assessed for elephant hide symptoms at harvest, 92 days after planting. The incidence of elephant hide was 55.7% and severity 1.26. R. solani AG2-2IIIB was consistently reisolated from the symptomatic tubers, and identity of the isolate was confirmed as described previously, thus confirming Koch’s postulates. No symptoms were observed on control plants. The experiment was conducted twice with the same results. Until now, only AG 3-PT was reported to be associated with elephant hide in South Africa (Muzhinji et al. 2014). Therefore, this is the first report of R. solani AG2-2IIIB causing elephant hide on potato tubers in South Africa, and the AG should be considered when developing disease control strategies to effectively manage this disease.

Sensitivity of Rhizoctonia spp. to flutolanil and characterization of the point mutation in succinate dehydrogenase conferring fungicide resistance

Rhizoctonia are the primary pathogens associated with damping-off disease of sugar beet seedlings in China. Flutolanil is an important member of the succinate dehydrogenase (SDH) inhibitors, and exhibits a high level of antifungal activity against Rhizoctonia. The sensitivity of Rhizoctonia associated with sugar beet seedling damping-off disease to flutolanil has not been comprehensively examined, nor has the underlying basis for resistance. In the present study, a total of 221 collected Rhizoctonia isolates were found to be extremely sensitive to flutolanil in vitro, having a mean median effective concentration (EC50) value of 0.1727 ± 0.0074 μg mL−1. Two flutolanil-resistant isolates were generated using flutolanil-amended media. The resistant isolates, relative to the parental sensitive isolate, exhibited a slower rate of mycelial growth at certain temperatures and slightly decreased virulence on sugar beet seedlings. Flutolanil resistance was stable in the two generated resistant isolates after growing them for ten generations on potato dextrose agar (PDA) plates without fungicide. Flutolanil resistance was positively correlated with cross-resistance to thifluzamide, penthiopyrad, and tebuconazole. Molecular characterization and amino acid polymorphism analysis of the translated SDHA, SDHB, SDHC genes in Rhizoctonia indicated that there were no amino acid substitutions in the SDHA or SDHB subunits, however, a replacement of phenylalanine (Phe) by leucine (Leu) at position 48 (F48 L) in the SDHC subunit was observed. This study is the first documentation of flutolanil-resistance in R. solani anastomosis group (AG)-4HGI isolates with a point mutation in the SDHC subunit.

The rice CYP78A gene BSR2 confers resistance to Rhizoctonia solani and affects seed size and growth in Arabidopsis and rice

The fungal pathogen Rhizoctonia solani causes devastating diseases in hundreds of plant species. Among these, R. solani causes sheath blight, one of the three major diseases in rice. To date, few genes have been reported that confer resistance to R. solani. Here, rice-FOX Arabidopsis lines identified as having resistance to a bacterial pathogen, Pseudomonas syringae pv. tomato DC3000, and a fungal pathogen, Colletotrichum higginsianum were screened for disease resistance to R. solani. BROAD-SPECTRUM RESISTANCE2 (BSR2), a gene encoding an uncharacterized cytochrome P450 protein belonging to the CYP78A family, conferred resistance to R. solani in Arabidopsis. When overexpressed in rice, BSR2 also conferred resistance to two R. solani anastomosis groups. Both Arabidopsis and rice plants overexpressing BSR2 had slower growth and produced longer seeds than wild-type control plants. In contrast, BSR2-knockdown rice plants were more susceptible to R. solani and displayed faster growth and shorter seeds in comparison with the control. These results indicate that BSR2 is associated with disease resistance, growth rate and seed size in rice and suggest that its function is evolutionarily conserved in both monocot rice and dicot Arabidopsis.

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8.

The soilborne fungus Rhizoctonia solani anastomosis group (AG) 8 is a major pathogen of grain crops resulting in substantial production losses. In the absence of resistant cultivars of wheat or barley, a sustainable and enduring method for disease control may lie in the enhancement of biological disease suppression. Evidence of effective biological control of R. solani AG8 through disease suppression has been well documented at our study site in Avon, South Australia. A comparative metatranscriptomic approach was applied to assess the taxonomic and functional characteristics of the rhizosphere microbiome of wheat plants grown in adjacent fields which are suppressive and non-suppressive to the plant pathogen R. solani AG8. Analysis of 12 rhizosphere metatranscriptomes (six per field) was undertaken using two bioinformatic approaches involving unassembled and assembled reads. Differential expression analysis showed the dominant taxa in the rhizosphere based on mRNA annotation were Arthrobacter spp. and Pseudomonas spp. for non-suppressive samples and Stenotrophomonas spp. and Buttiauxella spp. for the suppressive samples. The assembled metatranscriptome analysis identified more differentially expressed genes than the unassembled analysis in the comparison of suppressive and non-suppressive samples. Suppressive samples showed greater expression of a polyketide cyclase, a terpenoid biosynthesis backbone gene (dxs) and many cold shock proteins (csp). Non-suppressive samples were characterised by greater expression of antibiotic genes such as non-heme chloroperoxidase (cpo) which is involved in pyrrolnitrin synthesis, and phenazine biosynthesis family protein F (phzF) and its transcriptional activator protein (phzR). A large number of genes involved in detoxifying reactive oxygen species (ROS) and superoxide radicals (sod, cat, ahp, bcp, gpx1, trx) were also expressed in the non-suppressive rhizosphere samples most likely in response to the infection of wheat roots by R. solani AG8. Together these results provide new insight into microbial gene expression in the rhizosphere of wheat in soils suppressive and non-suppressive to R. solani AG8. The approach taken and the genes involved in these functions provide direction for future studies to determine more precisely the molecular interplay of plant-microbe-pathogen interactions with the ultimate goal of the development of management options that promote beneficial rhizosphere microflora to reduce R. solani AG8 infection of crops.

Screening for soybean varieties suited to Belgian growing conditions based on maturity, yield components and resistance to Sclerotinia sclerotiorum and Rhizoctonia solani anastomosis group 2-2IIIB

AbstractPolicy makers and farmers in north-west Europe are expressing a growing interest in soybean production. However, cool and wet climatic conditions in this region pose challenges for this crop in terms of reaching maturity and producing sufficient yield and create additional disease pressure from the fungal pathogens Sclerotinia sclerotiorum and Rhizoctonia solani. To increase the chance for successful introduction of this new crop in Belgium and to determine the main issues for local soybean breeding programmes, 14 early maturing varieties were screened over a 2-year-period for their agronomic performance. Based on novel bioassays, susceptibility to S. sclerotiorum and R. solani anastomosis group (AG) 2-2IIIB was evaluated. The varieties tested were able to reach sufficient maturity (average seed moisture content of 19.0%) by the beginning of October. Significant differences were observed in most agronomic characteristics, with seed yield and protein content ranging from 2002 to 2916 kg dry matter/ha and 35.5–43.3%, respectively. Taller varieties ripened later but reached higher protein levels compared with shorter varieties. Tolerance to lodging was correlated with seed and protein yield but was not correlated with plant height. Large seeds corresponded with a high protein content. Susceptibility to S. sclerotiorum reflected significant differences between varieties. In contrast, levels of susceptibility to R. solani AG 2-2IIIB were similar between most varieties, with only the variety Primus showing significantly less disease. The results of the current study hold promise for a successful introduction of soybean cultivation in north-west Europe and areas for further crop improvement have been identified.

First Report of Lily Root Rot Caused by Thanatephorus cucumeris AG 2-1 in the United States

A survey was undertaken on April 2016 to profile soilborne fungal pathogens causing root rot and lesions on lily (Lilium longiflorum) cv. Nellie White in Brookings, Curry County, Oregon. Diseased roots were either blackened or rotted. Sections of diseased roots including the epidermis were surface sterilized and placed on sterile water agar plates containing 100 μg/ml chloramphenicol. From the emerging mycelia, pure cultures were obtained by collecting hyphal tips and placing them on potato dextrose agar (PDA) medium. Recently, we demonstrated the presence of pathogenic Fusarium oxysporum, F. tricinctum, and Ceratobasidium sp. AG-I isolates in eight randomly selected fungal isolates from diseased roots of lilies (Lakshman et al. 2017). In this investigation, three additional fungal isolates showed four to six nuclei per cell under the microscope with lactophenol staining at 400× magnification. The hyphae were branched at right angles, and septa were present near the point of branching. The respective fungal isolates produced dark brown microsclerotia of 2 mm or less in diameter, mostly at the edge of PDA plates. Total DNA from each of the three cultures was PCR amplified with ITS1 and ITS4 ribosomal DNA (rDNA) primers (White et al. 1990) and cloned into a TOPO TA cloning vector (Thermo Fisher Scientific, Waltham, MA). Nucleotide sequences of a randomly chosen clone from each of the three isolates were 706 bp long and identical in sequence. Hence, all were assumed to have originated from a single haplotype and numerated as ELRF 11. The rDNA amplicon deposited in GeneBank (accession no. MF972486) showed 100% homology with the corresponding region of two isolates of Rhizoctonia solani (Teleomorph: Thanatephorus cucumeris) anastomosis group (AG) 2-1 (gb|KP662692 and gb|JQ676881). For pathogenicity tests, 5-mm-diameter plugs from the margin of a 5-day-old culture were placed near the roots of axenically grown lily seedlings, two replicates per treatment and repeated two times, for 10 days at 22°C. Necrotic brown lesions appeared on the roots of such seedlings whereas control inoculation with only PDA plugs did not produce any symptoms on roots. Lactophenol staining and microscopy showed both inner and outer mycelia colonization on infected roots. Additionally, the ELRF 11 caused necrosis and rot upon inoculation of roots of diploid strawberry runners (Hawaii4 F7-3) and necrotic spots on detached leaves of Nicotiana glutinosa, N. benthamiana, and N. paniculata. The onset of necrotic symptoms on those plants occurred 4 to 7 days after inoculation. Fungus with identical morphology was reisolated from root lesions, thus proving Koch’s postulate. No fungus could be isolated from respective roots and leaves of control seedlings. AG 2-1 isolates are reported to be pathogenic on roots, bulbs, and leaves of various hosts, including strawberry and Nicotiana spp. (Yang and Li 2012). Furthermore, both pathogenic and nonpathogenic isolates of AG 2-1 were reported on bulbous crops in the Netherlands (Schneider et al. 1997). To our knowledge, this is the first report of T. cucumeris AG 2-1 causing root rot of lily in the field plots of Oregon or anywhere else in the United States. As various AGs may differ in sensitivity to fungicides and biocontrol agents (Amaradasa et al. 2014), a systematic survey of Rhizoctonia and other pathogens infecting lily under field conditions is required in order to develop effective disease management strategies.

Draft Genome Sequence of Rhizoctonia solani Anastomosis Group 1 Subgroup 1A Strain 1802/KB Isolated from Rice.

ABSTRACTSheath blight, caused by Rhizoctonia solani anastomosis group 1 subgroup 1A (AG1-1A), is one of the most devastating rice diseases worldwide. Here, we report the draft genome sequence of R. solani AG1-1A strain 1802/KB isolated from a popular Malaysian rice variety. To the best of our knowledge, this is the second reported representative genome from AG1-1A.

First report of Rhizoctonia disease of lily caused by Rhizoctonia solani AG-11 in Japan

Blight on leaves, stems and bulbs of lilies grown in a greenhouse were found in Hokkaido, Japan, in 2012. Two isolates obtained from the lesions were identified as Rhizoctonia solani anastomosis group (AG)-11 based on morphology and molecular analysis. Original symptoms were reproduced after artificial inoculation with the isolates. Except for R. solani AG-2-1 and AG-4 HG-I, none of the AGs have been reported as pathogens causing lily Rhizoctonia disease in Japan; therefore, we propose adding AG-11 as a pathogen of the disease. More importantly, we report the first appearance of crop disease caused by AG-11 in Japan.

The transcriptional landscape of Rhizoctonia solani AG1-IA during infection of soybean as defined by RNA-seq.

Rhizoctonia solani Kühn infects most plant families and can cause significant agricultural yield losses worldwide; however, plant resistance to this disease is rare and short-lived, and therefore poorly understood, resulting in the use of chemical pesticides for its control. Understanding the functional responses of this pathogen during host infection can help elucidate the molecular mechanisms that are necessary for successful host invasion. Using the pathosystem model soybean-R. solani anastomosis group AG1-IA, we examined the global transcriptional responses of R. solani during early and late infection stages of soybean by applying an RNA-seq approach. Approximately, 148 million clean paired-end reads, representing 93% of R. solani AG1-IA genes, were obtained from the sequenced libraries. Analysis of R. solani AG1-IA transcripts during soybean invasion revealed that most genes were similarly expressed during early and late infection stages, and only 11% and 15% of the expressed genes were differentially expressed during early and late infection stages, respectively. Analyses of the differentially expressed genes (DEGs) revealed shifts in molecular pathways involved in antibiotics biosynthesis, amino acid and carbohydrate metabolism, as well as pathways involved in antioxidant production. Furthermore, several KEGG pathways were unique to each time point, particularly the up-regulation of genes related to toxin degradation (e.g., nicotinate and nicotinamid metabolism) at onset of necrosis, and those linked to synthesis of anti-microbial compounds and pyridoxine (vitamin B6) biosynthesis 24 h.p.o. of necrosis. These results suggest that particular genes or pathways are required for either invasion or disease development. Overall, this study provides the first insights into R. solani AG1-IA transcriptome responses to soybean invasion providing beneficial information for future targeted control methods of this successful pathogen.