Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus

Characterization of Fusarium Diversity and Head Microbiota Associated with Rice Spikelet Rot Disease

Rice spikelet rot disease (RSRD) affects the production and market price of rice, and can be harmful to humans and livestock. In this study, 51 strains of Fusarium spp. were isolated from rice spikelets in the Lin'an, Yuhang, and Fuyang regions. The isolates comprised four composite species: Fusarium incarnatum-equiseti species complex (FIESC), Fusarium asiaticum species complex (FSAMSC), Fusarium fujikuroi species complex (FFSC), Fusarium commune species complex (FNSC), and five species of Fusarium spp. (F. luffae, F. sulawesiense, F. asiaticum, F. fujikuroi, and F. commune). The separation rate of F. sulawesiense was the highest (41.2%), followed by F. asiaticum at 37.3%. The results of this study, compared with those of other studies, found that the newly discovered species of Fusarium spp. associated with RSRD were FSAMSC (F. asiaticum) and FNSC (F. commune). Temperature is one of the important factors causing RSRD; the optimal growth temperature for F. sulawesiense and F. commune was 30 °C, and the optimal growth temperature for other species was 25 °C. A high temperature of 35 °C did not inhibit the growth of Fusarium, as F. commune and F. fujikuroi could grow at this temperature. At 20-30 °C, the growth rate of F. asiaticum was higher than those of other strains. To determine whether the occurrence of RSRD is related to the correlation between Fusarium and other fungi in rice spikelets under different health conditions, the genetic diversity of fungi in rice spikelets was analyzed by amplicon Internal Transcribed Spacer (ITS) sequencing, and the correlations between strains of Fusarium spp. were measured. The results showed that the fungal diversity of diseased rice spikelets (RD) was higher than that of relatively healthy rice spikelets (RH). Curvularia spp., which was affected by the condition of the spikelets, was negatively correlated with Fusarium spp. in RH and positively correlated with Fusarium spp. in RD. Therefore, Fusarium spp. and Curvularia spp. can jointly cause the occurrence of RSRD. The results of the study are significant for understanding the occurrence of RSRD and formulating prevention and control measures.

Fungal Species Associated with Tuber Rot of Foshou Yam (Dioscorea esculenta) in China

Foshou yam (Dioscorea esculenta) is a tuber food crop in China. It is a rare species of the yam family and known for its high nutritional value. From 2019 to 2021, tuber rot was observed in Foshou yam in Wuxue, Hubei Province, China. Fungal strains were isolated from diseased tubers, and ten representative strains were identified based on microscopical characterization and multi-locus phylogenetic analysis. A total of five different species were identified, including Curvularia geniculata, Curvularia muehlenbeckiae, Fusarium commune, Penicillium oxalicum, and Penicillium sclerotigenum. Pathogenicity test revealed that these fungi are the pathogens of tuber rot in Foshou yam. Among them, P. oxalicum exhibited the strongest pathogenicity. To our knowledge, this is the first report of tuber rot in D. esculenta caused by these five species worldwide. This study provides important information for the future management of tuber rot in Foshou yam.

Morpho-Molecular Characterization of Hypocrealean Fungi Isolated from Rice in Northern Thailand

Hypocreales is one of the largest orders within the class Sordariomycetes and is renowned for its diversity of lifestyles, encompassing plant, insect, and human pathogens, as well as endophytes, parasites, and saprobes. In this study, we focused on saprobic hypocrealean fungi isolated from rice in northern Thailand. Species identification was conducted using morphological characteristics and multilocus phylogenetic analyses, including the internal transcribed spacer region (ITS), 28S large subunit nuclear ribosomal DNA (LSU), translation elongation factor 1-alpha (tef1-α), RNA polymerase II second-largest subunit (rpb2), and calmodulin (cmdA). This research confirmed the presence of 14 species of hypocrealean taxa, viz. Fusarium (9), Ochronectria (1), Sarocladium (2), Trichothecium (1), and Waltergamsia (1). Among these were two new species (Fusarium chiangraiense and F. oryzigenum), four new host records (Fusarium kotabaruense, Ochronectria thailandica, Sarocladium bactrocephalum, and Waltergamsia fusidioides), and three new geographical records (Fusarium commune, F. guilinense, and F. hainanese).

Morphological and phylogenetic analyses reveal new species and records of Fusarium (Nectriaceae, Hypocreales) from China

Species of Fusarium are important phytopathogens, saprobes, and endophytes around the world. Some species can affect plant health and cause yield loss of economic plants. Fusarium species are widely distributed in China, and many species were found from different plant hosts. The Fusariumincarnatum-equiseti species complex (FIESC) is one of the most significant species complexes within the genus. Based on morphological and three-gene (cal, rpb2, and tef1) phylogenetic analyses, two new species are in the Incarnatum clade, and two new host records are identified and described, viz. Fusariumfici sp. nov., Fusariumxylosmatis sp. nov., Fusariumfecundum, and Fusariumweifangense.

Three new species of Fusarium (Nectriaceae, Hypocreales) isolated from Eastern Cape dairy pastures in South Africa

A survey of the fungal diversity associated with mixed pastures from Eastern Cape dairy farms in South Africa led to the isolation of 155 Fusarium strains that belong to the Fusariumincarnatum-equiseti species complex (FIESC). Using single and multigene phylogenies based on partial sequences of the translation elongation factor 1-alpha (TEF), calmodulin (CaM), and the partial RNA polymerase second largest subunit (RPB2) genes, we identified 11 species. They included F.brevicaudatum, F.clavus, F.coffeatum, F.croceum, F.goeppertmayerae, and F.heslopiae, with five species that were found to be new. Based on morphological and phylogenetic data, three new species are formally described here as F.cumulatum, F.mariecurieae, and F.pascuum. We also provided a description for F.goeppertmayerae, as the authors who identified and named this species did not include one. We have chosen to not describe the remaining species, as our cultures lack proper morphological structure development. This study shows that mixed pastures harbour a diverse range of Fusarium species and highlights the need for further studies into their potential to impact animal health.

An integrative re-evaluation of the Fusarium sambucinum species complex

The species-rich Fusarium sambucinum species complex (FSAMSC; Fusarium, Nectriaceae, Hypocreales) is well-known for including devastating plant pathogens and toxigenic species. However, this group of grass-loving fungi also accommodates soil saprobes, endophytes, mycoparasites and rare opportunistic pathogens of humans and other animals. Recent publications have highlighted the vast phylogenetic and biochemical diversity of the FSAMSC, although a large number of taxa in FSAMSC have not been systematically described and still lack Latin binomials. In this study we established the phylogenetic breadth of the FSAMSC using an integrative approach including morphological, multilocus phylogenetic, and coalescence analyses based on five gene regions (calmodulin, RNA polymerase II largest and second largest subunits, translation elongation factor 1-α, and β-tubulin). Results obtained support the recognition of 75 taxa in FSAMSC, including all the currently known species segregates of the Fusarium head-blight pathogen F. graminearum s. lat. Thirty novel species are formally described and illustrated, while four phylogenetic species remain undescribed. An epitype is proposed for the generic type of Fusarium, F. sambucinum, from recently collected material identified by means of morphology, phylogenetics and mating experiments, fixing the phylogenetic application of the name. Additional notes are included on the typification of Fusisporium cerealis (syn. Fusarium cerealis). Taxonomic novelties: New species: Fusarium agreste Sand.-Den., J.Z. Groenew. & Crous, Fusarium amblysporum Sand.-Den., M.M. Costa, Fusarium bananae Sand.-Den., M.M. Costa, Fusarium bellum Sand.-Den., J.Z. Groenew. & Crous, Fusarium brachypes Sand.-Den., J.Z. Groenew. & Crous, Fusarium carinatum Sand.-Den., J.Z. Groenew. & Crous, Fusarium cultriforme Sand.-Den., M.M. Costa, Fusarium cuspidatum Sand.-Den., J.Z. Groenew. & Crous, Fusarium cygneum Sand.-Den., J.Z. Groenew. & Crous, Fusarium dimorphosporum Sand.-Den., M.M. Costa, J.Z. Groenew. & Crous, Fusarium dolichosporum Sand.-Den., J.Z. Groenew. & Crous, Fusarium gladiolum Sand.-Den., J.Z. Groenew. & Crous, Fusarium hamatum Sand.-Den., M.M. Costa, J.Z. Groenew. & Crous, Fusarium leptum Sand.-Den., J.Z. Groenew. & Crous, Fusarium longicolle Sand.-Den., J.Z. Groenew. & Crous, Fusarium magnum Sand.-Den., J.Z. Groenew. & Crous, Fusarium mastigosporum Sand.-Den., M.M. Costa, J.Z. Groenew. & Crous, Fusarium minutum Sand.-Den., J.Z. Groenew. & Crous, Fusarium mucronatum Sand.-Den., J.Z. Groenew. & Crous, Fusarium parabolicum Sand.-Den., J.Z. Groenew. & Crous, Fusarium platysporum Sand.-Den., J.Z. Groenew. & Crous, Fusarium pratense Sand.-Den., J.Z. Groenew. & Crous, Fusarium procumbens Sand.-Den., J.Z. Groenew. & Crous, Fusarium pseudolongipes Sand.-Den., J.Z. Groenew. & Crous, Fusarium sagittatum Sand.-Den., J.Z. Groenew. & Crous, Fusarium seculiforme Sand.-Den., J.Z. Groenew. & Crous, Fusarium subcylindroides Sand.-Den., J.Z. Groenew. & Crous, Fusarium symmetricum Sand.-Den., J.Z. Groenew. & Crous, Fusarium tropicale Sand.-Den., M.M. Costa, J.Z. Groenew. & Crous, Fusarium vermicularioides Sand.-Den., J.Z. Groenew. & Crous. Epitype: Fusarium sambucinum Fuckel. Citation: Sandoval-Denis M, Costa MM, Broders K, Becker Y, Maier W, Yurkov A, Kermode A, Buddie AG, Ryan MJ, Schumacher RK, Groenewald JZ, Crous PW (2024). An integrative re-evaluation of the Fusarium sambucinum species complex. Studies in Mycology 110: 1-110 doi: 10.3114/sim.2025.110.01.

Rapid and Sensitive On-Site Nucleic Acid Detection of Three Main Fusarium Pathogens of Maize Stalk Rot Based on RPA-CRISPR/Cas12a

Maize stalk rot is a soilborne disease that poses a serious threat to maize production worldwide, with the most significant cause being fungal stalk rot. The development of a visual and rapid detection method for the maize stalk rot pathogen is significant for its prompt and accurate identification, enhancing agricultural production efficiency, and implementing timely preventive measures. These measures will help safeguard the maize yield and quality, ultimately reducing agricultural losses. In this study, we aimed to develop an efficient method to detect maize stalk rot pathogens. We focused on three pathogenic fungi commonly found in maize-producing regions worldwide: Fusarium verticillioides, F. proliferatum, and F. graminearum. Based on translation elongation factor 1-α, we developed a rapid detection technique using recombinase polymerase amplification-CRISPR/Cas12a, combined with test strips to develop an on-site rapid visual detection test for these pathogens. The method showed detection sensitivity for F. verticillioides, F. proliferatum, and F. graminearum within 20 min at concentrations of 7.8 pg/μl, 0.11 ng/μl, and 0.13 ng/μl, respectively. The sensitivity increased with increasing reaction time. Testing of field disease samples indicated that the method is effective in detecting nucleic acids obtained through crude extraction methods. In conclusion, we developed a visually rapid detection technology that does not rely on complex instruments and equipment for the on-site early detection of F. verticillioides, F. proliferatum, and F. graminearum in the field to implement effective control measures, ensuring stable and high maize yields.

Fungal Pathogen Diversity and Fungicide Resistance Assessment in Fusarium Crown Rot of Wheat in the Huanghuai Region of China

Fusarium crown rot (FCR) poses a major threat to wheat production in the Huanghuai wheat region of China. This study aims to enhance understanding of pathogen populations causing FCR, focusing on their pathogenicity, trichothecene genotypes, and fungicide resistance. During the 2022-2023 growing seasons, we collected 1820 fungal isolates from 233 locations in this region. Our results identified Fusarium pseudograminearum, Fusarium graminearum, and Fusarium asiaticum as the primary pathogens, with F. pseudograminearum exhibiting the highest virulence. Three trichothecene genotypes were identified, including nivalenol, 3-acetyldeoxynivalenol, and 15-acetyldeoxynivalenol. No correlation was observed between trichothecene genotype and virulence, except in F. asiaticum. Antifungal assays demonstrated that all six tested fungicides effectively inhibited F. pseudograminearum, with fludioxonil being particularly effective. Field surveys identified isolates resistant to difenoconazole and pyraclostrobin. Laboratory analysis also revealed strains with FpSdhC1A83 V and FpSdhC1S80N mutations conferring resistance to cyclobutrifluram. These findings offer critical insights for developing effective control strategies to manage FCR.

Identification and Pathogenicity of Fusarium Species from Herbaceous Plants on Grassland in Qiaojia County, China

The Fusarium species is an important plant pathogen that can cause plant diseases in grassland, leading to the degradation of grassland quality. However, the morphology of Fusarium is greatly affected by environmental factors, which makes it difficult to identify its species. In addition, the pathogenic ability of different Fusarium species in plants has not been fully studied. In this study, Fusarium isolates were obtained from grassland herbaceous plants via tissue separation. Through morphological means and based on ITS, RPB2, and TEF-1 gene sequences, we compared and constructed polygenic phylogenetic trees to classify and identify the Fusarium species. In addition, the pathogenicity of different Fusarium species was also analyzed. The results showed that a total of 24 Fusarium strains were successfully isolated from grassland, from which ten species were identified: F. flagelliforme, F. longifundum, F. clavum, F. scirpi, F. ipomoeae, F. oxysporum, etc. and were included in four complexes: Fusarium incarnatum-equiseti species complex (FIESC), Fusarium oxysporum species complex (FOSC), Fusarium tricinctum species complex (FTSC), and Fusarium sambucinum species complex (FSAMSC). Pathogenicity tests demonstrated that except for F. ipomoeae QJ5211, F. sambucinum QJ203, and F. acuminatum QJ1662, other Fusarium species had different degrees of pathogenic ability. This is the first study that discusses the effect of Fusarium on grassland disease control in this area. This study further provides clear pathogen information for the prevention and control of grassland diseases.

Maize-Fusarium associations and their mycotoxins: Insights from South Africa

For maize, a staple food in South Africa, there is a lack of comprehensive knowledge on the mycotoxin-producing fungal diversity. In this study, a fungal community profile was established using culture-dependent methods for 56 maize seed samples that were also analysed for 13 mycotoxins. The fungal isolates were identified by morphology and DNA sequencing. A total of 723 fungal isolates from 21 genera and 99 species were obtained and characterised. Fusarium was the most common genus (isolated from 52 samples), followed by Cladosporium (n = 45), Aspergillus (n = 41), Talaromyces (n = 40), and Penicillium (n = 38). Fusarium communities were dominated by the Fusarium fujikuroi species complex, which includes species such as Fusarium verticillioides and Fusarium temperatum, while Fusarium awaxy and Fusarium mirum are reported here for the first time from South Africa. As for the deoxynivalenol (DON) producing species, only Fusarium boothii and Fusarium graminearum were isolated to a lesser extent. DON (n = 37), fumonisins (FUM) (n = 32), and zearalenone (ZEA) (n = 6) were detected. The presence of a particular species did not guarantee the presence of the corresponding mycotoxins, while the inverse was also true. The occurrence of DON and/or FUM in South African maize remains a health concern, so continuous monitoring of both fungal species and their mycotoxins is important.

Sporocadaceae revisited

Sporocadaceae is a species-rich and cosmopolitan fungal family including species of plant pathogens, endophytes or saprobes, and parasites of humans and animals. The taxonomy of Sporocadaceae has recently been revised using a polyphasic approach. However, much remains unknown about the diversity of species and their host associations. A collection of 488 strains, mostly from China and associated with 129 host plant species, was studied based on morphological comparisons and multi-locus (LSU, ITS, tef-1α, tub2, and rpb2) phylogenies. Our results revealed that they belonged to 86 species, one new genus (Cavernicola gen. nov.) and seven known genera, including Discosia, Monochaetia, Neopestalotiopsis, Pestalotiopsis, Seimatosporium, Seiridium and Sporocadus. Of these, 43 new species and three new combinations (Dis. kaki, Mon. bulbophylli, and Neo. keteleeriae) are proposed in this paper. In addition, Neo. vaccinii, Pes. kaki and Pes. nanjingensis are synonymised under Neo. hispanica, Pes. menhaiensis and Pes. sichuanensis, respectively. We also corrected seven problematic sequences of type materials of previously published species, namely Neo. iranensis (tef-1α, ITS, tub2), Pes. jesteri (tef-1α), Pes. photinicola (ITS, tub2) and Pes. yunnanensis (ITS). Based on this study, Pestalotiopsis and Neopestalotiopsis are the most commonly detected genera within the Sporocadaceae family, associated with 84 and 70 plant species, respectively. Furthermore, considering the importance of Sporocadaceae and the fact that commonly used loci provide little valid information for species delimitation in this family, especially for Neopestalotiopsis and Pestalotiopsis, we initiated a phylogenomic project in this study. It will not only contribute to the knowledge of species boundaries but will also provide an important basis for evolutionary studies and research on secondary metabolites in Sporocadaceae. Taxonomic novelties: New genus: Cavernicola P. Razaghi, F. Liu & L. Cai. New species: Cavernicola guangxiensis P. Razaghi, F. Liu & L. Cai, Discosia ascidiata P. Razaghi, F. Liu & L. Cai, Discosia jiangxiensis P. Razaghi, F. Liu & L. Cai, Discosia navicularis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis ageratinae P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis castanopsidis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis celtidis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis collariata P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis dimorphospora P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis dolichoconidiophora P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis fijiensis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis fimbriata P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis fuzhouensis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis guangxiensis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis guizhouensis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis jiangxiensis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis liquidambaris P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis machili P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis megabetaspora P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis moniliformis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis nanningensis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis phyllostachydis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis poae P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis smilacis P. Razaghi, F. Liu, M. Raza & L. Cai, Pestalotiopsis alloschemones P. Razaghi, F. Liu & L. Cai, Pestalotiopsis americana P. Razaghi, F. Liu & L. Cai, Pestalotiopsis biappendiculata P. Razaghi, F. Liu & L. Cai, Pestalotiopsis cratoxyli P. Razaghi, F. Liu, M. Raza & L. Cai, Pestalotiopsis exudata P. Razaghi, F. Liu & L. Cai, Pestalotiopsis fusiformis P. Razaghi, F. Liu & L. Cai, Pestalotiopsis ganzhouensis P. Razaghi, F. Liu & L. Cai, Pestalotiopsis leucospermi P. Razaghi, F. Liu & L. Cai, Pestalotiopsis lobata P. Razaghi, F. Liu & L. Cai, Pestalotiopsis machili P. Razaghi, F. Liu & L. Cai, Pestalotiopsis multiappendiculata P. Razaghi, F. Liu & L. Cai, Pestalotiopsis pruni P. Razaghi, F. Liu & L. Cai, Pestalotiopsis rubrae P. Razaghi, F. Liu, M. Raza & L. Cai, Pestalotiopsis wulichongensis P. Razaghi, F. Liu, M. Raza & L. Cai, Seimatosporium tibetense P. Razaghi, F. Liu & L. Cai, Seiridium rhododendri P. Razaghi, F. Liu & L. Cai, Sporocadus cavernicola P. Razaghi, F. Liu & L. Cai, Sporocadus hyperici P. Razaghi, F. Liu & L. Cai, Sporocadus tibetensis P. Razaghi, F. Liu & L. Cai. New combinations: Discosia kaki (Kaz. Tanaka et al.) P. Razaghi, F. Liu & L. Cai, Monochaetia bulbophylli (S.F. Ran & Yong Wang bis) P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis keteleeriae (Y. Song et al.) P. Razaghi, F. Liu & L. Cai. Citation: Razaghi P, Raza M, Han SL, Ma ZY, Cai L, Zhao P, Chen Q, Phurbu D, Liu F (2024). Sporocadaceae revisited. Studies in Mycology 109: 155-272. doi: 10.3114/sim.2024.109.03.

Unraveling the antifungal composition of bitter orange decoction against the melon pathogen Fusarium jinanense

Bitter orange (Citrus aurantium) is an important source of essential oils with high antimicrobial activities, however the composition and antifungal potential of the decoction peels is little explored. This study assessed the peel decoction's chemical profile at the secondary metabolism level and its antifungal activity against the melon phytopathogen Fusarium jinanense. The decoction's antifungal potential was investigated using a bioassay-guided fractionation approach based on Solid-Phase Extraction (SPE) and LC-HRMS/MS analysis. Coumarins and flavones were the most abundant classes of compounds in the high-value fractions responsible for up to 61% of the mycelial inhibition of F. jinanense. Overall, this study has presented for the first time the chemical composition, the antifungal potential of the decoction of C. aurantium peels and the compounds associated with these results. This strategy can guide the exploration of under-explored food sources and add value to compounds or fractions enriched with bioactive compounds.

Morpho-phylogenetic identification and characterization of new causal agents of Fusarium species for postharvest fruit rot disease of muskmelon in northern Thailand and their sensitivity to fungicides

A significant global problem affecting muskmelon (Cucumis melo L.) is fruit rot caused by phytopathogenic fungi, which results in unsaleable products and substantial financial losses. In 2022 and 2023, fruit rot on muskmelon was found during the postharvest storage period in Phayao Province of northern Thailand. The aim of the current study was to isolate the species of fungi causing the fruit rot lesions. Out of the rot lesions on muskmelons, nine fungal isolates were received. All isolates of fungi were identified through a combination of morphological characteristics and molecular analyses. Based on their morphological traits, all isolated fungal isolate was assigned to the genus Fusarium. All the fungal isolates were determined to belong to the Fusarium incarnatum-equiseti species complex through multi-gene phylogenetic analysis employing the calmodulin (cam), RNA polymerase second largest subunit (rpb2), and translation elongation factor 1-alpha (tef1-α) genes. These isolates were identified as F. compactum (SDBR-CMU483), F. jinanense (SDBR-CMU484, SDBR-CMU485, and SDBR-CMU486), F. mianyangense (SDBR-CMU487 and SDBR-CMU488), and F. sulawesiense (SDBR-CMU489, SDBR-CMU490, and SDBR-CMU491). Moreover, pathogenicity tests were subsequently carried out, and the results indicated that all fungal isolates caused symptoms of fruit rot on inoculated muskmelon fruits. Notably, this result was consistent with the symptoms observed throughout the postharvest storage period. In the fungicide screening test, all fungal isolates showed sensitivity to copper oxychloride. However, all isolates showed insensitivity to benalaxyl-M + mancozeb, carbendazim, mancozeb, and metalaxy. To the best of our knowledge, the present study is the first to identify F. compactum, F. jinanense, and F. mianyangense as new causative agents of muskmelon fruit rot in Thailand and other regions globally. This is also the first report of postharvest fruit rot on muskmelons caused by F. sulawesiense in Thailand. Furthermore, the fungicide screening results indicate that fungicide resistance can be beneficial in developing potential management strategies against postharvest fruit rot disease of muskmelon caused by these four pathogenic Fusarium species.

Fusarium amaranthi sp. nov. from Amaranth Is an Emergent Species Closely Related to F. circinatum

Amaranth (Amaranthus spp. L) is not native to South Korea but is cultivated in small scales for ornamental purposes as well as leafy vegetables and pseudo cereals. In this study, a new species within the genus Fusarium was isolated from amaranth, showing stem rot symptoms from a farmer field in Hwaseong, South Korea. The disease is characterized by dark-brown spots with black borders, leading to withering. Phylogenetic analysis-based concatenated sequences of translation elongation factor 1-alpha (TEF1), beta-tubulin (tub2), calmodulin (cmdA), RNA polymerase largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) genes revealed that the obtained isolates formed a distinct clad within the Fusarium fujikuroi species complex and is closely related to F. circinatum. Cultural and morphological characteristics and pathogenicity on healthy amaranth plants (stem and leaves) were examined. The isolates readily differentiated from F. circinatum based on one- to five-septate macroconidia and the absence of sterile hyphae. Based on molecular and morphological characteristics, this fungus is demonstrated to be a new species and is described here as F. amaranthi, the causal agent of stem rot of amaranth in South Korea.

Phylogenomic approaches reveal a robust time-scale phylogeny of the Terminal Fusarium Clade

The Terminal Fusarium Clade (TFC) is a group in the Nectriaceae family with agricultural and clinical relevance. In recent years, various phylogenies have been presented in the literature, showing disagreement in the topologies, but only a few studies have conducted analyses on the divergence time scale of the group. Therefore, the evolutionary history of this group is still being determined. This study aimed to understand the evolutionary history of the TFC from a phylogenomic perspective. To achieve this objective, we performed a phylogenomic analysis using the available genomes in GenBank and ran eight different pipelines. We presented a new robust topology of the TFC that differs at some nodes from previous studies. These new relationships allowed us to formulate new hypotheses about the evolutionary history of the TFC. We also inferred new divergence time estimates, which differ from those of previous studies due to topology discordances and taxon sampling. The results suggested an important diversification process in the Neogene period, likely associated with the diversification and predominance of terrestrial ecosystems by angiosperms. In conclusion, we presented a robust time-scale phylogeny that allowed us to formulate new hypotheses regarding the evolutionary history of the TFC.

White root rot of Bletilla striata: the pathogen, biological characterization, and fungicide screening

Bletilla striata is an endangered traditional medicinal herb in China. In May 2020, the emergence of white root rot severely impacted the quality and yield of B. striata, affecting about 5% of the plants at plant nurseries of the Chengdu Academy of Agricultural and Forestry Sciences. Through a series of experiments and evaluations, the pathogen was identified as Fusarium solani. This is the first report of B. striata white root rot caused by F. solani in Sichuan, China. To better understand this disease and provide data support for its control, a combination of morphological, molecular characterisation and pathogenicity determination was used in this study for assessment. Meanwhile, the effects of different carbon and nitrogen sources, culture medium, temperature, photoperiod and pH on mycelial growth and spore production of F. solani were investigated. In addition, effective fungicides were screened and the concentration ratios of fungicides were optimized using response surface methodology (RSM). The experimental results showed that sucrose was the optimum carbon source for the pathogen, and the optimum temperature and pH were 25°C and pH 7, respectively, while light did no significant effect. Effective fungicides were screened, among which difenoconazole showed the strongest inhibition with EC50 of 142.773 µg/mL. The optimum fungicide concentration scheme (difenoconazole, pyraclostrobin, and thiophanate-methyl at 395.42, 781.03, and 561.11 µg/mL, respectively) was obtained using response surface methodology (RSM) to improve the inhibition rate of 92.24 ± 0.34%. This study provides basic data for the pathogen characterization of B. striata white root rot and its potential fungicides in Sichuan, China. In addition, the optimal fungicide concentration ratios were obtained through response surface methodology (RSM) optimization, which significantly enhanced the fungicidal effect and provided a scientific basis for the future control of B. striata white root rot.

IMA Genome - F19 : A genome assembly and annotation guide to empower mycologists, including annotated draft genome sequences of Ceratocystis pirilliformis, Diaporthe australafricana, Fusarium ophioides, Paecilomyces lecythidis, and Sporothrix stenoceras

The pace at which Next Generation Sequence data is being produced continues to accelerate as technology improves. As a result, such data are increasingly becoming accessible to biologists outside of the field of bioinformatics. In contrast, access to training in the methods of genome assembly and annotation are not growing at a similar rate. In this issue, we report on a Genome Assembly Workshop for Mycologists that was held at the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, South Africa and make available the 12 draft genome sequences emanating from the event. With the aim of making the process of genome assembly and annotation more accessible to biologists, we provide a step-by-step guide to both genome assembly and annotation, intended to encourage and empower mycologists to use genome data in their research.

Molecular assessment of oat head blight fungus, including a new genus and species in a family of Nectriaceae

Head blight (HB) of oat (Avena sativa) has caused significant production losses in oats growing areas of western China. A total of 314 isolates, associated with HB were collected from the major oat cultivating areas of Gansu, Qinghai, and Yunnan Provinces in western China. Based on morphological characters, the isolates were initially classified into three genera, as differentiation to species was a bit difficult. Taxonomic analysis of these isolates based on muti-gene phylogenetic analyses (ITS, TEF1, TUB2, and RPB2) revealed four known Fusarium species, F. proliferatum, F. avenaceum, F. poae, and F. sibiricum, and one Acremonium specie (A. sclerotigenum). In addition, a new genus Neonalanthamala gen. nov., similar to genus Nalanthamala was introduced herein with a new combination, Neonalanthamala graminearum sp. nov., to accommodate the HB fungus. The molecular clock analyses estimated the divergence time of the Neonalanthamala and Nalanthamala based on a dataset (ITS, TUB2, RPB2), and we recognized the mean stem ages of the two genera are 98.95 Mya, which showed that they evolved from the same ancestor. N. graminearum was the most prevalent throughout the surveyed provinces. Pathogenicity test was carried out by using two different methods: seed inoculation and head inoculation. Results showed that F. sibiricum isolates were the most aggressive on the seed and head. A. sclerotigenum isolates were not pathogenic to seeds, and were developed less symptoms to the head compared to other species. Data analyses showed that the correlation of the germination potential, germination index, and dry weight of seed inoculation and disease index of plant inoculation had a highly significant negative correlation (P < 0.001). These results showed that the development of HB might be predicted by seed tests for this species. A. sclerotigenum and N. graminearum causing HB are being firstly reported on oat in the world. Similarly, F. proliferatum, F. avenaceum, F. poae and F. sibiricum causing oat HB are firstly reported in China.

Didymellaceae species associated with tea plant (Camelliasinensis) in China

Tea plant is one of the most important commercial crops worldwide. The Didymellaceae fungi can cause leaf blight disease of tea plant. In this study, 240 isolates were isolated from tea plant leaves of 10 provinces in China. Combined with multi-locus (ITS, LSU, RPB2 and TUB2) phylogenetic analysis and morphological characteristics, these isolates were identified as 25 species of six genera in Didymellaceae, including 19 known species Didymellacoffeae-arabicae, D.pomorum, D.segeticola, D.sinensis, Epicoccumcatenisporum, E.dendrobii, E.draconis, E.italicum, E.latusicollum, E.mackenziei, E.oryzae, E.poaceicola, E.rosae, E.sorghinum, E.tobaicum, Neoascochytamortariensis, Paraboeremialitseae, Remotididymellaanemophila and Stagonosporopsiscaricae, of which 15 species were new record species and six novel species, named D.yunnanensis, E.anhuiense, E.jingdongense, E.puerense, N.yunnanensis and N.zhejiangensis. Amongst all isolates, D.segeticola was the most dominant species. Pathogenicity tests on tea plant leaves showed that E.anhuiense had the strongest virulence, while E.puerense had the weakest virulence. Besides, D.pomorum, D.yunnanensis, E.dendrobii, E.italicum, E.jingdongense, E.mackenziei, E.oryzae, E.rosae, E.tobaicum, N.mortariensis, N.yunnanensis, N.zhejiangensis and R.anemophila were non-pathogenic to the tea plant.

Virulent Fusarium isolates with diverse morphologies show similar invasion and colonization strategies in alfalfa

Root rot is a major disease that causes decline of alfalfa production, and Fusarium is a major pathogen associated with root rot. In this study, 13 Fusarium isolates were obtained from alfalfa with root rot in Gansu Province, the major alfalfa production region in China. The isolates were characterized by molecular genotyping (ITS, TEF 1-α and RPB2 fragments) and identified as six species, which included the F. acuminatum, F. incarnatum, F. oxysporum, F. proliferatum, F. redolens, and F. solani. We found that their morphology varied significantly at both the macro- and micro-levels, even for those from the same species. We developed a low cost and fast pathogenicity test and revealed that all isolates were pathogenic to alfalfa with typical root rot symptoms such as leaf yellowing and brown lesions on the root and stem. However, the virulence of the isolates differed. We also found that the conidia of all isolates germinated as early as 24 hours post inoculation (hpi), while hyphae colonized the root extensively and invaded the xylem vessel by 48 hpi. Together our results reveal that different virulent Fusarium isolates use a similar invasion strategy in alfalfa. This natural plant-fungus pathosystem is intriguing and warrants further examination, particularly with regard to efforts aimed at mitigating the impact of multiple similar vascular pathogens on infected alfalfa plants.

Diversity of culturable fungi in six Tibetan Plateau lakes, with descriptions of eight new taxa

The combination of low temperatures, oligotrophic conditions, high altitude, and varying salinity in Tibetan Plateau lakes endows them with a wealth of distinctive fungal resources. This study aimed to investigate the diversity of culturable fungi in sediment and water samples collected from six lakes located on the Tibetan Plateau at elevations above 4,500 m. A total of 843 fungal strains were isolated by dilution plate method using four different media. Initial ITS analyses revealed that they belong to 156 species across 83 genera, spanning 50 families, 26 orders, 12 classes, and 6 phyla. Further morphological and multi-locus phylogenetic analyses were conducted, resulting in the formal descriptions of a new genus, Xizangia, and seven new species, including Alternaria xizangensis, Emericellopsis ovoidea, Myceliophthora xizangica, Preussia cylindricalis, Preussia sedimenticola, Pseudeurotium sedimenticola, and Xizangia sedimenticola. This research provides insights into the biodiversity of culturable fungi in the unique and extreme ecosystem, shedding light on the potential discovery of novel species and genera.

An evolutionary view of the Fusarium core genome

Fusarium, a member of the Ascomycota fungi, encompasses several pathogenic species significant to plants and animals. Some phytopathogenic species have received special attention due to their negative economic impact on the agricultural industry around the world. Traditionally, identification and taxonomic analysis of Fusarium have relied on morphological and phenotypic features, including the fungal host, leading to taxonomic conflicts that have been solved using molecular systematic technologies. In this work, we applied a phylogenomic approach that allowed us to resolve the evolutionary history of the species complexes of the genus and present evidence that supports the F. ventricosum species complex as the most basal lineage of the genus. Additionally, we present evidence that proposes modifications to the previous hypothesis of the evolutionary history of the F. staphyleae, F. newnesense, F. nisikadoi, F. oxysporum, and F. fujikuroi species complexes. Evolutionary analysis showed that the genome GC content tends to be lower in more modern lineages, in both, the whole-genome and core-genome coding DNA sequences. In contrast, genome size gain and losses are present during the evolution of the genus. Interestingly, core genome duplication events positively correlate with genome size. Evolutionary and genome conservation analysis supports the F3 hypothesis of Fusarium as a more compact and conserved group in terms of genome conservation. By contrast, outside of the F3 hypothesis, the most basal clades only share 8.8% of its genomic sequences with the F3 clade.

Fusarium species associated with citrus blackfly (Aleurocanthus woglumi) from an agroecological polyculture in Brazil, including an augmented description of F. volatile

The objectives of this study were to report Fusarium species associated with Aleurocanthus woglumi (Hemiptera: Aleyrodidae) collected from citrus leaves from an agroecological polyculture in Brazil, assess sexual reproductive mode of the species with unknown sexual stages, and provide an augmented description of F. volatile, for which we discovered a sexual stage. Nineteen Fusarium isolates were recovered from A. woglumi. These fungi belong to three species complexes, i.e., the F. chlamydosporum species complex (FCSC), the F. fujikuroi species complex (FFSC), and the F. incarnatum-equiseti species complex (FIESC). Based on multilocus phylogenetic analyses, the species were identified as F. annulatum, F. chlamydosporum, F. pernambucanum, F. sulawesiense, F. verticillioides, and F. volatile. Our results suggest that three species whose sexual stages are unknown (F. chlamydosporum, F. sulawesiense, and F. volatile) are also heterothallic. Intraspecific crosses of F. sulawesiense and F. volatile produced protoperithecia, whereas 66.7% of F. volatile crosses produced fertile perithecia. We provide an augmented description of the latter species to include characteristics of its sexual morph and those observed in the asexual morph that had not yet been described for the species. This study highlights the potential of researching insect-associated fungi to increase knowledge about the diversity, taxonomy, and versatility of Fusarium in ecosystems.

Diversity and Pathogenicity of Fusarium Species Associated with Stalk and Crown Rot in Maize in Northern Italy

The genus Fusarium includes several agronomically important and toxin-producing species that are distributed worldwide and can cause a wide range of diseases. Crown and stalk rot and grain infections are among the most severe symptoms that Fusarium spp. can cause in maize. Disease development usually occurs during germination, but it may also affect the later phases of plant growth. The purpose of this study was to investigate the diversity and pathogenicity of 41 isolates recovered from symptomatic seedlings collected in Northern Italy and seeds of five different geographical origins in 2019 and 2020. The pathogenicity was tested and confirmed in 23 isolates causing rotting in maize seedlings, with disease indexes from 20% to 90%. A multilocus phylogeny analysis based on four genomic loci (tef1-α, rpb2, calm and tub2) was performed on 23 representative isolates. Representative isolates were identified as species belonging to three species complexes (SC), including Fusarium verticillioides and F. annulatum in the F. fujikuroi SC. Fusarium commune was identified in the F. nisikadoi SC, and three different lineages were found in the Fusarium oxysporum SC. This study reports F. annulatum and two lineages of the Fusarium oxysporum SC as maize pathogens for the first time in Italy.