Tolerance Evaluation of Celery Commercial Cultivars and Genetic Variability of Fusarium oxysporum f. sp. apii

Celery (Apium graveolens var. dulce) is affected by several plant diseases, such as Fusarium oxysporum f. sp. apii (Foa). Four Foa races have been found in the US. The goals of this study were to determine which races are present in Costa Rica and to quantify the tolerance of the imported commercial cultivars of celery produced in the country. Isolates from 125 symptomatic celery plants from three different geographical locations were analyzed, 65 of which were selected for phylogenetic analysis. All isolates presented a short sequence of five nucleotides that differentiates Foa race 3 in the IGS rDNA region. Three different haplotypes closely related to race 3 were found, which were highly virulent, produced great losses, and affected all cultivars (resistant to races 2 and 4) of imported commercial celery. Additionally, five different cultivars of celery were evaluated against seven pathogen isolates identified as race 3 in greenhouse conditions. Two of the cultivars showed significantly less chlorosis, wilting, mortality, and higher fresh weight. Most of the Foa isolates significantly increased chlorosis, wilting, and mortality compared to non-inoculated control. Celery producers in Costa Rica lack access to seeds resistant to the Foa race 3 present in the country.

Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers

Tomato is one of the most prominent crops in global horticulture and an important vegetable crop in Kazakhstan. The lack of data on the genetic background of local varieties limits the development of tomato breeding in the country. This study aimed to perform an initial evaluation of the breeding collection of tomato varieties from the point of view of their genetic structure and pathogen resistance using a set of PCR based molecular markers, including 13 SSR markers for genetic structure analysis, and 14 SCAR and CAPS markers associated with resistance to five pathogens: three viruses, fungus Fusarium oxysporum, and oomycete P hytophthora infestans. Nine SSR markers were with a PIC value varying from 0.0562 (low information content) to 0.629 (high information content). A weak genetic structure was revealed in the samples of varieties including local cultivars and, predominantly, varieties from Russia and other ex-USSR countries. The local varieties were closely related to several groups of cultivars of Russian origin. Screening for a set of resistance markers revealed the common occurrence of the resistance locus I against Fusarium oxysporum and only the occasional presence of resistance alleles of other markers. No markers of resistance to the three considered viruses were revealed in local tomato varieties. Only two local cultivars had markers of resistance to P. infestans, and only the 'Meruert' cultivar had a combination of resistance markers against P. infestans and F. oxysporum. The obtained results have demonstrated the need for further studies of local tomato varieties with a wider range of molecular markers and source germplasm to lay a foundation for the development of tomato breeding in Kazakhstan.

Role of seed infection for the near and far distance dissemination of wheat blast caused by Magnaporthe oryzae pathotype Triticum

Magnaporthe oryzae pathotype Triticum (MoT) is a devastating fungal phytopathogen causing wheat blast disease which threatens wheat production particularly in warmer climate zones. Effective disease control is hampered by the limited knowledge on the life cycle, epidemiology, and pathogenicity of MoT. Since MoT mainly infects and colonizes the inflorescences of wheat, infection, invasion routes and colonization of MoT on wheat ears and in wheat seeds were investigated in order to assess potential seed transmission pathways. MoT was spray inoculated on two wheat cultivars (Sumai 3, susceptible and Milan, resistant) at three ear maturity stages [full ear emergence, growth stage (GS) 59; mid flowering, GS 65; and end of flowering, GS 69]. Incidence of MoT on Sumai 3 seeds was 100% and 20-25% on Milan. MoT sporulation rate on Sumai 3 contaminated seeds was more than 15 times higher than on Milan. Repeated washes of seed samples for removing paraffin fixation hampers seed microscopy. To overcome the damage of seed samples, we used hand-sectioned seed samples instead of paraffin-fixed microtome samples to facilitate microscopy. The colonization of MoT within various seed tissues was followed by light and confocal laser scanning microscopy (CLSM). Invasion of MoT in seeds predominantly occurred in the caryopsis germ region, but entry via other seed parts was also observed, confirming the potential of intense colonization of MoT in wheat grains. Fungal spread in wheat plants growing from MoT infected seeds was monitored through plating, microscopic and molecular techniques. Under greenhouse conditions, no spread of MoT from infected seeds to seedlings later than GS 21 or to ears was detected, neither in Milan nor in Sumai 3. We therefore conclude, that MoT may not systemically contaminate inflorescences and seeds in neither susceptible nor resistant wheat cultivars. However, initial blast symptoms, only found on seedlings of Sumai 3 but not Milan, resulted in the formation of new conidia, which may serve as inoculum source for plant-to-plant dissemination by airborne infection of plant stands in the field (short distance spread). Ultimately the inoculum may infect young inflorescences in the field and contaminate seeds. Our findings again stress the risk of long-distance dissemination of wheat blast across continents through MoT-contaminated seeds. This underlines the importance of mandatory use of healthy seeds in strategies to control any further spread of wheat blast.

Fungal Pathogens and Seed Storage in the Dry State

Seeds can harbor a wide range of microorganisms, especially fungi, which can cause different sanitary problems. Seed quality and seed longevity may be drastically reduced by fungi that invade seeds before or after harvest. Seed movement can be a pathway for the spread of diseases into new areas. Some seed-associated fungi can also produce mycotoxins that may cause serious negative effects on humans, animals and the seeds themselves. Seed storage is the most efficient and widely used method for conserving plant genetic resources. The seed storage conditions used in gene banks, low temperature and low seed moisture content, increase seed longevity and are usually favorable for the survival of seed-borne mycoflora. Early detection and identification of seed fungi are essential activities to conserve high-quality seeds and to prevent pathogen dissemination. This article provides an overview of the characteristics and detection methods of seed-borne fungi, with a special focus on their potential effects on gene bank seed conservation. The review includes the following aspects: types of seed-borne fungi, paths of infection and transmission, seed health methods, fungi longevity, risk of pathogen dissemination, the effect of fungi on seed longevity and procedures to reduce the harmful effects of fungi in gene banks.

Alien and cryptogenic fungi and oomycetes in Austria: an annotated checklist (2nd edition)

Fungal invasions can have far-reaching consequences, and despite increasing relevance, fungi are notoriously underrepresented in invasion science. Here, we present the second annotated checklist for alien and cryptogenic fungi and oomycetes in Austria. This list contains 375 taxa of which 278 are classified as established; compared to the first checklist from 2002, this amounts to an almost five-fold increase and the number of decade-wise first records is steadily rising since the mid-twentieth century. The introduction pathway is unclear for the vast majority of taxa, while the main means of spread within the country is unassisted secondary spread. Fungi were predominantly introduced from the Northern Hemisphere, especially North America and Temperate Asia. Rates of newly recorded alien fungi differ among phyla; the majority belongs to the Ascomycota, which experienced an 9.6-fold increase in numbers. Orders found most frequently are powdery mildews (Erysiphales, Ascomycota), downy mildews (Peronosporales, Oomycota), agarics (Agaricales, Basidiomycota), Mycosphaerellales (Ascomycota), rusts (Pucciniales, Basidiomycota) and Pleosporales (Ascomycota). The majority (about 80%) of the taxa are plant pathogens, while animal pathogens are few but severely affecting their native hosts. The dominance of pathogens in our checklist underlines the need of better tackling fungal invasions-especially in the light of emerging infectious diseases-and highlights potential knowledge gaps for ectomycorrhizal and saprobic alien fungi, whose invasion processes are often much more inconspicuous. Our results show that fungal invasions are a phenomenon of increasing importance, and collaborative efforts are needed for advancing the knowledge and management of this important group.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10530-022-02896-2.

Illumina Sequencing of 18S/16S rRNA Reveals Microbial Community Composition, Diversity, and Potential Pathogens in 17 Turfgrass Seeds

The increasing need for turfgrass seeds is coupled with the high risk of dangerous microbial pathogens being transmitted through the domestic and international trade of seeds. Concerns continue to be raised about seed safety and quality. Here, we show that next-generation sequencing (NGS) of DNA represents an effective and reliable tactic to monitor the microbial communities within turfgrass seeds. A comparison of DNA sequence data with reference databases revealed the presence of 26 different fungal orders. Among them, serious plant disease pathogens such as Bipolaris sorokiniana, Boeremia exigua, Claviceps purpurea, and Rhizoctonia zeae were detected. Seedborne bacteria, including Erwinia persicina and Acidovorax avenae, were identified from different bacterial orders. Our study indicated that the traditional culturing method and the NGS approach for pathogen identification complement each other. The reliability of culturing and NGS methods was further validated by PCR with specific primers. The combination of these different techniques ensures maximum sensitivity and specificity for turfgrass seed pathogen testing assay.

Phytosanitary Interventions for Safe Global Germplasm Exchange and the Prevention of Transboundary Pest Spread: The Role of CGIAR Germplasm Health Units

The inherent ability of seeds (orthodox, intermediate, and recalcitrant seeds and vegetative propagules) to serve as carriers of pests and pathogens (hereafter referred to as pests) and the risk of transboundary spread along with the seed movement present a high-risk factor for international germplasm distribution activities. Quarantine and phytosanitary procedures have been established by many countries around the world to minimize seed-borne pest spread by screening export and import consignments of germplasm. The effectiveness of these time-consuming and cost-intensive procedures depends on the knowledge of pest distribution, availability of diagnostic tools for seed health testing, qualified operators, procedures for inspection, and seed phytosanitation. This review describes a unique multidisciplinary approach used by the CGIAR Germplasm Health Units (GHUs) in ensuring phytosanitary protection for the safe conservation and global movement of germplasm from the 11 CGIAR genebanks and breeding programs that acquire and distribute germplasm to and from all parts of the world for agricultural research and food security. We also present the challenges, lessons learned, and recommendations stemming from the experience of GHUs, which collaborate with the national quarantine systems to export and distribute about 100,000 germplasm samples annually to partners located in about 90 to 100 countries. Furthermore, we describe how GHUs adjust their procedures to stay in alignment with evolving phytosanitary regulations and pest risk scenarios. In conclusion, we state the benefits of globally coordinated phytosanitary networks for the prevention of the intercontinental spread of pests that are transmissible through plant propagation materials.

Interspecific Competition for Colonization of Maize Plants Between Fusarium proliferatum and Fusarium verticillioides

Fusarium proliferatum and F. verticillioides are mycotoxin-producing, seedborne pathogens of maize. They are often asymptomatic in seed, eluding symptom-based detection. Experiments were conducted in nonsterile soil to determine whether interspecific competition influenced establishment in maize plants of an introduced isolate of F. proliferatum or F. verticillioides. Hygromycin-resistant, green fluorescent protein (GFP) transformed (GFP-tagged) F. proliferatum (F. proliferatum-green) and hygromycin-resistant, monomeric red fluorescent protein (mRFP) transformed (mRFP-tagged) F. verticillioides (F. verticillioides-red) strains were developed to provide molecular markers to track fungal establishment. Heat-killed Fusarium-free maize seed, colonized with F. proliferatum-green or F. verticillioides-red by immersion in a spore suspension for 16 h, served as the source of inoculum. The ability of F. proliferatum-green and F. verticillioides-red to colonize viable maize plants already colonized by the other species was determined. Maize plants were retrieved from soil after 14 days and DNA was extracted from three consecutive root segments and three consecutive stem segments. A TaqMan multiplex real-time quantitative PCR protocol was developed to identify and quantify F. proliferatum-green and F. verticillioides-red from each plant segment from each treatment; the experiment was repeated three times. This experiment confirmed that F. proliferatum-green and F. verticillioides-red effectively colonized roots and stems of the maize plant already colonized with the other species. Prior colonization of maize tissues by F. verticillioides-red (P = 0.6749) and other seedborne microorganisms (P = 0.1910) reduced but did not prevent subsequent colonization by F. proliferatum-green. Similarly, prior colonization of maize tissues by F. proliferatum-green (P = 0.7032) and other seedborne microorganisms (P = 0.1447) reduced but did not prevent subsequent colonization by F. verticillioides-red.

Microbiota in the Rhizosphere and Seed of Rice From China, With Reference to Their Transmission and Biogeography

Seeds play key roles in the acquisition of plant pioneer microbiota, including the transmission of microbes from parent plants to offspring. However, the issues about seed microbial communities are mostly unknown, especially for their potential origins and the factors influencing the structure and composition. In this study, samples of rice seed and rhizosphere were collected from northeast and central-south China in two harvest years and analyzed using a metabarcoding approach targeting 16S rRNA gene region. A higher level of vertical transmission (from parent seed microbiota to offspring) was revealed, as compared to the acquisition from the rhizosphere (25.5 vs 10.7%). The core microbiota of the rice seeds consisted of a smaller proportion of OTUs (3.59%) than that of the rice rhizosphere (7.54%). Among the core microbiota, species in Arthrobacter, Bacillus, Blastococcus, Curtobacterium, Pseudomonas, and Ramlibacter have been reported as potential pathogens and/or beneficial bacteria for plants. Both the seed and the rhizosphere of rice showed distance-decay of similarity in microbial communities. Seed moisture and winter mean annual temperature (WMAT) had significant impacts on seed microbiota, while WMAT, total carbon, available potassium, available phosphorus, aluminum, pH, and total nitrogen significantly determined the rhizosphere microbiota. Multiple functional pathways were found to be enriched in the seed or the rhizosphere microbiota, which, to some extent, explained the potential adaptation of bacterial communities to respective living habitats. The results presented here elucidate the composition and possible sources of rice seed microbiota, which is crucial for the health and productivity management in sustainable agriculture.

Morphological and Molecular Identification of Seedborne Fungi in Squash (Cucurbita maxima, Cucurbita moschata)

Squash is one of the most important crops of tropical and temperate regions, and it can be affected by several fungal pathogens. Most of these pathogens infect the seeds, which become an efficient vehicle to disperse seedborne pathogens over long distances, with consequent severe crop losses. The main objective of this study was the identification of the principal seedborne fungi in seeds extracted from 66 samples of asymptomatic and symptomatic squash fruit (Cucurbita maxima, Cucurbita moschata) collected in two countries, Tunisia and Italy. The symptoms of fruit decay were identified and classified according to lesion size. Following the blotter test, 14 fungal species were detected from the seeds. Seedborne fungi were identified in all fruit samples tested, including asymptomatic fruit. The most frequent fungi from Tunisian seeds were Alternaria alternata (25.1%), followed by Stagonosporopsis cucurbitacearum (24.6%), Fusarium solani (16.6%), Rhizopus stolonifer (13.3%), F. fujikuroi (7.8%), Albifimbria verrucaria (3.3%), and Stemphylium vesicarium (2.3%). For the fruits from Italy, the most frequently identified fungal species in seed samples were Alternaria alternata (40.0%), followed by F. fujikuroi (20.8%), Stemphylium vesicarium (3.0%), and Curvularia spicifera (2.1%). Morphological identification was confirmed by molecular diagnosis using the available species-specific primers. Furthermore, specific primers were designed to identify Albifimbria verrucaria, Paramyrothecium roridum, and Stemphylium vesicarium. Application of seed-health testing methods, including such conventional and molecular diagnostic tools, will help to improve seed quality and crop yields.

Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA

Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.

Prevalence and Distribution of Beet Necrotic Yellow Vein Virus Strains in North Dakota and Minnesota

Beet necrotic yellow vein virus (BNYVV) is the causal agent of rhizomania, a disease of global importance to the sugar beet industry. The most widely implemented resistance gene to rhizomania to date is Rz1, but resistance has been circumvented by resistance-breaking (RB) isolates worldwide. In an effort to gain greater understanding of the distribution of BNYVV and the nature of RB isolates in Minnesota and eastern North Dakota, sugar beet plants were grown in 594 soil samples obtained from production fields and subsequently were analyzed for the presence of BNYVV as well as coding variability in the viral P25 gene, the gene previously implicated in the RB pathotype. Baiting of virus from the soil with sugar beet varieties possessing no known resistance to rhizomania resulted in a disease incidence level of 10.6% in the region examined. Parallel baiting analysis of sugar beet genotypes possessing Rz1, the more recently introgressed Rz2, and with the combination of Rz1 + Rz2 resulted in a disease incidence level of 4.2, 1.0, and 0.8%, respectively. Virus sequences recovered from sugar beet bait plants possessing resistance genes Rz1 and/or Rz2 exhibited reduced genetic diversity in the P25 gene relative to those recovered from the susceptible genotype while confirming the hypervariable nature of the coding for amino acids (AAs) at position 67 and 68 in the P25 protein. In contrast to previous reports, we did not find an association between any one specific AA signature at these positions and the ability to circumvent Rz1-mediated resistance. The data document ongoing virulence development in BNYVV populations to previously resistant varieties and provide a baseline for the analysis of genetic change in the virus population that may accompany the implementation of new resistance genes to manage rhizomania.

Seed and Root Endophytic Fungi in a Range Expanding and a Related Plant Species

Climate change is accelerating the spread of plants and their associated species to new ranges. The differences in range shift capacity of the various types of species may disrupt long-term co-evolved relationships especially those belowground, however, this may be less so for seed-borne endophytic microbes. We collected seeds and soil of the range-expanding Centaurea stoebe and the congeneric Centaurea jacea from three populations growing in Slovenia (native range of both Centaurea species) and the Netherlands (expanded range of C. stoebe, native range of C. jacea). We isolated and identified endophytic fungi directly from seeds, as well as from roots of the plants grown in Slovenian, Dutch or sterilized soil to compare fungal endophyte composition. Furthermore, we investigated whether C. stoebe hosts a reduced community composition of endophytes in the expanded range due to release from plant-species specific fungi while endophyte communities in C. jacea in both ranges are similar. We cultivated 46 unique and phylogenetically diverse endophytes. A majority of the seed endophytes resembled potential pathogens, while most root endophytes were not likely to be pathogenic. Only one endophyte was found in both roots and seeds, but was isolated from different plant species. Unexpectedly, seed endophyte diversity of southern C. stoebe populations was lower than of populations from the north, while the seed endophyte community composition of northern C. stoebe populations was significantly different southern C. stoebe as well as northern and southern C. jacea populations. Root endophyte diversity was considerably lower in C. stoebe than in C. jacea independent of plant and soil origin, but this difference disappeared when plants were grown in sterile soils. We conclude that the community composition of fungal endophytes not only differs between related plant species but also between populations of plants that expand their range compared to their native habitat. Our results suggest that fungal endophytes of two Centaurea species are not able to systemically infect plants. We highlight that endophytes remain poorly studied and further work should investigate the functional importance of endophytes.

Epidemiology and Management of Fusarium Wilt of China Asters

The epidemiology and strategies for management of Fusarium wilt of China aster (Callistephus chinensis) were studied in Connecticut and Florida, USA, by examining seed contamination, on-farm disease incidence, sanitation, host resistance, and various soil treatments. Five out of 25 commercial seed packages from three separate distribution companies assayed in Connecticut had seeds contaminated with the pathogen Fusarium oxysporum f. sp. callistephi. Farm surveys of two cut-flower farms in Connecticut had disease incidences of 32 and 58%, while in Florida, the incidence of the disease ranged from 0.002 to 71.2% in two cut-flower operations. All pathogenic isolates from seed and symptomatic plants in Connecticut were vegetatively compatible, suggesting a common origin. Pathogenic isolates from Florida and nonpathogenic isolates fell into different vegetative compatibility groups and may have had another origin. Sodium hypochlorite solutions (1%) eliminated the fungus from seeds and Styrofoam when applied as a soak or spray, respectively. Soil fumigation with methyl bromide + chloropicrin, 1,3-dichloropropene + chloropicrin, or metam sodium maintained Fusarium wilt at low levels at a Florida cut-flower production facility. Evaluations of disease resistance of 44 cultivars in the greenhouse identified eight cultivars with moderate resistance. Four cultivars were identified with moderate resistance in field trials and thus could serve as a source of resistant germplasm for future breeding programs. These findings should encourage growers to use sanitation protocols to prevent entry of the pathogen into their fields and to choose commercially available cultivars that have moderate resistance.

The Arabidopsis thaliana-Alternaria brassicicola pathosystem: A model interaction for investigating seed transmission of necrotrophic fungi

BACKGROUND

Seed transmission constitutes a major component of the parasitic cycle for several fungal pathogens. However, very little is known concerning fungal or plant genetic factors that impact seed transmission and mechanisms underlying this key biological trait have yet to be clarified. Such lack of available data could be probably explained by the absence of suitable model pathosystem to study plant-fungus interactions during the plant reproductive phase.

RESULTS

Here we report on setting up a new pathosystem that could facilitate the study of fungal seed transmission. Reproductive organs of Arabidopsis thaliana were inoculated with Alternaria brassicicola conidia. Parameters (floral vs fruit route, seed collection date, plant and silique developmental stages) that could influence the seed transmission efficiency were tested to define optimal seed infection conditions. Microscopic observations revealed that the fungus penetrates siliques through cellular junctions, replum and stomata, and into seed coats either directly or through cracks. The ability of the osmosensitive fungal mutant nik1Δ3 to transmit to A. thaliana seeds was analyzed. A significant decrease in seed transmission rate was observed compared to the wild-type parental strain, confirming that a functional osmoregulation pathway is required for efficient seed transmission of the fungus. Similarly, to test the role of flavonoids in seed coat protection against pathogens, a transparent testa Arabidopsis mutant (tt4-1) not producing any flavonoid was used as host plant. Unexpectedly, tt4-1 seeds were infected to a significantly lower extent than wild-type seeds, possibly due to over-accumulation of other antimicrobial metabolites.

CONCLUSIONS

The Arabidopsis thaliana-Alternaria brassicicola pathosystem, that have been widely used to study plant-pathogen interactions during the vegetative phase, also proved to constitute a suitable model pathosystem for detailed analysis of plant-pathogen interactions during the reproductive phase. We demonstrated that it provides an excellent system for investigating the impact of different fungal or plant mutations on the seed transmission process and therefore paves the way towards future high-throughput screening of both Arabidopsis and fungal mutant.

Biodiversity and biogeography of Fusarium species from northeastern North American asparagus fields based on microbiological and molecular approaches

Sixteen Fusarium species were recovered from 52 asparagus commercial fields, representing all major ecological (edaphic and climatic) area of asparagus production in the province of Québec, eastern Canada. This study extends our understanding of the geographic range of these species. It also provides climatological and edaphic properties linked to community changes and adaptations. Fusarium oxysporum and F. proliferatum were omnipresent and abundant in all five ecological area under study, whereas F. redolens was less frequently found. Species of Fusarium that produce carmine red pigmentation on potato dextrose agar, i.e., F. acuminatum, F. avenaceum, etc., were common at the northern limit of asparagus production. Abundance of red Fusarium species corresponded with a low isolation frequency of F. proliferatum. Nevertheless, F. proliferatum had a high recovery rate throughout Québec asparagus growing areas, under climatic conditions as cold as those of northern Europe where this species is uncommon in asparagus fields. In the light of these results, redefinition of the geographical distribution of F. proliferatum in asparagus fields is proposed. Intraspecific molecular differences in F. proliferatum and F. oxysporum were detected in the EF-1 alpha sequences and compared with well-characterized strains of North America.