Cladosporium from caves of the Brazilian savannah (Cerrado) and the description of six new species
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Pensoft Publishers
Abstract
Caves are important but understudied reservoirs of fungal diversity, particularly for genera such as Cladosporium (Cladosporiales, Dothideomycetes). This study aimed to characterise the richness of Cladosporium species from six caves in the Brazilian savannah (Cerrado) using an integrative approach combining morphology and multi-locus phylogenetic analyses (ACT, ITS, RPB2, TEF1-α, and TUB). To improve species recognition in Cladosporium, selected ex-type strains were studied, for which RPB2 and TUB barcodes were also sequenced. Species were delimited using morphology and phylogenetic inferences, supplemented by the pairwise homoplasy index (PHI) test to evaluate species boundaries. Twenty-three species were identified among 94 Cladosporium isolates. The polyphasic approach resulted in the description of six new species: five in the C. cladosporioides complex (C. carsi, C. lacerdae, C. mambaiense, C. nogueirae, and C. propiciense) and one in the C. sphaerospermum complex (C. mesquitapaivae). Additionally, analyses based on morphology, genealogical concordance phylogenetic species recognition (GCPSR), and the PHI test resulted in the synonymisation of C. ribis and C. speluncae under C. bambusicola, C. brigadeirense under C. puris, and C. marinisedimentum under C. sphaerospermum. Among the previously known species identified, 11 represent new records for cave environments, with C. bambusicola being the most frequent (29.17%). These findings substantially expand the known diversity of Cladosporium in Neotropical caves, highlighting the Brazilian Cerrado as a hotspot of mycodiversity. Furthermore, ACT, RPB2, TEF1-α, and TUB are proposed as the primary phylogenetic barcodes for distinguishing closely related Cladosporium species, particularly within the C. cladosporioides complex. This study further emphasises the necessity of using a polyphasic approach to achieve accurate taxonomic resolution among Cladosporium species, trace their distribution in caves, and help to understand their ecology.
Description
DATA AVAILABILITY : Fungal isolates are deposited in public culture collections in Brazil, DNA sequences are available in GenBank, and alignments were deposited in Figshare.
SUPPLEMENTARY IMAGES
FIGURE S1 : Explanation note: Maximum-likelihood IQTree tree of C. cladosporioides SC based on an individual dataset of ACT sequences. The species obtained in this study are highlighted in bold. Ex-type strains = T. IQ-TREE-BS values ≥ 70% and RAxML-BS ≥ 70% are included next to the nodes. The tree was rooted with Cladosporium herbarum (CBS 121621 and CBS 300.49).
FIGURE S2 : Explanation note: Maximum-likelihood IQTree tree of C. cladosporioides SC based on an individual dataset of ITS sequences. The species obtained in this study are highlighted in bold. Ex-type strains = T. IQ-TREE-BS values ≥ 70% and RAxML-BS ≥ 70% are included next to the nodes. The tree was rooted with Cladosporium herbarum (CBS 121621 and CBS 300.49).
FIGURE S3 : Explanation note: Maximum-likelihood IQTree tree of C. cladosporioides SC based on an individual dataset of TEF1-α sequences. The species obtained in this study are highlighted in bold. Ex-type strains = T. IQ-TREE-BS values ≥ 70% and RAxML-BS ≥ 70% are included next to the nodes. The tree was rooted with Cladosporium herbarum (CBS 121621 and CBS 300.49).
FIGURE S4 : Explanation note: Maximum-likelihood IQTree tree of C. sphaerospermum SC based on an individual dataset of ACT sequences. The species obtained in this study are highlighted in bold. Ex-type strains = T. IQ-TREE-BS values ≥ 70% and RAxML-BS ≥ 70% are included next to the nodes. The tree was rooted with Cladosporium herbarum (CBS 121621 and CBS 300.49).
FIGURE S5 : Explanation note: Maximum-likelihood IQTree tree of C. sphaerospermum SC based on an individual dataset of ITS sequences. The species obtained in this study are highlighted in bold. Ex-type strains = T. IQ-TREE-BS values ≥ 70%, and RAxML-BS ≥ 70% are included next to the nodes. The tree was rooted with Cladosporium herbarum (CBS 121621 and CBS 300.49).
FIGURE S6 : Explanation note: Maximum-likelihood IQTree tree of C. sphaerospermum SC based on an individual dataset of TEF1-α sequences. The species obtained in this study are highlighted in bold. Ex-type strains = T. IQ-TREE-BS values ≥ 70% and RAxML-BS ≥ 70% are included next to the nodes. The tree was rooted with Cladosporium herbarum (CBS 121621 and CBS 300.49).
FIGURE S7 : Explanation note: Maximum-likelihood IQTree tree of C. cladosporioides SC and C. sphaerospermum SC based on an individual dataset of RPB2 sequences. The species obtained in this study are highlighted in bold. Ex-type strains = T. IQ-TREE-BS values ≥ 70% and RAxML-BS ≥ 70% are included next to the nodes. The tree was rooted with Cercospora beticola (CBS 116456).
FIGURE S8 : Explanation note: Maximum-likelihood IQTree tree of C. cladosporioides SC and C. sphaerospermum SC based on an individual dataset of TUB sequences. The species obtained in this study are highlighted in bold. Ex-type strains = T. IQ-TREE-BS values ≥ 70% and RAxML-BS ≥ 70% are included next to the nodes. The tree was rooted with Cercospora beticola (CBS 116456).
SUPPLEMENTARY TABLES : Explanation note: table SS1. Feature summaries of the studied caves, including geographic coordinates, number of sampling points, count of fungal isolates by substrate (air and soil), temperature, and humidity. table SS2. Checklist of Cladosporium species reported in caves of different Brazilian biomes, with details on the location, substrate, and reference for each record.
These datasets are made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Keywords
Cave fungi, Fungal taxonomy, New taxa, Phylogeny, Speleomycology
Sustainable Development Goals
SDG-15: Life on land
Citation
Félix-Oliveira, P.H., Prazeres, J.F.S.A., Ferro, L.O. et al. 2026, 'Cladosporium from caves of the Brazilian savannah (Cerrado) and the description of six new species', IMA Fungus, vol. 17, art. e191673, pp. 1-68, doi : 10.3897/imafungus.17.191673,