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DNA barcoding survey of Trichoderma diversity in soil and litter of the Colombian lowland Amazonian rainforest reveals Trichoderma strigosellum sp. nov. and other species.

López-Quintero CA, Atanasova L, Franco-Molano AE, Gams W, Komon-Zelazowska M, Theelen B, Müller WH, Boekhout T, Druzhinina I - Antonie Van Leeuwenhoek (2013)

Bottom Line: DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %).Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov.Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.

View Article: PubMed Central - PubMed

Affiliation: CBS Fungal Biodiversity Centre (CBS-KNAW), Utrecht, The Netherlands.

ABSTRACT
The diversity of Trichoderma (Hypocreales, Ascomycota) colonizing leaf litter as well as the rhizosphere of Garcinia macrophylla (Clusiaceae) was investigated in primary and secondary rain forests in Colombian Amazonia. DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %). Four ITS 1 and 2 phylotypes (13 strains) could not be identified with certainty. Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov. Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.

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Position of T. strigosellum sp. nov. in the tef1 Bayesian phylogenetic tree. Black circles indicate nodes supported by posterior probabilities higher than 0.94. Arrows indicate branches that lead to species clades. Numbers correspond to GenBank accessions
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Fig1: Position of T. strigosellum sp. nov. in the tef1 Bayesian phylogenetic tree. Black circles indicate nodes supported by posterior probabilities higher than 0.94. Arrows indicate branches that lead to species clades. Numbers correspond to GenBank accessions

Mentions: To reveal the exact phylogenetic position of isolates identified as T. cf. strigosum in section Trichoderma we applied the exact sequence of the 4th large intron of tef1 (as retrieved by TrichoMARK, www.isth.info, Druzhinina et al. 2005) to sequence similarity search (blastn) against NCBI GeneBank. The application of the precise intron sequence without flanking coding areas is necessary to get the most accurate identification result that is not biased by strong similarities of less polymorphic coding regions (exons). The taxonomy report obtained from this search revealed that besides T. strigosum, the query isolates are related to Hypocrea valdunensis (1 hit), T. viride (teleomorph H. rufa, 79 hits) and T. viridescens (4 hits) (listed in decreasing similarity). The Bayesian phylogram constructed with tef1 sequences of T. strigosum and the query isolates (Fig. 1) demonstrated that T. strigosum and T. cf. strigosum are monophyletic and both belong to a statistically supported clade together with T. valdunensis and T. viride, while T. viridescens is the most distanced genetic neighbor of them. Interestingly, isolates of T. strigosum and T. cf. strigosum formed two statistically supported subclades what allowed us to hypothesize that they may represent two sister species. To test this we constructed Bayesian phylograms based on cal1 and chi18-5 phylogenetic markers (both unlinked to tef1, see Trichoderma genomes on Mycocosm portal of DOE JGI and Kubicek et al. 2011). This analysis demonstrated that both subclades were also present on chi18-5 and cal1 phylogenetic trees. The same result, the two statistically supported subclades corresponding to T strigosum and T. strigosellum sp. nov. were also present of a concatenated phylogram with tef1, ITS1 and 2, cal1 and chi18-5 loci (Supplementary materials). Thus, the isolates of T. cf. strigosum fulfill the criteria of the genealogical concordance phylogenetic species recognition concept (Taylor et al. 2000) and represent a new species described below as T. strigosellum sp. nov. The phylogenetic position of isolates identified as T. strigosum was also confirmed by this analysis (Figs. 1 and 2).Fig. 1


DNA barcoding survey of Trichoderma diversity in soil and litter of the Colombian lowland Amazonian rainforest reveals Trichoderma strigosellum sp. nov. and other species.

López-Quintero CA, Atanasova L, Franco-Molano AE, Gams W, Komon-Zelazowska M, Theelen B, Müller WH, Boekhout T, Druzhinina I - Antonie Van Leeuwenhoek (2013)

Position of T. strigosellum sp. nov. in the tef1 Bayesian phylogenetic tree. Black circles indicate nodes supported by posterior probabilities higher than 0.94. Arrows indicate branches that lead to species clades. Numbers correspond to GenBank accessions
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3824238&req=5

Fig1: Position of T. strigosellum sp. nov. in the tef1 Bayesian phylogenetic tree. Black circles indicate nodes supported by posterior probabilities higher than 0.94. Arrows indicate branches that lead to species clades. Numbers correspond to GenBank accessions
Mentions: To reveal the exact phylogenetic position of isolates identified as T. cf. strigosum in section Trichoderma we applied the exact sequence of the 4th large intron of tef1 (as retrieved by TrichoMARK, www.isth.info, Druzhinina et al. 2005) to sequence similarity search (blastn) against NCBI GeneBank. The application of the precise intron sequence without flanking coding areas is necessary to get the most accurate identification result that is not biased by strong similarities of less polymorphic coding regions (exons). The taxonomy report obtained from this search revealed that besides T. strigosum, the query isolates are related to Hypocrea valdunensis (1 hit), T. viride (teleomorph H. rufa, 79 hits) and T. viridescens (4 hits) (listed in decreasing similarity). The Bayesian phylogram constructed with tef1 sequences of T. strigosum and the query isolates (Fig. 1) demonstrated that T. strigosum and T. cf. strigosum are monophyletic and both belong to a statistically supported clade together with T. valdunensis and T. viride, while T. viridescens is the most distanced genetic neighbor of them. Interestingly, isolates of T. strigosum and T. cf. strigosum formed two statistically supported subclades what allowed us to hypothesize that they may represent two sister species. To test this we constructed Bayesian phylograms based on cal1 and chi18-5 phylogenetic markers (both unlinked to tef1, see Trichoderma genomes on Mycocosm portal of DOE JGI and Kubicek et al. 2011). This analysis demonstrated that both subclades were also present on chi18-5 and cal1 phylogenetic trees. The same result, the two statistically supported subclades corresponding to T strigosum and T. strigosellum sp. nov. were also present of a concatenated phylogram with tef1, ITS1 and 2, cal1 and chi18-5 loci (Supplementary materials). Thus, the isolates of T. cf. strigosum fulfill the criteria of the genealogical concordance phylogenetic species recognition concept (Taylor et al. 2000) and represent a new species described below as T. strigosellum sp. nov. The phylogenetic position of isolates identified as T. strigosum was also confirmed by this analysis (Figs. 1 and 2).Fig. 1

Bottom Line: DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %).Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov.Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.

View Article: PubMed Central - PubMed

Affiliation: CBS Fungal Biodiversity Centre (CBS-KNAW), Utrecht, The Netherlands.

ABSTRACT
The diversity of Trichoderma (Hypocreales, Ascomycota) colonizing leaf litter as well as the rhizosphere of Garcinia macrophylla (Clusiaceae) was investigated in primary and secondary rain forests in Colombian Amazonia. DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %). Four ITS 1 and 2 phylotypes (13 strains) could not be identified with certainty. Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov. Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.

Show MeSH