Matthew H. Laurence

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.

Biogeography and phylogeography of Fusarium: a review

Fusarium is a large, complex genus that causes a wide variety of plant diseases, produces a number of mycotoxins and is becoming increasingly recognized as a significant human pathogen. These fungi occur in ecosystems in all parts of the globe, which makes them useful as a model to better understand biogeographic processes affecting the distribution of fungi. Here we review the information available on the biogeography of different species and clades of Fusarium and some of the likely processes affecting dispersal and speciation.

Fusarium species associated with plants in Australia

Fusarium species associated with plants as pathogens, saprobes and endophytes in Australia are listed with notes on their pathogenicity and toxicity provided. A list of Fusarium species not known to occur in Australia also is provided and their quarantine significance evaluated.

Genealogical concordance phylogenetic species recognition in the Fusarium oxysporum species complex

Fusarium oxysporum is an important plant and human pathogenic ascomycetous group, with near ubiquity in agricultural and non-cultivated ecosystems. Phylogenetic evidence suggests that F. oxysporum is a complex of multiple morphologically cryptic species. Species boundaries and limits of genetic exchange within this complex are poorly defined, largely due to the absence of a sexual state and the paucity of morphological characters. This study determined species boundaries within the F. oxysporum species complex using Genealogical Concordance Phylogenetic Species Recognition (GCPSR) with eight protein coding loci. GCPSR criteria were used firstly to identify independent evolutionary lineages (IEL), which were subsequently collapsed into phylogenetic species. Seventeen IELs were initially identified resulting in the recognition of two phylogenetic species. Further evidence supporting this delineation is discussed.

Fusarium: two endophytic novel species from tropical grasses of northern Australia

Two new species of Fusarium associated with Australian indigenous grasses in natural ecosystems are described as F. lyarnte and F. werrikimbe on the basis of morphology, DNA fingerprinting and phylogenetic analysis of EF-1α and β-tubulin sequence data. Isolates of these species were initially recovered from soil in the McGraths Creek area of central Australia and subsequently recovered from soil and stems of the indigenous grass Sorghum interjectum from Litchfield National Park in the Northern Territory, and from Sorghum leiocladum from Werrikimbe National Park in New South Wales. The common feature of both of these species is the production of large globose microconidia in false heads on polyphialides. Attempts to apply the biological species concept were unsuccessful.

High levels of diversity in Fusarium oxysporum from non-cultivated ecosystems in Australia

The Fusarium oxysporum species complex (FOSC) is a ubiquitous ascomycetous group that includes both pathogenic and non-pathogenic strains, the former being responsible for disease in over 100 cultivated plant species. Previous phylogenetic studies have uncovered at least four major clades within the FOSC, with Clade 1 hypothesised as being ancestral. However, the origin of these clades and pathogenic strains is poorly understood. Due to an emphasis on agricultural isolates in previous studies, the underlying diversity of this species complex in non-cultivated soils is largely unknown. To address this imbalance an extensive survey of isolates associated with native vegetation geographically isolated from cultivation throughout the Australian continent was conducted. A multi-gene phylogenetic analysis of the translation elongation factor (EF-1α) and the mitochondrial small subunit (mtSSU) rDNA loci did not recover any novel clades. However, the Australian isolates had high levels of intra-Clade diversity based on EF-1α sequence type (ST) comparison with a global dataset. The ST diversity was not equally distributed across the four clades, with the majority of novel STs recovered from Clade 1. Implications on the origin of the FOSC are discussed.

Six novel species of Fusarium from natural ecosystems in Australia

Six new species of Fusarium associated with soil and plant hosts from ecosystems of minimal anthropogenic disturbance in Australia are described. Fusarium coicis from Coix gasteenii, F. goolgardi from Xanthorrhoea glauca, F. mundagurra from soil and Mangifera indica, F. newnesense from soil, F. tjaetaba from Sorghum interjectum and F. tjaynera from soil, Triodia microstachya, Sorghum interjectum and Sorghum intrans. Morphology and phylogenetic analysis of EF-1α, RPB1 and RPB2 sequence data were used to delineate species boundaries. The new species were phylogenetically distributed in the Fusarium sambucinum, F. fujikuroi, and F. chlamydosporum species complexes, and two novel species complexes. These six new species have particular phylogeographic significance as not only do they provide further insight into the geographic patterns of Fusarium evolution but also challenge current phylogeographic hypotheses.

Variation in type A trichothecene production and trichothecene biosynthetic genes in Fusarium goolgardi from natural ecosystems of Australia.

Fusarium goolgardi, isolated from the grass tree Xanthorrhoea glauca in natural ecosystems of Australia, is closely related to fusaria that produce a subgroup of trichothecene (type A) mycotoxins that lack a carbonyl group at carbon atom 8 (C-8). Mass spectrometric analysis revealed that F. goolgardi isolates produce type A trichothecenes, but exhibited one of two chemotypes. Some isolates (50%) produced multiple type A trichothecenes, including 4,15-diacetoxyscirpenol (DAS), neosolaniol (NEO), 8-acetylneosolaniol (Ac-NEO) and T-2 toxin (DAS-NEO-T2 chemotype). Other isolates (50%) produced only DAS (DAS chemotype). In the phylogenies inferred from DNA sequences of genes encoding the RNA polymerase II largest (RPB1) and second largest (RPB2) subunits as well as the trichothecene biosynthetic genes (TRI), F. goolgardi isolates were resolved as a monophyletic clade, distinct from other type A trichothecene-producing species. However, the relationships of F. goolgardi to the other species varied depending on whether phylogenies were inferred from RPB1 and RPB2, the 12-gene TRI cluster, the two-gene TRI1-TRI16 locus, or the single-gene TRI101 locus. Phylogenies based on different TRI loci resolved isolates with different chemotypes into distinct clades, even though only the TRI1-TRI16 locus is responsible for structural variation at C-8. Sequence analysis indicated that TRI1 and TRI16 are functional in F. goolgardi isolates with the DAS-NEO-T2 chemotype, but non-functional in isolates with DAS chemotype due to the presence of premature stop codons caused by a point mutation.

Identification of Fusarium solani f.sp. phalaenopsis in Australia

Fusarium solani is responsible for leaf yellowing and root and collar rot across a broad range of orchid species. The forma specialis, ‘phalaenopsis’, of Fusarium solani has recently been described using molecular methods as being the causal organism of disease in Phalaenopsis and Cymbidium orchids, and is the predominant pathogen of Taiwanese glasshouse-grown Phalaenopsis orchids. A study in 1996 reported F. solani as the causal agent of root necrosis of Cymbidium in NSW, Australia, but the study did not use molecular methods and predated the forma specialis ‘phalaenopsis’ designation. By comparing the phylogeny of the Australian isolates of F. solani from glasshouse-grown orchids with isolates of F. solani f.sp. phalaenopsis from Taiwan, the current study showed that the Australian and Taiwanese isolates were identical on the basis of the internal transcribed spacer (ITS) and β-tubulin (benA) regions and resulted in the first identification of F. solani f.sp. phalaenopsis in Australia.

First report of Fusarium fujikuroi in the Lao PDR

The isolation of Fusarium fujikuroi from rice plants with elongated stems typical of bakanae disease in the Lao PDR is reported for the first time. The identification was based on both molecular and morphological markers. Koch’s postulates were fulfilled. Bakanae disease has long been recognized in the Lao PDR based on symptomatology, but the etiology of the disease has not been clearly defined. This study was part of a continuing program to assist with the development of checklists of pathogens and plant diseases for Lao PDR for biosecurity purposes and integrated disease management.