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Research Article
Two new species of Penicillium and a new genus in Xylariomycetidae from the forest dump-sites in Chiang Mai, Thailand
expand article infoTanapol Thitla, Jutamart Monkai§, Weiqian Meng, Surapong Khuna, Ning Xie, Sinang Hongsanan§, Saisamorn Lumyong|§
‡ Shenzhen University, Shenzhen, China
§ Chiang Mai University, Chiang Mai, Thailand
| Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
Open Access

Abstract

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.

Key words:

Eurotiomycetes, new taxa, Pseudoleptodontidium, soil fungi, Sordariomycetes, taxonomy

Introduction

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 (Lin et al. 2020; Wanthongchai et al. 2021). Soil serves as a natural habitat for a wide range of fauna and flora, including fungi. Fungi are a major component of soil ecosystems, playing crucial roles in the cycling of nutrients and the decomposition of organic materials (Frąc et al. 2018; Coleine et al. 2022). The most abundant soil fungi belong to the Ascomycota, which includes the classes Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Leotiomycetes and Sordariomycetes (Tedersoo et al. 2021; Gomes de Farias et al. 2023). Amongst these, Fusarium, Penicillium and Phoma are the most frequently isolated genera (Tedersoo et al. 2021; Yasanthika et al. 2023). However, contamination with pollutants may adversely affect their diversity, population and ecological functions (Frąc et al. 2018; Schloter et al. 2018; Coleine et al. 2022). The ability to synthesise a wide range of enzymes for breaking down various substrates enables soil fungi to adapt and thrive in diverse environments and harsh conditions (Singh et al. 2021; Coleine et al. 2022; Sun et al. 2024).

Extensive studies have focused on isolating and characterising soil fungi from contaminated areas, landfills and urban dump-sites (Sangale et al. 2019; Verma and Gupta 2019; Ren et al. 2021; Khan et al. 2022; Gong et al. 2023; Sathiyabama et al. 2024; Sun et al. 2024). These studies have revealed diverse soil fungal communities and identified numerous new fungal taxa and strains from these polluted habitats. Moreover, they have demonstrated a significant potential for biodegradation and bioremediation. For example, Yasanthika et al. (2021) studied soil ascomycetes in China and reported a new species, Juxtiphoma yunnanensis, as well as two new records, Lecanicillium dimorphum and Scopulariopsis brevicaulis, from urban-industrialised soils. Ren et al. (2021) isolated 29 fungal strains from soils contaminated with explosive materials in China. Amongst them, the isolate of Fusarium solani demonstrated the ability to decompose alkyne-terminated polybutadiene with urethane segments (PUPB) (Ren et al. 2021). Similarly, Sangale et al. (2019) obtained 109 fungal isolates from the dumping sites of mangrove rhizosphere soil and revealed that the strains of Aspergillus terreus and A. sydowii were the most effective in breaking down polythene. Additionally, the strain of Penicillium citrinum, isolated from municipal landfill soils in Bhopal, India, has demonstrated efficacy in degrading low-density polyethylene (LDPE) without prior pretreatment (Khan et al. 2022).

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 (Kooch et al. 2023; Sun et al. 2024). It is essential for exploring novel soil fungi from this habitat in order to determine fungal diversity and investigate their biodegradation strategies. Therefore, the present study aims to isolate and identify soil ascomycetes from disposal sites located in forests of northern Thailand. The topsoil samples from forest dump-sites in Chiang Mai Province were collected and isolated for fungi, leading to the discovery of five novel Ascomycota strains. Based on molecular analyses and morphological characteristics, two new species of Penicillium and a new genus in Xylariomycetidae were introduced and described.

Materials and methods

Fungal isolation

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. 1). The collection details were noted (Rathnayaka et al. 2024) and the soil samples were placed in plastic bags and taken to the Sustainable Development of Biological Resources Laboratory (SDBR), at the Department of Biology, Faculty of Science, Chiang Mai University, Thailand. Upon arrival, soil fungi were isolated immediately using the serial dilution plating method with three serial dilutions in sterile water (Yasanthika et al. 2022). After dilution, 100 µl of the soil suspension was dropped and spread on potato dextrose agar (PDA; CONDALAB, Spain) supplemented with 100 µg/ml of streptomycin. The isolation plates were incubated at 25 °C in the dark for 5 days. The appearing fungal colonies were transferred to fresh PDA using the hyphal tip method (Korhonen and Hintikka 1980). The pure cultures were deposited and permanently preserved in a metabolically inactive state at the Culture Collection of Microbial Shenzhen University (MBSZU), Shenzhen University, China.

Figure 1. 

Forest dump-sites used for soil fungal isolation in this study A Papae, Mae Tang District, Chiang Mai Province B Suthep, Muang Chiang Mai District, Chiang Mai Province C Mae Sa, Mae Rim District, Chiang Mai Province.

Morphological characterisation

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 (Visagie et al. 2014; Khuna et al. 2023). Micro-morphologically, the characteristics of conidiophores, stipes, conidiogenous cells, conidia or other structures were observed under a light microscope (Nikon DS-Ri2; Nikon, Japan), using fungal colonies grown on MEA at 25 °C in darkness for 7 days. Size data were evaluated by at least 50 measurements per structure.

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.

DNA extraction, amplification and sequencing

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 1). PCR amplifications were performed in 20 µl reaction mixtures, consisting of 1 µl of genomic DNA, 1 µl of each primer, 10 µl of 2× Phanta Max Master Mix (Dye Plus) (Vazyme, China) and 7 µl of deionised water. The PCR amplification was performed using a T100 Thermal Cycler (BIO-RAD, USA), with an initial denaturation step at 95 °C for 5 min, followed by 35 cycles of denaturation, annealing and elongation steps. The denaturation and elongation steps were performed at 95 °C for 30 s and 72 °C for 60 s, respectively. The annealing step was performed at different conditions depending on each target locus (Table 1). A final elongation step was performed at 72 °C for 10 minutes. The success or failure of the PCR product was determined through 1% agarose gel electrophoresis, followed by purification of the product using the E.Z.N.A® Gel Extraction Kit (Omega, USA). The quality and quantity of the purified PCR products were assessed using 1% agarose gel electrophoresis and a Nanodrop 2000 Spectrophotometer (Thermo Scientific, USA). Subsequently, the products were sequenced by BGI-Shenzhen Company (Shenzhen, Guangdong, China).

Table 1.

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 White et al. (1990)
LSU LR0R/LR5 52 30 Vilgalys and Hester (1990); Rehner and Samuels (1994)
CAM CF1/CF4 51 60 Peterson et al. (2005)
Cmd5/Cmd6 58 30 Hong et al. (2006)
RPB2 fRPB2-5F/ fRPB2-7cR 56 60 Liu et al. (1999)
TUB Bt2a/Bt2b 52 30 Glass and Donaldson (1995)
T1/Bt2b 55 45 Glass and Donaldson (1995); O’Donnell and Cigelnik (1997)

The bidirectional sequence data were assembled using the software Sequencher 5.4.6 (Nishimura 2000). The consensus sequence data were searched for sequence similarity via the Basic Local Alignment Search Tool (BLAST) in the National Center for Biotechnology Information (NCBI) website.

Phylogenetic analysis

The multi-loci phylogenetic dataset was obtained, based on previous studies of Penicillium section Exilicaulis (Ansari et al. 2023; Liu et al. 2023; Wang et al. 2023b; Visagie et al. 2024a, 2024b), Penicillium section Lanata-Divaricata (Lenz et al. 2022; Liu et al. 2023; Wang et al. 2023b; Araújo et al. 2024; Visagie et al. 2024b) and Xylariomycetidae (Samarakoon et al. 2022; Crous et al. 2023; Li et al. 2024; Samarakoon 2024) (Suppl. material 1: tables S1–S3). The sequence data for each locus were individually aligned using MUSCLE through the software MEGA 6 (Edgar 2004) and manually adjusted in BioEdit v.7.2.5 (Hall 2004). The concatenation of the ITS, TUB, CAM and RPB2 loci was performed for the phylogenetic analysis of Penicillium; in contrast, the combined ITS, LSU, RPB2 and TUB loci were used for the analysis of Xylariomycetidae. Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were applied to generate a phylogenetic tree. The ML analysis was conducted with 25 categories and 1,000 bootstrap (BS) replications under the GTRCAT model using RAxML-HPC2 on XSEDE (v.8.2.12) in the CIPRES web portal (Felsenstein 1985; Stamatakis 2006; Miller et al. 2009). The best-fit models of nucleotide substitution for individual locus were determined by using MrModelTest v.2.3 based on the Akaike Information Criterion (AIC) (Nylander 2004). The GTR+I+G substitution model was the best fit for all loci. The BI analysis was performed using MrBayes v.3.2.6 (Ronquist and Huelsenbeck 2003). Bayesian Posterior Probability (PP) was examined by Markov Chain Monte Carlo (MCMC) sampling. Six simultaneous Markov chains were run with random initial trees, wherein every 100th generation was sampled. The first 20% of generated trees, representing the burn-in phase of the analysis, were discarded, while the remaining trees were used to calculate PP in the majority-rule consensus tree. The tree topologies were visualised in FigTree v.1.4.0 with BS support and PP values equal to or higher than 75% and 0.95, respectively, in branches (Rambaut 2019). The final alignment and phylogram were submitted to TreeBASE (http://purl.org/phylo/treebase/phylows/study/TB2:S32075, accessed 19 March 2025).

Results

Phylogenetic analysis

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. 2). These fungal strains formed a sister clade with P. laeve DTO270G8 (BS 99% and PP 1.00) and belonged to the series Erubescentia.

Figure 2. 

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. 3). These strains also formed a sister clade with P. brefeldianum CBS 235.81 (BS 100% and PP 1.00) within the Series Janthinella clade.

Figure 3. 

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. 4).

Figure 4. 

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.

Taxonomy

Penicillium terrae Thitla, Monkai, Lumyong & Hongsanan, sp. nov.

MycoBank No: 857423

Etymology.

The specific epithet terrae refers to the soil substrate, from which this species was isolated.

Holotype.

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.

Colony diam.

(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.

Culture characteristics.

Colonies at 25 °C for 7 days on CREA thin colonies; acid production absent (Fig. 5A). Colonies on CYA circular, convex, wrinkled texture, entire margin; white mycelia; soluble pigment absent; reverse yellowish-brown (Fig. 5B). Colonies on CYAS barely growing, circular, raised, wrinkled texture, undulate margin; white mycelia; soluble pigment absent; reverse white (Fig. 5C). On CZ thin colonies, circular, flat, entire margin; white mycelia; soluble pigment absent; reverse white (Fig. 5D). On DG18 circular, flat, wrinkled at the centre, margin smooth and entire; grey mycelia at the centre, white mycelia at the margin; soluble pigment absent; reverse greenish-grey to light yellow (Fig. 5E). Colonies on MEA circular, flat, smooth texture, entire margin; light grey mycelia; soluble pigment absent; reverse light yellow to white (Fig. 5F). On MEAbl circular, flat, wrinkled at the centre, margin smooth and entire; light grey at the centre, white at the margin; soluble pigment absent; reverse yellowish-brown (Fig. 5G). On OA circular, flat, smooth textured, entire margin; light brown mycelia at the centre, white mycelia at the margin; soluble pigment absent; reverse white (Fig. 5H). Colonies on PDA circular, flat, wrinkled texture, entire margin; white mycelia; soluble pigment absent; reverse white to light yellow (Fig. 5I). Colonies on YES circular, convex, wrinkled texture, entire margin; white mycelia; soluble pigment absent; reverse light brown (Fig. 5J). Sporulation abundantly produces on all media.

Figure 5. 

Penicillium terrae (MBSZU 24-008, 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−P conidiophores, phialides and conidia Q conidia. Scale bar: 2 cm (A–J); 10 µm (K); 5 µm (L–Q).

Micromorphology.

Conidiophores mononematous, growing out at right angles from hyphae, unbranched, smooth, hyaline, 3–14 × 1–3 µm (Fig. 5K–P). Phialides solitary, terminal, ampulliform, smooth, hyaline, 5–12 × 1–4 µm (Fig. 5K–P). Conidia globose to subglobose, 2–4 µm diam., smooth, hyaline (Fig. 5K–N, Q). Sclerotia not observed. Sexual morph absent.

Additional strain examined.

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.

Habitat and distribution.

Soil; only known from Chiang Mai Province, Thailand.

Notes.

Penicillium section Exilicaulis was first established by Pitt (1980), with P. restrictum as the type species. This section was initially proposed to accommodate Penicillium species characterised by monoverticillate conidiophores and non-vesiculated stipes. Subsequently, phylogenetic studies expanded the section to include species with bi-verticillate conidiophores and those with conidiophores bearing solitary phialides (Houbraken and Samson 2011; Visagie et al. 2016a, b; da Silva et al. 2023). Species of the sect. Exilicaulis have been isolated from diverse environments, including soil, marine ecosystems, air, plants and insects (Ansari et al. 2023). Currently, this section comprises over 60 species across six series: Alutacea, Citreonigra, Corylophila, Erubescentia, Lapidosa and Restricta (Ansari et al. 2023; Visagie et al. 2024a).

Penicillium terrae is classified within section Exilicaulis, series Erubescentia. Phylogenetically, this species is closely related to P. laeve and P. ovatum (Fig. 2). However, P. laeve and P. ovatum were unable to grow on CREA and CYAS media, while P. terrae can grow on these media. Regarding growth rates, P. laeve exhibited slower growth than P. terrae, including CYA (8–9 mm), DG18 (5–7 mm), OA (7–8 mm) and YES (8–9 mm) at 25 °C, as well as CYA at 30 °C (4–5 mm) (Visagie et al. 2016a). Similarly, P. ovatum also demonstrated slower growth compared to P. terrae on CYA (10–11 mm), DG18 (9–11 mm), MEA (7–8 mm) and OA (10–11 mm) at 25 °C (Visagie et al. 2016a). Micromorphologically, the phialides of P. laeve (4–6 µm × 2–3 µm) and P. ovatum (4.5–7 µm × 2–3 µm) were shorter than P. terrae (Visagie et al. 2016a). In terms of conidia, P. terrae produced globose to subglobose conidia with 2–4 µm, while P. leave produced globose conidia measuring 2.5–3 µm diam. and P. ovatum produced ellipsoidal conidia with 2–3 × 1.5–2 µm (Visagie et al. 2016a). Furthermore, a pairwise nucleotide comparison between P. terrae and P. laeve showed differences of 0.86% (5/581 bp, including gaps) in ITS, 2.87% (13/453 bp, including gaps) in TUB, 2.62% (13/497 bp, including gaps) in CAM and 1.39% (13/938 bp, including gaps) in RPB2. Similarly, the comparison between P. terrae and P. ovatum revealed nucleotide differences of 2.64% (15/569 bp, including gaps) in ITS, 14.41% (65/451 bp, including gaps) in TUB, 17.74% (91/513 bp, including gaps) in CAM and 12.37% (116/938 bp, including gaps) in RPB2.

Penicillium chiangmaiense Thitla, Monkai, Lumyong & Hongsanan, sp. nov.

MycoBank No: 857424

Etymology.

The specific epithet “chiangmaiense” refers to the type locality “Chiang Mai Province, Thailand”.

Holotype.

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.

Colony diam.

(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.

Culture characteristics.

Colonies at 25 °C for 7 days on CREA thin colonies; acid production absent (Fig. 6A). Colonies on CYA and CYAS wrinkled texture, velvety, circular, flat, entire margin; white mycelia; soluble pigment absent; reverse light brown (Fig. 6B, C). On CZ, thin colonies, circular, flat, filamentous margin; white mycelia; soluble pigment absent; reverse white (Fig. 6D). On DG18, wrinkled texture, velvety, circular, flat, entire margin; white mycelia; soluble pigment absent; reverse white to pale yellow (Fig. 6E). Colonies on MEA and MEAbl smooth texture, circular, flat, entire margin; pale yellow at the centre, white at the margin; soluble pigment absent; reverse pale brown to white (Fig. 6F, G). On OA, smooth textured, velvety, circular, flat, entire margin; white mycelia; soluble pigment absent; reverse light yellow to white (Fig. 6H). Colonies on PDA circular, flat, smooth texture, entire margin; white mycelia; soluble pigment absent; reverse white to light yellow (Fig. 6I). Colonies on YES circular, flat, wrinkled texture, velvety, entire margin; white mycelia; soluble pigment absent; reverse brownish-yellow (Fig. 6J). Sporulation abundantly produces on DG18, MEA and MEAbl media. Sclerotia produces MEA, MEAbl and OA (Fig. 6P).

Figure 6. 

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).

Micromorphology.

Conidiophores monoverticillate, sometimes divaricate. Stipes hyaline, smooth–walled, 80–270 × 2–3 µm (Fig. 6K–N). Phialides terminal, ampulliform, hyaline, smooth–walled 6–17 × 2–3.5 µm (Fig. 6K–N). Conidia globose to subglobose, 2–4 µm diam., smooth, hyaline (Fig. 6K–O). Sclerotia pale brown to brown, globose to irregular, 180–260 µm diam. (Fig. 6P). Sexual morph absent.

Additional strain examined.

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.

Habitat and distribution.

Soil; only known from Chiang Mai Province, Thailand.

Notes.

Penicillium section Lanata-Divaricata was established by Thom (1930) to include species with biverticillate conidiophores, which usually contain a main conidiophore axis and metulae that diverge (referred to as divaricate conidiophores), as well as broadly spreading colonies (Houbraken and Samson 2011; Pangging et al. 2021). Species within this section have been isolated from various sources, including soil, air, fluvial sediments and plants (Nóbrega et al. 2024). Currently, the section is divided into five series: Dalearum, Janthinella, Oxalica, Rolfsiorum and Simplicissima (Ansari et al. 2023; Visagie et al. 2024a).

Penicillium chiangmaiense is classified within section Lanata-Divaricata, series Janthinella. In the phylogenetic tree (Fig. 3), the new species is closely related to P. brefeldianum, P. limosum and P. michoacanense. However, P. brefeldianum produces sexual structures on cornmeal agar and P. limosum produces on CZ, MEA and OA, while P. chiangmaiense does not exhibit any sexual features (Dodge 1933; Ueda 1995). Furthermore, the growth rate of P. limosum on MEA (42 mm in 14 days) was slower than that of P. chiangmaiense (47–51 mm in 7 days) (Ueda 1995). In the case of P. michoacanense, the stipes (15–60 × 1–1.5 µm) and phialides (4–5 × 1.5 µm) were shorter than those of P. chiangmaiense (stipes 80–270 × 2–3 µm; phialides 6–17 × 2–3.5 µm) (Rodríguez-Andrade et al. 2021). Moreover, P. michoacanense produced weak acid on CREA, while P. chiangmaiense does not produce it (Rodríguez-Andrade et al. 2021). Additionally, the pairwise nucleotide comparison of P. chiangmaiense with related species revealed significant differences. The comparison of P. chiangmaiense to P. brefeldianum showed 0.90% (5/556 bp) difference in ITS, 4.73% (21/444 bp) in TUB, 4.28% (24/561 bp) in CAM and 1.46% (11/755 bp) in RPB2, including gaps. Differences in P. chiangmaiense and P. limosum were 1.09% (6/548 bp) in ITS, 5.00% (22/440 bp) in TUB, 6.28% (35/557 bp) in CAM and 0.93% (7/755 bp) in RPB2, including gaps. In comparison between P. chiangmaiense and P. michoacanense, the differences were 0.73% (4/548 bp) in ITS, 2.84% (11/388 bp) in TUB, 8.35% (34/407 bp) in CAM and 1.61% (12/745 bp) in RPB2, including gaps.

Pseudoleptodontidium Thitla, Monkai, Lumyong & Hongsanan, gen. nov.

MycoBank No: 857466

Etymology.

The name refers to its morphological similarity to Leptodontidium.

Classification.

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.

Type species.

Pseudoleptodontidium chiangmaiense Thitla, Monkai, Lumyong & Hongsanan, sp. nov.

Notes.

Hernández-Restrepo et al. (2017) established Leptodontidium in Leptodontidiaceae (Helotiales, Leotiomycetes), characterised by erect conidiophores and conidiogenous cells with a long rachis bearing denticles, as well as the presence of a Beauveria-like synasexual morph. Neoleptodontidium was introduced by Crous et al. (2023) due to its morphological resemblance to Leptodontidium, but it differs in having minute, terminal and lateral exophiala-like phialides. Based on LSU phylogeny, the type species of Neoleptodontidium (N. aquaticum) clustered with Leptodontidium aciculare (Crous et al. 2023). Hence, Crous et al. (2023) transferred L. aciculare to Neoleptodontidium as N. aciculare by the morphological and phylogenetic congruence.

Pseudoleptodontidium is morphologically similar to Neoleptodontidium, sharing septate, subcylindrical conidiophores, terminal and lateral phialidic conidiogenous cells and aseptate subcylindrical conidia (Crous et al. 2023). However, Pseudoleptodontidium can be distinguished from Neoleptodontidium by its obclavate, sympodially proliferating, denticulate conidiogenous cells and subglobose to ellipsoidal conidia. The phylogeny, based on a combined ITS, LSU, RPB2 and TUB dataset, revealed that Pseudoleptodontidium forms an independent lineage, sister to Neoleptodontidium with significant support (BS 96% ML and PP 1.00; Fig. 4). Although Crous et al. (2023) placed Neoleptodontidium in Xylariales genera incertae sedis, our phylogeny indicates that Pseudoleptodontidium and Neoleptodontidium are closely related to the Amphisphaeriaceae, Cylidriaceae, Phlogicylindriaceae and Amphisphaeriales genera incertae sedis (Neoarthrinium, Pidoplitchkoviella) (Fig. 4). Therefore, due to their distinct morphology and phylogeny, Pseudoleptodontidium is introduced as a genus incertae sedis in Amphisphaeriales, with Ps. chiangmaiense designated as the type species.

Pseudoleptodontidium chiangmaiense Thitla, Monkai, Lumyong & Hongsanan, sp. nov.

MycoBank No: 857467

Etymology.

The specific epithet chiangmaiense refers to the type locality, Chiang Mai Province, Thailand.

Holotype.

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.

Colony diam.

(in mm) 14 days, 25 °C: PDA 36–40 and MEA 31–38.

Culture characteristics.

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. 7A). Colonies on MEA velvety, circular, flat, entire margin; dark green to black at the centre, yellowish-green to white at the margin; soluble pigment absent; reverse dark green at the centre, pale yellow to white at the margin (Fig. 7B).

Figure 7. 

Pseudoleptodontidium chiangmaiense (MBSZU 25-005, ex-type living culture) A, B colonies from surface and reverse view at 25 °C for 14 days on PDA and MEA, respectively C−J conidiophores, conidiogenous cells and conidia K conidia L chlamydospore. Scale bar: 2 cm (A, B); 10 µm (C–L).

Micromorphology.

Mycelium composed of hyaline to black, thin- to thick-walled, smooth, branched, septate, 2–4.5 µm diam. hyphae (Fig. 7C–L). Conidiophores arising from hyphae, solitary, erect, cylindrical, pale brown to dark brown, thick-walled, occasionally roughened on lower part, septate, 7–70 × 2.5–5 µm (Fig. 7C–G). Conidiogenous cells terminal and intercalary on conidiophores, occasionally lateral on hyphae, obclavate, sympodially proliferate, denticulate, hyaline to pale brown, smooth, 0-1 septate, 7.5–26 × 3–5 µm (Fig. 7C–J). Conidia hyaline, smooth, aseptate, subglobose to ellipsoidal, slightly curved, 3–7.5 × 1.5–4 µm (Fig. 7K). Chlamydospores solitary, terminal on hyphae, medium brown to dark brown, smooth, thick-walled, aseptate, subglobose, 6–8 × 4.5–6 µm (Fig. 7L). Sexual morph absent.

Habitat and distribution.

Soil; only known from Chiang Mai Province, Thailand.

Notes.

Pseudoleptodontidium chiangmaiense has a close relationship with Neoleptodontidium aciculare and N. aquaticum (Fig. 4). However, their morphological characteristics are distinct: Ps. chiangmaiense has broader conidiogenous cells (7.5–26 × 3–5 µm) than N. aciculare (15–30 × 2–3 µm) and N. aquaticum (10–30 × 2–2.5 µm) and larger conidia (3–7.5 × 1.5–4 µm) than N. aciculare (3–4 × 1–2 µm) and N. aquaticum (3–4 × 1.5 µm) (Rao and De Hoog 1986; Hernández-Restrepo et al. 2017). The pairwise nucleotide comparison between Ps. chiangmaiense and N. aciculare revealed differences of 16.38% (95/580 bp, including gaps) in the ITS region and 4.92% (40/813 bp, including gaps) in the LSU region. Additionally, the comparison between Ps. chiangmaiense and N. aquaticum revealed differences of 16.23% (87/536 bp, including gaps) in the ITS region and 4.80% (39/813 bp, including gaps) in the LSU region.

Discussion

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 26).

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 (Oshikata et al. 2013; Perrone and Susca 2017; Costa et al. 2019; Toghueo and Boyom 2020; Wolski 2023; Suwannarach et al. 2024). The genus was proposed by Link (1809) and currently comprises two subgenera, 34 sections, 102 series and 535 accepted species (Visagie et al. 2024a). Penicillium was traditionally identified, based on macro-morphology (such as colony characteristics and pigment production) and micro-morphology (including conidiophores, branches, metula, phialides and conidia) (Khuna et al. 2023). However, relying solely on morphological characteristics has proven insufficient for accurate identification. Consequently, an integrated approach combining morphology, molecular data and extrolite analysis is currently used to identify species within the genus Penicillium (Visagie et al. 2014; Labuda et al. 2021; Nguyen and Pham 2022; Visagie et al. 2024a, 2024b). In section Exilicaulis, key genetic data for species identification include the internal transcribed spacer region (ITS), beta-tubulin (TUB), calmodulin (CAM) and RNA polymerase II subunit (RPB2) genes (Visagie et al. 2016c). Initially, P. laeve and P. ovatum were introduced under the genus Torulomyces as T. laevis and T. ovatus, respectively (Ando et al. 1998). Subsequently, phylogenetic analyses using RNA polymerase II largest subunit (RPB1), RPB2, the protein required for processing of 20S pre-rRNA in the cytoplasm (Tsr1) and the subunit of the cytosolic chaperonin Cct ring complex (Cct8) led to transfer to Penicillium section Torulomyces (Houbraken and Samson 2011). Visagie et al. (2016a) reclassified these species into section Exilicaulis using ITS, TUB, CAM and RPB2 sequence data. Currently, P. laeve and P. ovatum belong to the series Erubescentia, characterised by species with monoverticillate conidiophores, short stipes and the ability to grow at 37 °C (Houbraken et al. 2020). However, both P. laeve and P. ovatum, along with P. terrae, produce conidiophores with solitary phialides and were unable to grow at 37 °C. Additionally, the phylogenetic clade of these species formed a basal clade with other species in this series with strong support (BS 97% and PP 1.00) (Fig. 2). In our opinion, this distinct clade may represent a potential new series within section Exilicaulis and should be further studied in the future.

Prior to this study, P. laeve was the only species in section Exilicaulis reported from Thailand (Ando et al. 1998). The discovery of P. terrae from soil in Thailand marks the second species from this section identified in the country. Furthermore, this new species represents the 69th global species in section Exilicaulis, as shown in Suppl. material 1: table S1, excluding P. janthinellum and P. limosum. In addition, this study proposed a new species, P. chiangmaiense in section Lanata-Divaricata, which is the second species recorded in Thailand from this section, following the first species (P. singorense) described by Visagie et al. (2014b). Additionally, this new species represents the 108th global species in section Lanata-Divaricata, as outlined in Suppl. material 1: table S2, excluding P. alogum and P. stolkiae.

Ecologically, Penicillium species have been isolated from different environments (Ansari et al. 2023; Nóbrega et al. 2024). For instance, P. chiangmaiense and its closely-related species, including P. brefeldianum, P. limosum and P. michoacanense, have been found in the human digestive tract, marine sediments and soil (Dodge 1933; Ueda 1995; Rodríguez-Andrade et al. 2021). Similarly, P. terrae and its relatives, including P. laeve and P. ovatum, have primarily been reported from soil, with P. laeve specifically found in forest soils in Thailand (Ando et al. 1998). These findings highlight the ecological plasticity of Penicillium species, which can potentially thrive in disturbed ecosystems. Future studies examining their functional traits and metabolic profiles could further enhance better understanding of their ecological significance.

Xylariomycetidae is a large subclass within Sordariomycetes comprising numerous taxa that are polyphyletic and paraphyletic (Wendt et al. 2017; Daranagama et al. 2018; Konta et al. 2020; Samarakoon et al. 2022). The taxonomic classification of Xylariomycetidae has undergone considerable change (Maharachchikumbura et al. 2016; Samarakoon et al. 2016, 2022). Earlier, Amphisphaeriales was considered a synonym of Xylariales (Maharachchikumbura et al. 2016). However, based on morphology, molecular data, divergence estimates and ancestral state reconstruction, Samarakoon et al. (2016, 2022) subsequently reclassified Amphisphaeriales, Delonicicolales and Xylariales in Xylariomycetidae. Molecular phylogeny, based on concatenated ITS, LSU, RPB2, TUB and TEF-1α sequence data, demonstrated the placement of Amphisphaeriales in a sister clade to Xylariales (Samarakoon et al. 2022), which is consistent with our study (Fig. 4). However, we did not incorporate TEF-1a into the phylogenetic tree, as the number of taxa with available sequence data was low. The classification of taxa within Xylariomycetidae remains ambiguous, as more than 50 incertae sedis genera await taxonomic resolution (Samarakoon et al. 2022). Likewise, our study was unable to assign the novel genus Pseudoleptodontidium to any family within the Xylariomycetidae (Fig. 4). The new lineage of Pseudoleptodontidium and Neoleptodontidium also lacks significant statistical support for placement within other taxa and families in Amphisphaeriales, though it is likely linked to Amphisphaeriaceae, Cylidriaceae and Phlogicylindriaceae (Fig. 4). Further taxonomic and phylogenetic studies, including the collection of new specimens and the examination of additional isolates, are necessary to confirm the familial placement of Pseudoleptodontidium and Neoleptodontidium.

Members of Xylariomycetidae have a worldwide distribution and occupy various ecological niches, including saprobes, endophytes and pathogens (U’Ren et al. 2016; Daranagama et al. 2018; Sugita et al. 2022; Samarakoon 2024). Recently, several new taxa have been reported as saprobes on dead plant materials from Thailand (Monkai et al. 2022; Afshari et al. 2023; Samarakoon et al. 2023; Karimi et al. 2023, 2024; Samarakoon 2024; Thakshila et al. 2024). In this study, Pseudoleptodontidium was isolated from soil associated with a forest dump-site in Thailand, whereas Neoleptodontidium species have been found in hydroponic water and decomposing wood in the USA and India (Rao and De Hoog 1986; Hernández-Restrepo et al. 2017). This demonstrates that these taxa have a broad distribution range, highlighting their adaptability in diverse environments.

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 (Toghueo and Boyom 2020; Becker and Stadler 2021; Wang et al. 2023a; Wolski 2023). The discovery of novel fungi in forest dump areas presents an opportunity to explore and characterise these fungi for various applications. Therefore, further research is necessary to evaluate the capabilities of new fungal strains for extracellular enzyme production and the degradation of synthetic materials.

Acknowledgements

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).

Additional information

Conflict of interest

The authors have declared that no competing interests exist.

Ethical statement

No ethical statement was reported.

Funding

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).

Author contributions

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.

Author ORCIDs

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

Data availability

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 1: tables S1–S3). Additionally, the datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

References

  • Afshari N, Karimi O, De Farias ARG, Suwannarach N, Bhunjun CS, Zeng X-Y, Lumyong S (2023) Additions to Diatrypaceae (Xylariales): Novel taxa and new host associations. Journal of Fungi (Basel, Switzerland) 9: 1151. https://doi.org/10.3390/jof9121151
  • Ando K, Nawawi A, Manoch L, Pitt JI (1998) Three new species and a new combination in the genus Torulomyces from soil. Mycoscience 39(3): 313–318. https://doi.org/10.1007/BF02464014
  • Ansari L, Asgari B, Zare R, Zamanizadeh HR (2023) Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran. International Journal of Systematic and Evolutionary Microbiology 73(9). https://doi.org/10.1099/ijsem.0.006028
  • Araújo KS, Alves JL, Pereira OL, de Queiroz MV (2024) Five new species of endophytic Penicillium from rubber trees in the Brazilian Amazon. Brazilian Journal of Microbiology 55: 3051–3074. https://doi.org/10.1007/s42770-024-01478-9
  • Crous PW, Akulov A, Balashov S, Boers J, Braun U, Castillo J, Delgado MA, Denman S, Erhard A, Gusella G, Jurjević Ž, Kruse J, Malloch DW, Osieck ER, Polizzi G, Schumacher RK, Slootweg E, Starink-Willemse M, Van Iperen AL, Verkley GJM, Groenewald JZ (2023) New and Interesting Fungi. 6. Fungal Systematics and Evolution 11: 109–156. https://doi.org/10.3114/fuse.2023.11.09
  • da Silva IJS, Sousa TF, de Queiroz CA, Castro GDS, Caniato FF, de Medeiros LS, Angolini CFF, Hanada RE, Koolen HHF, da Silva GF (2023) Penicillium amapaense sp. nov., section Exilicaulis, and new records of Penicillium labradorum in Brazil isolated from Amazon River sediments with potential applications in agriculture and biotechnology. Mycological Progress 22(4): 23. https://doi.org/10.1007/s11557-023-01868-7
  • Daranagama DA, Hyde KD, Sir EB, Thambugala KM, Tian Q, Samarakoon MC, McKenzie EHC, Jayasiri SC, Tibpromma S, Bhat JD, Liu X, Stadler M (2018) Towards a natural classification and backbone tree for Graphostromataceae, Hypoxylaceae, Lopadostomataceae and Xylariaceae. Fungal Diversity 88: 1–165. https://doi.org/10.1007/s13225-017-0388-y
  • Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution; International Journal of Organic Evolution 39: 783–791. https://doi.org/10.2307/2408678
  • Glass NL, Donaldson GC (1995) Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Applied and Environmental Microbiology 61: 1323–1330. https://doi.org/10.1128/aem.61.4.1323-1330.1995
  • Gomes de Farias AR, Yasanthika WAE, Monkai J (2023) Insights into the profile of soil fungal diversity in Thailand. Asian Journal of Mycology, 305–317. https://doi.org/10.5943/ajom/6/2/11
  • Gong Z, Jin L, Yu X, Wang B, Hu S, Ruan H, Sung Y-J, Lee H-G, Jin F (2023) Biodegradation of low density polyethylene by the fungus Cladosporium sp. recovered from a landfill Site. Journal of Fungi (Basel, Switzerland) 9: 605. https://doi.org/10.3390/jof9060605
  • Hernández-Restrepo M, Gené J, Castañeda-Ruiz RF, Mena-Portales J, Crous PW, Guarro J (2017) Phylogeny of saprobic microfungi from Southern Europe. Studies in Mycology 86: 53–97. https://doi.org/10.1016/j.simyco.2017.05.002
  • Hong SB, Cho HS, Shin HD, Frisvad JC, Samson RA (2006) Novel Neosartorya species isolated from soil in Korea. International Journal of Systematic and Evolutionary Microbiology 56: 477–486. https://doi.org/10.1099/ijs.0.63980-0
  • Houbraken J, Kocsubé S, Visagie CM, Yilmaz N, Wang XC, Meijer M, Kraak B, Hubka V, Bensch K, Samson RA, Frisvad JC (2020) Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): An overview of families, genera, subgenera, sections, series and species. Studies in Mycology 95: 5–169. https://doi.org/10.1016/j.simyco.2020.05.002
  • Karimi O, Afshari N, Asghari R, Li Q, Chethana KWT, Hyde KD, Alotibi FO (2024) Novel discoveries of Xylariomycetidae (Ascomycota) taxa from peat swamp forests and other terrestrial habitats in Thailand. MycoKeys 107: 219–247. https://doi.org/10.3897/mycokeys.107.127749
  • Khan S, Ali SA, Ali AS (2022) Biodegradation of low density polyethylene (LDPE) by mesophilic fungus ‘Penicillium citrinum’ isolated from soils of plastic waste dump yard, Bhopal, India. Environmental Technology 44: 2300–2314. https://doi.org/10.1080/09593330.2022.2027025
  • Khuna S, Kumla J, Thitla T, Hongsanan S, Lumyong S, Suwannarach N (2023) Penicillium thailandense (Aspergillaceae, Eurotiales), a new species isolated from soil in northern Thailand. Phytotaxa 612(1): 033–045. https://doi.org/10.11646/phytotaxa.612.1.2
  • Konta S, Hyde KD, Phookamsak R, Xu JC, Maharachchikumbura SSN, Daranagama DA, McKenzie EH, Boonmee S, Tibpromma S, Eungwanichayapant PD, Samarakoon MC (2020) Polyphyletic genera in Xylariaceae (Xylariales): Neoxylaria gen. nov. and Stilbohypoxylon. Mycosphere 11: 2629–2651. https://doi.org/10.5943/mycosphere/11/1/17
  • Kooch Y, Nouraei A, Haghverdi K, Kolb S, Francaviglia R (2023) Landfill leachate has multiple negative impacts on soil health indicators in Hyrcanian forest, northern Iran. The Science of the Total Environment 896: 166341. https://doi.org/10.1016/j.scitotenv.2023.166341
  • Labuda R, Bacher M, Rosenau T, Gasparotto E, Gratzl H, Doppler M, Sulyok M, Kubátová A, Berger H, Cank K, Raja HA, Oberlies NH, Schüller C, Strauss J (2021) Polyphasic approach utilized for the identification of two new toxigenic members of Penicillium section Exilicaulis, P. krskae and P. silybi spp. nov. Journal of Fungi (Basel, Switzerland) 7(7): 557. https://doi.org/10.3390/jof7070557
  • Lenz AR, Balbinot E, de Abreu FP, de Oliveira NS, Fontana RC, de Avila E, Silva S, Park MS, Lim YW, Houbraken J, Camassola M, Dillon AJP (2022) Taxonomy, comparative genomics and evolutionary insights of Penicillium ucsense: A novel species in series Oxalica. Antonie van Leeuwenhoek 115: 1009–1029. https://doi.org/10.1007/s10482-022-01746-4
  • Li WL, Liang RR, Yang J, Liu JK (2024) Morpho-molecular characterization reveals a new genus, three novel species and two new host records in Xylariomycetidae. Journal of Fungi (Basel, Switzerland) 10: 189. https://doi.org/10.3390/jof10030189
  • Lin D, Yang G, Dou P, Qian S, Zhao L, Yang Y, Fanin N (2020) Microplastics negatively affect soil fauna but stimulate microbial activity: Insights from a field-based microplastic addition experiment. Proceedings. Biological Sciences 287: 20201268. https://doi.org/10.1098/rspb.2020.1268
  • Link JHF (1809) Observationes in ordines plantarum naturales. Dissertatio I. Magazin Der Gesellschaft Naturforschenden Freunde Berlin 3: 3–42. [in Latin]
  • Liu C, Wang XC, Yu ZH, Zhuang WY, Zeng ZQ (2023) Seven new species of Eurotiales (Ascomycota) isolated from tidal flat sediments in China. Journal of Fungi (Basel, Switzerland) 9: 960. https://doi.org/10.3390/jof9100960
  • Maharachchikumbura SSN, Hyde KD, Jones EBG, McKenzie EHC, Bhat JD, Dayarathne MC, Huang S-K, Norphanphoun C, Senanayake IC, Perera RH, Shang Q-J, Xiao Y, D’souza MJ, Hongsanan S, Jayawardena RS, Daranagama DA, Konta S, Goonasekara ID, Zhuang W-Y, Jeewon R, Phillips AJL, Abdel-Wahab MA, Al-Sadi AM, Bahkali AH, Boonmee S, Boonyuen N, Cheewangkoon R, Dissanayake AJ, Kang J, Li Q-R, Liu JK, Liu XZ, Liu Z-Y, Luangsa-Ard JJ, Pang K-L, Phookamsak R, Promputtha I, Suetrong S, Stadler M, Wen T, Wijayawardene NN (2016) Families of Sordariomycetes. Fungal Diversity 79: 1–317. https://doi.org/10.1007/s13225-016-0369-6
  • Monkai J, Phookamsak R, Tennakoon DS, Bhat DJ, Xu S, Li Q, Xu J, Mortimer PE, Kumla J, Lumyong S (2022) Insight into the taxonomic resolution of Apiospora: Introducing novel species and records from bamboo in China and Thailand. Diversity 14: 918. https://doi.org/10.3390/d14110918
  • Nguyen VD, Pham TT (2022) Penicillium vietnamense sp. nov., the first novel marine fungi species described from vietnam with a unique conidiophore structure and molecular phylogeny of Penicillium section Charlesia. Mycobiology 50(3): 155–165. https://doi.org/10.1080/12298093.2022.2068750
  • Nóbrega JP, do Nascimento Barbosa R, Lima JMdS, Bento DdM, de Souza-Motta CM, Melo RFR (2024) Six new Penicillium species in the section Lanata-Divaricata from a cave in Amazon rainforest, Brazil. Mycological Progress 23: 71. https://doi.org/10.1007/s11557-024-02007-6
  • Nylander JAA (2004) MrModeltest 2.0. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala.
  • O’Donnell K, Cigelnik E (1997) Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Molecular Phylogenetics and Evolution 7: 103–116. https://doi.org/10.1006/mpev.1996.0376
  • Oshikata C, Tsurikisawa N, Saito A, Watanabe M, Kamata Y, Tanaka M, Tsuburai T, Mitomi H, Takatori K, Yasueda H, Akiyama K (2013) Fatal pneumonia caused by Penicillium digitatum: A case report. BMC Pulmonary Medicine 13: 16. https://doi.org/10.1186/1471-2466-13-16
  • Peterson SW, Vega FE, Posada F, Nagai C (2005) Penicillium coffeae, a new endophytic species isolated from a coffee plant and its phylogenetic relationship to P. fellutanum, P. thiersii and P. brocae based on parsimony analysis of multilocus DNA sequences. Mycologia 97(3): 659–666. https://doi.org/10.1080/15572536.2006.11832796
  • Pitt JI (1980) [1979] The Genus Penicillium and its Teleomorphic States Eupenicillium and Talaromyces. Acdemic Press, London.
  • Rambaut A (2019) FigTree tree figure drawing tool version 131; Institute of Evolutionary 623 Biology (Edinburgh, Scotland: University of Edinburgh). http://treebioedacuk/software/figtree/ [Accessed November 2024]
  • Rao V, De Hoog GS (1986) New of critical hyphomycetes from India. Studies in Mycology 28: 1–84.
  • Rathnayaka AR, Tennakoon DS, Jones GE, Wanasinghe DN, Bhat DJ, Priyashantha AH, Stephenson SL, Tibpromma S, Karunarathna SC (2024) Significance of precise documentation of hosts and geospatial data of fungal collections, with an emphasis on plant-associated fungi. New Zealand Journal of Botany 63: 462–489. https://doi.org/10.1080/0028825X.2024.2381734
  • Ren GC, Pang AM, Gao Y, Wu SX, Ge ZQ, Zhang TF, Wanasinghe DN, Khan S, Mortimer PE, Xu JC, Gui H (2021) Polyurethane-degrading fungi from soils contaminated with rocket propellant and their ability to decompose alkyne terminated polybutadiene with urethane. Studies in Fungi 6: 224–239. https://doi.org/10.5943/sif/6/1/15
  • Rodríguez-Andrade E, Stchigel AM, Cano-Lira JF (2021) New xerophilic species of Penicillium from soil. Journal of Fungi (Basel, Switzerland) 7: 126. https://doi.org/10.3390/jof7020126
  • Samarakoon MC (2024) Additions to the Xylariomycetidae (Sordariomycetes) Fungal Flora from Northern Thailand: Amphisphaeria chiangmaiensis sp. nov. and A. hydei sp. nov. New Zealand Journal of Botany 62: 253–269. https://doi.org/10.1080/0028825X.2023.2284420
  • Samarakoon MC, Hyde KD, Promputtha I, Hongsanan S, Ariyawansa HA, Maharachchikumbura SSN, Daranagama DA, Stadler M, Mapook A (2016) Evolution of Xylariomycetidae (Ascomycota: Sordariomycetes). Mycosphere 7: 1746–1761. https://doi.org/10.5943/mycosphere/7/11/9
  • Samarakoon MC, Hyde KD, Maharachchikumbura SSN, Stadler M, Jones EBG, Promputtha I, Suwannarach N, Camporesi E, Bulgakov TS, Liu J-K (2022) Taxonomy, phylogeny, molecular dating and ancestral state reconstruction of Xylariomycetidae (Sordariomycetes). Fungal Diversity 112: 1–88. https://doi.org/10.1007/s13225-021-00495-5
  • Samarakoon MC, Lumyong S, Manawasinghe IS, Suwannarach N, Cheewangkoon R (2023) Addition of five novel fungal flora to the Xylariomycetidae (Sordariomycetes, Ascomycota) in northern Thailand. Journal of Fungi (Basel, Switzerland) 9: 1065. https://doi.org/10.3390/jof9111065
  • Sangale MK, Shahnawaz M, Ade AB (2019) Potential of fungi isolated from the dumping sites mangrove rhizosphere soil to degrade polythene. Scientific Reports 9: 5390. https://doi.org/10.1038/s41598-019-41448-y
  • Sathiyabama M, Boomija RV, Sathiyamoorthy T, Mathivanan N, Balaji R (2024) Mycodegradation of low-density polyethylene by Cladosporium sphaerospermum, isolated from platisphere. Scientific Reports 14: 8351. https://doi.org/10.1038/s41598-024-59032-4
  • Singh M, Singh D, Rai PK, Suyal DC, Saurabh S, Soni R, Giri K, Yadav AN (2021) Fungi in remediation of hazardous wastes: current status and future outlook. Fungal Biology, 195–224. https://doi.org/10.1007/978-3-030-68260-6_8
  • Sugita R, Hirayama K, Shirouzu T, Tanaka K (2022) Spirodecosporaceae fam. nov. (Xylariales, Sordariomycetes) and two new species of Spirodecospora. Fungal Systematics and Evolution 10: 217–229. https://doi.org/10.3114/fuse.2022.10.09
  • Sun Y, Xie S, Zang J, Wu M, Tao J, Li S, Du X, Wang J (2024) Terrestrial plastisphere as unique niches for fungal communities. Communications Earth & Environment 5: 483. https://doi.org/10.1038/s43247-024-01645-8
  • Suwannarach N, Khuna S, Chaiwong K, Senwanna C, Nuangmek W, Kumla J (2024) Identification and fungicide sensitivity of the blue mold pathogen in postharvest-stored elephant garlic Bulbs in Thailand. Studies in Fungi 0: 1–9. https://doi.org/10.48130/sif-0024-0015
  • Tedersoo L, Mikryukov V, Anslan S, Bahram M, Khalid AN, Corrales A, Agan A, Vasco-Palacios A-M, Saitta A, Antonelli A, Rinaldi AC, Verbeken A, Sulistyo BP, Tamgnoue B, Furneaux B, Ritter CD, Nyamukondiwa C, Sharp C, Marín C, Dai DQ, Gohar D, Sharmah D, Biersma EM, Cameron EK, De Crop E, Otsing E, Davydov EA, Albornoz FE, Brearley FQ, Buegger F, Gates G, Zahn G, Bonito G, Hiiesalu I, Hiiesalu I, Zettur I, Barrio IC, Pärn J, Heilmann-Clausen J, Ankuda J, Kupagme JY, Sarapuu J, Maciá-Vicente JG, Fovo JD, Geml J, Alatalo JM, Alvarez-Manjarrez J, Monkai J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan KI, Armolaitis K, Hyde KD, Newsham KK, Panksep K, Adebola LA, Lamit LJ, Saba M, Da Silva Cáceres ME, Tuomi M, Gryzenhout M, Bauters M, Bálint M, Wijayawardene N, Hagh-Doust N, Yorou NS, Kurina O, Mortimer PE, Meidl P, Nilsson RH, Puusepp R, Casique-Valdés R, Drenkhan R, Garibay-Orijel R, Godoy R, Alfarraj S, Rahimlou S, Põlme S, Dudov SV, Mundra S, Ahmed T, Netherway T, Henkel TW, Roslin T, Fedosov VE, Onipchenko VG, Yasanthika W, Lim YW, Piepenbring M, Klavina D, Kõljalg U, Abarenkov K (2021) The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. Fungal Diversity 111: 573–588. https://doi.org/10.1007/s13225-021-00493-7
  • Thakshila SAD, Bhunjun CS, Samarakoon MC, Rathnayaka AR, Gajanayake AJ (2024) Morpho-molecular analyses reveal a novel species, Xenoanthostomella thailandica (Gyrothricaceae, Xylariales), from northern Thailand. New Zealand Journal of Botany 62: 336–366. https://doi.org/10.1080/0028825X.2024.2304776
  • Thom C (1930) The Penicillia. The Williams & Wilkins Company, Baltimore.
  • U’Ren JM, Miadlikowska J, Zimmerman NB, Lutzoni F, Stajich JE, Arnold AE (2016) Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Molecular Phylogenetics and Evolution 98: 210–232. https://doi.org/10.1016/j.ympev.2016.02.010
  • Vilgalys R, Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 4238–4246. https://doi.org/10.1128/jb.172.8.4238-4246.1990
  • Visagie CM, Houbraken J, Frisvad JC, Hong SB, Klaassen CHW, Perrone G, Seifert KA, Varga J, Yaguchi T, Samson RA (2014) Identification and nomenclature of the genus Penicillium. Studies in Mycology 78: 343–371. https://doi.org/10.1016/j.simyco.2014.09.001
  • Visagie CM, Hirooka Y, Tanney JB, Whitfield E, Mwange K, Meijer M, Amend AS, Seifert KA, Samson RA (2014b) Aspergillus, Penicillium and Talaromyces isolated from house dust samples collected around the world. Studies in Mycology 78: 63–139. https://doi.org/10.1016/j.simyco.2014.07.002
  • Visagie CM, Houbraken J, Dijksterhuis J, Seifert KA, Jacobs K, Samson RA (2016a) A taxonomic review of Penicillium species producing conidiophores with solitary phialides, classified in section Torulomyces. Persoonia 36: 134–155. https://doi.org/10.3767/003158516X690952
  • Visagie CM, Renaud JB, Burgess KM, Malloch DW, Clark D, Ketch L, Urb M, Louis-Seize G, Assabgui R, Sumarah MW, Seifert KA (2016b) Fifteen new species of Penicillium. Persoonia 36: 247–280. https://doi.org/10.3767/003158516X691627
  • Visagie CM, Seifert KA, Houbraken J, Samson RA, Jacobs K (2016c) A phylogenetic revision of Penicillium sect. Exilicaulis, including nine new species from fynbos in South Africa. IMA Fungus 7: 75–117. https://doi.org/10.5598/imafungus.2016.07.01.06
  • Visagie CM, Yilmaz N, Kocsubé S, Frisvad JC, Hubka V, Samson RA, Houbraken J (2024a) A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species. Studies in Mycology 107: 1–66. https://doi.org/10.3114/sim.2024.107.01
  • Visagie CM, Houbraken J, Yilmaz N (2024b) The re-identification of Penicillium and Talaromyces (Eurotiales) catalogued in South African culture collections. Persoonia 53: 29–61. https://doi.org/10.3767/persoonia.2024.53.02
  • Wang X, Wanasinghe DN, Zhang J, Ma J, Zhou P, Zhang L, Lu Y, Zhang Z (2023a) Insights from the endophytic Fungi in Amphisphaeria (Sordariomycetes): A. orixae sp. nov. from Orixa japonica and Its Secondary Metabolites. Microorganisms 11: 1268. https://doi.org/10.3390/microorganisms11051268
  • Wang XC, Zhang ZK, Zhuang WY (2023b) Species diversity of Penicillium in Southwest China with discovery of forty-three new species. Journal of Fungi (Basel, Switzerland) 9: 1150. https://doi.org/10.3390/jof9121150
  • Wanthongchai K, Tanpipat V, Noochaiya P, Sirimongkonlertkun N, Macatangay R, Thammavongsa L, Oo TN, Bran SH, Solanki R (2021) Integrated highland wildfire, smoke, and haze management in the Upper Indochina region. APN Science Bulletin 11: 133–143. https://doi.org/10.30852/sb.2021.1704
  • Wendt L, Sir EB, Kuhnert E, Heitkämper S, Lambert C, Hladki AI, Romero AI, Luangsa-Ard JJ, Srikitikulchai P, Peršoh D, Stadler M (2017) Resurrection and emendation of the Hypoxylaceae, recognised from a multigene phylogeny of the Xylariales. Mycological Progress 17: 115–154. https://doi.org/10.1007/s11557-017-1311-3
  • White TJ, Bruns T, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innes MA, Gelfand DH, Sninsky JJ, White TJ (Eds) PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
  • Wolski EA (2023) The versatility of Penicillium species to degrade organic pollutants and its use for wastewater treatment. Studies in Fungi 8: 1–10. https://doi.org/10.48130/SIF-2023-0002
  • Yasanthika E, Wanasinghe DN, Ren G-C, Karunarathna SC, Tennakoon DS, Monkai J, Gui H, Mortimer PE, Lumyong S, Hyde KD (2021) Taxonomic and phylogenetic insights into novel Ascomycota from contaminated soils in Yunnan, China. Phytotaxa 513: 203–225. https://doi.org/10.11646/phytotaxa.513.3.2
  • Yasanthika W, Wanasinghe D, Mortimer P, Monkai J, Farias A (2022) The importance of culture-based techniques in the genomic era for assessing the taxonomy and diversity of soil fungi. Mycosphere : Journal of Fungal Biology 13: 724–751. https://doi.org/10.5943/mycosphere/13/1/8
  • Yasanthika WAE, De Farias ARG, Wanasinghe DN, Chethana KWT, Zare R, Cai L, Maharachchikumbura SSN, Tennakoon DS, Perera RH, Luangharn T, Chomnunti P (2023) a web-based platform for soil-inhabiting Ascomycota species. Studies in Fungi 8: 16. https://doi.org/10.48130/SIF-2023-0016

Tanapol Thitla1 and Jutamart Monkai contributed equally to this work.

Supplementary material

Supplementary material 1 

Additional information

Tanapol Thitla, Jutamart Monkai, Weiqian Meng, Surapong Khuna, Ning Xie, Sinang Hongsanan, Saisamorn Lumyong

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.

This dataset is 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.
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