Research Article |
Corresponding author: Sinang Hongsanan ( sinang333@gmail.com ) Corresponding author: Saisamorn Lumyong ( scboi009@gmail.com ) Academic editor: Samantha C. Karunarathna
© 2025 Tanapol Thitla, Jutamart Monkai, Weiqian Meng, Surapong Khuna, Ning Xie, Sinang Hongsanan, Saisamorn Lumyong.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Thitla T, Monkai J, Meng W, Khuna S, Xie N, Hongsanan S, Lumyong S (2025) Two new species of Penicillium and a new genus in Xylariomycetidae from the forest dump-sites in Chiang Mai, Thailand. MycoKeys 116: 275-301. https://doi.org/10.3897/mycokeys.116.150635
|
Waste accumulation in forest regions can have a severe impact on the soil mycobiome. However, research on soil fungi inhabiting forest disposal sites remains limited. Therefore, this study focused on the taxonomy and phylogeny of ascomycetes isolated from soil in forest dump-sites in Chiang Mai, Thailand. The fungal strains were identified using morphological characterisations and multigene phylogenetic reconstruction. A new genus, Pseudoleptodontidium, typified by Ps. chiangmaiense sp. nov. (Amphisphaeriales genera incertae sedis, Xylariomycetidae), along with two new species, Penicillium chiangmaiense (series Janthinella, section Lanata-Divaricata) and P. terrae (series Erubescentia, section Exilicaulis) (Aspergillaceae, Eurotiales), are described in detail and compared with closely-related species. Our discovery offers valuable insights into the soil ascomycetes associated with forest disturbances.
Eurotiomycetes, new taxa, Pseudoleptodontidium, soil fungi, Sordariomycetes, taxonomy
The disposal of waste materials through open burning, landfilling and dumping in land areas or water resources contributes to environmental issues, such as air pollution (PM2.5), as well as water and soil pollution, which can endanger the health and livelihood of humans, animals, plants and other organisms (
Extensive studies have focused on isolating and characterising soil fungi from contaminated areas, landfills and urban dump-sites (
Dump-sites, especially those located within forested areas, represent an underexplored yet ecologically significant niche. Forest dump-sites provide a distinctive habitat, characterised by decreased soil nutrients, fluctuating temperature and moisture levels and potential exposure to pollutants (
Soil samples (0–10 cm depth) were collected from three forest dump-sites in June 2024 in Chiang Mai Province, Thailand: (1) Papae, Mae Taeng District, (2) Suthep, Muang Chiang Mai District and (3) Mae Sa, Mae Rim District (Fig.
The morphological characteristics of the obtained fungi were observed in both macro-morphology and micro-morphology, with different details depending on each fungus.
To investigate the morphology of Penicillium (comprising MBSZU 24-007 to MBSZU 24-010), the colony characteristics, growth rate, pigment production, sporulation or related features were investigated on Blakeslee’s Malt extract agar (MEAbl), creatine sucrose agar (CREA), Czapek yeast autolysate agar with 5% NaCl (CYAS), Czapek’s agar (CZ), Dichloran 18% glycerol agar (DG18), malt extract agar (MEA), oatmeal agar (OA), PDA and yeast extract sucrose agar (YES) at 25 °C in darkness for 7 days. The experiment was also performed on Czapek yeast autolysate agar (CYA) at 25, 30 and 37 °C in darkness for 7 days to characterise the macro-morphology (
The colony characteristics, growth rate and pigment production of Pseudoleptodontidium (MBSZU 25-005) were studied on PDA and MEA at 25 °C in darkness for 14 days. Micro-morphology was observed under a light microscope using a fungal colony grown on PDA at 25 °C in darkness for 14–21 days. The size of each morphological structure was measured at least 50 times per structure.
Fungal genomic DNA from each strain was extracted from the fungal mycelium, which had grown on PDA at 25 °C for a week, using an E.Z.N.A® Tissue DNA Kit (Omega, USA). The polymerase chain reaction (PCR) technique was used to amplify each region. Each target locus was amplified using the specific primers (Table
The specific primer and annealing condition of each locus used in this study.
Loci* | Primer | Annealing condition | References | |
---|---|---|---|---|
Temperatures (°C) | Annealing period (s) | |||
ITS | ITS4/ITS5 | 52 | 30 |
|
LSU | LR0R/LR5 | 52 | 30 |
|
CAM | CF1/CF4 | 51 | 60 |
|
Cmd5/Cmd6 | 58 | 30 |
|
|
RPB2 | fRPB2-5F/ fRPB2-7cR | 56 | 60 |
|
TUB | Bt2a/Bt2b | 52 | 30 |
|
T1/Bt2b | 55 | 45 |
|
The bidirectional sequence data were assembled using the software Sequencher 5.4.6 (
The multi-loci phylogenetic dataset was obtained, based on previous studies of Penicillium section Exilicaulis (
Phylogenetic analysis of 72 taxa from Penicillium, section Exilicaulis (including P. terrae MBSZU 24-007 and MBSZU 24-008) was performed using a combined ITS, TUB, CAM and RPB2 sequence dataset. Penicillium janthinellum CBS 340.48 and P. limosum CBS 339.97 were selected as the outgroup. The combined dataset comprised 2,630 characters (ITS, 1−564 bp; TUB, 565−1,102 bp; CAM, 1,103−1,701 bp; RPB2, 1,702−2,630 bp), including gaps. RAxML analysis of the integrated dataset yielded the best-scoring tree with a final ML optimisation likelihood value of -26380.0905. The matrix contained 1,279 distinct alignment patterns, with 13.06% of the characters being undetermined or gaps. The estimated base frequencies were recorded as follows: A = 0.2238, C = 0.2765, G = 0.2706 and T = 0.2291, while the substitution rates were as follows: AC = 1.0947, AG = 3.5202, AT = 1.1705, CG = 0.7818, CT = 5.4306 and GT = 1.0000. The gamma distribution shape parameter alpha value was equal to 0.2342, while the tree length was equal to 2.4771. The final average standard deviation of the split frequencies at the end of the total MCMC generations was computed as 0.003644 via BI analysis.
Phylogenetic analysis of 111 taxa from Penicillium section Lanata-Divaricata (including P. chiangmaiense MBSZU 24-009 and MBSZU 24-010) was performed using a combined ITS, TUB, CAM and RPB2 sequence dataset. Penicillium alogum CBS 140996 and P. stolkiae CBS 315.67 were selected as outgroups. The combined dataset comprised 2,549 characters (ITS, 1−563 bp; TUB, 564−1,114 bp; CAM, 1,115−1,794 bp; RPB2, 1,795−2,549 bp), including gaps. RAxML analysis of the integrated dataset yielded the best scoring tree with a final ML optimisation likelihood value of -35195.9174. The matrix contained 1,381 distinct alignment patterns with 12.17% undetermined characters or gaps. The estimated base frequencies were recorded as follows: A = 0.2214, C = 0.2908, G = 0.2615 and T = 0.2263, while the substitution rates were as follows: AC = 1.1361, AG = 3.5568, AT = 1.5061, CG = 0.7521, CT = 5.3860 and GT = 1.0000. The gamma distribution shape parameter alpha value was equal to 0.2744, while the tree length was equal to 3.5928. The final average standard deviation of the split frequencies at the end of the total MCMC generations was computed as 0.005628 via BI analysis.
Phylogenetic analysis of species in subclass Xylariomycetidae was performed using a combined ITS, LSU, RPB2 and TUB sequence dataset of MBSZU 25-005 (proposed as Pseudoleptodontidium chiangmaiensis), together with 118 taxa of the subclass. Achaetomium macrosporum CBS 532.94, Chaetomium elatum CBS 374.66 and Sordaria fimicola CBS 723.96 were selected as outgroups. The combined dataset comprised 3,560 characters (ITS, 1−693 bp; LSU, 694−1,592 bp; RPB2, 1,593−2,656 bp; TUB, 2,657−3,560 bp), including gaps. RAxML analysis of the integrated dataset yielded the best scoring tree with a final ML optimisation likelihood value of -83630.121273. The matrix contained 2,615 distinct alignment patterns with 39.42% undetermined characters or gaps. The estimated base frequencies were recorded as follows: A = 0.256414, C = 0.231937, G = 0.280501 and T = 0.231149, while the substitution rates were as follows: AC = 0.888171, AG = 2.661198, AT = 1.161270, CG = 0.868099, CT = 3.494813 and GT = 1.000000. The gamma distribution shape parameter alpha value was equal to 0.351763, while the tree length was equal to 15.592567. The final average standard deviation of the split frequencies at the end of the total MCMC generations was computed as 0.009989 via BI analysis.
Topologically, the ML and BI phylogenetic trees of all fungal species had similar results; therefore, only the ML phylogram was demonstrated in this study. The phylogram of Penicillium section Exilicaulis showed that two new strains (MBSZU 24-007 and MBSZU 24-008) separated from other recognised species with 100% BS and 1.00 PP supports (Fig.
Phylogram generated from Maximum Likelihood analysis of 72 specimens belonging to the genus Penicillium section Exilicaulis, using the combined ITS, TUB, CAM and RPB2 genes. Penicillium janthinellum CBS 340.48 and P. limosum CBS 339.97 were used as the outgroup. The numbers above branches show bootstrap percentages (left) and Bayesian Posterior Probabilities (right). Bootstrap values ≥ 75% and Bayesian Posterior Probabilities ≥ 0.95 are shown. The scale bar reflects the estimated number of nucleotide substitutions per site. The fungal strains in this study are blue. Type species are bold.
While the phylogram of Penicillium section Lanata-Divaricata exhibited that MBSZU 24-009 and MBSZU 24-010 formed a distinct clade, clearly separated from other taxa with significant support (BS 100% and PP 1.00; Fig.
Phylogram generated from Maximum Likelihood analysis of 111 specimens belonging to the genus Penicillium section Lanata-Divaricata using the combined ITS, TUB, CAM and RPB2 genes. Penicillium alogum CBS 140996 and P. stolkiae CBS 315.67 were used as the outgroup. The numbers above branches show bootstrap percentages (left) and Bayesian Posterior Probabilities (right). Bootstrap values ≥ 75% and Bayesian Posterior Probabilities ≥ 0.95 are shown. The scale bar reflects the estimated number of nucleotide substitutions per site. The fungal strains in this study are red. Type species are bold.
The phylogram of Xylariomycetidae showed that MBSZU 25-005 clustered amongst families and taxa in Amphisphaeriales. This strain also formed a sister clade to Neoleptodontidium aciculare CBS 123.86 and N. aquaticum CBS 149455 (BS 96% and PP 1.00; Fig.
Phylogram generated from Maximum Likelihood analysis of 119 specimens belonging to the subclass Xylariomycetidae of the combined ITS, LSU, RPB2 and TUB genes. Achaetomium macrosporum CBS 532.94, Chaetomium elatum CBS 374.66 and Sordaria fimicola CBS 723.96 were used as the outgroup. The numbers above branches show bootstrap percentages (left) and Bayesian Posterior Probabilities (right). Bootstrap values ≥ 75% and Bayesian Posterior Probabilities ≥ 0.95 are shown. The scale bar reflects the estimated number of nucleotide substitutions per site. The fungal strains in this study are red. Type species are bold.
The specific epithet terrae refers to the soil substrate, from which this species was isolated.
Thailand • Chiang Mai Province, Mae Taeng District, Papae, on soil in the forest dump-sites, 20 June 2024, T. Thitla & J. Monkai; VR040 (SZU25-005, holotype); ex-type living culture, MBSZU 24-008, dried culture permanently preserved in a metabolically inactive state, SZU25-005.
(in mm) 7 days, 25 °C: CREA 8–11, CYA 13–18, CYAS 7–9, CZ 11–15, DG18 12–16, MEA 15–19, MEAbl 16–19, OA 13–19, PDA 12–15 and YES 9–13. 7 days, 30 °C: CYA 10–15. 7 days, 37 °C: CYA no growth.
Colonies at 25 °C for 7 days on CREA thin colonies; acid production absent (Fig.
Conidiophores mononematous, growing out at right angles from hyphae, unbranched, smooth, hyaline, 3–14 × 1–3 µm (Fig.
Thailand • Chiang Mai Province, Mae Taeng District, Papae, on soil in the forest dump-sites, 20 June 2024, T. Thitla & J. Monkai; CMUVR039; living culture, MBSZU 24-007, dried culture permanently preserved in a metabolically inactive state, CMUVR039.
Soil; only known from Chiang Mai Province, Thailand.
Penicillium section Exilicaulis was first established by
Penicillium terrae is classified within section Exilicaulis, series Erubescentia. Phylogenetically, this species is closely related to P. laeve and P. ovatum (Fig.
The specific epithet “chiangmaiense” refers to the type locality “Chiang Mai Province, Thailand”.
Thailand • Chiang Mai Province, Mae Rim District, Mae Sa, on soil in the forest dump-sites, 27 June 2024, T. Thitla & J. Monkai; VR005 (SZU25-006, holotype); ex-type living culture, MBSZU 24-009, dried culture permanently preserved in a metabolically inactive state, SZU25-006.
(in mm) 7 days, 25 °C: CREA 40–44, CYA 50–52, CYAS 35–38, CZ 48–49, DG18 34–39, MEA 47–51, MEAbl 51–53, OA 53–54, PDA 49–50 and YES 32–38. 7 days, 30 °C: CYA 59–61. 7 days, 37 °C: CYA 55–56.
Colonies at 25 °C for 7 days on CREA thin colonies; acid production absent (Fig.
Penicillium chiangmaiense (MBSZU 24-009, ex-type living culture) A–J colonies at 25 °C for 7 days on CREA, CYA, CYAS, CZ, DG18, MEA, MEAbl, OA, PDA and YES, respectively K−N conidiophores, phialides and conidia O conidia P sclerotia produced on culture media. Scale bar: 2 cm (A–J); 10 µm (K–O); 100 µm (P).
Conidiophores monoverticillate, sometimes divaricate. Stipes hyaline, smooth–walled, 80–270 × 2–3 µm (Fig.
Thailand • Chiang Mai Province, Mae Rim District, Mae Sa, on soil in the forest dump-sites, 27 June 2024, T. Thitla & J. Monkai; CMUVR005-2; living culture, MBSZU 24-010, dried culture permanently preserved in a metabolically inactive state, CMUVR005-2.
Soil; only known from Chiang Mai Province, Thailand.
Penicillium section Lanata-Divaricata was established by
Penicillium chiangmaiense is classified within section Lanata-Divaricata, series Janthinella. In the phylogenetic tree (Fig.
The name refers to its morphological similarity to Leptodontidium.
Sordariomycetes, Xylariomycetidae, Amphisphaeriales, incertae sedis.
Asexual morph: Mycelium composed of hyaline to black, thin- to thick-walled, smooth, branched, septate. Conidiophores arising from hyphae, solitary, erect, cylindrical, pale brown to dark brown, thick-walled, occasionally roughened on lower part, septate. Conidiogenous cells terminal and intercalary on conidiophores, occasionally lateral on hyphae, obclavate, sympodially proliferate, denticulate, hyaline to pale brown, smooth, septate. Conidia hyaline, smooth, aseptate, subglobose to ellipsoidal, slightly curved. Chlamydospores solitary, terminal on hyphae, medium brown to dark brown, smooth, thick-walled, aseptate, subglobose. Sexual morph: absent.
Pseudoleptodontidium chiangmaiense Thitla, Monkai, Lumyong & Hongsanan, sp. nov.
Pseudoleptodontidium is morphologically similar to Neoleptodontidium, sharing septate, subcylindrical conidiophores, terminal and lateral phialidic conidiogenous cells and aseptate subcylindrical conidia (
The specific epithet chiangmaiense refers to the type locality, Chiang Mai Province, Thailand.
Thailand•Chiang Mai Province, Mueang Chiang Mai District, Su Thep, on soil in the forest dump-sites, 21 June 2024, T. Thitla & J. Monkai; VR044 (SZU25-007, holotype); ex-type living culture, MBSZU 25-005, dried culture permanently preserved in a metabolically inactive state, SZU25-007.
(in mm) 14 days, 25 °C: PDA 36–40 and MEA 31–38.
Colonies at 25 °C for 14 days on PDA velvety, circular, flat, entire margin; dark green at the centre, greenish-yellow at the middle, white at the margin; soluble pigment absent; reverse dark green to pale yellow, white at the margin (Fig.
Mycelium composed of hyaline to black, thin- to thick-walled, smooth, branched, septate, 2–4.5 µm diam. hyphae (Fig.
Soil; only known from Chiang Mai Province, Thailand.
Pseudoleptodontidium chiangmaiense has a close relationship with Neoleptodontidium aciculare and N. aquaticum (Fig.
This study identifies a new genus in Xylariomycetidae, namely Pseudoleptodontidium, accommodating Ps. chiangmaiense sp. nov., along with two new species of Penicillium: P. terrae in section Exilicaulis and P. chiangmaiense in section Lanata-Divaricata. These species were isolated from soil collected in forest dump-sites in Chiang Mai Province, Thailand. They were characterised through morphological observations and multigene phylogenetic analyses (Figs
Penicillium is a highly impactful genus, with species ranging from mycotoxin-producing plant pathogens and opportunistic animal and human pathogens to valuable sources of enzymes, antibiotics and bioactive compounds (
Prior to this study, P. laeve was the only species in section Exilicaulis reported from Thailand (
Ecologically, Penicillium species have been isolated from different environments (
Xylariomycetidae is a large subclass within Sordariomycetes comprising numerous taxa that are polyphyletic and paraphyletic (
Members of Xylariomycetidae have a worldwide distribution and occupy various ecological niches, including saprobes, endophytes and pathogens (
These findings significantly contribute to our understanding of fungal diversity and ecology, particularly within the Ascomycota and highlight the richness and diversity of soil fungal communities in Thailand. Penicillium and some Xylariomycetidae taxa, such as Amphisphaeria, Annulohypoxylon and Hypoxylon are recognised for possessing a wide variety of secondary metabolites, which have prospective agricultural and therapeutic uses (
This research work is partially funded by Chiang Mai University. Shaun Pennycook is thanked for the nomenclatural advice. Sinang Hongsanan would like to thank the National Natural Science Foundation of China (32400012), 2023 Shenzhen Pengcheng Distinguished Positions and scientific research funds for high-tech talents /high-level talents and Shenzhen University 2035 Program for Excellent Research, Grant No. 2024C006. Ning Xie would like to thank the Natural Science Foundation of Guangdong Province (2024B1515020034) and National Key R&D Program of China (2021YFA0910800).
The authors have declared that no competing interests exist.
No ethical statement was reported.
This work was funded by the Natural Science Foundation of Guangdong Province (2024B1515020034), the International Research Fellowship (Visiting Researcher Program), Chiang Mai University (Grant No. 014/2567), and the National Key R&D Program of China (2021YFA0910800).
Conceptualisation: Tanapol Thitla, Jutamart Monkai, Sinang Hongsanan, Saisamorn Lumyong. Collection and morphological examinations: Tanapol Thitla, Jutamart Monkai, Weiqian Meng, Surapong Khuna. Molecular sequencing and phylogenetic analyses: Tanapol Thitla, Jutamart Monkai, Weiqian Meng, Surapong Khuna. Original draft preparation: Tanapol Thitla, Jutamart Monkai, Surapong Khuna. Review and editing, supervision: Tanapol Thitla, Jutamart Monkai, Weiqian Meng, Surapong Khuna, Ning Xie, Sinang Hongsanan, Saisamorn Lumyong. All authors have read and agreed to the published version of the manuscript.
Tanapol Thitla https://orcid.org/0000-0003-3092-0679
Jutamart Monkai https://orcid.org/0000-0001-6043-0625
Weiqian Meng https://orcid.org/0009-0006-3840-0992
Surapong Khuna https://orcid.org/0000-0003-1999-4001
Ning Xie https://orcid.org/0000-0002-5866-8535
Sinang Hongsanan https://orcid.org/0000-0003-0550-3152
Saisamorn Lumyong https://orcid.org/0000-0002-6485-414X
The datasets generated during and/or analysed during the current study are available in the MycoBank repository (included in the manuscript) and GenBank (included in Suppl. material
Additional information
Data type: docx
Explanation note: table S1. GenBank accession numbers of Penicillium section Exilicaulis used in multi-locus phylogenetic analysis. table S2. GenBank accession numbers of Penicillium section Lanata-Divaricata used in multi-locus phylogenetic analysis. table S3. GenBank accession numbers of taxa in Xylariomycetidae used in multi-genes phylogenetic analysis.