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In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine, and basic research. This phylogenetically guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi, and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. Here we present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.

Fusarium graminearum causes head blight disease in wheat and barley. To help understand the infection process on wheat, we studied global gene expression of F. graminearum in a time series from 24 to 196 h after inoculation, compared with a noninoculated control. The infection was rapid and, after 48 h, over 4,000 fungal genes were expressed. The number of genes expressed increased over time up to 96 h (>8,000 genes), and then declined at the 144- and 192-h post-inoculation time points. After subtraction of genes found expressed on complete medium, during carbon or nitrogen starvation, and on barley, only 355 were found exclusively expressed in wheat, mostly genes with unknown function (72.6%). These genes were mainly found in single-nucleotide polymorphism-enriched islands on the chromosomes, suggesting a higher evolutionary selection pressure. The annotated genes were enriched in functional groups predicted to be involved in allantoin and allantoate transport, detoxification, nitrogen, sulfur and selenium metabolism, secondary metabolism, carbohydrate metabolism, and degradation of polysaccharides and ester compounds. Several putative secreted virulence factors were also found expressed in wheat.

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Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani Species Complex (FSSC). Subsequently, this concept was challenged by one research group (Lombard et al. 2015 Studies in Mycology 80: 189-245) who proposed dividing Fusarium into seven genera, including the FSSC as the genus Neocosmospora, with subsequent justification based on claims that the Geiser et al. (2013) concept of Fusarium is polyphyletic (Sandoval-Denis et al. 2018; Persoonia 41:109-129). Here we test this claim, and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species recently described as Neocosmospora were recombined in Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural and practical taxonomic option available.

Fusarium graminearum is an important plant-pathogenic fungus and the major cause of cereal head blight. Here, we report the functional analysis of FgStuA, the gene for a transcription factor with homology to key developmental regulators in fungi. The deletion mutant was greatly reduced in pathogenicity on wheat heads and in production of secondary metabolites. Spore production was significantly impaired in ΔFgStuA, which did not develop perithecia and sexual ascospores, and lacked conidiophores and phialides, leading to delayed production of aberrant macroconidia. FgStuAp appears to act as a global regulator that may affect many diverse aspects of the life cycle of F. graminearum. Transcriptome analysis shows that thousands of genes are differentially expressed in the mutant during asexual sporulation and infection of wheat heads and under conditions that induce secondary metabolites, including many that could account for the mutant phenotypes observed. The primary regulatory targets of FgStuAp are likely genes involved in cell-cycle control, and the predicted FgStuAp sequence has an APSES domain, with homology to helix-loop-helix proteins involved in cell-cycle regulation. The Aspergillus StuAp response element (A/TCGCGT/ANA/C) was found highly enriched in the promoter sequences of cell-cycle genes, which was upregulated in the ΔFgStuA deletion mutant.

The phyllosphere is colonized by a wide variety of bacteria and fungi; it harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. However, little is known about how the bacterial community composition on leafy greens develops over time. The bacterial community of the leafy-green phyllosphere obtained from two plantings of rocket salad (Diplotaxis tenuifolia) and three plantings of lettuce (Lactuca sativa) at two farms in Norway were profiled by an Illumina MiSeq-based approach. We found that the bacterial richness of the L. sativa samples was significantly greater shortly (3 weeks) after planting than at harvest (5 to 7 weeks after planting) for plantings 1 and 3 at both farms. For the second planting, the bacterial diversity remained consistent at the two sites. This suggests that the effect on bacterial colonization of leaves, at least in part must, be seasonally driven rather than driven solely by leaf maturity. The distribution of phyllosphere communities varied between D. tenuifolia and L. sativa at harvest. The variability between these species at the same location suggests that the leaf-dwelling bacteria are not only passive inhabitants but interact with the host, which shapes niches favoring the growth of particular taxa. This work contributes to our understanding of host plant-specific microbial community structures and shows how these communities change throughout plant development.T he phyllosphere is a habitat on the surface of plant leaves colonized by a variety of bacteria, yeasts, and fungi (1). It harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. Microbial populations on leaf surfaces are highly influenced by rapid fluctuations in UV radiation, temperature, and humidity and are restricted by limited access to nutrients (1, 2). Resident bacteria on leaves can have neutral, negative, or positive influences on their host plants by serving as pathogens, preventing leaf colonization by pathogens, or acting as growth promoters (3). Traditionally, phyllosphere bacteria have been characterized by using culture-based approaches and much of the work on produce-associated bacteria has focused on a small number of pathogenic species. Culture-based methods will not include bacteria that are not able to grow on standard artificial media or are slow growing. This limits our understanding of the phyllosphere microbial community's ecology, genetics, and physiology (4). Bacterial communities associated with leafy greens have already been described by several culture-independent studies. "First-generation" molecular techniques have been used to describe variation in community structure in the context of leaf surface properties and microbial interactions (5), seasonal variation in the community structure (6), and monitoring of bacterial communities in the food chain (7). The introduction of culture-independent methods, in particular, microbial profiling using high-throughput sequencing to study microorganisms, has revealed more complexity and diversity of the...

Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6–43.1 MB, with 13217–13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.