Molecular Relationships of Fungi Within the Fusarium redolens-F. hostae Clade

Fusarium diversity from the Golden Gate Highlands National Park

Members from the genus Fusarium can infect a broad range of plants and threaten agricultural and horticultural production. Studies on the diversity of Fusarium occurring in natural ecosystems have received less attention than the better known phytopathogenic members of the genus. This study identified Fusarium species from soils with low anthropogenic disturbance found in the Golden Gate Highlands National Park (GGHNP), a part of the Drakensberg system in South Africa. Selective techniques were implemented to obtain 257 individual isolates from the selected soil samples for which the translation elongation factor 1α (tef-1α) gene region was sequenced and compared against the Fusarium MLST and FUSARIUM-ID databases. Phylogenetic analyses, based on maximum likelihood and Bayesian inference, were used to determine species diversity in relation to reference isolates. Species level identifications were made within three of the seven species complexes and identified F. brachygibbosum, F. sporotrichioides, F. andiyazi, and F. gaditjirri based on the FUSARIUM-ID database, with F. transvaalense and F. lyarnte identified against the Fusarium MLST database. This indicated highly diverse populations of Fusarium from soils with low anthropogenic disturbance from the Afromontane grassland region found in mountain ranges.

Multilocus molecular phylogenetic-led discovery and formal recognition of four novel root-colonizing Fusarium species from northern Kazakhstan and the phylogenetically divergent Fusarium steppicola lineage

In this study, DNA sequence data were used to characterize 290 Fusarium strains isolated during a survey of root-colonizing endophytic fungi of agricultural and nonagricultural plants in northern Kazakhstan. The Fusarium collection was screened for species identity using partial translation elongation factor 1-α (TEF1) gene sequences. Altogether, 16 different Fusarium species were identified, including eight known and four novel species, as well as the discovery of the phylogenetically divergent F. steppicola lineage. Isolates of the four putatively novel fusaria were further analyzed phylogenetically with a multilocus data set comprising partial sequences of TEF1, RNA polymerase II largest (RPB1) and second-largest (RPB2) subunits, and calmodulin (CaM) to assess their genealogical exclusivity. Based on the molecular phylogenetic and comprehensive morphological analyses, four new species are formally described herein: F. campestre, F. kazakhstanicum, F. rhizicola, and F. steppicola.

Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau

Introduction

Fritillaria przewalskii Maxim. is a Chinese endemic species with high medicinal value distributed in the northeastern part of the Tibetan Plateau. F. przewalskii root-associated rhizosphere bacterial communities shaped by soil properties may maintain the stability of soil structure and regulate F. przewalskii growth, but the rhizosphere bacterial community structure of wild F. przewalskii from natural populations is not clear.

Methods

In the current study, soil samples from 12 sites within the natural range of wild F. przewalskii were collected to investigate the compositions of bacterial communities via high-throughput sequencing of 16S rRNA genes and multivariate statistical analysis combined with soil properties and plant phenotypic characteristics.

Results

Bacterial communities varied between rhizosphere and bulk soil, and also between sites. Co-occurrence networks were more complex in rhizosphere soil (1,169 edges) than in bulk soil (676 edges). There were differences in bacterial communities between regions, including diversity and composition. Proteobacteria (26.47-37.61%), Bacteroidetes (10.53-25.22%), and Acidobacteria (10.45-23.54%) were the dominant bacteria, and all are associated with nutrient cycling. In multivariate statistical analysis, both soil properties and plant phenotypic characteristics were significantly associated with the bacterial community (p < 0.05). Soil physicochemical properties accounted for most community differences, and pH was a key factor (p < 0.01). Interestingly, when the rhizosphere soil environment remained alkaline, the C and N contents were lowest, as was the biomass of the medicinal part bulb. This might relate to the specific distribution of genera, such as Pseudonocardia, Ohtaekwangia, Flavobacterium (relative abundance >0.01), which all have significantly correlated with the biomass of F. przewalskii (p < 0.05).

Discussion

F. przewalskii is evidently averse to alkaline soil with high potassium contents, but this requires future verification. The results of the present study may provide theoretical guidance and new insights for the cultivation and domestication of F. przewalskii.

Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels

Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The interactions in microbial communities also influence the healthy growth of Fritillaria ussuriensis.

The Whole Genome Sequence of Fusarium redolens Strain YP04, a Pathogen that Causes Root Rot of American Ginseng

Fusarium redolens was previously reported as a plant pathogen or an endophyte that is closely related to F. oxysporum, a notoriously significant soilborne phytopathogen. Subsequent studies demonstrated the unique nature of F. redolens, which was considered a distinct species that causes multiple symptoms on multiple hosts. It was recently identified as a pathogen that causes root rot of American ginseng. Currently, few high-quality F. redolens genome sequences exist in the public database. Here, we report the whole-genome sequence of F. redolens strain YP04, based on a hybrid assembly of long- and short-read sequencing with PacBio and Illumina platforms, respectively. The assembly consists of 40 configs with a total length of 52.8 Mb nuclear genomic DNA and 49.6 kb complete mitochondrial genomic DNA, and encodes a total of 18,985 genes, including 18,517 protein-coding genes and 469 RNA genes which were functionally annotated. In total, 4,606 proteins were identified in the pathogen-host interactions database, suggesting that they were likely involved in pathogenicity and host-pathogen interactions, while 41 secondary metabolite synthesis clusters were predicted and annotated. This is the first high-quality whole genome of F. redolens, providing an important community resource for genome evolution, host-pathogen interaction, and secondary metabolite biosynthesis studies.

First Report of Crown Rot Caused by Fusarium redolens on Wheat in Kazakhstan

Fusarium crown rot, caused by several species within the genus, is a major constraint that results in significant losses in wheat production worldwide. In June 2019, diseased wheat plants with typical symptoms of crown rot, including discoloration on the first two or three internodes of the stem just above the soil line and stunted, dry rotted, and discolored roots were collected in several bread wheat fields during the maturity stage in Almaty, East Kazakhstan, and Karaganda Regions of Kazakhstan. For each field, approximately twenty tillers were randomly sampled. Symptomatic tissues were surface sterilized in 1% NaClO for 2 min, rinsed with sterile distilled water three times, air-dried in a laminar flow hood, and then transferred to Petri dishes containing one-fifth strength potato dextrose agar (PDA). After incubating in the dark at 23°C for 5 days, 79 single-spore isolates showing cultural and microscopic characteristics of Fusarium were obtained on PDA and Spezieller-Nährstoffarmer agar (SNA). Colonies were initially white but later produced a beige to pink diffusible pigment in PDA. Microconidia that formed on aerial monophialides were hyaline, 0 to 1 septum, oval- to kidney-shaped, and measured 4.3 to 10.3 × 1.9 to 3.4 µm (average 7.8 × 2.6 µm), whilst macroconidia were straight to slightly curved, 3 to 5 septate, and measured 18.7 to 38.8 × 2.9 to 6.6 µm (average 29.9 × 4.7 µm), with foot-shaped basal cells on SNA. Chlamydospores were present on PDA. Sequence analysis based on portions of translation elongation factor 1α (TEF1) and the nuclear ribosomal internal transcribed spacer region (ITS rDNA) loci with primers EF1/EF2 (O'Donnell et al. 1998) and ITS1/ITS4 (White et al. 1990) identified 29 of the 79 isolates as Fusarium redolens Wollenw. The sequences of the five representative isolates with 99.85% of similarity to those of F. redolens strains available in GenBank e.g., ITS (MT435063) and TEF1 (GU250584). The TEF1 (accession nos. MW403914-MW403918) and ITS rDNA (accession nos. MW397138-MW397142) sequences of the isolates were deposited in GenBank. The morphological features are consistent with the described features of F. redolens (Leslie and Summerell 2006). To confirm pathogenicity of the five isolates, five pre-germinated seeds of wheat cultivar Seri 82 were placed in a 9-cm-diameter pot filled with a sterile potting mix containing equal volumes of peat, vermiculite, and soil. An approximately 1-cm-diameter 7-day-old mycelial plug of each isolate was individually placed in contact with the seeds. Seeds were covered with the same potting mix, and then the pots were maintained for four weeks in a growth chamber at 23°C with a 12-h photoperiod. The experiment was conducted twice with three replicate 15-cm pots with 5 plants per pot. Controls were inoculated with sterile agar plugs using the same procedure. After four weeks, all the inoculated plants showed stunted growth with brown discoloration in most parts of the crown and roots, whereas no symptoms were observed in the control plants. The mean severity of the disease for each isolate was between 2.1 and 2.7 according to the scale of 1 to 5 described by Gebremariam et al. (2015). The pathogen was reisolated from crowns of diseased plants, but not from asymptomatic control tissues, and identified morphologically based on the methods described above, fulfilling Koch's postulates. Although several morphological features are shared by F. oxysporum and F. redolens, Baayen et al. (2001) showed that these species could be easily distinguished using molecular data. The pathogen was previously reported as F. redolens associated with crown rot of wheat in Turkey (Gebremariam et al. 2015) and Saskatchewan, Canada (Taheri et al. 2011). The presence of F. redolens causing crown rot is confirmed in the six wheat fields surveyed in Kazakhstan, for the first time. This pathogen may pose a risk for wheat production, and further studies needed to determine the impact on the crop in Kazakhstan.

American Ginseng Root Rot Caused by Fusarium redolens in China

American ginseng (Panax quinquefolium L.) originating from North America is one of important herbal medicine and economic crops . With the increasing market demand, China has become the third producer and the largest consumer country of American ginseng. However, continuous cropping obstacle has become the most serious problem for the production of American ginseng, and the continuous cropping of soils usually lead to accumulations of root fungal pathogens and increasing plant disease occurrence (1), root rot caused by the notorious soil-borne pathogenic fungi, Fusarium spp., results in a significant reduction of yield and quality of American ginseng. Investigation of American ginseng root rot was carried out in Liuba county, Shaanxi province, China from 2017 to 2019. About 20% of over 3-year-old American ginseng showed varied root rot symptoms in newly reclaimed fields, and more than 70% in continuous American ginseng planting fields. Among these root rot diseases, we found one kind of disease which shows symptoms of red leaves in initial stage and yellow or yellow brown lesions at the reed heads or taproots. The lesions mainly appear on the root surface; however, the vascular tissue has no discoloration. The aboveground parts become wilted and died, and the whole root appears dark brown rots. Fifteen Fusarium spp. isolates were obtained by cutting diseased rot roots into 5 × 5 mm2 pieces, disinfecting in 70% ethanol for 1 min, rinsing 2 ~ 3 times in sterile water for 1 min and isolating on PDA medium including 50 μg/mL streptomycin sulfate. All the isolates have identical morphological characteristics. The colony was white with curved and uplifted aerial hyphae in central region. The colony diameter was 48 ~51 mm after 6 days at room temperature. Microconidia were oval to cylindrical shape with 0 to 1 septa, ranged from 6.24 to10.09 μm long; the macroconidia were fusiform to conical with a hooked apical cell and a foot-shaped basal cell, usually 3 to 5 septa, ranged from 31.45 to 42.52 μm long. The chlamydospores were not found under our culture condition. Preliminary data analysis showed that the morphological characteristics of these isolates were consistent with the descriptions of Fusarium redolens (2). To clarify the fungus in the taxonomy , the rDNA internal transcribed spacer (ITS), the translation elongation factor 1 alpha (TEF1-α) and the RNA polymerase II subunit 1 (RPB1) fragments of two randomly selected isolates were amplified and sequenced. The sequences of the corresponding fragments of the two isolates were identical. The blast results in the GenBank and FUSARIUM-ID databases show the isolates belong to F. redolens (3). Previous study indicated F. redolens has an indistinguishable relative, F. hostae (4). Although the ITS sequence (MW331695) cannot provide enough information to distinguish them, the phylogenetic tree combined the sequence of TEF1-α (tempID: 2407237 ) and RPB1 (tempID: 2407229) clearly showed that the isolates are F. redolens. (Fig) The pathogenicity of a representative isolate, YP04, was tested on ginseng taproot by in vivo inoculation experiments with three replications. The taproot surface of 2-year-old healthy ginseng was washed and disinfested with 75% alcohol for 1 min and rinsed with sterile water, and dried. The surface of taproot was injured with sterilized steel needles and immersed in 1 × 106 /ml spore suspension (sterile water for control plants) for 30 min. The treatment and control plants were transplanted in 20 cm diameter flowerpots filled with sterilized humus and cultured in a greenhouse at 18-23°C. Six days after transplanting, the leaves began to turn red. The cortex of ginseng taproot showed yellow brown lesions and the vascular tissue turn to light yellow. Fifteen days after transplanting, the aboveground parts of treatment plants began to wilting and the taproots showed serious rots. no taproot rot was observed in the controls. The pathogen was re-isolated from the diseased taproots successfully. To our knowledge, this is the first report of F. redolens causing root rot of American ginseng in China.

An endophyte of Macrochloa tenacissima (esparto or needle grass) from Tunisia is a novel species in the Fusarium redolens species complex

Here, we report on the morphological, molecular, and chemical characterization of a novel Fusarium species recovered from the roots and rhizosphere of Macrochloa tenacissima (halfa, esparto, or needle grass) in central Tunisia. Formally described here as F. spartum, this species is a member of the Fusarium redolens species complex but differs from the other two species within the complex, F. redolens and F. hostae, by its endophytic association with M. tenacissima and its genealogical exclusivity based on multilocus phylogenetic analyses. To assess their sexual reproductive mode, a polymerase chain reaction (PCR) assay was designed and used to screen the three strains of F. spartum, 51 of F. redolens, and 14 of F. hostae for mating type (MAT) idiomorph. Genetic architecture of the MAT locus in the former two species suggests that if they reproduce sexually, it is via obligate outcrossing. By comparison, results of the PCR assay indicated that 13/14 of the F. hostae strains possessed MAT1-1 and MAT1-2 idiomorphs and thus might be self-fertile or homothallic. However, when the F. hostae strains were selfed, 11 failed to produce perithecia and one only produced several small abortive perithecia. Cirrhi with ascospores, however, were only produced by 8/28 and 4/84 of the variable size perithecia, respectively, of F. hostae NRRL 29888 and 29890. The potential for the three F. redolens clade species to produce mycotoxins, pigments, and phytohormones was assessed by screening whole genome sequence data and by analyzing extracts on cracked maize kernel cultures via liquid chromatography-mass spectrometry.

Molecular and Biological Characterization of the First Hypovirus Identified in Fusarium oxysporum

A novel mycovirus named Fusarium oxysporum f. sp. dianthi hypovirus 2 (FodHV2) has been identified infecting isolates Fod 408 and Fod 409 of Fusarium oxysporum f. sp. dianthi from Morocco. The genome of FodHV2 is 9,444 nucleotides long excluding the poly(A) tail, and has a single open reading frame encoding a polyprotein. The polyprotein contains three highly conserved domains of UDP glucose/sterol glucosyltransferase, RNA-dependent RNA polymerase, and viral RNA helicase. In addition, particular residues of Cys, Hys, and Gly detected in the N-terminal region suggest the presence of the catalytic site of a highly diverged papain-like protease. Genomic organization, presence of particular conserved motifs, and phylogenetic analyses based on multiple alignments clearly grouped FodHV2 with the members of the family Hypoviridae. FodHV2 was transferred by hyphal anastomosis to a recipient HygR-tagged virus-free strain. The comparison of the infected and non-infected isogenic strains showed that FodHV2 did not alter the vegetative growth, neither the conidiation nor the virulence of its fungal host. Efficiency of FodHV2 transmission through the conidia was 100% in both the original and the recipient infected-isolates. To the best of our knowledge, this is the first report of a hypovirus infecting the plant pathogen F. oxysporum, and also the first one of a hypovirus detected in a fungal strain from the African continent.

Merging FT-IR and NGS for simultaneous phenotypic and genotypic identification of pathogenic Candida species

The rapid and accurate identification of pathogen yeast species is crucial for clinical diagnosis due to the high level of mortality and morbidity induced, even after antifungal therapy. For this purpose, new rapid, high-throughput and reliable identification methods are required. In this work we described a combined approach based on two high-throughput techniques in order to improve the identification of pathogenic yeast strains. Next Generation Sequencing (NGS) of ITS and D1/D2 LSU marker regions together with FTIR spectroscopy were applied to identify 256 strains belonging to Candida genus isolated in nosocomial environments. Multivariate data analysis (MVA) was carried out on NGS and FT-IR data-sets, separately. Strains of Candida albicans, C. parapsilosis, C. glabrata and C. tropicalis, were identified with high-throughput NGS sequencing of ITS and LSU markers and then with FTIR. Inter- and intra-species variability was investigated by consensus principal component analysis (CPCA) which combines high-dimensional data of the two complementary analytical approaches in concatenated PCA blocks normalized to the same weight. The total percentage of correct identification reached around 97.4% for C. albicans and 74% for C. parapsilosis while the other two species showed lower identification rates. Results suggested that the identification success increases with the increasing number of strains actually used in the PLS analysis. The absence of reliable FT-IR libraries in the current scenario is the major limitation in FTIR-based identification of strains, although this metabolomics fingerprint represents a valid and affordable aid to rapid and high-throughput to clinical diagnosis. According to our data, FT-IR libraries should include some tens of certified strains per species, possibly over 50, deriving from diverse sources and collected over an extensive time period. This implies a multidisciplinary effort of specialists working in strain isolation and maintenance, molecular taxonomy, FT-IR technique and chemo-metrics, data management and data basing.

Veterinary Fusarioses within the United States

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67 Fusarium strains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within the Fusarium solani species complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme, Fusarium keratoplasticum, and Fusarium sp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of the F. falciforme strains (12/15) were recovered from equine keratitis infections; however, strains of F. keratoplasticum and Fusarium sp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that the Fusarium incarnatum-equiseti species complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance within Fusarium Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and the Fusarium oxysporum species complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes.

Development of a DNA Microarray-Based Assay for the Detection of Sugar Beet Root Rot Pathogens

Sugar beet root rot diseases that occur during the cropping season or in storage are accompanied by high yield losses and a severe reduction of processing quality. The vast diversity of microorganism species involved in rot development requires molecular tools allowing simultaneous identification of many different targets. Therefore, a new microarray technology (ArrayTube) was applied in this study to improve diagnosis of sugar beet root rot diseases. Based on three marker genes (internal transcribed spacer, translation elongation factor 1 alpha, and 16S ribosomal DNA), 42 well-performing probes enabled the identification of prevalent field pathogens (e.g., Aphanomyces cochlioides), storage pathogens (e.g., Botrytis cinerea), and ubiquitous spoilage fungi (e.g., Penicillium expansum). All probes were proven for specificity with pure cultures from 73 microorganism species as well as for in planta detection of their target species using inoculated sugar beet tissue. Microarray-based identification of root rot pathogens in diseased field beets was successfully confirmed by classical detection methods. The high discriminatory potential was proven by Fusarium species differentiation based on a single nucleotide polymorphism. The results demonstrate that the ArrayTube constitute an innovative tool allowing a rapid and reliable detection of plant pathogens particularly when multiple microorganism species are present.

Evolution of Nine Microsatellite Loci in the Fungus Fusarium oxysporum

The evolution of nine microsatellites and one minisatellite was investigated in the fungus Fusarium oxysporum and sister taxa Fusarium redolens and Fusarium verticillioides. Compared to other organisms, fungi have been reported to contain fewer and less polymorphic microsatellites. Mutational patterns over evolutionary time were studied for these ten loci by mapping changes in core repeat numbers onto a phylogeny based on the sequence of the conserved translation elongation factor 1-α gene. The patterns of microsatellite formation, expansion, and interruption by base substitutions were followed across the phylogeny, showing that these loci are evolving in a manner similar to that of microsatellites in other eukaryotes. Most mutations could be fit to a stepwise mutation model, but a few appear to have involved multiple repeat units. No evidence of gene conversion was seen at the minisatellite locus, which may also be mutating by replication slippage. Some homoplastic numbers of repeat units were observed for these loci, and polymorphisms in the regions flanking the microsatellites may provide better genetic markers for population genetics studies of these species.

DNA barcoding to map the microbial communities: current advances and future directions

During the last two decades, the DNA barcode development towards microbial community has increased dramatically. DNA barcode development is related to error-free and quick species identification which aid in understanding the microbial biodiversity, as well as the diseases related to microbial species. Here, we seek to evaluate the so-called barcoding initiatives for the microbial communities and the emerging trends in this field. In this paper, we describe the development of DNA marker-based DNA barcoding system, comparison between routine species identification and DNA barcode, and microbial biodiversity and DNA barcode for microbial communities. Two major topics, such as the molecular diversity of viruses and barcode for viruses have been discussed at the same time. We demonstrate the current status and the maker of DNA barcode for bacteria, algae, fungi, and protozoa. Furthermore, we argue about the promises, limitations, and present and future challenges of microbial barcode development.

Molecular and Pathogenic Characterization of Fusarium redolens, a New Causal Agent of Fusarium Yellows in Chickpea

The association of Fusarium redolens with wilting-like symptoms in chickpea in Lebanon, Morocco, Pakistan, and Spain is reported for the first time, together with the molecular and pathogenic characterization of isolates of the pathogen from chickpea of diverse geographic origin. Maximum parsimony analysis of sequences of the translation elongation factor 1α (TEF-1α) gene grouped all F. redolens isolates from chickpea in the same main clade. Pathogenicity assays using three chickpea cultivars and isolates from different geographic origins indicated that F. redolens is mildly virulent on chickpea. Moreover, infection of chickpea by F. redolens induces a disease syndrome similar to that caused by the yellowing pathotype of F. oxysporum f. sp. ciceris, including leaf yellowing and necrosis that develop upward from the stem base, and premature senescence of the plant. In contrast, F. redolens does not cause discoloration of the vascular tissues in chickpea but does cause brown necrotic lesions in the tap root and necrosis of lateral roots. F. redolens is not easily differentiated from F. oxysporum f. sp. ciceris using morphology-based diagnosis, and the two species cause similar symptoms on chickpea; therefore, the use of molecular protocols should help to avoid misdiagnoses of Fusarium yellows in chickpea.

Differentiation of eleven Fusarium spp. isolated from sugar beet, using restriction fragment analysis of a polymerase chain reaction-amplified translation elongation factor 1alpha gene fragment

Sugar beet in Europe is commonly grown in wheat and maize crop rotations and subsequently pile-stored for several weeks. Beet is threatened by the colonization of saprophytic as well as pathogenic Fusarium spp. A tool for reliable identification based on sequence information of the translation elongation factor 1alpha (TEF-1alpha) gene was developed for the numerous Fusarium spp. being isolated from sugar beets. In all, 65 isolates from different species (Fusarium avenaceum, F. cerealis, F. culmorum, F. equiseti, F. graminearum, F. oxysporum, F. proliferatum, F. redolens, F. solani, F. tricinctum, and F. venenatum) were obtained from sugar beet at different developmental stages from locations worldwide. Database sequences for additional species (F. sporotrichioides, F. poae, F. torulosum, F. hostae, F. sambucinum, F. subglutinans, and F. verticillioides), isolated from sugar beets in previous studies, were included in the analysis. Molecular sequence analysis of the partial TEF-1alpha gene fragment revealed sufficient variability to differentiate between the Fusarium spp., resulting in species-dependent separation of the isolates analyzed. This interspecific divergence could be translated into a polymerase chain reaction restriction fragment length polymorphism assay using only two subsequent restriction digests for the differentiation of 17 of 18 species.

Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria

Background

A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinformatic surveys is due to the presence of mobile introns in almost all the fungal mitochondrial genes. The aim of this work is to verify the incidence of this phenomenon in Ascomycota, testing, at the same time, a new bioinformatic tool for extracting and managing sequence databases annotations, in order to identify the mitochondrial gene regions where introns are missing so as to propose them as species markers.

Methods

The general trend towards a large occurrence of introns in the mitochondrial genome of Fungi has been confirmed in Ascomycota by an extensive bioinformatic analysis, performed on all the entries concerning 11 mitochondrial protein coding genes and 2 mitochondrial rRNA (ribosomal RNA) specifying genes, belonging to this phylum, available in public nucleotide sequence databases. A new query approach has been developed to retrieve effectively introns information included in these entries.

Results

After comparing the new query-based approach with a blast-based procedure, with the aim of designing a faithful Ascomycota mitochondrial intron map, the first method appeared clearly the most accurate. Within this map, despite the large pervasiveness of introns, it is possible to distinguish specific regions comprised in several genes, including the full NADH dehydrogenase subunit 6 (ND6) gene, which could be considered as barcode candidates for Ascomycota due to their paucity of introns and to their length, above 400 bp, comparable to the lower end size of the length range of barcodes successfully used in animals.

Conclusion

The development of the new query system described here would answer the pressing requirement to improve drastically the bioinformatics support to the DNA Barcode Initiative. The large scale investigation of Ascomycota mitochondrial introns performed through this tool, allowing to exclude the introns-rich sequences from the barcode candidates exploration, could be the first step towards a mitochondrial barcoding strategy for these organisms, similar to the standard approach employed in metazoans.

Multilocus phylogenetic diversity of Fusarium avenaceum pathogenic on lisianthus

Fusarium avenaceum is a globally distributed fungus commonly isolated from soil and a wide range of plants. Severe outbreaks of crown and stem rot of the flowering ornamental, lisianthus (Eustoma grandiflorum), have been attributed to F. avenaceum. We sequenced portions of the translation elongation factor 1-alpha (tef) and beta-tubulin (benA) protein coding genes as well as partial intergenic spacer (IGS) regions of the nuclear ribosomal genes in 37 Fusarium isolates obtained from lisianthus and other host plants. Isolates that were previously identified morphologically as F. acuminatum were included as an outgroup. Phylogenetic analyses of tef, benA, and IGS sequences showed that F. avenaceum isolates were an exclusive group with strong bootstrap support and no significant incongruence among gene genealogies. Isolates from lisianthus were scattered within this clade and did not form distinct groups based on host species or locality. Pathogenicity tests of F. avenaceum isolates obtained from several other hosts showed an ability to cause disease on lisianthus, suggesting that F. avenaceum may be pathogenic on lisianthus regardless of its phylogenetic origin. These findings have management implications and suggest that any host that supports F. avenaceum may serve as a source of inoculum for lisianthus growers.

Species-specific primers for Fusarium redolens and a PCR-RFLP technique to distinguish among three clades of Fusarium oxysporum

The currently available morphological and molecular diagnostic techniques for Fusarium redolens and the three phylogenetic clades of Fusarium oxysporum are problematic. Aligned translation elongation factor 1 alpha (TEF-1 alpha) gene sequences from these species and their close relatives were used to design F. redolens-specific primers, and to identify restriction sites that discriminate among the three clades of F. oxysporum. The F. redolens-specific primers distinguished this species from all others included in the study. There were three TEF-1 alpha-RFLP patterns among formae speciales of F. oxysporum. These PCR-RFLP patterns corresponded with the three clades. These techniques provide simple and inexpensive diagnostic methods for the identification of F. redolens and members of the three clades of F. oxysporum.

Transposition of a fungal miniature inverted-repeat transposable element through the action of a Tc1-like transposase

The mimp1 element previously identified in the ascomycete fungus Fusarium oxysporum has hallmarks of miniature inverted-repeat transposable elements (MITEs): short size, terminal inverted repeats (TIRs), structural homogeneity, and a stable secondary structure. Since mimp1 has no coding capacity, its mobilization requires a transposase-encoding element. On the basis of the similarity of TIRs and target-site preference with the autonomous Tc1-like element impala, together with a correlated distribution of both elements among the Fusarium genus, we investigated the ability of mimp1 to jump upon expression of the impala transposase provided in trans. Under these conditions, we present evidence that mimp1 transposes by a cut-and-paste mechanism into TA dinucleotides, which are duplicated upon insertion. Our results also show that mimp1 reinserts very frequently in genic regions for at least one-third of the cases. We also show that the mimp1/impala double-component system is fully functional in the heterologous species F. graminearum, allowing the development of a highly efficient tool for gene tagging in filamentous fungi.

Polyphasic classification of Alternaria isolated from hazelnut and walnut fruit in Europe

Brown apical necrosis of English walnut and grey necrosis of hazelnut are destructive fruit diseases caused by a complex of opportunistic fungi including several small-spored catenulate Alternaria taxa. Thirty Alternaria isolates recovered from walnut and hazelnut fruit that were pathogenic on their respective host were compared along with type or representative isolates of A. alternata, A. tenuissima, A. arborescens, and A. infectoria using morphological and molecular criteria. Morphological examination using standardized procedures separated the walnut and hazelnut isolates into three morphological groups: the A. alternata group, the A. tenuissima group, and the A. arborescens group based upon common characteristics of the conidium and the sporulation apparatus. To evaluate genetic relationships among these groups, AFLP markers, inter simple sequence repeat (ISSR) markers, and histone gene sequence data were compared. Based upon AFLP data, the A. alternata and A. tenuissima groups comprised a single lineage, and the A. arborescens group comprised a separate lineage. ISSR data supported the grouping by AFLP data except for three isolates of the A. alternata group that clustered with the A. arborescens group. Base substitution of the H4 gene supported the discrimination of the A. arborescens group from the A. alternata and A. tenuissima groups. Tests of hypotheses based upon groupings derived from the various data sets supported the discrimination of the A. arborescens group but did not support the discrimination of the A. alternata group from the A. tenuissima group.

Phylogenetic analyses reveal deeply divergent species lineages in the genus Sphaerobolus (Phallales: Basidiomycota)

Phylogenetic analyses of 27 artillery fungus (Sphaerobolus sp.) isolates were conducted to identify species boundaries in the genus Sphaerobolus. Multiple gene genealogies inferred from maximum likelihood, Bayesian, and maximum-parsimony analyses of sequence data from individual loci (mtSSU, ITS, EF 1-alpha, and LSU) and a combined dataset (mtSSU, ITS, and EF 1-alpha) concordantly indicate the existence of three deeply divergent lineages in the genus Sphaerobolus, each representing a phylogenetic species. These three phylogenetic species correspond to two known species: Sphaerobolus iowensis and Sphaerobolus stellatus, and a newly discovered species. Suprageneric phylogenetic analyses of the mtSSU and LSU datasets containing representatives of related genera of the gomphoid-phalloid clade of Homobasidiomycetes suggested that the undescribed taxon likely is more closely related to S. stellatus than to S. iowensis.

Fusarium oxysporum and its biocontrol

Fusarium oxysporum is well represented among the rhizosphere microflora. While all strains exist saprophytically, some are well-known for inducing wilt or root rots on plants whereas others are considered as nonpathogenic. Several methods based on phenotypic and genetic traits have been developed to characterize F. oxysporum strains. Results showed the great diversity affecting the soil-borne populations of F. oxysporum. In suppressive soils, interactions between pathogenic and nonpathogenic strains result in the control of the disease. Therefore nonpathogenic strains are developed as biocontrol agents. The nonpathogenic F. oxysporum strains show several modes of action contributing to their biocontrol capacity. They are able to compete for nutrients in the soil, affecting the rate of chlamydospore germination of the pathogen. They can also compete for infection sites on the root, and can trigger plant defence reactions, inducing systemic resistance. These mechanisms are more or less important depending on the strain. The nonpathogenic F. oxysporum are easy to mass produce and formulate, but application conditions for biocontrol efficacy under field conditions have still to be determined.

Effects of Cultural Practices and Temperature on Fusarium Root and Crown Rot of Container-Grown Hostas

Fusarium root and crown rot of hosta plants grown in containers is caused primarily by Fusarium hostae. In an effort to develop an integrated strategy for managing this disease at nurseries, the effects of wounding, container mix content, watering schedule, and temperature on disease development were investigated. Plants were not wounded or were wounded by severing the roots, severing the roots and making incisions in the crown, or severing the roots and removing a small piece of the crown. Plants were inoculated by dipping roots and crowns into a suspension of conidia from one of two isolates of F. hostae. In addition, some plants were inoculated by wounding crowns with a scalpel dipped in a conidium suspension. Disease development was examined on plants grown at different temperatures (18, 25, or 32°C), grown in different container mixes (100% Canadian sphagnum peat, 100% aged and processed pine bark, or a mixture of 50% peat and 50% bark), and watered on different schedules (which kept the container mix wet, moist, or dry). Significant levels of disease occurred only on plants that were wounded when inoculated. Fusarium root and crown rot was more severe when both the roots and crowns were wounded than when only the roots were wounded. Disease symptoms developed when crowns of plants were wounded with a scalpel infested with conidia, suggesting that contaminated tools used for vegetative propagation may transfer F. hostae. Disease development also was affected significantly by container mix content, watering schedule, and temperature. In separate experiments, disease was most severe on plants grown in 100% aged pine bark, in dry container mix, or at 18 to 25°C. Disease development was significantly less when plants were grown in 100% peat, in wet container mix, or at 32°C. These results suggest that altering or manipulating cultural practices used to produce hostas in containers at nurseries can reduce the impact from Fusarium root and crown rot.