title: Genus-Specific Primers for Study of Fusarium Communities in Field Samples.
abstract: 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 genus-specific 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.
authors.affiliation: Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden ida.karlsson@slu.se.
authors.forename: Ida
authors.identifier: http://orcid.org/0000-0002-5598-1200
authors.initials: I
authors.lastname: Karlsson
authors.affiliation: INRA, UMR 1347 Agroécologie, Pole IPM, Dijon, France.
authors.forename: Véronique
authors.initials: V
authors.lastname: Edel-Hermann
authors.affiliation: INRA, UMR 1347 Agroécologie, Pole IPM, Dijon, France.
authors.forename: Nadine
authors.initials: N
authors.lastname: Gautheron
authors.affiliation: Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Mikael Brandström
authors.initials: MB
authors.lastname: Durling
authors.affiliation: Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Anna-Karin
authors.initials: AK
authors.lastname: Kolseth
authors.affiliation: INRA, UMR 1347 Agroécologie, Pole IPM, Dijon, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Steinberg
authors.affiliation: Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Paula
authors.initials: P
authors.lastname: Persson
authors.affiliation: Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Hanna
authors.initials: H
authors.lastname: Friberg
mesh_terms: D000595:Amino Acid Sequence; D017931:DNA Primers / Q000235:genetics*; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics; D005670:Fusarium / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D020648:Peptide Elongation Factor 1 / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D013045:Species Specificity; D014908:Triticum / Q000382:microbiology
chemical_list: D017931:DNA Primers; D005656:Fungal Proteins; D020648:Peptide Elongation Factor 1