Multilocus Phylogenetic Diversity of <i>Fusarium avenaceum</i> Pathogenic on Lisianthus

Nalim, F. Ameena; Elmer, Wade H.; McGovern, Robert J.; Geiser, David M.

doi:10.1094/phyto-99-4-0462

Cited by 49 publications

(41 citation statements)

References 25 publications

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“…We detected several OTUs identified as F. avenaceum, revealing intraspecific diversity. This species has previously been reported to harbor high diversity (71). Up to eight OTUs were present in the same sample, indicating that species-specific PCR assays may soon become laborious when attempting to capture Fusarium diversity in cereals.…”

Section: Discussionmentioning

confidence: 93%

Genus-Specific Primers for Study of Fusarium Communities in Field Samples

Karlsson

Edel-Hermann

Gautheron

et al. 2016

Appl Environ Microbiol

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Fusarium is a large and diverse genus of fungi of great agricultural and economic importance, containing many plant pathogens and mycotoxin producers. To date, high-throughput sequencing of Fusarium communities has been limited by the lack of genusspecific primers targeting regions with high discriminatory power at the species level. In the present study, we evaluated two Fusarium-specific primer pairs targeting translation elongation factor 1 (TEF1). We also present the new primer pair Fa؉7/Ra؉6. Mock Fusarium communities reflecting phylogenetic diversity were used to evaluate the accuracy of the primers in reflecting the relative abundance of the species. TEF1 amplicons were subjected to 454 high-throughput sequencing to characterize Fusarium communities. Field samples from soil and wheat kernels were included to test the method on more-complex material. For kernel samples, a single PCR was sufficient, while for soil samples, nested PCR was necessary. The newly developed primer pairs Fa؉7/Ra؉6 and Fa/Ra accurately reflected Fusarium species composition in mock DNA communities. In field samples, 47 Fusarium operational taxonomic units were identified, with the highest Fusarium diversity in soil. The Fusarium community in soil was dominated by members of the Fusarium incarnatum-Fusarium equiseti species complex, contradicting findings in previous studies. The method was successfully applied to analyze Fusarium communities in soil and plant material and can facilitate further studies of Fusarium ecology.

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Section: Discussionmentioning

confidence: 93%

Genus-Specific Primers for Study of Fusarium Communities in Field Samples

Karlsson

Edel-Hermann

Gautheron

et al. 2016

Appl Environ Microbiol

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“…Fusarium avenaceum is known to harbor high intra-specific diversity (Nalim et al, 2009). One of the F. avenaceum OTUs dominated with 24% of the reads followed by three minor ones (<2% of the reads).…”

Section: Discussionmentioning

confidence: 99%

Agricultural factors affecting Fusarium communities in wheat kernels

Karlsson

Friberg

Kolseth

et al. 2017

International Journal of Food Microbiology

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Fusarium head blight (FHB) is a devastating disease of cereals caused by Fusarium fungi. The disease is of great economic importance especially owing to reduced grain quality due to contamination by a range of mycotoxins produced by Fusarium. Disease control and prediction is difficult because of the many Fusarium species associated with FHB. Different species may respond differently to control methods and can have both competitive and synergistic interactions. Therefore, it is important to understand how agricultural practices affect Fusarium at the community level.Lower levels of Fusarium mycotoxin contamination of organically produced cereals compared with conventionally produced have been reported, but the causes of these differences are not well understood. The aim of our study was to investigate the effect of agricultural factors on Fusarium abundance and community composition in different cropping systems. Winter wheat kernels were collected from 18 organically and conventionally cultivated fields in Sweden, paired based on their geographical distance and the wheat cultivar grown. We characterised the Fusarium community in harvested wheat kernels using 454 sequencing of translation elongation factor 1-a amplicons. In addition, we quantified Fusarium spp. using real-time PCR to reveal differences in biomass between fields.We identified 12 Fusarium operational taxonomic units (OTUs) with a median of 4.5 OTUs per field. Fusarium graminearum was the most abundant species, while F. avenaceum had the highest occurrence. The abundance of Fusarium spp. ranged two orders of magnitude between fields. Two pairs of Fusarium species co-occurred between fields: F. poae with F. tricinctum and F. culmorum with F. sporotrichoides. We could not detect any difference in Fusarium communities between the organic and conventional systems. However, agricultural intensity, measured as the number of pesticide applications and the amount of nitrogen fertiliser applied, had an impact on Fusarium communities, specifically increasing the abundance of F. tricinctum. There were geographical differences in the Fusarium community composition where F. graminearum was more abundant in the western part of Sweden. The application of amplicon sequencing provided a comprehensive view of the Fusarium community in cereals. This gives us better opportunities to understand the ecology of Fusarium spp., which is important in order to limit FHB and mycotoxin contamination in cereals.

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“…This is in accordance with results of several previous studies. Nalim et al (2009) demonstrated the absence of phylogenetic separation between F. avenaceum isolates from lisianthus and those from other hosts and suggested that the ability to cause diseases on this ornamental occurs broadly within the species. Harrow et al (2010) revealed high intraspecific polymorphism of TEF1α and β-TUB sequences between F. avenaceum isolates from cereal and grassland sites of New Zealand but did not find strict phylogenetic structure with relation to host and indicated capability of this species to infect a wide range of plants.…”

Section: Discussionmentioning

confidence: 99%

“…Another promising target used for phylogenetic analysis of enniatinproducing Fusarium species is enniatin synthetase gene (Stępień and Waśkiewicz, 2013). There were several studies of intraspecific diversity of F. avenaceum Nalim et al, 2009) and its relationship with other species (Harrow et al, 2010;Yli-Mattila et al, 2002b, 2004b. At the same time, there is little information on genetic variation between isolates of F. avenaceum and closest relatives from Russia, especially Siberia and Far East.…”

Section: Introductionmentioning

confidence: 99%