Polyphasic re-examination of Yarrowia lipolytica strains and the description of three novel Candida species: Candida oslonensis sp. nov., Candida alimentaria sp. nov. and Candida hollandica sp. nov

The type strain of Yarrowia lipolytica and 38 strains identified as Yarrowia lipolytica, four strains of Candida deformans, including the type and two subcultures of the type, two strains of Candida galli and six unidentified strains that resembled Y. lipolytica were examined by PCR fingerprints using primers M13 and (GAC)5. The same strains, together with four strains of the recently introduced Candida yakushimensis nom. inval., were sequenced for the D1/D2 domain of the 26S rRNA gene and parts of the ITS domain and also studied for their physiological properties. Of the strains identified previously as Y. lipolytica, CBS 2076 had the same fingerprint as the type of C. deformans and strain CBS 4855 was distinct from all other strains. The six strains that resembled Y. lipolytica were separated into two groups distinct from any of the other clades. A total of six groups obtained by fingerprint and sequence data were evaluated by performing DNA reassociation reactions. Mating experiments among the 35 strains of Y. lipolytica sensu stricto showed that 15 strains represented one mating type and 16 strains represented the opposite mating type, while four strains were self-sporulating. Teleomorph states were not produced by C. deformans, C. galli or any of the unidentified isolates. However, positive mating reactions were rarely observed in crosses among C. galli and some strains of Y. lipolytica and C. deformans. Consequently, sharing the same mating type system, C. deformans and C. galli could be considered anamorphs of unnamed Yarrowia species. Results from PCR fingerprints, sequencing and mating studies support the grouping of the studied strains into Y. lipolytica, C. galli, C. deformans, C. yakushimensis nom. inval. and three novel species in the Yarrowia clade: Candida oslonensis sp. nov. (type strain CBS 10146T =NRRL Y-48252T; Mycobank number MB 510769), Candida alimentaria sp. nov. (type strain CBS 10151T =NRRL Y-48253T; Mycobank number MB 510770) and Candida hollandica sp. nov. (type strain CBS 4855T =NRRL Y-48254T; Mycobank number MB 510771).

DNA microarray to detect and identify trichothecene- and moniliformin-producing Fusarium species

AIMS

To develop a DNA microarray for easy and fast detection of trichothecene- and moniliformin-producing Fusarium species.

METHOD AND RESULTS

A DNA microarray was developed for detection and identification of 14 trichothecene- and moniliformin-producing species of the fungal genus Fusarium. The array could also differentiate between four species groups. Capture probes were designed based on recent phylogenetic analyses of translation elongation factor-1 alpha (TEF-1alpha) sequences. Particular emphasis was put on designing capture probes corresponding to groups or species with particular mycotoxigenic synthetic abilities. A consensus PCR amplification of a part of the TEF-1alpha is followed by hybridization to the Fusarium chip and the results are visualized by a colorimetric Silverquant detection method. We validated the Fusarium chip against five naturally infected cereal samples for which we also have morphological and chemical data. The limit of detection was estimated to be less than 16 copies of genomic DNA in spiked commercial wheat flour.

CONCLUSIONS

The current Fusarium chip proved to be a highly sensitive and fast microarray for detection and identification of Fusarium species. We postulate that the method also has potential for (semi-)quantification.

SIGNIFICANCE AND IMPACT OF THE STUDY

The Fusarium chip may prove to be a very valuable tool for screening of cereal samples in the food and feed production chain, and may facilitate detection of new or introduced Fusarium spp.

Simultaneous detection and identification of trichothecene- and moniliformin-producing Fusarium species based on multiplex SNP analysis

AIM

To develop a multiplex identification method for trichothecene- and moniliformin-producing Fusarium species.

METHOD AND RESULTS

In this article, we present a single nucleotide polymorphism (SNP) assay to simultaneously detect and identify 16 trichothecene- and moniliformin-producing Fusarium species. A number of SNP primers are designed to detect clades of species with particular mycotoxigenic synthetic abilities. The assay is based on minisequencing using SNaPshot reactions and the SNP primers are designed based on motifs derived from phylogenetic analyses of translation elongation factor-1alpha sequences. The present version of the Fusarium SNP assay can distinguish major groups of trichothecene producers; the strict-type-A, the strict-type-B, the type-A and type-B trichothecene producers and the putative moniliformin producers. The SNP assay was validated against five naturally infected cereal samples that previously had been analysed morphologically, chemically and by a multiplex DNA array hybridization.

CONCLUSIONS

The Fusarium SNP assay reveals the advantages of using SNPs for multiplex species identification.

SIGNIFICANCE AND IMPACT OF THE STUDY

The current assay may qualify as a high-throughput screening method for small-grain cereals in the feed and food chain, and may facilitate detection of new or introduced Fusarium species.

An integrated taxonomic study of Fusarium langsethiae, Fusarium poae and Fusarium sporotrichioides based on the use of composite datasets

An integrated systematic study was carried out to clarify the taxonomical position and relationship of Fusarium langsethiae to other taxa within the Fusarium section Sporotrichiella. Strains of this species were compared with strains of the closely related species Fusarium poae and Fusarium sporotrichioides using a composite dataset. This set consisted of DNA sequences derived from the ribosomal internal transcribed spacer (ITS) regions, partial sequences of the ribosomal intergenic spacer (IGS) region, the beta-tubulin and translation elongation factor-1 alpha (EF-1alpha) genes, AFLP fingerprints, chromatographic data on secondary metabolites and morphological data and growth characteristics. From these combined data, a consensus matrix was calculated by taking the mean of all pairwise distances between single isolates over all separate datasets. The consensus matrix was used as the basis for the construction of a UPGMA dendrogram and a multidimensional scaling, both of which revealed a clear separation of the three taxa. Partial IGS, EF-1alpha and beta-tubulin sequence-as well as chromatography-and AFLP-derived similarities turned out to be comparably consistent, while ITS sequence- and morphology-derived similarity matrices were rather divergent.

Phylogenetic analyses of the Fusarium poae, Fusarium sporotrichioides and Fusarium langsethiae species complex based on partial sequences of the translation elongation factor-1 alpha gene

Phylogenetic relationships between four Fusarium species were studied using parts of the nuclear translation elongation factor-1 alpha (EF-1alpha) gene as a phylogenetic marker. Sequences from 12 isolates of Fusarium poae, 10 isolates of Fusarium sporotrichioides and 12 isolates of Fusarium langsethiae yielded 4, 5 and 5 haplotypes, respectively. In addition, we included one isolate of Fusarium kyushuense. The aligned sequences were subjected to neighbor-joining (NJ), maximum parsimony and maximum likelihood (ML) analyses. The results from the different analyses were highly concordant. The EF-1alpha-based phylogenies support the classification of F. langsethiae as a separate taxon in the section Sporotrichiella of Fusarium, as the closest sister taxon to F. sporotrichioides, while F. kyushuense is the sister taxon to F. poae. This corresponds well with the ability of F. langsethiae and F. sporotrichioides to produce T-2 and HT-2 toxins. In contrast, morphological characters indicate a closer relationship between F. langsethiae and F. poae on the one hand, and between F. sporotrichioides and F. kyushuense on the other hand.

Detection and traceability of genetically modified organisms in the food production chain

Both labelling and traceability of genetically modified organisms are current issues that are considered in trade and regulation. Currently, labelling of genetically modified foods containing detectable transgenic material is required by EU legislation. A proposed package of legislation would extend this labelling to foods without any traces of transgenics. These new legislations would also impose labelling and a traceability system based on documentation throughout the food and feed manufacture system. The regulatory issues of risk analysis and labelling are currently harmonised by Codex Alimentarius. The implementation and maintenance of the regulations necessitates sampling protocols and analytical methodologies that allow for accurate determination of the content of genetically modified organisms within a food and feed sample. Current methodologies for the analysis of genetically modified organisms are focused on either one of two targets, the transgenic DNA inserted- or the novel protein(s) expressed- in a genetically modified product. For most DNA-based detection methods, the polymerase chain reaction is employed. Items that need consideration in the use of DNA-based detection methods include the specificity, sensitivity, matrix effects, internal reference DNA, availability of external reference materials, hemizygosity versus homozygosity, extrachromosomal DNA, and international harmonisation. For most protein-based methods, enzyme-linked immunosorbent assays with antibodies binding the novel protein are employed. Consideration should be given to the selection of the antigen bound by the antibody, accuracy, validation, and matrix effects. Currently, validation of detection methods for analysis of genetically modified organisms is taking place. In addition, new methodologies are developed, including the use of microarrays, mass spectrometry, and surface plasmon resonance. Challenges for GMO detection include the detection of transgenic material in materials with varying chromosome numbers. The existing and proposed regulatory EU requirements for traceability of genetically modified products fit within a broader tendency towards traceability of foods in general and, commercially, towards products that can be distinguished from each other. Traceability systems document the history of a product and may serve the purpose of both marketing and health protection. In this framework, segregation and identity preservation systems allow for the separation of genetically modified and non-modified products from "farm to fork". Implementation of these systems comes with specific technical requirements for each particular step of the food processing chain. In addition, the feasibility of traceability systems depends on a number of factors, including unique identifiers for each genetically modified product, detection methods, permissible levels of contamination, and financial costs. In conclusion, progress has been achieved in the field of sampling, detection, and traceability of genetically modified products, while some issues remain to be solved. For success, much will depend on the threshold level for adventitious contamination set by legislation.

The use of AFLP to relate cheese-contaminating Penicillium strains to specific points in the production plants

Amplified fragment length polymorphism (AFLP) analysis was performed on isolates of Penicillium commune and Penicillium palitans originating from cheese and indoor environment in four cheese factories. The AFLP method was found to be a useful tool for identification of P. commune and P. palitans on, as well as below, species level. However, AFLP in combination with M13 fingerprinting described in a previous paper provided better resolution at the intraspecific level than either of the methods alone. Specific P. commune and P. palitans strains were found in the same factories over a period of more than a year and showed that the cheese factories have contaminating strains that are well established. The majority of the P. commune and P. palitans strains were found only within a single factory, but several were found in different cheese factories. The combined fingerprinting data could relate strains isolated from cheese to specific points in the production plants. Several of cheese-contaminating Penicillium strains could be related to air in the wrapping room, which must be considered to be a critical point for contamination of cheese.

A molecular genetic analysis of Eragrostis tef (Zucc.) Trotter: non-coding regions of chloroplast DNA, 18S rDNA and the transcription factor VP1

The non-coding chloroplast DNA sequences of the trnL (UAA) intron and the trnL-trnF (GAA) intergeneric spacer (IGS), the coding sequences of nuclear 18S rDNA, and the transcription factor Vp1 of the cereal tef (Eragrostis tef (Zucc.) Trotter) were studied. No intraspecific variation was found among the 6 studied tef varieties. However, the study displayed that Eragrostis tef has a number of unique traits compared to other grasses. Phylogenetic analysis of the chloroplast DNA gave three grass clades, joining Eragrostis with sorghum and maize in one. In the analysis of the 18S rDNA sequences, the three grass species were joined in a monophyletic trichotomy in the cladogram, in which maize is the most divergent, rice the least and tef intermediate. The Vp1 is highly conserved. The Vp1 phylogeny showed that the tef Vp1-sequence is the hitherto most divergent Vp1-sequence reported from a grass.

Structural characteristics and possible horizontal transfer of group I introns between closely related plant pathogenic fungi

We have characterized structural features and the distribution pattern of nuclear group I introns found in ribosomal DNA (rDNA) of closely related plant pathogenic fungi of the family Sclerotiniaceae. Sixteen introns, at two distinct positions in the small-subunit (SSU) and large-subunit (LSU) rDNA, were sequenced and analyzed among the 29 taxa included in the initial screening. Genera found to contain introns were Botrytis, Dumontinia, Encoelia, Grovesinia, Myriosclerotinia, and Sclerotinia. Secondary-structure analyses of the group I introns concluded that all belong to the common IC1 subclass. Interestingly, the SSU rDNA intron from Myriosclerotinia caricisampullacea contains an insertion-like sequence extension which may be a relic of an open reading frame. Incongruent branching patterns of intron-based and rDNA-based (internal transcribed spacer) phylogenetic trees suggest that the fungal host genomes and the group I introns do not share a common evolutionary history. A model to explain how horizontal intron transfers may have occurred among the closely related fungal taxa is proposed.

The postfire discomycete Geopyxis carbonaria (Ascomycota) is a biotrophic root associate with Norway spruce (Picea abies) in nature

The hypothesis that the postfire discomycete Geopyxis carbonaria (Ascomycota, Pezizales, Pyronemataceae) has a biotrophic association with roots of Norway spruce (Picea abies) in nature was tested by isolation of fungal strains from fresh, brown, smooth mycorrhiza-like root tips of Norway spruce collected from below the depth of detrimental heat penetration in a postfire site. The morphology of seven culture isolates originating from the smooth mycorrhiza-like root tips of two different spruce trees was congruent with the morphology of axenic culture isolates obtained from ascospores of G. carbonaria. DNA sequences of the nuclear ribosomal internal transcribed spacers ITS1 and ITS2 from these root-derived cultures and the ascosporic G. carbonaria culture isolates were found to be identical, further supporting the conclusion that the isolates were conspecific. The extensive ascocarp and ascospore formation of G. carbonaria which succeeds a forest fire may be explained in terms of a fungal escape from a moribund tree associate. Possible ecological adaptations of G. carbonaria to the pre- and postfire community are discussed.

Molecular phylogeny and evolution of Monilinia (Sclerotiniaceae) based on coding and noncoding rDNA sequences

The nuclear internal transcribed spacers, the 5.8S subunit, ~560 bp of the small subunit, and ~320 bp of the large subunit of the nuclear ribosomal DNA repeat from 17 species of Monilinia and eight species of closely related genera were sequenced. Phylogenies were constructed using maximum parsimony. The results support the hypothesis that Monilinia is not monophyletic. A fundamental distinction was found between the section Junctoriae and the section Disjunctoriae. Four evolutionary lineages were identified within the Disjunctoriae: one species on Crataegus, one group of species on dry stone fruits of rosaceous hosts, one group of species on capsular fruits of ericaceous hosts, and one group of species on sweet berry fruits of ericaceous hosts. Comparisons between branching topologies of hosts and Monilinia species suggest that although cospeciation among hosts and parasites has been the rule, several host jumps have taken place. Sclerotinia pirolae was determined to be a true member of the Disjunctoriae. The closest taxon groups to the Junctoriae were found to be Botrytis and Sclerotinia, with Ciborinia being the closest taxon group to the Disjunctoriae. There is evidence of an increased rate of ssrRNA evolution in the lineage of species that attack ericaceous berries.