Diversity and taxonomy of Chaetomium and chaetomium-like fungi from indoor environments

Wang, X.W.; Houbraken, J; Groenewald, J.Z.; Meijer, M. M.; Andersen, Birgitte; Nielsen, K.F.; Crous, P.W.; Samson, R.A.

doi:10.1016/j.simyco.2016.11.005

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Diversity and taxonomy of Chaetomium and chaetomium-like fungi from indoor environments

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Author(s): X.W. Wang ¹ ^, ² ^, ^∗ , J. Houbraken ² , J.Z. Groenewald ² , M. Meijer ² , B. Andersen ³ , K.F. Nielsen ³ , P.W. Crous ² ^, ⁴ ^, ⁵ , R.A. Samson ² ^, ^∗

Publication date (Electronic): 08 December 2016

Journal: Studies in Mycology

Publisher: CBS Fungal Biodiversity Centre

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Abstract

During a study of indoor fungi, 145 isolates belonging to Chaetomiaceae were cultured from air, swab and dust samples from 19 countries. Based on the phylogenetic analyses of DNA-directed RNA polymerase II second largest subunit ( rpb2), β-tubulin ( tub2), ITS and 28S large subunit (LSU) nrDNA sequences, together with morphological comparisons with related genera and species, 30 indoor taxa are recognised, of which 22 represent known species, seven are described as new, and one remains to be identified to species level. In our collection, 69 % of the indoor isolates with six species cluster with members of the Chaetomium globosum species complex, representing Chaetomium sensu stricto. The other indoor species fall into nine lineages that are separated from each other with several known chaetomiaceous genera occurring among them. No generic names are available for five of those lineages, and the following new genera are introduced here: Amesia with three indoor species, Arcopilus with one indoor species, Collariella with four indoor species, Dichotomopilus with seven indoor species and Ovatospora with two indoor species. The generic concept of Botryotrichum is expanded to include Emilmuelleria and the chaetomium-like species B. muromum (= Ch. murorum) in which two indoor species are included. The generic concept of Subramaniula is expanded to include several chaetomium-like taxa as well as one indoor species. Humicola is recognised as a distinct genus including two indoor taxa. According to this study, Ch. globosum is the most abundant Chaetomiaceae indoor species (74/145), followed by Ch. cochliodes (17/145), Ch. elatum (6/145) and B. piluliferum (5/145). The morphological diversity of indoor Chaetomiaceae as well as the morphological characteristics of the new genera are described and illustrated. This taxonomic study redefines the generic concept of Chaetomium and provides new insight into the phylogenetic relationships among different genera within Chaetomiaceae.

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Most cited references 82

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Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous.

K. O'Donnell, E Cigelnik (1997)

The evolutionary history of the phytopathogenic Gibberella fujikuroi complex of Fusarium and related species was investigated by cladistic analysis of DNA sequences obtained from multiple unlinked loci. Gene phylogenies inferred from the mitochondrial small subunit (mtSSU) rDNA, nuclear 28S rDNA, and beta-tubulin gene were generally concordant, providing strong support for a fully resolved phylogeny of all biological and most morphological species. Discordance of the nuclear rDNA internal transcribed spacer 2 (ITS2) gene tree is due to paralogous or xenologous ITS2 sequences. PCR and sequence analysis demonstrated that every strain of the ingroup species tested possesses two highly divergent nonorthologous ITS2 types designated type I and type II. Only the major ITS2 type, however, is discernable when PCR products are amplified and sequenced directly with conserved primers. The minor ITS2 type was recovered using ITS2 type-specific PCR primers. Distribution of the major ITS2 type within the species lineages exhibits a homoplastic pattern of evolution, thus obscuring true phylogenetic relationships. The results suggest that the ancestral ITS2 types may have arisen following an ancient interspecific hybridization or gene duplication which occurred prior to the evolutionary radiation of the Gibberella fujikuroi complex and related species of Fusarium. The results also indicate that current morphological-based taxonomic schemes for these fungi are unnatural and a new classification is required.

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Can three incongruence tests predict when data should be combined?

C. Cunningham (1997)

Advocates of conditional combination have argued that testing for incongruence between data partitions is an important step in data exploration. Unless the partitions have had distinct histories, as in horizontal gene transfer, incongruence means that one or more data support the wrong phylogeny. This study examines the relationship between incongruence and phylogenetic accuracy using three tests of incongruence. These tests were applied to pairs of mitochondrial DNA data partitions from two well-corroborated vertebrate phylogenies. Of the three tests, the most useful was the incongruence length difference test (ILD, also called the partition homogeneity test). This test distinguished between cases in which combining the data generally improved phylogenetic accuracy (P > 0.01) and cases in which accuracy of the combined data suffered relative to the individual partitions (P < 0.001). In contrast, in several cases, the Templeton and Rodrigo tests detected highly significant incongruence (P < 0.001) even though combining the incongruent partitions actually increased phylogenetic accuracy. All three tests identified cases in which improving the reconstruction model would improve the phylogenetic accuracy of the individual partitions.

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Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics.

Anthony S. Amend, Robert Samson, Thomas D. Bruns … (2010)

Fungi are ubiquitous components of indoor human environments, where most contact between humans and microbes occurs. The majority of these organisms apparently play a neutral role, but some are detrimental to human lifestyles and health. Recent studies that used culture-independent sampling methods demonstrated a high diversity of indoor fungi distinct from that of outdoor environments. Others have shown temporal fluctuations of fungal assemblages in human environments and modest correlations with human activity, but global-scale patterns have not been examined, despite the manifest significance of biogeography in other microbial systems. Here we present a global survey of fungi from indoor environments (n = 72), using both taxonomic and phylogeny-informative molecular markers to determine whether global or local indoor factors determine indoor fungal composition. Contrary to common ecological patterns, we show that fungal diversity is significantly higher in temperate zones than in the tropics, with distance from the equator being the best predictor of phylogenetic community similarity. Fungal composition is significantly auto-correlated at the national and hemispheric spatial scales. Remarkably, building function has no significant effect on indoor fungal composition, despite stark contrasts between architecture and materials of some buildings in close proximity. Distribution of individual taxa is significantly range- and latitude-limited compared with a null model of randomized distribution. Our results suggest that factors driving fungal composition are primarily global rather than mediated by building design or function.

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Author and article information

Contributors

X.W. Wang

R.A. Samson

Journal

Journal ID (nlm-ta): Stud Mycol

Journal ID (iso-abbrev): Stud. Mycol

Title: Studies in Mycology

Publisher: CBS Fungal Biodiversity Centre

ISSN (Print): 0166-0616

ISSN (Electronic): 1872-9797

Publication date PMC-release: 08 December 2016

Publication date (Print): June 2016

Publication date (Electronic): 08 December 2016

Volume: 84

Pages: 145-224

Affiliations

[1 ]State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3, 1st Beichen West Road, Chaoyang District, Beijing 100101, China

[2 ]CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

[3 ]DTU Bioengineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark

[4 ]Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa

[5 ]Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

Author notes

[∗ ] Correspondence: X.W. Wang; R.A. Samson x.wang@ 123456cbs.knaw.nl r.samson@ 123456cbs.knaw.nl

Article

Publisher ID: S0166-0616(16)30019-7

DOI: 10.1016/j.simyco.2016.11.005

PMC ID: 5226397

PubMed ID: 28082757

SO-VID: 1254ddf5-6f60-4696-9765-632dff6d6558

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This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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Subject: Research Paper

ScienceOpen disciplines: Plant science & Botany

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ScienceOpen disciplines: Plant science & Botany

Diversity and taxonomy of Chaetomium and chaetomium-like fungi from indoor environments

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Abstract

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Plant MYBs

Most cited references 82

Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous.

Can three incongruence tests predict when data should be combined?

Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics.

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