Bacillus subtilis and Bacillus amyloliquefaciens Mix Suppresses Rhizoctonia Disease and Improves Rhizosphere Microbiome, Growth and Yield of Potato (Solanum tuberosum L.)

Black scurf and stem canker caused by Rhizoctonia solani is a significant disease problem of potatoes. Currently, chemical methods are the primary means of controlling this pathogen. This study sought to explore an alternative approach by harnessing the biocontrol potential of a bacterial mix of Bacillus subtilis and Bacillus amyloliquefaciens against black scurf, and to determine their effect on rhizosphere microorganisms of soil microbiota. This study showed that these bacteria demonstrate antagonistic activity against Rhizoctonia solani. Reduced damage to potato plants during the growing season in Siberia was observed. The index of disease development decreased from 40.9% to 12.0%. The treatment of tubers with this mix of bacteria also led to a change in the composition of the rhizosphere microbiota (according to CFU, 16S and ITS sequencing). This effect was accompanied by a positive change in plant physiological parameters (spectrophotometric analysis). The concentration of chlorophyll in potatoes with the bacterial mix treatment increased by 1.3 fold (p ≤ 0.001), and of carotenoids by 1.2 fold (p ≤ 0.01) compared with the control. After bacterial mix treatment, the length of the aerial parts of plants was 1.3 fold higher (p ≤ 0.001), and the number of stems 1.4 fold higher (p ≤ 0.05). The yield of potatoes was increased by 8.2 t/ha, while the large tuber fraction was increased by 16% (p ≤ 0.05). The bacteria mix of Bacillus subtilis and Bacillus amyloliquefaciens suppressed the plant pathogenic fungus Rhizoctonia solani, and simultaneously enhanced the physiological parameters of potato plants. This treatment can be used to enhance the yield/quality of potato tubers under field conditions.

A novel species of Microsphaeropsis causing cankers on Rafnia amplexicaulis in South Africa

Cankers leading to branch, stem and plant death were observed on the South African endemic Rafnia amplexicaulis (Fabaceae) in the Cederberg Wilderness Area, South Africa, during September 2021. Conidiomatal pycnidia were found developing on the cankers, and isolations consistently yielded a Microsphaeropsis species. Phylogenetic analysis based on partial nucleotide sequences of the internal transcribed spacers (ITS), the nuclear large subunit (LSU) and RNA polymerase II second largest subunit (RPB2) regions showed that the fungus represented an undescribed species. Based on the multigene phylogeny and morphological characteristics, we describe the species here as M. rafniae sp. nov. Pathogenicity tests and the fulfilment of Koch's postulates confirmed that M. rafniae sp. nov. is the cause of the cankers of R. amplexicaulis. Presently, this disease is known from a single location in South Africa, and further surveys are required to determine its distribution and relative importance. Citation: Paap T, Marincowitz S, Pham NQ, Roets F, Basson RJ, Wingfield BD, Oberlander K, Wingfield MJ (2023). A novel species of Microsphaeropsis causing cankers on Rafnia amplexicaulis in South Africa. Fungal Systematics and Evolution 12: 73-80. doi: 10.3114/fuse.2023.12.05.

First report of Diaporthe sojae causing stem canker on blueberry in China

Blueberry (Vaccinium corymbosum) plants are popular all over the world due to their high nutritional value and health benefits. In October 2020, blueberry stems (cv. O'Neal) displaying reddish brown necrotic lesions were observed from a blueberry field in Anqing (Anhui, China), with the incidence of approximately 90%. The affected plants were somewhat stunted that had smaller fruit, and in severe cases, partial or whole plant died. We randomly selected three sampling sites to collect stems with the symptoms. Samples at the margin between diseased and healthy tissues were taken out, cut into 5 mm pieces in length，and then mixed them together. Twenty small samples were surface-sterilized, and plated onto potato dextrose agar (PDA). The plates were incubated at 25°C in the dark until fungal colonies were observed. After subculturing single hyphal tips, 9 out of 12 fungal isolates with similar morphologies were obtained. The representative isolate, LMKY12 was selected for further identification. The colonies on PDA showed white, fluffy aerial mycelia with 7.9  0.2 mm (n=5) diameter after inoculation in darkness at 25°C for one week. The colony darkens in color with age, yellowish pigmentation in reverse were observed. After 15 days of incubation, dark brown, irregular hard particles (fruiting bodies in sexual stage) accumulated on the surface of the colonies. Asci were 8-spored, sessile, club-like, hyaline, and 35-46 x 6-9 μm (n=30) in size. The ascospores were oval or spindle shaped, two-celled, constricted at division, and containing four guttulates with larger guttules at centre and smaller one at ends, measured 9-11 x 2-4 um (n=50). No sporulation observed on blueberry stems after inoculated 30 days. In order to induce the production of conidiophores, mycelial plugs were placed on blueberry leaves and cultured in darkness at 25°C. There are two types of conidia observed after 20 days of inoculation. Alpha conidia were aseptate, hyaline, smooth, ovate to ellipsoidal, often biguttulate, measured 5.33-7.26 x 1.65-2.53 μm (n=50). Beta conidia were hyaline, linear, measured 12.60-17.91 x 0.81-1.38 μm (n=30). The morphological characteristics matched the previous description of D. sojae (Udayanga et al. 2015; Guo et al. 2020). To confirm the identification, the mycelial genomic DNA of LMKY12 was extracted as a template. The rDNA internal transcribed spacer (ITS), translation elongation factor 1-α gene (TEF1-α), and calmodulin (CAL) were amplified and sequenced using primers ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R, and CAL-228F/CAL-737R (Carbone and Kohn 1999), respectively. BLAST analysis revealed that the ITS (ON545758), CAL (OP886852), and TEF1-α (OP886853) sequences were 100% (527/527 base pairs), 99.21% (504/508 base pairs), and 99.41% (336/338 base pairs) similar to the strain FAU636 of D. sojae (KJ590718, KJ612115, KJ590761), respectively. Phylogenetic analysis based on concatenated sequences of ITS, TEF1-α, and CAL using MEGA 7.0 by maximum likelihood attributed the isolate LMKY12 to the D. sojae clade. Pathogenicity tests were performed on blueberry cv. O'Neal using detached stems (n=8) in laboratory, one-year-old potted plants (n=4) in greenhouse. Inoculations were done by placing mycelial plugs (7 mm in diameter) taken from a 7-day-old PDA culture on wounded stems. Inoculations with uncolonized agar plugs served as negative controls. Reddish dark brown lesions similar to the symptoms were observed on all inoculated stems 7 days after inoculation. No symptoms developed on control stems. Reisolations were successfully made from all the inoculated stems, and the pathogen was confirmed by the presence of pycnidia, alpha conidia and beta conidia. To our knowledge, this is the first report of D. sojae causing blueberry stem canker in China.

Pestalotiopsis Species Associated with Blueberry Leaf Spots and Stem Cankers in Sichuan Province of China

Blueberry leaf spots and stem cankers caused by Pestalotiopsis spp. have become a serious threat for the production of blueberry in Sichuan Province. To characterize the etiology of the diseases connected with these fungi, samples showing leaf spot and stem canker symptoms were collected from the 12 main blueberry-growing areas of Sichuan Province from 2015 to 2020 and used for pathogen isolation. In total, 91 fungal isolates were obtained with preliminary morphological identification and 48 representative strains were selected for further pathogenicity test and molecular identification. Four species, including Pestalotiopsis clavispora (Neopestalotiopsis clavispora) (57.14%), P. trachicarpicola (28.57%), P. chamaeropis (13.19%), and P. adusta (1.10%), were identified based on conidial morphology, cultural characteristics, and phylogenetic analysis of the internal transcribed spacer region, partial sequence of the β-tubulin gene, and the translation elongation factor 1-α. Pathogenicity tests showed that four species were pathogenic to leaves and stems of blueberry. Among them, P. clavispora (N. clavispora) was the most aggressive as the predominant species to cause both leaf spot and stem canker. P. trachicarpicola and P. chamaeropis were mainly isolated from leaves but also pathogenic to stems. P. adusta was only isolated from stems but also pathogenic to leaves. To the best of our knowledge, this is the first report of P. chamaeropis and P. adusta as pathogens causing leaf spots and stem canker on blueberry. The results provide helpful information in disease diagnosis and management of blueberry.

Anastomosis Groups of Rhizoctonia solani and Binucleate Rhizoctonia Associated with Potatoes in Idaho

A survey of the relative incidence of anastomosis groups (AGs) of Rhizoctonia spp. associated with potato disease was conducted in Idaho, the leading potato producing state in the U.S.A. In total, 169 isolates of Rhizoctonia solani and seven binucleate Rhizoctonia (BNR) isolates were recovered from diseased potato plants. The AG of each isolate was determined through real-time PCR assays for AG 3-PT and phylogenetic analysis of the internal transcribed spacer region of ribosomal DNA. AG 3-PT was the predominant AG, accounting for 85% of isolates recovered, followed by AG 2-1 (5.7%) and AG 4 HG-II (4.5%). Two different subsets of AG 2-1 isolates were recovered (subset 2 and 3). Three isolates each of AG A and AG K were recovered, as well as one isolate each of AG 5 and AG W. An experiment carried out under greenhouse conditions with representative isolates of the different AGs recovered from Idaho potatoes showed differences in aggressiveness between AGs to potato stems, with AG 3-PT being the most aggressive followed by an isolate of AG 2-1 (subset 3). The three BNR isolates representative of AG A, AG K, and AG W appeared to be less aggressive to potato stems than the R. solani isolates except for the AG 2-1 (subset 2) isolate. This is the first comprehensive study of the relative incidences of Rhizoctonia species associated with Idaho potatoes and the first study to report the presence of BNR AG W outside of China.

First Report of Stem Canker on Dangshen (Codonopsis pilosula) Caused by Binucleate Rhizoctonia AG-K in China

Dangshen (Codonopsis pilosula) is a well-known medicinal and food homologous plant in China, which is widely used as a tonic agent and has good immunomodulatory effects (Bai et al. 2020; Luan et al. 2021). To retain the best medicinal properties, growers imitated the original ecological planting method for cultivating C. pilosula in hillside fields in Wutai county, Shanxi province, China. In July and August 2021 and 2022, stem canker disease was observed in C. pilosula. The basal part of the stems showed slightly sunken brown lesions, and the disease incidence was up to 20% in the investigated fields (6.67 ha). To identify the causal agents of stem canker, 12 small pieces (approximately 5 mm long) from 12 diseased samples (one piece per sample) were cut from the border of the lesions, surface-sterilized (70% ethanol for 30 s, 0.5% NaClO for 3 min), washed three times with sterile water, and then incubated on water agar (WA) at 25 °C for 24 h. Isolates with right-angle branching, a septum near the branch, and a slight constriction at the branch base were selected, and their hyphal tips were transferred onto potato dextrose agar (PDA) plates. After incubation at 25 °C, 12 Rhizoctonia-like isolates (Dcp-19 to Dcp-30) with white colonies were obtained. White monilioid cells in aerial mycelia formed as they aged but did not produce sclerotia. Based on nuclear fluorescence staining with 1 μg·mL-1 4'-6-diamidino-2-phenylindole as described by Ahvenniemi et al. (2009), there were two nuclei per hyphal cell for all the 12 isolates. Moreover, the sequences of internal transcribed spacer region of ribosomal DNA (rDNA-ITS) of all the 12 isolates were amplified using the primers ITS1/ITS4 (White et al. 1990). For identical sequences, only the rDNA-ITS sequence (674 bp) of Dcp-19 has been deposited in GenBank (accession no. ON004932) and BLASTn analyses showed 100% homology with Rhizoctonia AG-K (MF070696). Maximum likelihood phylogenetic analysis further confirmed the identification. Healthy C. pilosula plants grown for two years in hillside fields were transplanted into sterile soil for pathogenicity testing. And the 12 isolates were all done in this test. Sterilized wheat seeds were placed on a 2-day-old colony of the isolate and incubated for 7 days. One fungus-infested seed was placed at the base of the stem and covered with sterilized soil. Control plants were inoculated with sterilized wheat seeds. Tests were performed on three plants for each isolate. The experiment was repeated twice. All the plants were cultivated at 22 °C and 50% relative humidity. After three weeks, the basal stems of the control plants were still healthy and did not have lesions, but the treated plants exhibited sunken brown canker lesions. The mean disease incidence of all the 12 isolates was 58.33%. The AG-K isolates re-isolated from the lesions of treated plants were confirmed by the morphological and molecular characteristics mentioned above, fulfilling Koch's postulates. To our knowledge, this is the first report of stem canker on C. pilosula caused by binucleate Rhizoctonia AG-K in China.

A new avirulence gene of Leptosphaeria maculans, AvrLm14, identifies a resistance source in American broccoli (Brassica oleracea) genotypes

In many cultivated crops, sources of resistance to diseases are sparse and rely on introgression from wild relatives. Agricultural crops often are allopolyploids resulting from interspecific crosses between related species, which are sources of diversity for resistance genes. This is the case for Brassica napus (oilseed rape, canola), an interspecific hybrid between Brassica rapa (turnip) and Brassica oleracea (cabbage). B. napus has a narrow genetic basis and few effective resistance genes against stem canker (blackleg) disease, caused by the fungus Leptosphaeria maculans, are currently available. B. rapa diversity has proven to be a valuable source of resistance (Rlm, LepR) genes, while B. oleracea genotypes were mostly considered susceptible. Here we identified a new resistance source in B. oleracea genotypes from America, potentially effective against French L. maculans isolates under both controlled and field conditions. Genetic analysis of fungal avirulence and subsequent cloning and validation identified a new avirulence gene termed AvrLm14 and suggested a typical gene-for-gene interaction between AvrLm14 and the postulated Rlm14 gene. AvrLm14 shares all the usual characteristics of L. maculans avirulence genes: it is hosted in a genomic region enriched in transposable elements and heterochromatin marks H3K9me3, its expression is repressed during vegetative growth but shows a strong overexpression 5-9 days following cotyledon infection, and it encodes a small secreted protein enriched in cysteine residues with few matches in databases. Similar to the previously cloned AvrLm10-A, AvrLm14 contributes to reduce lesion size on susceptible cotyledons, pointing to a complex interplay between effectors promoting or reducing lesion development.

Effectiveness of Augmentative Biological Control of Streptomyces griseorubens UAE2 Depends on 1-Aminocyclopropane-1-Carboxylic Acid Deaminase Activity against Neoscytalidium dimidiatum

To manage stem canker disease on royal poinciana, actinobacterial isolates were used as biological control agents (BCAs) based on their strong in vitro inhibitory effects against Neoscytalidiumdimidiatum. Streptomyces griseorubens UAE2 and Streptomyces wuyuanensis UAE1 had the ability to produce antifungal compounds and cell-wall-degrading enzymes (CWDEs). Only S. griseorubens, however, restored the activity of 1-aminocyclopropane-1-carboxylate (ACC) deaminase (ACCD). In vivo apple fruit bioassay showed that lesion development was successfully constrained by either isolates on fruits inoculated with N. dimidiatum. In our greenhouse and container nursery experiments, S. griseorubens showed almost complete suppression of disease symptoms. This was evident when the preventive treatment of S. griseorubens significantly (p < 0.05) reduced the numbers of conidia of N. dimidiatum and defoliated leaves of royal poinciana seedlings to lesser levels than when S. wuyuanensis was applied, but comparable to control treatments (no pathogen). The disease management of stem canker was also associated with significant (p < 0.05) decreases in ACC levels in royal poinciana stems when S. griseorubens was applied compared to the non-ACCD-producing S. wuyuanensis. This study is the first to report the superiority of antagonistic actinobacteria to enhance their effectiveness as BCAs not only for producing antifungal metabolites and CWDEs but also for secreting ACCD.

Integrated Transcriptome and Metabolome Analysis Revealed That Flavonoid Biosynthesis May Dominate the Resistance of Zanthoxylum bungeanum against Stem Canker

Stem canker of Zanthoxylum bungeanum is a devastating disease that seriously affects the plantation and industrial development of Z. bungeanum due to a lack of effective control measures. The objective of this study was to screen out resistant Z. bungeanum varieties and further explore their resistance mechanisms against stem canker. Results showed that the most resistant and susceptible varieties were, respectively, Doujiao (DJ) and Fengxian Dahongpao (FD). Combining transcriptomic and metabolomic analyses, we found that the genes and metabolites associated with the phenylpropanoid metabolism, especially flavonoid biosynthesis, were highly significantly enriched in DJ following pathogen infection compared with that in FD, which indicated that the flavonoid metabolism may positively dominate the resistance of Z. bungeanum. This finding was further confirmed by quantitative real-time polymerase chain reaction analysis, through which higher expression levels of core genes involved in flavonoid metabolism in resistant variety were observed. Moreover, by analyzing the differences in the flavonoid content in the stems of resistant and susceptible varieties and the antifungal activities of flavonoids extracted from Z. bungeanum stems, the conclusion that flavonoid metabolism positively regulates the resistance of Z. bungeanum was further supported. Our results not only aid in better understanding the resistance mechanisms of Z. bungeanum against stem canker but also promote the breeding and utilization of resistant varieties.

First Report of Stem Canker of Almond Trees Caused by Fusarium solani in Greece

Almond (Prunus dulcis) is an important crop for Greece grown on 15.130 ha in 2019. In September 2019, a severe stem canker disease was observed in 6-year-old trees of cv Marta grafted on the rootstock 'F675C14', in a new almond grove of cvs Marta, Soleta, Antonela, Belona and Laurete, in Vlachiana, Heraklion, Crete, Greece. Only cv Marta trees were affected. Diseased trees exhibited cankers on trunks and branches with pale yellow to red-colored gum excreting from cankers, yellowing, leaf fall, twig and branch dieback, bark and wood tissue discoloration. Severely affected trees were killed. A Fusarium-like fungus was consistently isolated from symptomatic wood tissue previously surface-disinfested with 95% ethanol, on acidified potato dextrose agar (APDA). Emerging colonies were transferred to new PDA and the growth rate of the fungus was 7.86 mm/day at 24 °C in the dark. The abundant aerial mycelium was initially white, turning into pale orange in the centre after 7 days of growth on PDA. Microscopic observations revealed hyaline conidiophores measuring 26.74 ± 20.44 μm in length, developing microconidia 5.00 to 9.50 × 2.50 to 4.75 μm (average 6.64 × 3.50 μm) and macroconidia 10.00 to 23.25 × 3.75 to 5.50 μm (average 16.42 × 4.50 μm) in size. DNA from one representative single-spore isolate (code KOUB.AM.VR1) was extracted and the internal transcribed spacer region (ITS) of ribosomal DNA and translation elongation factor 1-alpha (EF 1-a) genes were amplified using the primer pairs ITS1/ITS4 (White et al. 1990) and EF1-F/EF2-R (O'Donnell et al. 1998), respectively. The PCR products were sequenced and deposited in GenBank (accession Nos. MW547397 and MW554492). Based on morphological characteristics (Leslie and Summerell 2006) and a BLAST search with 100.00% and 99.38% identity to published F. solani ITS and EF 1-a sequences in GenBank (KX034335.1, DQ247636.1) the fungus was identified as F. solani. Eight 3-year-old almond trees of cv. Marta were artificially inoculated in March 2020 by making a 6.0-mm-diameter hole into the trunk, inserting a 6-mm-diameter mycelial disc taken from a 10-day-old PDA culture, sealing the hole with cellophane membrane and covering with adhesive paper tape. Another eight trees of the same cultivar were mock-inoculated with sterilized PDA discs and served as controls. Potted trees were kept under ambient conditions. One month post inoculation, yellow gum was evident excreting around the inoculation point in F. solani-treated trees but not in the controls. Seven months post inoculation, longitudinal and transverse sections of inoculated trunks revealed internal and external symptoms similar to those observed under natural infection conditions and F. solani was steadily re-isolated from symptomatic wood tissue and identified by colony morphology. Neither symptoms nor positive isolations were observed in control trunks. Pathogenicity tests were repeated twice. Fusarium solani has been reported as the causal agent of stem canker or wood decay diseases in several woody hosts including bitternut hickory, black walnut, mulberry and pistachio trees (Crespo et al. 2019; Markakis et al. 2017; Park and Juzwik 2012; Tisserat 1987). To the best of our knowledge, this is the first worldwide report of stem canker caused by F. solani on almond tree. This disease could potentially be an increasing problem in almond growing areas and result in severe crop losses. Hence, effective management practices should be investigated and applied.

First Report of Diaporthe phaseolorum Causing Stem Canker of Hemp (Cannabis sativa)

Hemp is an annual herbaceous plant that is used for its fiber and oil in a variety of commercial and industrial products. In Florida, it is currently being explored as a new specialty crop. During a field trial from October to January 2019 in Wimauma, FL, a stem canker was observed on up to 60% of three-month-old plants of 'Eletta Campana', 'Carmagnola Selezionata', and 'Tygra'. Symptoms started on the main stems with light-to-dark brown lesions of different sizes and shapes. Over time, the lesions coalesced into large necrotic areas and bore pycnidia. Isolations were made from diseased stem tissues on General Isolation medium (Amiri et al. 2018) after surface disinfestation (Marin et al. 2020). The plates were placed in a growth chamber at 25°C under a 12/12 photoperiod. A fungus with white, floccose, aerial mycelium and pycnidia producing alpha and beta conidia was consistently isolated. Three single spore isolates were chosen for identification and pathogenicity tests. Pycnidia on PDA were globose to irregular and ranged from 170 to 250 μm long (210 ± 2.5, n = 50) and 140 to 220 μm wide (180 ± 2.7, n = 50). The alpha conidia were unicellular, hyaline, ellipsoidal to fusiform and ranged from 5.3 to 7.7 μm long (6.5 ± 1.6, n = 50) and 1.5 to 4.6 μm wide (2.8 ± 1.8, n = 50). The beta conidia were hyaline, elongated, filiform, straight or curved and ranged from 10.2 to 17.7 μm long (16.1 ± 2.2, n = 50) and 0.5 to 1.8 μm wide (0.8 ± 0.2, n = 50). Perithecia were not observed. Based on morphological features, the fungus was similar to anamorphs of Diaporthe spp. (Santos et al. 2011; Udayanga et al. 2015). DNA from the same three isolates was extracted using the FastDNA kit, and the ribosomal internal transcribed spacer (ITS), β-tubulin (TUB), and calmodulin (CAL) regions were amplified following Udayanga et al. (2014), and Sanger sequenced by Genewiz. Sequences were deposited in GenBank (accession no. MT497039 to MT497047 for ITS, TUB, and CAL). BLASTn searches revealed isolates 20-58, 20-59, and 20-60 were 96.34% identical to the epitype isolate D. phaseolorum AR4203 for ITS (KJ590738.1, 527 bp out of 547 bp), 100% for TUB (KJ610893.1, 459 bp out of 459 bp), and 100% for CAL (KJ612135.1, 522 bp out of 522 bp) (Udayanga et al. 2015). Their identity was confirmed by phylogenetic analyses using maximum likelihood and Bayesian inference methods. To complete Koch's postulates, pycnidia of the same three isolates were harvested and crushed in 2 mL Eppendorf tubes containing 0.01% Tween 20. Conidia suspensions were adjusted to 106 spores/mL. Three 5-week-old potted plants of 'Eletta Campana' and 'Carmagnola Selezionata' per isolate were inoculated using a 1 mL syringe with a needle by injecting 200 µL of the suspension into the stem. Plants were placed inside clear plastic bags for 48 h and maintained in the greenhouse. Control plants were injected with sterile deionized water and kept under the same conditions. The pathogenicity test was repeated once. Four weeks after inoculation, inoculated plants developed stem cankers from which the same pathogen was isolated, whereas controls remained healthy. To our knowledge, this is the first report of D. phaseolorum causing stem canker on hemp. This pathogen has been reported causing canker on sunflower and Phaseolus spp. (Gomzhina and Gannibal 2018; Udayanga et al. 2015; Vrandecic et al. 2009). This discovery may help shape future research into disease epidemiology and management for a crop in which very limited disease information is available at the moment.

Impact of a resistance gene against a fungal pathogen on the plant host residue microbiome: The case of the Leptosphaeria maculans-Brassica napus pathosystem

Oilseed rape residues are a crucial determinant of stem canker epidemiology as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterize the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify microorganisms interacting with this pathogen during residue degradation. We used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterized by metabarcoding. A combination of linear discriminant analysis and ecological network analysis was used to compare the microbial communities and to identify microorganisms interacting with L. maculans. Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonization of the residues by fungi. Direct interactions with other members of the community involved many fungal and bacterial amplicon sequence variants (ASVs). L. maculans appeared to play a minor role in networks, whereas one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) from the Leptosphaeria species complex may be considered a keystone taxon in the networks at harvest. This approach could be used to identify and promote microorganisms with beneficial effects against residue-borne pathogens and, more broadly, to decipher the complex interactions between multispecies pathosystems and other microbial components in crop residues.

Phytophthora palmivora-Cocoa Interaction

Phytophthora palmivora (Butler) is an hemibiotrophic oomycete capable of infecting over 200 plant species including one of the most economically important crops, Theobroma cacao L. commonly known as cocoa. It infects many parts of the cocoa plant including the pods, causing black pod rot disease. This review will focus on P. palmivora’s ability to infect a plant host to cause disease. We highlight some current findings in other Phytophthora sp. plant model systems demonstrating how the germ tube, the appressorium and the haustorium enable the plant pathogen to penetrate a plant cell and how they contribute to the disease development in planta. This review explores the molecular exchange between the oomycete and the plant host, and the role of plant immunity during the development of such structures, to understand the infection of cocoa pods by P. palmivora isolates from Papua New Guinea.

Quantitative PCR Assays Developed for Diaporthe helianthi and Diaporthe gulyae for Phomopsis Stem Canker Diagnosis and Germplasm Screening in Sunflower (Helianthus annuus)

Phomopsis stem canker of sunflower is caused by two fungal pathogens, Diaporthe helianthi and Diaporthe gulyae, in the United States. In this study, two quantitative PCR (qPCR) assays were developed to detect and quantify D. helianthi and D. gulyae in sunflower. The two assays differentiated the two fungi from each other, other species of the genus Diaporthe, and pathogens, and they have high efficiency (>90%). The qPCR assays detected the two pathogens on plant samples exhibiting Phomopsis stem canker symptoms sampled from commercial sunflower fields in Minnesota, Nebraska, North Dakota, and South Dakota. Furthermore, the assays were used to screen cultivated sunflower accessions for resistance to D. helianthi and D. gulyae. The disease severity index (DSI) of the accessions significantly correlated (P < 0.0001) with the amount of pathogen DNA from the qPCR assays. The qPCR assays identified PI664232 and PI561918 to be significantly less susceptible (P ≤ 0.05) to D. helianthi and D. gulyae, respectively, when compared with the susceptible check cultivar HA 288, and this was in agreement with the DSI. These results suggest that the qPCR assays for D. helianthi and D. gulyae can be used as a reliable tool to diagnose Phomopsis stem canker and screen sunflower germplasm for disease resistance.

Molecular Characterization and Disease Control of Stem Canker on Royal Poinciana (Delonix regia) Caused by Neoscytalidium dimidiatum in the United Arab Emirates

In the United Arab Emirates (UAE), royal poinciana (Delonix regia) trees suffer from stem canker disease. Symptoms of stem canker can be characterized by branch and leaf dryness, bark lesions, discoloration of xylem tissues, longitudinal wood necrosis and extensive gumming. General dieback signs were also observed leading to complete defoliation of leaves and ultimately death of trees in advanced stages. The fungus, Neoscytalidium dimidiatum DSM 109897, was consistently recovered from diseased royal poinciana tissues; this was confirmed by the molecular, structural and morphological studies. Phylogenetic analyses of the translation elongation factor 1-a (TEF1-α) of N. dimidiatum from the UAE with reference specimens of Botryosphaeriaceae family validated the identity of the pathogen. To manage the disease, the chemical fungicides, Protifert®, Cidely® Top and Amistrar® Top, significantly inhibited mycelial growth and reduced conidial numbers of N. dimidiatum in laboratory and greenhouse experiments. The described "apple bioassay" is an innovative approach that can be useful when performing fungicide treatment studies. Under field conditions, Cidely® Top proved to be the most effective fungicide against N. dimidiatum among all tested treatments. Our data suggest that the causal agent of stem canker disease on royal poinciana in the UAE is N. dimidiatum.

Teratosphaeria stem canker of Eucalyptus: two pathogens, one devastating disease

BACKGROUND

Teratosphaeria gauchensis and T. zuluensis are closely related fungi that cause Teratosphaeria (previously Coniothyrium) stem canker disease on Eucalyptus species propagated in plantations for commercial purposes. This disease is present in many countries in which Eucalyptus trees are planted, and continues to spread with the international trade of infected plant germplasm.

TAXONOMY

Fungi, Ascomycota, Pezizomycotina, Dothideomycetes, Dothideomycetidae, Capnodiales, Teratosphaeriaceae, Teratosphaeria.

IDENTIFICATION

The causal agents form dark masses of pycnidia that are visible on the surface of distinct stem cankers that typically form on young green stem tissues. Accurate diagnosis of the causal agents requires DNA sequence data.

HOST RANGE

Nine species of Eucalyptus are known to be affected. Of these, E. grandis and its hybrids, which include some of the most important planting stock globally, appear to be particularly vulnerable.

DISEASE SYMPTOMS

Small necrotic lesions develop on young green stem tissue. These lesions coalesce to form large cankers that exude gum. Epicormic shoots develop below the girdling canker and, in severe cases, trees die.

USEFUL WEBSITES

Mycobank, https://www.mycobank.org; Publications of the Forestry and Agricultural Biotechnology Institute (FABI), https://www.fabinet.up.ac.za/index.php/journals.

Caliciopsis pleomorpha sp. nov. (Ascomycota: Coryneliales) causing a severe canker disease of Eucalyptus cladocalyx and other eucalypt species in Australia

Caliciopsis pleomorpha sp. nov. is described from a severe stem canker disease of cultivated Eucalyptus cladocalyx ‘Nana’ (dwarf sugar gum) in Australia. The fungus is a pleomorphic ascomycete (Coryneliales), with pycnidial (pleurophoma-like) and hyphomycetous (phaeoacremonium-like) morphs, and differs in these respects and in ITS sequences from other Caliciopsis spp. The fungus was also found associated with cankers on other Eucalyptus species growing in native habitats, and was successfully inoculated under glasshouse conditions into a wide range of Eucalyptus species on which it caused cankers of varying severity.

MoNSTR-seq, a restriction site-associated DNA sequencing technique to characterize Agrobacterium-mediated transfer-DNA insertions in Phomopsis longicolla

Phomopsis longicolla (Hobbs) causes Phomopsis seed decay and stem lesions in soybean (Glycine max). In this study, a novel, high-throughput adaptation of RAD-seq termed MoNSTR-seq (Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions) was developed to determine the genomic location of T-DNA insertions in P. longicolla mutants. Insertional mutants were created via Agrobacterium tumefaciens-mediated transformation, and one mutant, strain PL343, was further investigated due to impaired stem lesion formation. Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions, in which DNA libraries are created with two distinct restriction enzymes and customized adapters to simultaneously enrich both T-DNA insertion borders, was developed to characterize the genomic lesion in strain PL343. MoNSTR-seq successfully identified a T-DNA insertion in the predicted promoter region of a gene encoding a cellobiose dehydrogenase (CDH1), and the position of the T-DNA insertion in strain PL343 was confirmed by Sanger sequencing. Thus, MoNSTR-seq represents an effective tool for molecular genetics in P. longicolla, and is readily adaptable for use in diverse fungal species.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study describes MoNSTR-seq (Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions), an adaptation of restriction site-associated DNA sequencing (RAD-seq) to identify the position of transfer-DNA (T-DNA) insertions in the genome of Phomopsis longicolla, an important pathogen of soybean. The technique enables high-throughput characterization of mutants generated via Agrobacterium tumefaciens-mediated transformation (ATMT), thus accelerating gene discovery via forward genetics. This technique represents a significant advancement over existing approaches to characterize T-DNA insertions in fungal genomes. With minor modifications, this technique could be easily adapted to taxonomically diverse fungal pathogens and additional mutagenesis cassettes.

Unusual evolutionary mechanisms to escape effector-triggered immunity in the fungal phytopathogen Leptosphaeria maculans

Leptosphaeria maculans is the fungus responsible for the stem canker disease of oilseed rape (Brassica napus). AvrLm3 and AvrLm4-7, two avirulence effector genes of L. maculans, are involved in an unusual relationship: AvrLm4-7 suppresses the Rlm3-mediated resistance. Here, we assessed AvrLm3 polymorphism in a collection of 235 L. maculans isolates. No field isolates exhibited deletion or inactivating mutations in AvrLm3, as observed for other L. maculans avirulence genes. Eleven isoforms of the AvrLm3 protein were found. In isolates virulent towards both Rlm3 and Rlm7 (a3a7), the loss of the Rlm3-mediated resistance response was due to two distinct mechanisms. First, when AvrLm4-7 was inactivated (deletion or inactivating mutations), amino acid substitutions in AvrLm3 generated virulent isoforms of the protein. Second, when only point mutations were observed in AvrLm4-7, a3a7 isolates still contained an avirulent allele of AvrLm3. Directed mutagenesis confirmed that some point mutations in AvrLm4-7 were sufficient for the fungus to escape Rlm7-mediated resistance while maintaining the suppression of the AvrLm3 phenotype. Signatures of positive selection were also identified in AvrLm3. The complex evolutionary mechanisms enabling L. maculans to escape Rlm3-mediated resistance while preserving AvrLm3 integrity, along with observed reduced aggressiveness of isolates silenced for AvrLm3, serves to emphasize the importance of this effector in pathogenicity towards B. napus. While the common response to resistance gene pressure is local selection of isolates depleted in the cognate avirulence gene, this example contributes to complexify the gene-for-gene concept of plant-pathogen evolution with a 'camouflaged' model allowing retention of nondispensable avirulence effectors.

3-Methylthiopropionic Acid of Rhizoctonia solani AG-3 and Its Role in the Pathogenicity of the Fungus

Studies were conducted to determine the role of 3-methylthioproprionic acid (MTPA) in the pathogenicity of potato stem canker, Rhizoctonia solani, and the concentrations required to inhibit growth of R. solani under laboratory and plant house-based conditions. The experiments were laid out in a completely randomized design with five treatments and five replications. The treatments were 0, 1, 2, 4, and 8 mM concentrations of MTPA. The purified toxin exhibited maximal activity at pH 2.5 and 30°C. MTPA at 1, 2, 4, and 8 mM levels reduced plant height, chlorophyll content, haulm fresh weight, number of stolons, canopy development, and tuber weight of potato plants, as compared to the control. MTPA significantly affected mycelial growth with 8 mM causing the highest infection. The potato seedlings treated with MTPA concentrations of 1.0-8.0 mM induced necrosis of up to 80% of root system area. Cankers were resulted from the injection of potato seedling stems with 8.0 mM MTPA. The results showed the disappearance of cell membrane, rough mitochondrial and cell walls, change of the shape of chloroplasts, and swollen endoplasmic reticulum. Seventy-six (76) hours after toxin treatment, cell contents were completely broken, cytoplasm dissolved, and more chromatin were seen in the nucleus. The results suggested that high levels of the toxin concentration caused cell membrane and cytoplasm fracture. The integrity of cellular structure was destroyed by the phytotoxin. The concentrations of the phytotoxin were significantly correlated with pathogenicity and caused damage to the cell membrane of potato stem base tissue.

Survival Analysis to Determine the Length of the Incubation Period of Camellia Twig Blight Caused by Colletotrichum gloeosporioides

Camellia twig blight, caused by Colletotrichum gloeosporioides, is a disease common to several Camellia species in the southern United States. To determine the potential seasonal differences in incubation periods, stems of Camellia sasanqua 'Rosea' plants grown in pine bark under ambient conditions were wounded and inoculated monthly with C. gloeosporioides mycelium. The time until appearance of the first symptom of disease (incubation period length) was recorded for all stems. Stems that did not display a disease symptom by the last day of the observation period were recorded as censored observations. Survival analysis using Kaplan-Meier estimates, Cox proportional hazards, and extended Cox models was used to analyze the data. Incubation period length was regressed against stem diameter, monthly mean hours per day in a specified temperature range (15 to 30°C), and a categorical season variable approximating the four host growth stages (winter dormancy, spring leaf and stem growth, summer stem hardening and bud set, fall cessation of leaf and stem growth and opening of flowers) at the time stems were inoculated. Stems of thicker diameter tended to have greater incubation period length, while higher monthly mean hours per day in the specified temperature range decreased incubation period length. In comparison to winter months, spring, summer, and fall months were all associated with significantly higher risks for disease symptom appearance. The median incubation period lengths for the spring, summer, fall, and winter months were 18, 23, 28, and 57 days, respectively.

Replacement Series: A Tool for Characterizing Competition between Phytoparasitic Nematodes

The replacement series approach was used to detect and define competition between Meloidogyne incognita (Mi) and Rotylenchulus reniformis (Rr) on soybean. In three greenhouse tests, soybean cv. Davis seedlings were inoculated with 1,000 vermiform nematodes in the following Mi:Rr ratios: 0:0, 100:0, 75:25, 50:50, 25:75, and 0:100. After 86 days, relative nematode-yield values (number of each species in mixed culture divided by number in nonmixed culture) were calculated based on nematodes in soil per gram of dry root tissue. Calculated values were plotted and the resulting line compared with a reference line representing equal inter- and intraspecific competition predicted by the replacement series. Relative yields for Mi were higher than predicted at all ratios where Mi and Rr occurred together (lack-of-fit regression, F= 5.9401, P = 0.0008), indicating increased reproduction in the presence of Rr. Relative yields for Rr did not differ from predicted yields (lack-of-fit regression, F= 0.7565, P = 0.5203), indicating no effect of Mi on Rr. These relationships were not detected using analysis of variance. The relationship between Mi and Rr was independent of host colonization by Diaporthe phaseolorum var. caulivora, the stem canker fungus.

Development of Heterodera glycines on Soybean Damaged by Soybean Looper and Stem Canker

Short-term greenhouse studies with soybean (Glycine max cv. Bragg) were used to examine interactions between the soybean cyst nematode (Heterodera glycines) and two other common pests of soybean, the stem canker fungus (Diaporthe phaseolorum var. caulivora) and the soybean looper (Pseudoplusia includens), a lepidopterous defoliator. Numbers of cyst nematode juveniles in roots and numbers of cysts in soil and roots were reduced on plants with stem cankers. Defoliation by soybean looper larvae had the opposite effect; defoliation levels of 22 and 64% caused stepwise increases in numbers of juveniles and cysts in both roots and soil, whereas numbers of females in roots decreased. In two experiments, stem canker length was reduced 40 and 45% when root systems were colonized by the soybean cyst nematode. The absence of significant interactions among these pests indicates that the effects of soybean cyst nematode, stem canker, and soybean looper on plant growth and each other primarily were additive.