Sequences Of Internal Transcribed Spacer Region Research Articles

First Report of Penicillium olsonii Causing Postharvest Fruit Rot of Grape (Vitis vinifera) in China.

Grapes (Vitis vinifera L.) are very popular in China as fresh fruit. Due to its storability, some grape varieties can be kept fresh until winter, increasing the popularity of fruit grapes. However, in 2019, rot symptoms were observed on cv. Crimson in Wuhan, Hubei (30°52'N, 114°31'E), and Chengdu, Sichuan (30°67'N, 104°06'E). Subsequently, from 2019 to 2021, Liangshan (28°33'N, 102°42'E, cv.Crimson), Ya'an (29°40'N, 102°66'E, cv. Red globe), and Nanchong (30°80'N, 106°06'E, cv. Victoria), Sichuan also experienced the same decay symptoms. Initial symptoms of this disease were slightly sunken lesions on the berries 5 to 7 days in storage at 28℃, and then white mycelial growth on the surface of lesions. The growth became bluish-green following the occurrence of abundant sporulation, along with softening and collapsing the whole berry (Fig. 1a). Twenty symptomatic berries from each city were collected (100 samples in total) and twenty isolates were obtained using the single spore isolation technique developed by Chomnunti et al. (2014). The colony on PDA media initially appeared as white mycelium, and later developed into greenish-gray to grayish-green sporulation with white margins, the colony diameter reached 32.5 to 34.5 mm after ten days of incubation at 28±1℃. The reverse side of the colony was oblive-brown or grayish-yellow. Morphological characteristics of the twenty isolates showed that the conidiophores were broom-shaped and verticillate, the stipes smooth-walled and measured 120 to 300 × 2.5 to 4.0 μm; the ramus (n = 2 to 3) measured 6.0 to 15 × 2.5 to 3.6 μm; the metulas (n = 2 to 4) were verticillate, with sizes ranging from 8.7 to 9.8 × 2.0 to 3.2 μm; the phialides (n = 3 to 7) were elongate and ampulliform, with sizes ranging from 2.0 to 3.5 × 2.0 to 2.4 μm; the conidia (2.0 to 3.5 × 2.0 to 2.4 μm) were sub-globose to ellipsoidal in shape, with thick and finely roughened walls. Based on these cultural and morphological characteristics, the isolates were identified as Penicillium olsonii Bainier & Sartory (Frisvad et al., 1990). A multi-locus approach was performed to accurately identify a representative WHG5 isolate. The internal transcribed spacer regions (ITS), calmodulin (CaM,), beta tubulin (BenA), and 18S ribosomal RNA (18S) of isolate WHG5 were amplified and sequenced as described by Walker et al. (2012). The pairwise alignments of ITS, CaM, BenA, and 18S sequences was nearly 100% identical to Penicillium olsonii with GenBank accession numbers KX056230.1 (524/524 bp, 100%), DQ645807.1 (570/572 bp, 99%), AY674444.1 (472/472 bp, 99%), and FJ717701.1 (1299/1301 bp, 99%), respectively. The resulting sequences were deposited in GenBank (Accession no. ITS: MW192867; CaM: MZ936474; BenA: MZ936475; and 18S: MZ936476). The phylogenetic analysis performed with the Neighbor-Joining method classified WGH5 into the P. olsonii clade with a posterior probability of 100% based on the concatenated sequences of the ITS CaM, BenA, and 18S (Fig. 2). Combined with the above morphological characteristics, we finally confirmed the identity of isolate WGH5 as P. olsonii. To fulfill Koch's postulates and confirm the pathogenicity of WGH5, a 10 μL conidial suspension (1 × 106 spores/mL) aliquot was inoculated into the healthy grape berry (cv. Crimson) while using sterile distilled water as a control. Thirty berries were surface disinfected with 2% sodium hypochlorite then artificially wounded prior to inoculation with the conidial suspension. The artificial wound was made using a sterilized steel needle with a diameter of 0.5 mm and a depth of 0.3 cm. All the inoculated fruits were placed in sealed and sterilized Petri dishes and incubated at 28±1℃. The experiments were done in triplicate. After five days, the inoculated grape berries showed typical symptoms (Fig. 1b) while the control remained asymptomatic. Using the same protocol as above, the fungus P. olsonii was re-isolated from the symptomatic inoculated berries but not successfully from mock-inoculated berries. Previously, P. olsonii has been reported from Portuguese wine grapes (Serra et al., 2007). This study is the first time that P. olsonii was reported as a plant pathogen in China. Since the grapes were collected from grocery stores, details of post-harvest management that could have affected disease presence and progression of rotting were not available.

Morphological and Molecular Analysis of Fungal Species Associated with Blast and Brown Spot Diseases of Oryza sativa.

Fungal diseases blast and brown spot in rice cause severe yield losses worldwide. Blast is caused by Magnaporthe oryzae, and Bipolaris oryzae is reported as the main causal organism of brown spot. Both diseases cause leaf lesions that are difficult differentiate until the later stages. Early detection and differentiation of the lesions would help the adoption of disease management strategies specific to the pathogens and prevent reductions in the quality and quantity of rice yields. This study was conducted in the Northern Province of Sri Lanka over five consecutive rice cultivating seasons to characterize the causal fungi of rice blast and brown spot diseases by morphological and molecular means and to develop a visual guide to differentiate the two diseases. Disease incidence was recorded in 114 fields from 2017 to 2019, and fungal isolates associated with the lesions of both diseases were cultured and subjected to morphological and molecular characterization. Competitive growth interactions between M. oryzae and the more common individual fungal isolates of the brown spot lesions were evaluated. Fungal metagenomic analysis was conducted for the fungal species isolated from brown spot lesions. A suppression of blast accompanied by an increased incidence of brown spot disease was observed during the study period. M. oryzae was confirmed to be the causal organism of the blast, and >20 species of fungi were identified to be associated with brown spot lesions through morphological and molecular studies and metagenomic analyses. Fungal internal transcribed spacer region sequencing revealed genetic variation in the highly conserved region of DNA sequences of blast and brown spot fungal isolates. B. oryzae, Curvularia, and Microdochium species were commonly isolated from brown spot lesions. In vitro competitive growth interactions between the fungal isolates revealed growth suppression of M. oryzae by the fungal isolates associated with brown spot lesions. Similarly, it can be speculated that the abundance and severity of blast in the field may have an influence on brown spot-associated fungi. A simple visual guide was developed to differentiate blast and brown spot lesions. The findings would be highly useful in the timely management of these major fungal diseases affecting rice.

Identification of Monilia Species in Tibet and Characterization of M. yunnanensis in China.

Samples of peach and plum fruits with brown rot symptoms were collected from Tibet in 2019 and 2020, and the causal agent was identified as Monilia yunnanensis, which represents the first characterization of Monilia spp. on peach and plum in Tibet. Morphological investigation showed that some conidia from naturally diseased fruits were larger than those observed in previously isolated M. yunnanensis. Some conidia of M. yunnanensis isolates from Tibet produced more than two, even up to six germ tubes from different parts of each conidium, instead of one or two germ tubes developing from the pointy sides of each conidium. The alignment of ribosomal internal transcribed spacer region sequences revealed that some isolates from Tibet displayed a mutation at the 374th position from adenine (A) to cytosine (C). Although abovementioned differences were observed between isolates from Tibet and other regions, phylogenetic analysis indicated that all of the M. yunnanensis isolates from different stone fruits and different regions in China were clustered together without obvious genetic differentiation. These results revealed that hosts and geographic environments did not play a major role in the evolution of M. yunnanensis.

The creeping bentgrass microbiome: Traditional culturing and sequencing results compared with metagenomic techniques

AbstractRecent metagenomic studies have probed the fungal microbiome of intensively managed turfgrasses to better understand the organisms present, which may be beneficial or harmful, but the taxonomic resolution is often limited to the family or genus level. This may relate to the common practice of targeting short ribosomal DNA sequences for estimating fungal abundance and phylogenetic relationships. We collected samples of intensively managed creeping bentgrass (Agrostis stolonifera L.) from Guelph, ON, across two growing seasons and obtained 2,204 foliar epiphytic fungal isolates. Sequencing the entire internal transcribed spacer (ITS) region of 251 representative isolates resolved these to 54 species in 31 genera. A comparison of the taxa identified here versus those reported in five metagenomic studies revealed similarities. However, of the 31 genera we identified by sequencing, 13 genera (42%) were not reported in the metagenomic studies related to intensively managed turfgrass systems. The five metagenomic studies identified an average of 44 genera, with 46% (ranging from 4 to 72%) on average being unique to each study. In addition to revealing genera that were not reported in other studies, full‐length ITS sequencing had the advantage of being able to resolve to the species level. We could resolve 248 of the sequenced isolates to species with an e‐value of 10−50, with three left at the genus level. Until sequencing technologies can yield full‐length ITS sequencing, laborious traditional culturing followed by sequencing of the entire ITS region can give insights into microbiomes not revealed by current metagenomic methods.

Pichia bovicola sp. nov., a yeast species associated with small-intestinal content of cattle.

Three yeast strains, DMKU-MP6-4T, DMKU-MP2-6 and DMKU-MP5-1, were isolated from the small-intestinal content or Pia of cattle in Thailand during the investigation of yeast diversity in this habitat. According to the D1/D2 domain of the large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) region sequence analysis, these strains represent a novel yeast species in the genus Pichia. The species produced one to four ascospores per ascus with spherical to ellipsoidal shape and heterogenous in terms of size. These three strains were identical and differed from their closely related species, Pichia exigua NRRL Y-10920T by 2% (six nucleotide substitutions and five gaps) in the D1/D2 domain of the large subunit rRNA gene, while ITS region sequences differed by 3.1% (16 nucleotide substitutions and 27 gaps), 3.7% (19 nucleotide substitutions and 28 gaps) and 3.1% (16 nucleotide substitutions and 27 gaps) for DMKU-MP6-4T, DMKU-MP2-6 and DMKU-MP5-1, respectively. The name, Pichia bovicola, is proposed to accommodate these species. The holotype is DMKU-MP6-4T (TBRC 15616T=PYCC 8905T).

Species diversity, systematic revision and molecular phylogeny of Ganodermataceae (Polyporales, Basidiomycota) with an emphasis on Chinese collections.

Ganodermataceae is one of the main families of macrofungi since species in the family are both ecologically and economically important. The double-walled basidiospores with ornamented endospore walls are the characteristic features of Ganodermataceae. It is a large and complex family; although many studies have focused on Ganodermataceae, the global diversity, geographic distribution, taxonomy and molecular phylogeny of Ganodermataceae still remained incompletely understood. In this work, taxonomic and phylogenetic studies on worldwide species of Ganodermataceae were carried out by morphological examination and molecular phylogenetic analyses inferred from six gene loci including the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), the second largest subunit of RNA polymerase II gene (rpb2), the translation elongation factor 1-α gene (tef1), the small subunit mitochondrial rRNA gene (mtSSU) and the small subunit nuclear ribosomal RNA gene (nSSU). A total of 1 382 sequences were used in the phylogenetic analyses, of which 817 were newly generated, including 132 sequences of ITS, 139 sequences of nLSU, 83 sequences of rpb2, 124 sequences of tef1, 150 sequences of mtSSU and 189 sequences of nSSU. The combined six-gene dataset included sequences from 391 specimens representing 146 taxa from Ganodermataceae. Based on morphological and phylogenetic analyses, 14 genera were confirmed in Ganodermataceae: Amauroderma, Amaurodermellus, Cristataspora, Foraminispora, Furtadoella, Ganoderma, Haddowia, Humphreya, Magoderna, Neoganoderma, Sanguinoderma, Sinoganoderma, Tomophagus and Trachydermella. Among these genera, Neoganoderma gen. nov. is proposed for Ganoderma neurosporum; Sinoganoderma gen. nov. is proposed for Ganoderma shandongense; Furtadoella gen. nov. is proposed to include taxa previously belonging to Furtadoa since Furtadoa is a homonym of a plant genus in the Araceae; Trachydermella gen. nov. is proposed to include Trachyderma tsunodae since Trachyderma is a homonym of a lichen genus in the Pannariaceae. Twenty-three new species, viz., Ganoderma acaciicola, G. acontextum, G. alpinum, G. bubalinomarginatum, G. castaneum, G. chuxiongense, G. cocoicola, G. fallax, G. guangxiense, G. puerense, G. subangustisporum, G. subellipsoideum, G. subflexipes, G. sublobatum, G. tongshanense, G. yunlingense, Haddowia macropora, Sanguinoderma guangdongense, Sa. infundibulare, Sa. longistipitum, Sa. melanocarpum, Sa. microsporum and Sa. tricolor are described. In addition, another 33 known species are also described in detail for comparison. Scanning electron micrographs of basidiospores of 10 genera in Ganodermataceae are provided. A key to the accepted genera of Ganodermataceae and keys to the accepted species of Ganoderma, Haddowia, Humphreya, Magoderna, Sanguinoderma and Tomophagus are also provided. In total, 278 species are accepted as members of Ganodermataceae including 59 species distributed in China. Taxonomic novelties: New genera: Furtadoella B.K. Cui & Y.F. Sun, Neoganoderma B.K. Cui & Y.F. Sun, Sinoganoderma B.K. Cui, J.H. Xing & Y.F. Sun and Trachydermella B.K. Cui & Y.F. Sun; New species: Ganoderma acaciicola B.K. Cui, J.H. Xing & Y.F. Sun, G. acontextum B.K. Cui, J.H. Xing & Vlasák, G. alpinum B.K. Cui, J.H. Xing & Y.F. Sun, G. bubalinomarginatum B.K. Cui, J.H. Xing & Y.F. Sun, G. castaneum B.K. Cui, J.H. Xing & Y.F. Sun, G. chuxiongense B.K. Cui, J.H. Xing & Y.F. Sun, G. cocoicola B.K. Cui, J.H. Xing & Y.F. Sun, G. fallax B.K. Cui, J.H. Xing & Vlasák, G. guangxiense B.K. Cui, J.H. Xing & Y.F. Sun, G. puerense B.K. Cui, J.H. Xing & Y.F. Sun, G. subangustisporum B.K. Cui, J.H. Xing & Y.F. Sun, G. subellipsoideum B.K. Cui, J.H. Xing & Y.F. Sun, G. subflexipes B.K. Cui, J.H. Xing & Y.F. Sun, G. sublobatum B.K. Cui, J.H. Xing & Y.F. Sun, G. tongshanense B.K. Cui, J.H. Xing & Y.F. Sun, G. yunlingense B.K. Cui, J.H. Xing & Y.F. Sun, Haddowia macropora B.K. Cui, Vlasák & Y.F. Sun, Sanguinoderma guangdongense B.K. Cui & Y.F. Sun, Sa. infundibulare B.K. Cui & Y.F. Sun, Sa. longistipitum B.K. Cui & Y.F. Sun, Sa. melanocarpum B.K. Cui & Y.F. Sun, Sa. microsporum B.K. Cui & Y.F. Sun and Sa. tricolor B.K. Cui & Y.F. Sun; New combinations: Furtadoella biseptata (Costa-Rezende et al.) B.K. Cui & Y.F. Sun, Fu. brasiliensis (Singer) B.K. Cui & Y.F. Sun, Fu. corneri (Gulaid & Ryvarden) B.K. Cui & Y.F. Sun, Neoganoderma neurosporum (J.S. Furtado) B.K. Cui & Y.F. Sun, Sinoganoderma shandongense (J.D. Zhao & L.W. Xu) B.K. Cui, J.H. Xing & Y.F. Sun and Trachydermella tsunodae (Yasuda ex Lloyd) B.K. Cui & Y.F. Sun. Citation: Sun Y-F, Xing J-H, He X-L, Wu D-M, Song C-G, Liu S, Vlasák J, Gates G, Gibertoni TB, Cui B-K (2022). Species diversity, systematic revision and molecular phylogeny of Ganodermataceae (Polyporales, Basidiomycota) with an emphasis on Chinese collections. Studies in Mycology 101: 287-415. doi: 10.3114/sim.2022.101.05.

Morphological and pathogenic characterization of Corynespora cassiicola isolates reveals specific genotypic interactions in soybean

AbstractSoybean target spot, caused by the fungus Corynespora cassiicola, is an important disease in northwestern Argentina (NWA). A cultural, morphological, and virulence characterization of 24 C. cassiicola isolates from different geographic localities in NWA was performed. The isolates were classified into five different cultural phenotypes, one of which has not been previously described. The ribosomal DNA internal transcribed spacer region sequence from five representative isolates (587 bp) exhibited 100% identity with C. cassiicola. A high variability of conidial morphology was observed among isolates, but no correlation with cultural phenotype was observed. When the soybean cultivar A 8000 RG was challenged with the 24 isolates, different degrees of virulence were observed, ranging from highly virulent to nonvirulent. No association of virulence with cultural or morphological characters was observed, but a relationship with geographical origin was demonstrated. Histopathological studies were performed on a nonvirulent and a highly virulent isolate. Microscopic observations of infected tissues of the former showed low mycelium development restricted to the upper epidermis, a thickening of the cuticle and primary wall of subepidermal cells, and accumulation of callose in phloematic vessels. In tissue infected with the latter, there was abundant mycelium development accompanied by cellular disorganization in mesophyll cells. Pathological challenges of isolates on nine different cultivars indicated that the degree of virulence of isolates depends on the plant genotype, demonstrating that the C. cassiicola–soybean interaction is highly specific. Understanding the genetic basis of this interaction will provide new information for better disease management and breeding strategies.

First report of Fusarium concentricum causing wilt on Podocarpus macrophyllus in China.

Podocarpus macrophyllus (Thunb.) D. Don is used in many fields, including landscape, medicine, and forest interplanting. In July 2019, shoot blight was observed on P. macrophyllus at three nurseries in Harbin, China. Approximately 15% of plants had symptoms of the disease, which included rapid, synchronized death of leaves on individual branches. Eventually the whole plant wilted. Leaves and stems turned dark blue to brown. Ten infected vascular tissue samples from 10 individual plants were surface-disinfested in 0.5% NaOCl for 5 min, rinsed 3 times in sterile distilled water, and cultured on potato dextrose agar (PDA) amended with 50 µg/ml streptomycin at 26°C. Six similar fungal isolates from ten samples were isolated and subcultured. Single-conidium isolates were generated with methods reported previously (Leslie and Summerell 2006). Colonies on PDA consisted of densely floccose aerial hyphae with light yellow and pinkish pigments. Microconidia were oval to obovoid or allantoid, 3.8 to 11.8 μm in length and 2.8 to 4.6 μm in width, mostly non-septate on carnationleafagar (CLA). Macroconidia were naviculate-to-fusiform slender, 24.9 to 57.2 μm in length and 2.8 to 4.5 μm in width with 3- to 5- septate, with a beaked apical cell and a foot-shaped basal cell. According to these morphological characteristics, all isolates were identified as Fusarium spp. (Aoki et al. 2001 ). Genomic DNA was extracted from a representative isolate LHS1. Theinternal transcribed spacer regions (ITS), translation elongation factor 1-alpha gene (TEF-1ɑ)andβ-tubulin (TUB2) gene were amplified using the primers ITS1 and ITS4 (Yin et al. 2012)，EF1-728F/EF1-986R (Carbone and Kohn 1999)and T1/Bt2b (Glass and Donaldson 1995), respectively. DNA sequences of LHS1 were deposited in GenBank (accession nos. MT914496 for ITS, MT920920 for TEF-1ɑ and MT920921 for TUB2, respectively). MegaBLAST analysis of the ITS, TEF-1a, and TUB2 sequences indicated 100%, 97.7% and 100% similarity withFusarium concentricum isolate CBS 450.97 (accession no. MH862659.1 for ITS, MT010992.1 for TEF-1a, and MT011040.1 for TUB2, respectively). To determine pathogenicity, P. macrophyllus plants were grown in 10-cm pots containing a commercial potting mix (five plants/pot). At the 10 to 12 leaf stage, 10 healthy plants (2 pots) were inoculated by spraying 5 ml of a conidial suspension (4×106spores/ml) onto every plant. Ten plants treated with sterile distilled water served as a control. Thetestwasrepeatedtwice. All plants were placed in a humidity chamber (>95% RH, 26℃) for 48 h after inoculation and then transferred to a greenhouse at 22/28°C (night/day). All inoculated wilted with leaves and stems turning dark blue to brown 15 days after inoculation. No symptoms were observed on the control plants. The fungus was re-isolated and confirmed to be F. concentricum according to morphological characteristics and molecular identification. To our knowledge, this is the first report of F. concentricum on P. macrophyllus in world. The disease caused a large number of plants to wilt and die, seriously impacting the ability of the horticulture industry to produce P. macrophyllus. Although this pathogen causes leaf and shoot blight symptoms, it is not clear if the pathogen is also a vascular wilt disease. The occurrence of the new disease caused by F. concentricum highlights the importance of developing management strategiestoprotect P. macrophyllus.

Stemphylium lycopersici Causing Leaf Spot of Watermelon (Citrullus lanatus) in China.

Watermelon (Citrullus lanatus) is an important cucurbit crop in China. During September 2020, an unknown leaf spot disease was observed onwatermelon in two greenhouses (640m2 per greenhouse) of Sangzi town, Jizhou district, in Tianjin,China(117°10'E, 39°55'N), where approximately 10% of plants were infected. Disease symptoms began as small, circular, brown spots on leaves. As these spots increased in size, they developed confluent, irregular lesions surrounded by dark brown edges. Severely affected plants had many wilted leaves followed by defoliation. Ten symptomatic leaves were collected for pathogen isolation. Diseased tissues (3×3 mm) were cut from the margins of lesions and surface disinfected with 1% NaClO for 1 min, rinsed three times with sterile distilled water and then placed on potato dextrose agar (PDA) at 25±2°C with a 12-h photoperiod for 7 to 10 days. Seven morphologically similar isolates were obtained from the ten infected leaves and purified by single-spore culturing for further study. The initial growth of the isolates on PDA appeared grayish white in obverse and bright yellow pigmentation in reverse. Colony color gradually deepened to grayish brown in obverse and brownish red in reverse. Conidia (n=50) were solitary, light brown, oblong to long elliptic, pointed or obtuselyrounded atthetop, constricted at the transverse septum, with verrucous processes on the surface, 36.3 to 64.2×16.6 to 25.1 μm, and the L/W ratio of conidia was 1.5-2.5. All characteristics were consistent with the description of Stemphylium lycopersici (Ellis 1971; Woudenberg et al. 2017). Total genomic DNA was extracted from a representative isolate (XG2-2) using a Fungal DNA Kit (GBCBIO, Guangzhou, China). The internal transcribed spacer (ITS) and translation elongation factor 1-α (EF1-α) genes (Sun et al. 2015) were amplified and sequenced with the primer pairs ITS1/ITS4 (5'-TCCGTAGGTGAACCTGCGG-3'/5'-TCCTCCGCTTATTGATATGC-3') and EF-1α-F/EF-1α-R(5'-TCACTTGATCTACAAGTGCGGTGG-3'/5'-CGATCTTGTAGACATCCTGGAGG-3'), respectively. The two sequences of strain XG2-2 (GenBank Accession No. MW362344 and MW664941) showed 100% and 99% identity toS. lycopersici strain 01 and strain KuNBY1 (GenBank Accession No. KR911814 and AB828256) respectively. The phylogenetic analysis using MEGA7 based on the sequences of ITS and EF1-α regions showed that the isolate XG2-2 was clustered withS. lycopersiciisolates (strain 01 and strain KuNBY1). For the pathogenicity test, a spore suspension (1×106 spores/ml) in sterile distilled water from a 7-day-old culture of the fungus grown on PDA and counted with a hemacytometer was sprayed on leaves and stems of five healthy watermelon plants, grown for 2 months in the greenhouse at 25 to 30 °C, with 85% relative humidity. Conditions remained the same for inoculation experiments. Negative controls were healthy plants inoculated with sterile distilled water. The experiment was repeated twice. Six days after inoculation, typical leaf spot symptoms were observed on inoculated leaves, whereas control leaves remained symptomless. To satisfy Koch's postulates, the causal fungus was re-isolated from the lesions of inoculated plants, with morphological and cultural characteristics identical with the original isolate. Stemphylium lycopersici is a common fungus with a relatively extensive host range (Kee et al. 2018). In recent years, new host plants infected by S. lycopersici have been reported in Asia including Physali (Yange et al. 2020), common bean (Li et al. 2019), and potato (Kee et al. 2018). To our knowledge, this is a new host record for S. lycopersici causing leaf spot on watermelon in China. Sangzi watermelon is a special local product in the Jizhou district of Tianjin. At present the cultivated area in 1000 ha including 667 ha in controlled conditions and 333 ha of field-grown plants with a total annual output of 45000 Mg. In this survey, we found the disease caused by S. lycopersici on watermelon only in these two greenhouses, but cannot rule out the possibility of large-scale spread in the future. Therefore, integrated management strategies for this fungus need to be developed to reduce economic losses in commercial cultivation.

First Report of Root Rot onkiwifruitsCaused byAthelia rolfsiiin Hefei, China.

Kiwifruits (Actinidia ssp.), known as "King of vitamin C", have been wildly cultivated. In August 2020, about 15% of A. deliciosa (cv. Xuxiang) and A. macrosperma (rootstock) plants displayed symptoms typical of root rot at a farm in Hefei (117°25'E, 31°86'N), Anhui Province of China (Fig.1 a-b). Symptoms first appeared at the root and stem junction which were covered by cottony white mycelium during warm and humid summer. Then, the infected tissues were rotted, and subsequently the whole plant withered. Tan to brown sclerotia were observed on the basal stem epidermis and soil surface surrounding the stem (Fig.1 c-d). Infected plant tissues and sclerotia were collected for isolating the fungal pathogen. The samples were surface sterilized in 70% alcohol for 30 s, followed by 2% sodium hypochlorite for 3 min, washed five times with sterile double-distilled water (ddH2O), dried, placed on potato dextrose agar, and incubated at 25 °C in the dark. In total, twelve fungal isolates were obtained. The mycelia of all the isolates were white with a fluffy appearance (Fig.1 e). Sclerotia formed after 7 days were initially white (Fig.1 f) and gradually turned to dark brown (Fig.1 g) measuring 0.67 to 2.03 mm in diameter (mean = 1.367 ± 0.16 mm;n= 30). Hyphae were hyaline, septate. Some cells possessed multiple nuclei (Fig.1 h) and clamp connections (Fig.1 i). No spores were observed. For species-level identification, ITS1/ITS4 and EF1-983F/EF1-2218R primers were used to amplify the internal transcribed spacer regions (ITS) and translation elongation factor-1 alpha regions (TEF-1α), respectively (White et al. 1990; Rehner & Buckley 2005). Based on ITS and TEF-1α sequence analyses, all 12 isolates were categorized into two groups, group one including isolates NC-1 and NC-6~10 and group two containing NC-2~5 and NC-11~12. The length of ITS sequences for NC-1 (MW311079) was 684bp and 99% to 100% similar to Athelia rolfsii (MN610007.1, MN258360.1). Similarly, ITS sequences for NC-2 (MW311080) were 99% to 100% similar to A. rolfsii (MH858139.1; MN872304.1). Also, TEF-1α sequences of NC-1 (MW322687) and NC-2 (MW322688) were 96% to 99% similar to sequences of A. rolfsii (MN702794.1, GU187681.1, MN702789.1). Based on morphology and phylogenetic analyses (Fig.1 j&k), the isolates NC-1 and NC-2 were identified as Athelia rolfsii (anamorph Sclerotium rolfsii) (Mordue. 1974; Punja. 1985). To fulfill Koch's postulates, ten sclerotia of NC-1 were incorporated into the soil near stems of healthy Xuxiang plants (Fig.2 a). Similar treatments were also used for plants of A. macrosperma or A. arguta (Fig.2 g&m). Each control group had the same number of plants (n=3) for inoculating with ddH2O. The plants were kept in an incubator with a relative humidity of 80% and temperature of 28°C with 16/8 hours light/dark photoperiod. After twenty days, the pathogen-inoculated plants developed similar symptoms of root rot observed in the field (Fig.2 b-d, h-j, n-o). Similarly, four days after inoculation with sclerotia, leaves developed water-soaked lesions (Fig.2 e, k&p). No significant difference in pathogenicity was observed between NC-1 and NC-2. Non-inoculated control plants remained disease-free (Fig.2 f, l&q). The pathogenicity experiments were repeated three times. The pathogen was re-isolated from infected tissues and sclerotia, and isolates were confirmed as A. rolfsii by the ITS sequences. A. rolfsii has been reported to cause root rot in kiwifruit in the USA (Raabe. 1988). To our knowledge, this is the first report A. rolfsiicausing root rot on kiwifruits in China.

First Report of Spot Blotch Caused by Bipolaris sorokiniana on Winter Rye in Kentucky.

The Kentucky distilling industry ranks as one of the state's largest industries and continues to expand. In 2017, the Kentucky distilling industry was responsible for approximately $235 million in state and local tax revenues (Coomes and Kornstein, 2019). Rye (Secale cereale L.) grains are a vital component for production of some distilled spirits. Although winter rye is produced on relatively few hectares in Kentucky currently, a recent initiative has supported expanding production to help meet the growing demand of local distilleries. University of Kentucky winter rye research field trials were visited in Caldwell and Logan Counties, KY in May 2018, and in Fayette County, KY in May 2019. Leaves were collected that had dark brown, oval to irregular-shaped lesions with definite margins and yellow halos. Symptoms were present on approximately 50% to 80% of the flag leaves, with severity ranging from 5% to 30% of the flag leaf area affected. Leaves were surface-disinfested by soaking in a 2% NaOCl solution for 1 min and rinsed twice in sterilized water and then placed in a humidity chamber (plastic bag with moist paper towels) at room temperature (approximately 24°C) to induce fungal sporulation. Seventeen single-spore isolates were obtained and stored at -80°C in 15% glycerol solution. Isolates were grown on potato dextrose agar under 12 h cycles of white light/darkness for 5 days. Colonies were gray to black. Conidia that formed were mostly straight or slightly curved, dark olivaceous brown, 3-7 septate, and 41.0-90.4 × 15.2-29.3 µm. Based on the symptoms observed on the collected leaves and these morphological characteristics similar to those described by Chang and Hwang (2000) and Manamgoda et al. (2014), the fungus was tentatively identified as Bipolaris sorokiniana (Sorokin) Shoemaker. The sequence of internal transcribed spacer regions (ITS) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were used to identify three isolates (18Bs004, 18Bs111 and 19Bs064) using primer ITS1/ITS4 (White et al. 1990) and GPD1/GPD2 (Berbee et al. 1999), respectively. The sequences were deposited in GenBank with accession numbers MT457817, MT457818 and MZ066635 for ITS sequences and MZ073644 to MZ073646 for GAPDH sequences. BLAST searches with ITS and GAPDH sequences matched 100% identity (344/344 bp and 515/515 bp for ITS and GAPDH sequences, respectively) to B. sorokiniana (GenBank accession No. MT254731 and MH844813, respectively). To prove pathogenicity, a conidial suspension (1 × 105 conidia/ml) was used to inoculate 15-day-old cultivar 'Serafino' winter rye plants in the greenhouse. Leaves of 8 plants were inoculated with 50 ml of the conidial suspension using a spray bottle. Plants were covered with a transparent plastic bag for 48 h, and symptoms were observed 10 days after inoculation. Leaf lesions, similar to those described above, were present on all inoculated plants, but no symptoms were observed on non-inoculated control plants. Bipolaris sorokiniana was reisolated from symptomatic leaves and the identity of the pathogen was confirmed based on the morphology previously described. To our knowledge, this is the first report of spot blotch caused by B. sorokiniana on winter rye in Kentucky, but B. sorokiniana has been reported on rye in the neighboring state of Virginia (Roane 2009). Kentucky produces approximately 150,000 and 4,000 ha of winter wheat (Triticum aestivum) and winter barley (Hordeum vulgare) annually, respectively, which are both known hosts of B. sorokiniana (Kumar et al. 2002). An isolate of B. sorokiniana from rye was reported by Ghazvini and Tekauz (2007) to be less virulent on barley differential lines. Further research is needed to better understand spot blotch distribution, susceptibility in winter rye cultivars, and potential yield and quality loss implications in winter rye production and end use. It is unknown how susceptible various winter rye cultivars grown in Kentucky are to spot blotch.

First Identification and Genotyping of Enterocytozoon bieneusi and Prevalence of Encephalitozoon intestinalis in Patients with Acute Diarrhea in the Republic of Korea.

Encephalitozoon intestinalis and Enterocytozoon bieneusi can cause diarrhea in humans, especially severe diarrhea in immunocompromised patients. However, there have been few studies on Enc. intestinalis and Ent. bieneusi in patients with acute diarrhea in the Republic of Korea (ROK). In this study, fecal samples were collected from 1241 patients with acute diarrhea in 2020. Among these, 24 cases of Enc. intestinalis and one case of Ent. bieneusi were detected via PCR amplification of small subunit ribosomal RNA. Genotyping of the internal transcribed spacer region sequence revealed that the detected Ent. bieneusi genotype was in Group 1. This study provides the first evidence that Ent. bieneusi exists in humans in addition to animals in the ROK. To identify the causative agent, continuous monitoring of Enc. intestinalis and Ent. bieneusi is necessary for patients with acute diarrhea in the ROK.

First Report of Meloidogyne graminicola on Rice in Henan Province, China.

Rice (Oryza sativa) is an important food crop in China and root-knot nematode Meloidogyne graminicola has been one of the most important diseases on rice in recently five years (Ju et al. 2020). In August 2020, rice plants were found to be maldeveloped, yellow leaves and hooked root tips in an irrigated paddy field of Yuanyang County, Xinxiang City, Henan Province. Fifty rice plants were randomly collected and 84.0 percent plants were infected with root-knot nematodes, with root-gall index of 56.0. Then nematodes from rice roots were isolated with 100-μm and 25-μm sieves. A large number of females, some third-stage juveniles (J3s), and a small number of males of Meloidogyne spp. were found in root galls of all samples after dissected, and then were identified and measured under the microscope. In females (n = 20), the perineal pattern was dorsoventrally oval with low and round dorsal arch, and the lateral field was not obvious or absent, striae are usually smooth, with occasional short and irregular striatal fragmentation. The morphological data of females are as follows: body length (BL) = 516.9 ± 72.5 μm (424.2 to 611.6 μm), body width (BW)= 328.4 ± 80.7 μm (232.1 to 437.4 μm), stylet length = 11.2 ± 1.3 μm (7.7 to 13.9 μm), dorsal pharyngeal gland orifice to stylet base (DGO) = 3.9 ± 0.5 μm (3.2 to 4.5 μm), vulval slit length = 24.3 ± 4.6 μm (15.2 to 31.4 μm), vulval slit to anus distance = 16.2 ± 2.5 μm (10.1 to 20.2 μm). Males are long cylindrical, wormlike, with a short round tail. Morphological measurements of males (n = 20) were BL = 1,218.0 ± 150.7μm (1,085.7 to 1,692.2 μm), BW = 34.2 ± 4.6 μm (28.5 to 39.7 μm), stylet = 17.4 ± 0.7 μm (15.9 to 19.3 μm), DGO = 3.6 ± 0.7 μm (2.5 to 4.5 μm), tail = 10.8 ± 2.1 μm (8.0 to 14.8 μm), spicule = 30.3 ± 2.6 μm (24.7 to 36.3 μm). The egg masses from the females were incubated at 28℃ for 48 hours. Measurements of J2s (n = 20) were BL = 444.2 ± 37.8 μm (315.7 to 547.5 μm), BW = 21.2 ± 2.7 μm (16.7 to 26.4 μm), stylet = 14.2 ± 0.3 μm (13.6 to 14.8 μm), DGO = 3.5 ± 0.5 μm (2.7 to 4.5 μm), tail = 70.8 ± 5.1 μm (61.3 to 80.8 μm), hyaline tail length = 21.0 ± 2.5 μm (16.3 to 26.1 μm). These morphological features are consistent with the original description by Golden and Birchfield (1965). DNA of a single female from each sample was extracted for molecular identification. Primer pairs D2A/D3B (5´-ACAAGTACCGTGAGGGAAAGTTG-3´/ 5´-TCGGAAGGAACCAGCTACTA-3´) (De Ley et al. 1999) and the species-specific primers Mg-F3/Mg-R2 (5'-TTATCGCATCATTTTATTTG-3'/ 5'-CGCTTTGTTAGAAAATGACCCT-3') (Htay et al. 2016) were used to amplify D2/D3 region of 28S RNA and the internal transcribed spacer (ITS) region, respectively. The amplified sequences of D2/D3 region (GenBank MW490724, 766 bp) shared 99.9% and 99.7% homology with the sequences of M. graminicola (MN647592, MT576694) isolated from Guangxi and Anhui Province (Ju et al. 2020), respectively, while ITS region sequences (MW487239, 369 bp) shared 100% and 99.7% homology to M. graminicola isolate GXL3 (MN636702) and FQJJ01 (MT159690), respectively. In order to verify the pathogenicity of nematodes, about 300 J2s were inoculated on ten 14-week-old rice (Oryza sativa cv. Nipponbare) planted in pots with sterilized sandy soil, respcectively, and maintained in a greenhouse at 28°C/26°C with a 16h/8h light/dark photoperiod and 75% relative humidity. At 14 days post inoculation, obvious symptoms of hook galls were observed on roots in all inoculated rice plants, and females and males in the same shape as the collected samples were found in the root galls under the stereoscopic microscope. No symptoms were observed on non-inoculated rice plants. After 28 days, the growth of the inoculated rice plants was significantly worse than that of uninoculated ones, with yellow leaves and short plants. These results confirmed the pathogenicity of M. graminicola on rice and it indicated that M. graminicola was already spread from the main rice-producing areas to the wheat and rice rotation areas. To our knowledge, this is the first report of M. graminicola in the Henan Province of China.

Characterization of root-associated bacterial species of Leklek variety of common bean (Phaseolus sp.)

The common bean is a valuable food source in the human diet. Leklek is a local variety of common bean (Phaseolus sp.) widely grown in Mersin's Gülnar district, but little is known about this variety. In the present study, bacterial species from root nodules of this common bean variety were identified by PCR-amplified 16S ribosomal RNA (rRNA) gene and 16S-23S ribosomal RNA (rRNA) Internal Transcribed Spacer (ITS) region and sequencing. The partial 16S rRNA gene and 16S-23S rRNA ITS region sequences were submitted to the NCBI database (accession numbers MT967369, MT968518, respectively). Amplified sequences were used to construct a phylogenetic tree. Phylogenetic analysis based on the identified sequences showed that the isolate belonged to the genus Microbacterium and was closely related to Microbacterium paraoxydans. The findings presented here will provide a clue for understanding this bacterium's role in nodule formation in Phaseolus sp. (variety Leklek).

Enrichment of microbial taxa after the onset of wheat yellow mosaic disease

Soil-borne Chinese wheat mosaic virus causes yellow mosaic disease in winter wheat and is transmitted by its vector—Polymyxa graminis—in rhizosphere soil. However, the mechanism underlying the protective effect of belowground plant-associated microbes against infection by soil-borne viruses is unknown. Here, we used comprehensive bacterial 16S rRNA gene and fungal internal transcribed spacer region sequencing to explore changes of belowground plant-associated microbes and their network associations in response to wheat yellow mosaic disease. Following infection, the alpha diversity of root-associated microbiota significantly increases, whereas the microbial community structure becomes more homogeneous from the bulk soil to the root endosphere. Nevertheless, significant differences occur in taxonomic composition with different degrees of plant disease. For example, certain phyla, including Firmicutes, Gemmatimonadetes, Bacteroidetes, Chloroflexi, Nitrospirae, Armatimonadetes, and Acidobacteria, as well as specific genera, namely, Streptomyces, Stenotrophomonas, Bradyrhizobium, Sphingomonas and Bacillus, are greatly enriched following disease outbreak and may contribute to pathogen suppression. Moreover, following disease occurrence, the scale, connectivity, and complexity of the rhizosphere and root endosphere co-occurrence network increased compared with those of healthy plants. Moreover, the rhizosphere and root endosphere co-occurrence network of diseased plants contains more plant beneficial taxa and nitrogen cycle-related bacterial taxa as the keystone taxa, including the genera Bosea (Bradyrhizobiaceae), Stenotrophomonas, Thermomonas (Xanthomonadaceae), Novosphingobium (Sphingomonadaceae), and Methylibium (Comamonadaceae), implying that these potential beneficial taxa may regulate microbial networks and prevent the collapse of belowground microbial networks after disease emerging. It also implies that there is potential niche competition between beneficial bacteria and pathogen. In conclusion, our findings provide important insights into the relationship between the occurrence of soil-borne virus diseases and changes in the belowground microbial communities. This work may facilitate future research on the use of specific rhizosphere microbial communities to inhibit soil-borne virus infection.

Morphological and molecular characterization of Eustrongylides excisus larvae (Nematoda: Dioctophymatidae) in Sander lucioperca (L.) from Northern Turkey.

The genus Eustrongylides Jägerskiöld, 1909 includes parasitic nematodes (Dioctophymatidae) affecting various fish species and piscivorous birds of freshwater ecosystems. Currently, there is little information on the molecular characterization of E. excisus based on nuclear ribosomal internal transcribed spacer (ITS) rDNA regions. However, before the present study, there had been no reports of characterizing the E. excisus using nuclear small subunit ribosomal RNA (SSU rRNA) and mitochondrial cytochrome c oxidase subunit I (COI) genes sequences. In the present study, Eustrongylides spp. larvae were collected from pike-perch Sander lucioperca (L.) in Northern Turkey, and characterized by sequencing of ITS regions, SSU rRNA, and COI markers. Larvae herein morphologically identified as the fourth stage of Eustrongylides spp. were genetically identified as E. excisus based on the ITS sequence analysis. This study is the first record of SSU rRNA and COI sequences for E. excisus in GenBank. This is also a molecular characterization of E. excisus for the first time in Turkey. The ITS, SSU rRNA, and COI sequences of E. excisus can be used to establish the phylogenetic relationships of Eustrongylides species from Turkey and worldwide for further studies.

Genetic identification of medicinally used Salacia species by nrDNA ITS sequences and a PCR-RFLP assay for authentication of Salacia-related health foods

Ethnopharmacological relevanceThe roots and stems of several Salacia species have been used as traditional medicines, especially in Ayurvedic medical system for the treatment of diabetes, rheumatism, gonorrhea, amenorrhea, skin diseases, etc. Due to reported evidence supporting Salacia's beneficial effects in early-stage diabetes and other lifestyle-related diseases, Salacia-based dietary supplements and health foods have been gaining popularity in Japan and other countries in recent years. However, due to the morphological similarities between Salacia plants, particularly in the medicinally used parts (roots and stems), the authentication of the botanical identities of Salacia-derived products is challenging. Aim of this studyThis study aims to develop a genetic approach to authenticate the medicinally used Salacia species and to determine the botanical sources of the commercially available Salacia-derived products. Materials and methodsThe sequences of nuclear DNA internal transcribed spacer (ITS) and chloroplast trnK-rps16 region were determined and compared between 10 plant specimens from three medicinally used Salacia species as well as 48 samples of commercial crude drugs. Moreover, a PCR-restriction fragment length polymorphism (RFLP) assay was developed for rapid identification based on the ITS sequences. ResultsThe plant specimens from the three medicinally used Salacia species showed three main types of sequences in both ITS (types I, II, III) and trnK-rps16 (i, ii, iii) regions. Combined the sequences of ITS and trnK-rps16 regions, S. reticulata and S. oblonga had type I-i and type III-iii or similar sequences, respectively. S. chinensis had type II-ii or II(536M)-i sequences. Forty-eight samples of commercial crude drugs were identified based on ITS and trnK-rps16 DNA barcode. A convenient PCR-RFLP assay using Cac8I restriction enzyme was established and applied to identify the botanical sources of health food products purchased from online retailers. All the twelve samples were identified as S. chinensis. ConclusionThe nrDNA ITS sequences provided useful information to authenticate Salacia species and to elucidate the phylogenetic relationship within the Salacia genus. Genetic identification results revealed that S. chinensis and S. reticulata are the major sources of commercially available Salacia-products. Based on the ITS sequences, a convenient PCR-RFLP assay was established for the identification of the medicinally used Salacia species as well as their derived health food products.

The endangered epiphytic orchid Dendrobium okinawense has a highly specific mycorrhizal association with a single Tulasnellaceae fungus

ABSTRACT Epiphytic orchids, which account for 68% of vascular epiphytes, contribute substantially to plant species diversity in forest canopies. Many orchid species are naturally rare and have limited geographical distributions. All orchids rely on mycorrhizal fungi for nutrient acquisition during seed germination and seedling establishment, and many species retain these associations throughout their lifecycle. Due to their reliance on mycorrhizal fungi, epiphytic orchid species with highly specific mycorrhizal associations may be geographically restricted and are often rare. Dendrobium okinawense is a rare epiphytic orchid endemic to the Yambaru Forest in Japan and to southern Taiwan. We hypothesized that this species exhibits high mycorrhizal specificity and tested this hypothesis via identification of the species’ mycorrhizal associates. We collected root samples of this orchid from four tree species and assessed mycorrhizal fungi in 25 root fragments harvested from 10 plants. Fungi were identified using molecular methods based on fungal isolates and DNA extracted from mycorrhizal roots. Detected fungi were assigned to 21 operational taxonomic units (OTUs) based on 97% sequence similarity of nuclear ribosomal DNA internal transcribed spacer region sequences. TU11, an OTU belonging to Tulasnellaceae (Basidiomycota), was the most frequently detected OTU, occurring in 20 root fragments from all 10 sampled individuals. Our results indicate that Dendrobium okinawense has a highly specific association with TU11. Further, this specificity may be high relative to the Dendrobium species assessed in other studies. These findings support the hypothesis that Dendrobium okinawense exhibits high mycorrhizal specificity.

Diversity and Spatiotemporal Dynamics of Fungal Communities in the Rhizosphere Soil of Cotton in the Arid Region of Northwest China.

This study aimed to investigate the fungal diversity and its temporal and spatial dynamics in the rhizosphere soil of healthy cotton by high-throughput sequencing. We studied species richness, composition, and distribution of cotton rhizosphere fungal community with respect to location (Alaer, Kuerle, Tumushuke, Hami, Shihezi, Wusu, and Jinghe) and plant growth period (seedling stage, bud stage, flowering stage, and boll-opening stage) using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. A total of 1,838,454 fungal nuclear ribosomal internal transcribed spacer region sequences (rRNA ITS) were obtained from all cotton plants sampled at different growth stages in the seven locations in Xinjiang. The most abundant fungal group in the cotton rhizosphere was the Ascomycota (78.72%), followed by the Zygomycota (9.56%) and Basidiomycota (2.77%). These sequences revealed an enormous number of operational taxonomic units (OTUs) in cotton (1802 unique OTUs), with 67-464 OTUs in a single cotton sample, at a 3% threshold and a sequencing depth of 30,000 sequences. We identified 33 classes and 389 genera from the resulting 1,800,714 sequences. Sordariomycetes was the most frequent class in all samples, followed by Leotiomycetes and Eurotiomycetes. There were some differences in OTUs among different growth stages, but the differences were not significant, with 382 OTUs (14.66%) being common to each of the stages. A marked difference in the diversity of fungi in the rhizosphere soil of cotton was evident among the different locations, with the highest number of OTUs being detected in Jinghe (1084 OTUs) and clusters of OTUs representative of northern and eastern Xinjiang being detected. There were significantly more tags of Mortierella in Jinghe and Wusu than in the other sampling sites. The dynamics of the rhizosphere fungal communities were influenced by sampling sites. To the best of our knowledge, the current study is the first application of PCR-based Illumina to characterize and compare the fungal biodiversity in multiple rhizosphere soil samples from cotton.

The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements.

The dietary supplement industry is rapidly growing yet, a recent study revealed that up to 60% of supplements may have substituted ingredients, some of which can be harmful contaminants or additives. When ingredients cannot be verified morphologically or biochemically, DNA barcoding complemented with a molecular phylogenetic analysis can be a powerful method for species authentication. We employed a molecular phylogenetic analysis for species authentication of the commonly used fungal supplement, reishi (Ganoderma lingzhi), by amplifying and sequencing the nuclear ribosomal internal transcribed spacer regions (ITS) with genus-specific primers. PCR of six powdered samples and one dried sample all sold as G. lucidum representing independent suppliers produced single, strong amplification products in the expected size-range for Ganoderma. Both best-hit BLAST and molecular phylogenetic analyses clearly identified the presence of G. lingzhi DNA in all seven herbal supplements. We detected variation in the ITS sequences among our samples, but all herbal supplement samples fall within a large clade of G. lingzhi ITS sequences. ITS-based phylogenetic analysis is a successful and cost-effective method for DNA-based species authentication that could be used in the herbal supplement industry for this and other fungal and plant species that are otherwise difficult to identify.