Unveiling fungal diversity associated with coffee trees in China using a polyphasic approach and a global review of coffee saprobic fungi

Li Lu; Samantha C. Karunarathna; Kunhiraman C. Rajeshkumar; Abdallah M. Elgorban; Ruvishika S. Jayawardena; Sinang Hongsanan; Nakarin Suwannarach; Jaturong Kumla; Yin-Ru Xiong; Kevin D. Hyde; Mei-Yan Han; De-Ge Zheng; Qiang Li; Dong-Qin Dai; Saowaluck Tibpromma

doi:10.3897/imafungus.16.144874

Research Article

Unveiling fungal diversity associated with coffee trees in China using a polyphasic approach and a global review of coffee saprobic fungi

Li Lu^‡§, Samantha C. Karunarathna^|‡, Kunhiraman C. Rajeshkumar^¶, Abdallah M. Elgorban^#, Ruvishika S. Jayawardena^§, Sinang Hongsanan^|, Nakarin Suwannarach^|, Jaturong Kumla^|, Yin-Ru Xiong^§¤, Kevin D. Hyde^§¤, Mei-Yan Han^‡, De-Ge Zheng^‡, Qiang Li^‡, Dong-Qin Dai^‡, Saowaluck Tibpromma^‡

‡ Qujing Normal University, Qujing, China

§ Mae Fah Luang University, Chiang Rai, Thailand

| Chiang Mai University, Chiang Mai, Thailand

¶ National Fungal Culture Collection of India (NFCCI), Biodiversity & Palaeobiology (Fungi) Group, Agharkar Research Institute, Maharashtra, India

# King Saud University, Riyadh, Saudi Arabia

¤ Zhongkai University of Agriculture and Engineering, Guangzhou, China

Corresponding author: Dong-Qin Dai ( cicidaidongqin@gmail.com )

Corresponding author: Saowaluck Tibpromma ( saowaluckfai@gmail.com )

Academic editor: Fang Liu

© 2025 Li Lu, Samantha C. Karunarathna, Kunhiraman C. Rajeshkumar, Abdallah M. Elgorban, Ruvishika S. Jayawardena, Sinang Hongsanan, Nakarin Suwannarach, Jaturong Kumla, Yin-Ru Xiong, Kevin D. Hyde, Mei-Yan Han, De-Ge Zheng, Qiang Li, Dong-Qin Dai, Saowaluck Tibpromma.

This is an open access article distributed under the terms of the CC0 Public Domain Dedication.

Citation: Lu L, Karunarathna SC, Rajeshkumar KC, Elgorban AM, Jayawardena RS, Hongsanan S, Suwannarach N, Kumla J, Xiong Y-R, Hyde KD, Han M-Y, Zheng D-G, Li Q, Dai D-Q, Tibpromma S (2025) Unveiling fungal diversity associated with coffee trees in China using a polyphasic approach and a global review of coffee saprobic fungi. IMA Fungus 16: e144874. https://doi.org/10.3897/imafungus.16.144874

Abstract

Arabica coffee (Coffea arabica) is the most cultured and popular coffee bean in today’s world. Yunnan Province is well known as China’s largest arabica coffee cultivation region. Fungi represent an important group of microorganisms associated with coffee, profoundly influencing its yield and quality. In this study, twelve fungal collections growing on dead and decaying twigs of coffee were collected and isolated to systematically document microfungi associated with coffee plants in Yunnan Province. Ten novel species, each representing a unique family within Pleosporales, were identified and introduced, based on comprehensive morphological analyses and multigene phylogenetic studies. The ten new species belong to the families Bambusicolaceae, Didymellaceae, Didymosphaeriaceae, Longiostiolaceae, Lophiostomataceae, Massarinaceae, Neomassariaceae, Occultibambusaceae, Roussoellaceae and Thyridariaceae with each family containing one new species. Macro- and micro-characteristics, descriptions and phylogenetic trees indicating the placement of the new taxa are provided. In addition, pairwise homoplasy index (PHI) test results and morphological comparisons between the new species and closely-related taxa are given. This study also establishes a comprehensive global inventory of saprobic fungi associated with coffee, which is intended to help researchers and professionals worldwide with practical information. This research enhances the understanding of coffee-associated fungal diversity in China and underscores the importance of introducing new saprobic fungal taxa related to coffee.

Key words:

Coffea arabica, Fungal diversity, new taxa, southwest China, taxonomy

Introduction

Coffea L. (Rubiaceae Juss.) is the world’s 124^th most-traded product and the second most popular beverage worldwide (Adhikari et al. 2020; ALAsmari et al. 2020). The coffee industry is a powerhouse, contributing to the economies of both exporting and importing countries. Its annual income is estimated to exceed $200 billion, providing livelihoods for around 100 million families (Adugna 2024; Freitas et al. 2024). The genus Coffea boasts over 120 species, but only two, Arabica coffee (Coffea arabica L., 75%) and Robusta coffee (Coffea canephora Pierre ex A. Froehner, 25%), hold significant economic importance, making them the key players in the industry (Lu et al. 2022e; Gole and Seyoum 2024). China now ranks as the 13^th largest coffee producer globally (https://colipsecoffee.com/blogs/coffee/countries) and the cultivation areas are mainly distributed in Yunnan and Hainan Provinces, with Yunnan’s coffee planting areas, production and agricultural output value accounting for more than 98% of the country’s total, making it a significant contributor to China’s economy (Neilson and Wang 2019; Zhang et al. 2021). Arabica coffee is the most widely grown and popular coffee in China, especially in Yunnan Province (Rigal et al. 2020; Zhang et al. 2021). It is worth noting that fungi are a common presence during the different stages of coffee processing, indicating the need for further research and development in this area (De Bruyn et al. 2017).

There are an estimated 2.5 million species of fungi, but only about 165,000 have been described thus far (Hyde et al. 2022; Niskanen et al. 2023; Kraisitudomsook et al. 2024; https://www.indexfungorum.org (accessed on 12 January 2025)). The first coffee-associated microorganism described was the arbuscular mycorrhizal fungi (AMF) colonising the roots of Coffea arabica and C. liberica Hiern (Janse 1897). Fungi associated with coffee exist in different life modes, including endophytes, pathogens and saprobes (Duong et al. 2020; Lu et al. 2022a). Based on the review of coffee-associated fungi, 648 species have been reported (Lu et al. 2022a). Amongst them, pathogens are the most widely studied fungi in coffee as their infection can impact coffee production and quality, with 295 species reported (Lu et al. 2022a). Coffee endophytes have also been extensively studied for their potential as biocontrol agents (Quesada-Moraga et al. 2014; Monteiro et al. 2020; Lu et al. 2022b), with 138 species reported (Lu et al. 2022a). However, the potential of using the saprobic microflora isolated from coffee berry surfaces to manage coffee berry disease, as shown by Masaba (1993) and Gichuru (2005), is an intriguing area of research, despite only 30 saprobic fungi being reported worldwide (Lu et al. 2022a). There were only a few reports on coffee-associated saprobic fungi in China before 2020. After 2020, there has been a significant increase in the reports of saprobic fungi on coffee in China, keeping the researchers informed and up-to-date (Lu et al. 2022c, d, e; Hyde et al. 2023; Lu et al. 2024; Liu et al. 2024).

The Greater Mekong Subregion (GMS) region in Yunnan Province has an enormous fungal diversity (Hyde et al. 2018; Chethana et al. 2021). In this study, we conducted a comprehensive study of microfungi collected from the GMS. Our efforts have led to the discovery of ten new species of Pleosporales Luttrell ex M.E. Barr, associated with dead branches of Coffea arabica, collected from Baoshan, Dali, Lincang, Pu’er and Xishuangbanna in Yunnan Province, China. These new species, distributed in ten different genera and families in Pleosporales, not only showcase the diversity of this group of fungi, but also have the potential to significantly impact future research on coffee-associated saprobic fungi in Yunnan Province. We provide full descriptions, photo plates of macro- and micro-morphological characteristics and comparisons with closely-related taxa and phylogenetic trees to indicate the placement of these meticulously researched new taxa. Furthermore, we have provided a comprehensive global list of 62 coffee-associated saprobic fungi (See Suppl. material 1: table S1), including the year, host and country. This global perspective is crucial for understanding these fungi’s full diversity and distribution. In addition, the diversity of coffee-associated saprobic fungi was analysed in the past four years and compared to previous studies. This comparison is not just a comparison; it is a testament to the thoroughness and comprehensive nature of our research, providing a valuable benchmark for our current findings.

Methods

Literature survey

To comprehensively review the diversity of saprobic fungi associated with coffee trees globally, we conducted a literature survey using academic databases, including the esteemed Google Scholar and the USDA Fungal Databases (https://fungi.ars.usda.gov/). Keywords such as “coffee”, “fungi” and “saprobic” were employed to identify relevant studies. The data we extracted on fungal species, geographic locations and host plants were compiled into Suppl. material 1: table S1.

Sample collection, morphological observation and isolation

Yunnan, one of China’s most biodiverse provinces, is a key region for studying fungal communities and their unique ecological roles in coffee ecosystems. We randomly obtained dead and decaying twigs of coffee plant samples with fungal fruiting bodies from coffee plantations in subtropical regions (Baoshan, Dali, Lincang and Pu’er) to tropical regions (Xishuangbanna) of Yunnan Province, China, from 2020 to 2022, noting important collection information (Rathnayaka et al. 2024). Saprobic fungi introduced in this study were isolated from Arabica coffee. Samples were put in paper bags, taken to the mycology laboratory at Qujing Normal University and kept in boxes until observed. The vertical portions of the fruiting body structures were prepared for photomicrography. The measurements were processed in Tarosoft (R) Image Frame Work v. 0.9.7 and photographic plates were made in Adobe Photoshop CC (2018). The single spore isolation method described by Senanayake et al. (2020) was followed to obtain pure cultures on potato dextrose agar (PDA) with antibiotic amoxicillin to prevent bacterial growth (for 500 ml PDA, 2 g of amoxicillin powder was added: Renhe brand amoxicillin capsules). Herbarium specimens were deposited in Kunming Institute of Botany Academia Sinica (HKAS) and Mycological Herbarium of Zhongkai University of Agriculture and Engineering (MHZU), living cultures growing on PDA were deposited in Kunming Institute of Botany Culture Collection (KUNCC) and culture collection of Zhongkai University of Agriculture and Engineering (ZHKUCC). Faces of fungi (FoF) numbers and Index Fungorum (IF) numbers were obtained, as explained in Jayasiri et al. (2015) and Index Fungorum (https://www.indexfungorum.org, accessed on 12 January 2025).

Molecular studies

The Biospin Fungus Genomic DNA Extraction Kit-BSC14S1 (BioFlux, China) was used to extract genomic DNA from fresh fungal mycelia cultivated on PDA for two weeks, following the manufacturer’s instructions. The polymerase chain reaction (PCR) amplification was conducted following the method described by Lu et al. (2022b). This study used six loci; their primers and amplification reactions are shown in Suppl. material 1: tables S2, S3. The PCR products were sequenced at Sango Biotechnology Co., Ltd. (Shanghai, China). All sequences generated in this study were deposited in GenBank (https://www.ncbi.nlm.nih.gov/genbank/) and used for the phylogenetic analysis. Information on all sequences used for phylogenetic analyses is available in the supplementary materials (See Suppl. material 1: tables S4–S13). All the obtained alignments and phylogenetic trees were deposited in Figshare (https://figshare.com/).

Phylogenetic analyses

Raw forward and reverse reads produced in this study were assembled with Geneious v. 9.1.2 (https://www.geneious.com) and initial identification was performed by BLASTn search in GenBank. The related sequence data were obtained from GenBank, based on the latest literature. Single gene sequence alignments were conducted with the online programme MAFFT v. 7.110 (https://mafft.cbrc.jp/alignment/server/). TrimAL v. 1.2 (http://trimal.cgenomics.org) was used to remove the uninformative gaps and ambiguous regions and Sequence Matrix v. 1.7.8 was used to concatenate the individual alignments (Vaidya et al. 2011). The fasta files were converted to Nexus files using AliView v. 1.28 (Larsson 2014). Maximum Likelihood (ML) and Bayesian Inference (BI) algorithms were used to perform phylogenetic analyses of the aligned sequences, as explained by Dissanayake et al. (2020), conducted on the CIPRES Science Gateway portal (https://www.phylo.org). A Maximum Likelihood analysis was performed using RAxML-HPC v.8, with rapid bootstrap analysis, followed by 1000 bootstrap replicates; the GTRGAMMA model was used for all partitions. The Bayesian analysis was used to evaluate posterior probabilities (PP) by MrBayes on XSEDE v. 3.2.7a; six simultaneous Markov Chains were run for two million generations and trees were sampled at every 200^th generation (resulting in 10,000 trees) and these chains stopped when all convergences met and the standard deviation fell below 0.01. The phylogenetic trees were viewed by FigTree v. 1.4.2 (Rambaut 2014) and edited using Microsoft Office PowerPoint (2020) and Adobe Illustrator CS6 (Adobe Systems Inc., USA). The bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 were mentioned above the nodes.

Genealogical concordance phylogenetic species recognition analysis

Genealogical concordance phylogenetic species recognition analysis (GCPSR) by the pairwise homoplasy index (PHI) test was used to determine the recombination level within closely-related species (Bruen et al. 2006). The data were analysed using the software SplitsTree v. 4 (Bruen et al. 2006; Huson and Bryant 2006). The relationships between closely-related taxa were visualised by constructing split graphs from concatenated datasets using the LogDet transformation and split decomposition options. If the PHI test value is lower than (Φw) ≤ 0.05, it indicates significant recombination within the dataset. This is an important method to provide further evidence to justify a species.

Results

Global diversity of coffee-associated saprobic fungi

The literature survey revealed a limited diversity of saprobic fungi associated with coffee trees globally, with only 62 species reported worldwide, including ten new species described in this study. A total of 62 coffee-associated saprobic species are distributed in 18 orders, 37 families and 47 genera (See Suppl. material 1: table S1), highlighting the global reach of our research. Amongst 62 species, 31 coffee-associated saprobic fungi were recorded worldwide from 1980 to 2020 and another 31 species were reported from Yunnan Province, China, from 2021 to 2024. The discovery of 31 new species in Yunnan, China, from 2021 to 2024 is a testament to the potential novelty of coffee-associated fungi in this region, a finding that is sure to spark scientific curiosity.

From 1980 to 2020, the 31 species reported were distributed across 13 orders, 18 families and 20 genera. In contrast, from 2021 to 2024, 31 species were reported across seven orders, 21 families and 27 genera (Fig. 1A, B). Additionally, no overlap in the species was reported between these two periods (Fig. 1B). This indicates that the diversity of coffee-associated saprobic fungi reported in Yunnan, China, is greater than that previously documented globally. This underscores the urgent and significant need for further exploration and study of saprobic fungi on coffee, a call to action for the scientific community.

Figure 1.

Analysis of the diversity of coffee-associated saprobic fungi from 1980 to 2020 (first period) and from 2021 to 2024 (Second period). A comparison of taxonomic distribution at the order and family levels between the two periods; B comparison of taxonomic distribution at the genus level between the two periods.

Amongst the 62 species, the most frequently segregated order is Pleosporales, encompassing 17 families, 22 genera and 35 species (Fig. 1A). This paper introduces ten new taxa within this order, distributed across different genera and families. The discovery of these new taxa is significant as it not only adds to the diversity of coffee-associated saprobic fungi, but also underscores the need for further exploration and study in this field.

Taxonomy

Fungi

Ascomycota Caval. Sm.

Dothideomycetes O. E. Erikss. & Winka.

Pleosporales Luttr. ex M.E. Barr, Prodr. Cl. Loculoasc. (Amherst): 67 (1987).

Bambusicolaceae D.Q. Dai & K.D. Hyde, Fungal Diversity 63 (1): 49 (2013).

Leucaenicola Jayasiri, E.B.G. Jones & K.D. Hyde, Mycosphere 10 (1): 37 (2019).

Notes.

Leucaenicola was introduced by Jayasiri et al. (2019) to accommodate two new coelomycetous species, with L. aseptata Jayasiri, E.B.G. Jones & K.D. Hyde, as the type species. Leucaenicola contains five species; only their anamorph has been documented (Jayasiri et al. 2019; Ariyawansa et al. 2020a, b; Hyde et al. 2024). Herein, we introduce a new species of Leucaenicola with both anamorph and teleomorph and this is the first report of Leucaenicola from Arabica coffee plants.

Leucaenicola coffeae L. Lu & Tibpromma, sp. nov.

Index Fungorum number: IF90099

Facesofungi number: FoF14724

Fig. 2

Etymology.

The species epithet “coffeae” refers to the host plant genus “Coffea” from which the fungus was isolated.

Diagnosis.

Differs from L. phraeana Jayasiri, E.B.G. Jones & K.D. Hyde, by the brown and large conidia (5–6 × 2.5–3.5 μm vs. 3–4 × 1.5–2 μm) and distinct guttules.

Holotype.

HKAS 137605.

Description.

Saprobic on decaying branch of C. arabica. Teleomorph: Ascomata 200–350 high × 200–300 µm diam. (x− = 239 × 273 µm), solitary or scattered, immersed, raised as brown to black spots on the substrate, globose to subglobose, coriaceous, uniloculate with ostioles. Peridium 25–35 μm wide (x− = 30 μm, n = 20), thin-walled, composed of dark brown and 2–4 layers of textura angularis cells, with the basal part composed of thinner, hyaline, smaller cells. Hamathecium 1.5–3.5 µm wide (x− = 2.7 µm, n = 20), dense, comprising numerous pseudoparaphyses, filamentous, hyaline, cellular, branched, with distinct septa. Asci 40–80 × 8–15 µm (x− = 57 × 9.6 µm, n = 20), 4–8-spored, bitunicate, fissitunicate, cylindrical, long-stalked with club-shape, apically rounded, with a shallow ocular chamber. Ascospores 15–25 × 4–8 µm (x− = 21 × 6 µm, n = 30), overlapping, uniseriate to biseriate, fusiform to ellipsoidal, straight, hyaline, mainly 1-septate, sometimes 2–3 septate, constricted at the centre septa, conical at both ends, upper cell wider than the lower cell, guttulate, mucilaginous sheath. Anamorph on PDA: Mycelium 1.5–2.5 μm broad (x− = 2.2 μm, n = 20), hyaline, septate, branched. Conidia 5–6 × 2.5–3.5 μm (x− = 5.6 × 3.1 μm, n = 30), ellipsoidal to cylindrical, hyaline when young, brown when mature, thin and smooth-walled, aseptate, with 1–2-guttules.

Culture characteristics.

Ascospores germinating on PDA within 24 h. Colonies reached 3.5 cm in diameter after one month at 25 °C. Colonies circular, slightly fluffy with an entire margin, white; the reverse is white to yellowish. After four months, conidia mass formed as globose to subglobose, dark brown to black spots in culture.

Materials examined.

China • Yunnan Province, Pu’er, on a decaying branch of Coffea arabica (Rubiaceae) (23°43'01"N, 101°73'90"E, 1085 m alt.), 18 November 2020, LiLu, MJ-C8 (HKAS 137605, holotype), isotype MHZU 23-0058, ex-type living culture KUNCC 24-18335 = KUNCC 24-18336, ex-isotype living culture ZHKUCC 23-0626 = ZHKUCC 23-0627.

Notes.

Based on the multi-gene sequence analysis, Leucaenicola coffeae forms an independent lineage allied to L. phraeana (Fig. 3). In the NCBI BLASTn searches, the ITS, LSU, SSU and TEF1-α sequences are similar to L. camelliae Ariyaw., I. Tsai & Thambugala, (MT112301, 98%), (MT071278, 90%), (MT071229, 99.9%) and (MT374091, 97%), respectively, while RPB2 is 97% similar to L. osmanthi Ariyaw., I. Tsai & Thambugala, (MN915020). Leucaenicola coffeae is the first species with a teleomorph known in Leucaenicola. The teleomorph characteristics of L. coffeae conform to the basic concept of Bambusicolaceae. The anamorph can be distinguished from L. phraeana by the brown and large conidia (5–6 × 2.5–3.5 μm vs. 3–4 × 1.5–2 μm) and distinct guttules (Fig. 2; Jayasiri et al. (2019)). Based on nucleotide comparisons, L. coffeae (ZHKUCC 23-0626) differs from L. phraeana (MFLUCC 18-0472) by 102/418 bp (24%, 3 gaps) in ITS, 80/844 bp (9%, without gaps) in LSU, 2/1017 bp (0.2%, without gaps) in SSU, 16/920 bp (1.7%, without gaps) in TEF1-α and 30/1036 bp (2.9%, without gaps) in RPB2; and differs from L. osmanthi (NTUCC 18-101-3) by 10/620 bp (1.6%, without gaps) in ITS, 78/756 bp (10%, without gaps) in LSU, 2/780 bp (0.2%, without gaps) in SSU, 21/816 bp (2.5%, without gaps) in TEF1-α and 26/818 bp (3%, without gaps) in RPB2. In addition, the PHI test results (Fig. 22a) revealed no significant recombination relationships between L. coffeae and its phylogenetically related taxa within the dataset. Therefore, we introduce L. coffeae as a new species in Leucaenicola with the first record of a teleomorph associated with the decaying branch of C. arabica.

Figure 2.

Leucaenicola coffeae (HKAS 137605, holotype). A, B appearance of ascomata on a decaying branch of C. arabica; C, D longitudinal section of ascomata; E peridium wall; F pseudoparaphyses; G–J asci; K germinated ascospores; L–O ascospores; P ascospores stained with Indian ink; Q conidia mass in culture after four months; R conidia; S culture on PDA from obverse and reverse. Scale bars: 150 μm (C, D); 50 μm (E); 100 μm (F); 20 μm (G–K); 10 μm (L–P, R).

Figure 3.

Phylogram generated from the best scoring RAxML tree, based on a combined ITS LSU, SSU, RPB2 and TEF1-α sequence dataset. Sulcatispora acerina Kaz. Tanaka & K. Hiray., (KT 2982) and S. berchemiae Kaz. Tanaka & K. Hiray., (KT 1607) are selected as the outgroup taxa. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are indicated at the nodes as ML/PP. All type strains are in bold and newly-generated sequences are in red.

Didymosphaeriaceae Munk, Dansk botanisk Arkiv 15 (2): 128 (1953).

Montagnula Berl., Icones Fungorum. Pyrenomycetes 2: 68 (1896).

Notes.

Berlese (1896) introduced Montagnula typified by M. infernalis (Niessl) Berl. Most species of Montagnula have been found on dead leaves and twigs by their teleomorph with a wide geographical and host distribution (Tibpromma et al. 2018; Mapook et al. 2020; Du et al. 2021). Only M. cylindrospora Valenz.-Lopez, Cano, Guarro & Stchigel, has been reported as a coelomycete (Crous et al. 2020). This study introduces a novel species from an Arabica coffee plant in Yunnan Province, China.

Montagnula coffeae L. Lu & Tibpromma, sp. nov.

Index Fungorum number: IF900999

Facesofungi number: FoF14725

Fig. 4

Etymology.

The species epithet “coffeae” refers to the host plant genus “Coffea” from which the fungus was isolated.

Diagnosis.

Differs from M. appendiculata (Aptroot) Wanas., E.B.G. Jones & K.D. Hyde, by 6–8-spored asci, differing from M. chromolaenae Mapook & K.D. Hyde, by guttulate ascospores and differing from M. chiangraiensis Mapook & K.D. Hyde, by the presence of appendages on its ascospores.

Holotype.

HKAS 137611.

Description.

Saprobic on decaying branch of C. arabica. Teleomorph: Ascomata 120–180 µm high × 150–220 µm diam. (x− = 150 × 183 µm, n = 15), immersed, separate beneath a clypeus or sometimes gregarious beneath fused clypei, visible as black, solitary or scattered, globose to subglobose, unilocular, black, with ostioles. Ostioles papillate, central. Clypeus brown or sometimes with a halo around the central pore, margin indistinct, consisting of dark, thick-walled hyphae in both epidermal and subepidermal cells. Peridium 7–11 µm wide (x− = 8.8 µm, n = 15), fused with host tissue, comprising 2–3 layers of pale brown to brown cells of textura prismatica. Hamathecium 3–6 µm wide (x− = 4 µm, n = 20) µm wide, branched, hyaline, septate, numerous pseudoparaphyses. Asci 60–75 × 6–10 µm (x− = 65 × 8.5 µm, n = 20), bitunicate, fissitunicate, 6–8-spored, clavate, long-stalked with club-shape, straight. Ascospores 12–16 × 3–6 µm (x− = 14 × 4.8 µm, n = 30), hyaline to yellowish when immature, brown to red-brown when mature, overlapping uniseriate or biseriate, fusiform to ellipsoid, 1-septate, guttulate, constricted at the septum, upper cell wider and shorter than lower cell and tapering towards ends, sheath drawn out to form polar appendages 4–9 µm long × 1.5–2.5 µm wide (x− = 6 × 1.9 µm, n = 30), from both ends of the ascospores, straight. Anamorph: Not observed.

Culture characteristics.

Ascospores germinating on PDA within 24 h, colonies reached 3.5–4 cm in diameter after one month at 25 °C. Colonies on PDA irregular, flat or slightly raised, filamentous, smooth, with undulate margin, from above, hyaline, from below, yellowish at the centre, hyaline at the edge.

Materials examined.

China • Yunnan Province, Lincang, on a decaying branch of Coffea arabica (Rubiaceae) (24°17'N, 99°99'E, 960 m alt.), 28 July 2022, LiLu, LC1-C5 (HKAS 137611, holotype), isotype MHZU 23-0060, ex-type living culture KUNCC 24-18337 = KUNCC 24-18338, ex-isotype living culture ZHKUCC 23-0630 = ZHKUCC 23-0631.

Notes.

In the concatenated phylogenetic analysis, Montagnula coffeae forms a distinct lineage and is basal to M. appendiculata, M. chromolaenae and M. chiangraiensis (Fig. 5). Based on nucleotide comparisons, M. coffeae (ZHKUCC 23-0630) differs from M. appendiculata (CBS 109027) by 30/497 bp (6%, without gaps) in ITS and 14/833 bp (1.7%, without gaps) in LSU; differs from M. chromolaenae (MFLUCC 17-1435) by 24/497 bp (4.8%, without gaps) in ITS, 12/903 bp (1.3%, without gaps) in LSU and 15/1006 bp (1.5%, without gaps) in SSU; differs from M. chiangraiensis (MFLUCC 17-1420) by 20/498 bp (4%, without gaps) in ITS, 13/903 bp (1.4%, without gaps) in LSU and 10/1006 bp (1%, without gaps) in SSU. The morphology of M. coffeae is similar to M. appendiculata and M. chromolaenae in having fusiform, brown and fusiform ascospores with appendages. However, M. coffeae has 6–8-spored asci, while M. appendiculata has 8-spored asci (Fig. 4; Aptroot (2004)). Montagnula coffeae have guttulate ascospores, while no guttules have been observed on the ascospores of M. chromolaenae (Mapook et al. 2020). Montagnula coffeae can be distinguished from M. chiangraiensis by the appendages on its ascospores (Mapook et al. 2020). In addition, the PHI test results (Fig. 22b) revealed no significant recombination relationships between M. coffeae and its phylogenetically related taxa. The morphological differences and phylogenetic analysis results support the discovery of M. coffeae as a new species.

Figure 4.

Montagnula coffeae (HKAS 137611, holotype). A, B ascomata on a decaying branch of C. arabica; C longitudinal section of an ascoma; D peridium wall; E pseudoparaphyses; F–J immature and mature asci; K germinated ascospore; L–Q ascospores; R culture on PDA from obverse and reverse. Scale bars: 50 μm (C); 20 μm (D–K); 10 μm (L–Q).

Figure 5.

Phylogram generated from the best scoring RAxML tree, based on a combined ITS, LSU, SSU and TEF1-α sequence dataset. Fuscostagonospora cytisi Jayasiri, Camporesi & K.D. Hyde, (MFLUCC 16-0622) and F. sasae Kaz. Tanaka & K. Hiray., (HHUF 29106) are selected as the outgroup taxa. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are given above the nodes. All type strains are in bold and newly-generated sequences are in red.

Didymellaceae Gruyter, Aveskamp & Verkley, Mycological Research 113 (4): 516 (2009).

Xenodidymella Qian Chen & L. Cai, Stud. Mycol. 82: 205 (2015).

Notes.

Xenodidymella typified by X. applanate (Niessl) Qian Chen & L. Cai, was established by Chen et al. (2015) to accommodate several phoma-like taxa. The new species, X. coffeae, is introduced here through phylogenetic and morphological comparisons and isolated from the Arabica coffee plant in China. This is the first Xenodidymella species reported from coffee.

Xenodidymella coffeae L. Lu & Tibpromma, sp. nov.

Index Fungorum number: IF901000

Facesofungi number: FoF14726

Fig. 6

Etymology.

The species epithet “coffeae” refers to the host plant genus “Coffea” from which the fungus was isolated.

Diagnosis.

Differs from X. clematidis Phukhams., Camporesi & K.D. Hyde, by shorter ostioles and cylindrical conidia.

Holotype.

HKAS 137610.

Description.

Saprobic on decaying branch of C. arabica. Teleomorph: Not observed. Anamorph: Conidiomata 50–80 µm high × 50–90 µm diam. (x− = 62 × 70 µm, n = 20), separate or scattered, semi-immersed, black, globose to subglobose or pyriform, pycnidial, with short ostioles. Conidiomatal wall 6–12 µm wide (x− = 9 µm, n = 30), composed of 1–3 layers of light brown to brown cells of textura angularis, heavily pigmented at the outer layers, lined with a hyaline layer bearing conidiogenous cells. Conidiophores inconspicuous or micronematous, often reduced to conidiogenous cells. Conidiogenous cells lining inner cavity, 4–6 × 4–7 µm (x− = 5.3 × 5.4 µm, n = 30), hyaline, globose to ampulliform, enteroblastic, phialidic. Conidia 10–15 × 3–4 µm (x− = 12 × 3.3 µm, n = 30), solitary, hyaline, oblong to cylindrical with rounded ends, aseptate, mostly straight, surface smooth or rough.

Culture characteristics.

Conidia germinating on PDA within 24 h, colonies reached 6 cm in diameter after two months at 25 °C, filamentous, filiform margin, smooth, flat, with aerial mycelium, from above, brown at the centre, dark brown at the edge, from below, dark brown to black.

Materials examined.

China • Yunnan Province, Dali, on a decaying branch of Coffea arabica (Rubiaceae) (26°09'N, 101°91'E, 1415 m alt.), 25 July 2022, LiLu, DL-C11 (HKAS 137610, holotype), isotype MHZU 23-0064, ex-type living culture KUNCC 24-18339 = KUNCC 24-18340, ex-isotype living culture ZHKUCC 23-0638 = ZHKUCC 23-0639.

Notes.

In the concatenated phylogenetic analysis, Xenodidymella coffeae shows a close relationship with X. clematidis and X. camporesii D. Pem, Doilom & K.D. Hyde (Fig. 7). Xenodidymella coffeae conforms to the characteristics of Xenodidymella by globose to ampulliform conidiogenous cells and hyaline conidia (Hyde et al. 2020). Xenodidymella coffeae has short ostioles and cylindrical conidia, while X. clematidis has long ostioles with oblong-elliptical or oval conidia (Fig. 6; Phukhamsakda et al. (2020)). Besides, the conidia of our species are larger than those of X. clematidis (10–15 × 3–4 µm vs. 4–8 × 2–5 μm). Xenodidymella camporesii has only been reported based on its teleomorph (Hyde et al. 2020). Based on nucleotide comparisons, X. coffeae (ZHKUCC 23-0638) is different from X. clematidis (MFLUCC 16-1365) by 8/482 bp (1.6%, without gaps) of the ITS, 11/786 bp (1.4%, without gaps) of the LSU; and different from X. camporesii (MFLUCC 17-2309) by 10/518 bp (2%, with one gap) of the ITS, 16/890 bp (1.8%, without gaps) of the LSU and 26/282 bp (9%, without gaps) of the TUB. In addition, the PHI test results (Fig. 22c) revealed no significant recombination relationships between X. coffeae and its phylogenetically related taxa. This fungus is, therefore, introduced as a new species of Xenodidymella, following the guidelines of Chethana et al. (2021) and Pem et al. (2021).

Figure 6.

Xenodidymella coffeae (HKAS 137610, holotype). A, B conidiomata on a decaying branch of C. arabica; C, D longitudinal section of a conidioma and conidioma wall; E conidiogenous cells with conidia; F–K conidia; L germinated conidium; M culture on PDA from obverse and reverse. Scale bars: 20 μm (C, D, K, L); 10 μm (E–J).

Figure 7.

Phylogram generated from the best scoring RAxML tree, based on a combined ITS LSU, TUB and RPB2 sequence dataset. Neodidymelliopsis cannabis (G. Winter) Qian Chen & L. Cai, (CBS 121.75) is selected as the outgroup taxon. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are given above the nodes. All type strains are in bold and newly-generated sequences are in red.

Lophiostomataceae Sacc., Syll. Fung. 2: 672 (1883).

Flabellascoma A. Hashim., K. Hiray. & Kaz. Tanaka, Studies in Mycology 90: 167 (2018).

Notes.

Flabellascoma was proposed by Hashimoto et al. (2018) and was typified by F. minimum A. Hashim., K. Hiray. & Kaz. Tanaka. Flabellascoma species were collected from terrestrial and freshwater habitats with anamorphs and teleomorphs (Hashimoto et al. 2018; Bao et al. 2019; Yu et al. 2022). A new species is added to Flabellascoma with a teleomorph from the Arabica coffee plant in Yunnan Province, China and this is the first report of Flabellascoma from coffee.

Flabellascoma coffeae L. Lu & Karun., sp. nov.

Index Fungorum number: IF901001

Facesofungi number: FoF14727

Fig. 8

Etymology.

The species epithet “coffeae” refers to the host plant genus “Coffea” from which the fungus was isolated.

Diagnosis.

Differs from F. fusiforme D.F. Bao, Z.L. Luo, K.D. Hyde & H.Y. Su, by an internal chamber at both ends of ascospores.

Holotype.

HKAS 137607.

Description.

Saprobic on decaying branch of C. arabica. Teleomorph: Ascomata 280–450 µm high × 200–280 µm diam. (x− = 356 × 230 µm, n = 20) (including neck), solitary, rarely clustered, immersed, visible as black, crest-like ostiolar neck on the substrate, globose to subglobose, uniloculate. Ostioles central, with a pore-like opening, periphysate. Peridium 15–30 µm wide (x− = 24 µm, n = 30), composed of several layers of brown, thick-walled cells of textura angularis. Hamathecium 1.5–3 µm wide (x− = 2.2 µm, n = 30), hyphae-like, septate, branched, pseudoparaphyses. Asci 60–100 × 10–15 µm (x− = 75 × 12 µm, n = 30), 8-spored, bitunicate, fissitunicate, cylindrical to clavate, straight, with a short furcate sessile, apically rounded with a broad ocular chamber. Ascospores 20–25 × 5–7 µm (x− = 22 × 6 µm, n = 30), overlapping biseriate, fusiform, hyaline, 1-septate, constricted at the septum, the upper cell slightly wider than the lower cell, guttulate, smooth-walled, with a narrow bipolar sheath. Sheath drawn-out at both ends, 4–7 µm long × 2–3 µm wide (x− = 5.6 × 2.5 µm, n = 30), with an internal chamber at both ends of ascospores. Anamorph: Not observed.

Culture characteristics.

Ascospores germinating on PDA within 24 h, colonies reached 1.5–2 cm in diameter after twenty days at 25 °C, circular, flat to umbonate, fluffy, smooth, with entire margin, from above, grey, from below, dark grey at the centre, white at the edge.

Materials examined.

China, Yunnan Province, Baoshan, on a decaying branch of Coffea arabica (Rubiaceae) (24°9'N, 98°8'E, 1050 m alt.), 30 July 2022, LiLu, BS1-C3 (HKAS 137607, holotype), isotype MHZU 23-0063, ex-type living culture KUNCC 24-18341 = KUNCC 24-18342, ex-isotype living culture ZHKUCC 23-0636 = ZHKUCC 23-0637; China, Yunnan Province, Dali, on a decaying branch of C. arabica, (26°09'N, 101°91'E, 1416.46 m alt.), 25 July 2022, LiLu, DL-C41 (HKAS 137612, paratype), isoparatype MHZU 23-0062, ex-paratype living culture KUNCC 24-18343 = KUNCC 24-18344, ex-isoparatype living culture ZHKUCC 23-0634 = ZHKUCC 23-0635.

Notes.

The phylogenetic result, based on SSU, ITS, LSU, RPB2 and TEF1-α sequence data, showed our new collection Flabellascoma coffeae is close to F. fusiforme (Fig. 9). Flabellascoma coffeae can be distinguished from F. fusiforme in having an internal chamber at both ends of ascospores (Fig. 8; Bao et al. (2019)). Flabellascoma coffeae also fits well with the morphological characteristics of Flabellascoma, such as immersed ascomata with crest-like ostiolar neck, cylindrical-clavate asci and fusiform, hyaline, 1-septate ascospores with a narrow bipolar sheath (Fig. 8; Hashimoto et al. (2018)). Based on nucleotide comparisons, F. coffeae (ZHKUCC 23-0636) is different from F. fusiforme (MFLUCC 18-1584) by 19/500 bp (3.8%, without gaps) of the ITS, 7/835 bp (0.8%, without gaps) of the LSU and 22/839 bp (2.7%, without gaps) of the TEF1-α. In addition, the PHI test results (Fig. 22d) revealed no significant recombination relationships between F. coffeae and its phylogenetically related taxa. Therefore, we introduce F. coffeae as a new species from coffee in China, based on morphology and multigene phylogeny.

Figure 8.

Flabellascoma coffeae (HKAS 137607, holotype). A, B ascomata on a decaying branch of C. arabica; C a longitudinal section of an ascoma; D ostioles; E peridium wall; F pseudoparaphyses; G germinated ascospore; H, I culture on PDA from the obverse and reverse; J–M asci; N–S ascospores (S: arrowheads indicate an internal chamber in ascospore). Scale bars: 100 μm (C); 20 μm (D–G, J–M); 10 μm (N–S).

Figure 9.

Phylogram generated from the best scoring RAxML tree, based on a combined ITS LSU, SSU, RPB2 and TEF1-α sequence dataset. Bambusicola guttulata X.D. Yu, S.N. Zhang & Jian K. Liu, (CGMCC 3.20935 and UESTCC 22.0002) are selected as the outgroup taxa. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are given above the nodes. All type strains are in bold and newly-generated sequences are in red.

Longiostiolaceae Phukhams., Doilom & K.D. Hyde, Fungal Diversity 102: 43 (2020).

Longiostiolum Doilom, Ariyaw. & K.D. Hyde, Fungal Diversity 78: 55 (2016).

Notes.

Longiostiolum was introduced by Li et al. (2016) in Pleosporales suborder Massarineae M.E. Barr, incertae sedis, with L. tectonae Doilom, D.J. Bhat & K.D. Hyde, as the type species. Later, Phukhamsakda et al. (2020) introduced the new family Longiostiolaceae to accommodate this distinct lineage, based on morphology and phylogenetic analysis. Longiostiolum is a monotypic genus with anamorphs and teleomorphs (Li et al. 2016). In this study, L. coffeae is introduced with a teleomorph from an Arabica coffee plant in Yunnan, China. This is the first report of Longiostiolum from a coffee host.

Longiostiolum coffeae L. Lu & Tibpromma, sp. nov.

Index Fungorum number: IF901002

Facesofungi number: FoF14728

Fig. 10

Etymology.

The species epithet “coffeae” refers to the host plant genus “Coffea” from which the fungus was isolated.

Diagnosis.

Differs from L. tectonae by the presence of sheath in ascospores.

Holotype.

HKAS 137602.

Description.

Saprobic on decaying branch of C. arabica. Teleomorph: Ascomata 160–280 µm high × 180–280 µm diam. (x− = 212 × 238 µm, n = 15), black spots on the substrate, solitary to scattered, immersed to semi-immersed, when cut horizontally, locules visible as white contents, unilocular, globose to subglobose, with central and short ostioles. Peridium 20–30 µm thick (x− = 23 µm, n = 15), outer layer consists of 2–4 layers of textura angularis, brown and thick-walled cells, inner layer consists of multi-layers of textura angularis, hyaline and thin-walled cells. Hamathecium 2–3 µm wide (x− = 2.5 µm, n = 20), numerous, hypha-like, filiform, septate, branched, cellular, pseudoparaphyses, embedded in a gelatinous matrix. Asci 90–140 × 20–28 µm (x− = 115 × 23 µm, n = 20), bitunicate, 8-spored, cylindrical to clavate, with a short pedicellate, apically rounded, with an ocular chamber. Ascospores 45–55 × 8–11 µm (x− = 47 × 9 µm, n = 20), overlapping uniseriate to 3-seriate, hyaline, fusoid, often enlarged at the fourth cell, with one transverse septum when young, 7–8 transverse septa when mature, constricted at the centre septa, slightly constricted at other septa, smooth-walled, sheath present. Anamorph: Not observed.

Culture characteristics.

Ascospores germinating on PDA within 24 h, colonies reached 4 cm in diameter after one month at 25 °C, circular, with filiform margin, aerial, medium spare, flat or effuse, from above, hyaline, from below, hyaline to light brown at the centre, hyaline at the edge.

Materials examined.

China, Yunnan Province, Lincang, on a decaying branch of Coffea arabica (Rubiaceae) (22°8'N, 99°4'E, 870 m alt.), 28 July 2022, LiLu, LC3-C3 (HKAS 137602, holotype), isotype MHZU 23-0059, ex-type living culture KUNCC 24-18345 = KUNCC 24-18346, ex-isotype living culture ZHKUCC 23-0628 = ZHKUCC 23-0629.

Notes.

In the concatenated phylogenetic analysis, Longiostiolum coffeae formed a sister branch with L. tectonae (MFLU 15-3532) (Fig. 11). Based on nucleotide comparisons, L. coffeae (HKAS 137602) is different from L. tectonae (MFLU 15-3532) by 70/480 bp (14%, without gaps) of the ITS, 13/863 bp (1.5%, without gaps) of the LSU, 4/665 bp (0.6%, without gaps) of the SSU and 75/920 bp (8%, without gaps) of the TEF1-α. Based on morphology, our novel taxon is similar to L. tectonae in the hyaline and fusoid ascospores, but differs in the sheath of ascospores, as L. tectonae lacks a sheath. Besides, our species has 1–8 transverse septa, while L. tectonae has 7–10 transverse septa (Fig. 10; Li et al. (2016); Phukhamsakda et al. (2020)). In addition, the PHI test results (Fig. 22e) revealed no significant recombination relationships between L. coffeae and its phylogenetically related taxa. The morphological differences and phylogenetic analyses support the discovery of L. coffeae as a new species.

Figure 10.

Longiostiolum coffeae (HKAS 137602, holotype). A, B ascomata on a decaying branch of C. arabica; C, D longitudinal section of ascomata; E peridium wall; F pseudoparaphyses; G–K asci; L–O ascospores; P an ascospore stained with Indian ink; Q culture on PDA from obverse and reverse. Scale bars: 100 μm (C, D); 20 μm (E–P).

Figure 11.

Phylogram generated from the best scoring RAxML tree, based on a combined ITS LSU, SSU, RPB2 and TEF1-α sequence dataset. Diatrype disciformis (Hoffm.) Fr., (AFTOL-ID 927), Graphostroma platystoma (Schwein.) Piroz. (CBS 270.87) and Sordaria fimicola (Roberge ex Desm.) Ces. & De Not., (AFTOL-ID 216) are selected as the outgroup taxa. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are given above the nodes. All type strains are in bold and newly-generated sequences are in red.

Massarinaceae Munk, Friesia 5 (3–5): 305 (1956).

Helminthosporium Link, Mag. Ges. Naturf. Freunde Berlin 3 (1): 10 (1809).

Notes.

Helminthosporium was established by Link (1809) and typified by H. velutinum Link; it is a polyphyletic genus in Massarinaceae of Pleosporales (Chen et al. 2022). Members of Helminthosporium mainly occur as anamorphs. Little is known about the teleomorph of Helminthosporium (Hughes 1953; Subramanian 1987; Tanaka et al. 2015). Herein, we introduce H. puerensis as a new species with a teleomorph from the Arabica coffee plant in Yunnan, China.

Helminthosporium puerensis L. Lu & Tibpromma, sp. nov.

Index Fungorum number: IF901003

Facesofungi number: FoF14729

Fig. 12

Etymology.

The epithet refers to the location “Pu’er“ from where the holotype was collected.

Diagnosis.

Differs from H. quercinum Voglmayr & Jaklitsch and H. microsorum D. Sacc., by the hyaline ascospores with inconspicuous sheath.

Holotype.

HKAS 137606.

Description.

Saprobic on decaying branch of C. arabica. Teleomorph: Ascomata 250–400 × 220–400 µm (x− = 320 × 310 µm, n = 15, including ostioles), solitary to scattered, immersed, visible as black dots with black hair on the host surface, globose to subglobose. Ostiolar neck central, cylindrical to papillate, surrounded by dark brown clypeus-like structure, without periphyses. Peridium 20–30 µm wide (x− = 26, n = 20), composed of 4–6 layers of textura angularis cells, polygonal to rectangular, light brown. Hamathecium 2–3 µm wide (x− = 2.2, n = 20), hyaline, filiform, branched, septate, pseudoparaphyses numerous. Asci 80–170 × 15–25 µm (x− = 130 × 19 µm, n = 20), 4–8-spored, fissitunicate, bitunicate, clavate, straight, rounded at the apex, with a narrow apical chamber and faint ring, short-stalked with club-shape, sometimes with long stipes. Ascospores 25–30 × 7–11 µm (x− = 26.5 × 9 µm, n = 30), mostly straight, 1–3-septate, constricted at the septum, asymmetric, with wider upper cell, hyaline, guttulate, smooth-walled, sheath present. Anamorph: Not observed.

Culture characteristics.

Ascospores germinating on PDA within 12 h, colonies reached 4 cm in diameter after two months at 25 °C, surface smooth, circular, flat, with entire margin, from above, hyaline to light yellow, from below, dark brown at the centre, hyaline at the margin.

Materials examined.

China, Yunnan Province, Pu’er, on a decaying branch of Coffea arabica (Rubiaceae) (22°70'12"N, 101°34'78"E, 900 m alt.), 6 September 2020, LiLu, QX-C7 (HKAS 137606, holotype), isotype MHZU 23-0055, ex-type living culture KUNCC 24-18347 = KUNCC 24-18348, ex-isotype living culture ZHKUCC 23-0620 = ZHKUCC 23-0621.

Notes.

Phylogenetic analyses show that Helminthosporium puerensis groups with H. chinense Y.P. Chen & Maharachch., (CGMCC 3.23570) and H. nanjingense Meng Zhang, Xiao J. Wang & H.Y. Wu, (HHAUF 020380) (Fig. 13). Helminthosporium chinense and H. nanjingense were only reported as anamorphs from decaying branches of palm trees (Sichuan Province, China) and dead branches of an unidentified tree (Jiangsu Province, China), respectively. Based on nucleotide comparisons, H. puerensis (ZHKUCC 23-0620) is different from H. chinense (CGMCC 3.23570) by 18/578 bp (3%, without gaps) of the ITS, 3/749 bp (0.4%, without gaps) of the LSU, 16/780 bp (2%, without gaps) of the SSU and 8/320 bp (2.5%, without gaps) of the TEF1-α. In comparison, it is different from H. nanjingense (HHAUF 020380) in 7/454 bp (1.5%, without gaps) of the ITS (H. nanjingense only has ITS sequence data available). Helminthosporium chinense and H. nanjingense showed only a small difference in ITS by 7/447 (1.6%, without gaps). Based on BLASTn search results of sequence data, ITS is 97.4% similar to H. chinense (ON557754), LSU, SSU and RPB2 are closely related to H. quercinum, with similarity rates of 97% (KY984338), 98.8% (NG_062196) and 92.5% (KY984398), respectively and TEF1-α is 94% (KY984448) similar to H. microsorum. In terms of morphological characteristics, our species can be distinguished from H. quercinum and H. microsorum by the hyaline ascospores with inconspicuous sheath; H. quercinum and H. microsorum are hyaline to brown ascospores with conspicuous sheath (Voglmayr and Jaklitsch 2017). Our species is most similar to the teleomorph H. massarinum in that it has ellipsoidal and hyaline ascospores (Fig. 12; Tanaka et al. (2015)). In addition, the PHI test results (Fig. 22f) revealed no significant recombination relationships between H. puerensis and its phylogenetically related taxa. Therefore, the morphological differences and phylogenetic analyses support the introduction of H. puerensis as a new species.

Figure 12.

Helminthosporium puerensis (HKAS 137606, holotype). A, B ascomata on a decaying branch of C. arabica; C, D vertical section of ascomata; E peridium wall; F pseudoparaphyses; G–K asci; L–P ascospores; Q an ascospore stained with Indian ink; R germinated ascospore; S culture on PDA from obverse and reverse. Scale bars: 100 μm (D); 20 μm (E–K); 10 μm (L–R).

Figure 13.

Phylogram generated from the best scoring RAxML tree, based on a combined ITS LSU, SSU, RPB2 and TEF1-α sequence dataset. Periconia pseudodigitata Kaz. Tanaka & K. Hiray., (KT 1395) and P. digitata (Cooke) Sacc., (CBS 510.77) are selected as the outgroup taxa. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are given above the nodes. All type strains are in bold and newly-generated sequences are in red.

Neomassariaceae H.A. Ariyaw., Jaklitsch & Voglmayr, Cryptogamie, Mycologie 39 (3): 367 (2018).

Neomassaria Mapook, Camporesi & K.D. Hyde, Fungal Diversity 80: 74 (2016).

Notes.

Neomassaria was proposed by Hyde et al. (2016) in Massariaceae Nitschke, with N. fabacearum Mapook, Camporesi & K.D. Hyde, as the type species. Later, Ariyawansa et al. (2018) collected a neomassaria-like species (N. formosana Ariyaw., Jaklitsch & Voglmayr), which formed a sister group with N. fabacearum and was well-separated from Massaria De Not. species (Massariaceae). Therefore, Neomassaria species were transferred to the new family Neomassariaceae (Ariyawansa et al. 2018; Yang et al. 2022). Neomassaria species comprise only teleomorphs (Hyde et al. 2016; Ariyawansa et al. 2018; de Silva et al. 2022; Yang et al. 2022). In this study, we introduce a new Neomassaria species with teleomorph, N. coffeae, from an Arabica coffee plant in Yunnan Province, China and this is the first report of Neomassaria from the coffee host.

Neomassaria coffeae L. Lu & Tibpromma, sp. nov.

Index Fungorum number: IF901004

Facesofungi number: FoF14730

Fig. 14

Etymology.

The species epithet “coffeae” refers to the host plant genus “Coffea” from which the fungus was isolated.

Diagnosis.

Differs from N. fabacearum by having guttulate ascospores with mucilaginous sheath and textura prismatica peridium.

Holotype.

HKAS 137608.

Description.

Saprobic on a decaying branch of C. arabica. Teleomorph: Ascomata 150–220 µm high × 150–250 µm diam. (x− = 191 × 210 µm, n = 15), solitary to gregarious, semi-immersed to immersed, coriaceous, visible as black dots on the substrate, unilocular, globose or subglobose, ostioles central. Peridium 10–20 µm wide (x− = 14 µm, n = 15), outer walls comprising 3–4 layers of textura prismatica cells, brown to dark brown, inner walls thin, hyaline and density. Hamathecium 1.5–2.5 µm wide (x− = 2 µm, n = 20), hyaline, filiform, septate, branched, cellular, numerous pseudoparaphyses. Asci 80–110 × 10–15 µm (x− = 93 × 13 µm, n = 20), 8-spored, bitunicate, fissitunicate, oblong to cylindrical, straight, sometimes with short pedicellate, with ocular chamber. Ascospores 15–18 × 5–7 µm (x− = 16.5 × 5.6 µm, n = 30), uniseriate to biseriate, hyaline, yellowish when mature, ellipsoid to broadly fusiform, 1-septate in the middle, constricted at the septum, guttulate, surrounded by mucilaginous sheath observed clearly when mature. Anamorph: Not observed.

Culture characteristics.

Ascospore germinating within 24 h on PDA. Colonies reached 4 cm in diameter after two months at 25 °C. Colonies obverse: circular, flat to slightly raised, fluffy, with filiform margin, white; reverse: brown in centre with yellowish to white edges.

Materials examined.

China, Yunnan Province, Baoshan, on a decaying branch of Coffea arabica (Rubiaceae) (24°9'N, 98°8'E, 1210 m alt.), 30 July 2022, LiLu, BS2-C19 (HKAS 137608, holotype), isotype MHZU 23-0066, ex-type living culture KUNCC 24-18349 = KUNCC 24-18350, ex-isotype living culture ZHKUCC 23-0642 = ZHKUCC 23-0643.

Notes.

According to the multi-gene phylogeny, Neomassaria coffeae forms a sister lineage to N. fabacearum (Fig. 15). Morphologically, N. coffeae can be distinguished from N. fabacearum by having guttulate ascospores with mucilaginous sheath and textura prismatica peridium (Fig. 14; Hyde et al. (2016)). Based on nucleotide comparisons, N. coffeae (ZHKUCC 23-0642) is different from the type species N. fabacearum (MFLU 16-1875) by 18/883 bp (2%, without gaps) of the LSU, 5/868 bp (0.6%, without gaps) of the SSU and 46/843 bp (5.5%, without gaps) of the TEF1-α. In addition, the PHI test results (Fig. 22g) revealed no significant recombination relationships between N. coffeae and its phylogenetically related taxa. Therefore, based on morphological characteristics and phylogenetic analyses, we introduce our strains as a new species, N. coffeae.

Figure 14.

Neomassaria coffeae (HKAS 137608, holotype). A, B ascomata on a decaying branch of C. arabica; C longitudinal section of an ascoma; D peridium wall; E pseudoparaphyses; F–J asci; K germinated ascospore; L–P ascospores; Q an ascospore stained with Indian ink; R culture on PDA from obverse and reverse. Scale bars: 50 μm (C); 10 μm (D, E, L–Q); 20 μm (F–K).

Figure 15.

Phylogram generated from the best scoring RAxML tree, based on a combined ITS LSU, SSU, RPB2 and TEF1-α sequence dataset. Berkleasmium longisporum Y.Z. Lu, J.C. Kang & K.D. Hyde, (MFLUCC 17-1999) and B. thailandicum (Tanney & A.N. Mill.) Y.Z. Lu & K.D. Hyde, (MFLUCC 17-2000) are selected as the outgroup taxa. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are given above the nodes. All type strains are in bold and newly-generated sequences are in red.

Occultibambusaceae D.Q. Dai & K.D. Hyde, Fungal Diversity 82: 25 (2016).

Neooccultibambusa Doilom & K.D. Hyde, Fungal Diversity 82: 126 (2016).

Notes.

Neooccultibambusa was introduced in Occultibambusaceae, based on phenotypic characteristics and phylogenetic analyses, with N. chiangraiensis Doilom & K.D. Hyde as the type species (Doilom et al. 2017). In this study, a new species of Neooccultibambusa is introduced from an Arabica coffee plant in Yunnan Province, China, which is the first report of Neooccultibambusa from a coffee host.

Neooccultibambusa coffeae L. Lu & Tibpromma, sp. nov.

Index Fungorum number: IF901005

Facesofungi number: FoF14731

Fig. 16

Etymology.

The species epithet “coffeae” refers to the host plant genus “Coffea” from which the fungus was isolated.

Diagnosis.

Differs from N. chiangraiensis and N. kaiyangensis X.D. Yu, S.N. Zhang & Jian K. Liu by the greyish-green ascospores.

Holotype.

HKAS 137604.

Description.

Saprobic on decaying branch of C. arabica. Teleomorph: Ascomata 140–180 × 200–250 µm (x− = 156 × 218 µm, n = 10), superficial to semi-immersed, solitary to gregarious, small, black spots on host surface, unilocular, globose or subglobose, some with ostiolate. Peridium 10–20 µm wide (x− = 15 µm, n = 20), outer walls comprising 2–4 layers of textura angularis cells, brown to dark brown, inner walls thin, hyaline and density. Hamathecium 2–4 µm wide (x− = 3.2 µm, n = 20), hyphae-like, hyaline, filiform, branched, pseudoparaphyses numerous. Asci 100–200 × 20–30 µm (x− = 156 × 24 µm, n = 20), 8-spored, bitunicate, cylindrical-clavate, straight, with a short furcate, apically rounded, with an ocular chamber. Ascospores 30–40 × 8–12 µm (x− = 36.6 × 10.3 µm, n = 50), overlapping biseriate, hyaline when young, greyish-green when mature, fusoid or elliptical, 1–3-septate, guttulate, smooth-walled, mucilaginous sheath present. Anamorph: Not observed.

Culture characteristics.

Ascospores germinating on PDA within 24 h, colonies reached 4 cm in diameter after two months at 25 °C, mycelia superficial, filamentous, with filiform margin, flat, smooth, from above, brown at the centre, dark brown at the edge, from below, dark brown.

Materials examined.

China, Yunnan Province, Xishuangbanna, Pu’wen Town, on a decaying branch of Coffea arabica (Rubiaceae) (22°31'18"N, 101°2'44"E, 850 m alt.), 15 September 2021, LiLu, JHPW 13 (HKAS 137604, holotype), isotype MHZU 23-0056, ex-type living culture KUNCC 24-18351, ex-isotype living culture ZHKUCC 23-0622; China, Yunnan Province, Pu’er, on a decaying branch of C. arabica, (22°36'2"N, 101°0'59"E, 1015 m alt.), 16 September 2021, LiLu, Pu’er 1-5 (HKAS 137603, paratype) , isoparatype MHZU 23-0057, ex-paratype living culture KUNCC 24-18353, ex-isoparatype living culture ZHKUCC 23-0624.

Notes.

In the concatenated phylogenetic analysis, Neooccultibambusa coffeae forms a distinct lineage within Neooccultibambusa, closely related to N. chiangraiensis and N. kaiyangensis (Fig. 17). Morphologically, the new species resembles N. chiangraiensis and N. kaiyangensis in shape, but differs in the colour of ascospores. The ascospores of N. coffeae are greyish-green when mature, while the ascospores of N. chiangraiensis and N. kaiyangensis are pale brown (Fig. 16; Doilom et al. (2017); Yu et al. (2021)). Based on nucleotide comparisons, N. coffeae (ZHKUCC 23-0622) is different from N. chiangraiensis (MFLUCC 12-0559) by 50/494 bp (10%, without gaps) of the ITS, 22/872 bp (2.5%, without gaps) of the LSU, 16/943 bp (1.6%, without gaps) of the SSU and 32/613 bp (5%, without gaps) of the TEF1-α; In comparison, it is different from N. kaiyangensis (CGMCC 3.20404) in 42/467 bp (9%, without gaps) of the ITS, 20/836 bp (2%, without gaps) of the LSU, 16/1009 bp (1.5%, without gaps) of the SSU, 42/963 bp (4%, without gaps) of the TEF1-α and 88/886 bp (10%, without gaps) of the RPB2. In the BLASTn NCBI GenBank database search of ITS, LSU, SSU, RPB2 and TEF1-α sequences, ITS results are similar to Brunneofusispora hyalina M.S. Calabon & K.D. Hyde, (MFLU 21-0016) with 90% similarity, LSU is similar to N. trachycarpi X.D. Yu, S.N. Zhang & Jian K. Liu, (CGMCC 3.20405) with 98% similarity, SSU is similar to Roussoella sp. (GMB1323) with 93% similarity, RPB2 and TEF1-α results are similar to N. kaiyangensis (MFLUCC 17-2128) with 90% and 96% similarity, respectively. In addition, the PHI test results (Fig. 22h) revealed no significant recombination relationships between N. coffeae and its phylogenetically related taxa. The morphological differences and phylogenetic analyses support the introduction of N. coffeae as a new species.

Figure 16.

Neooccultibambusa coffeae (HKAS 137604, holotype). A, B ascomata on a decaying branch of C. arabica; C longitudinal section of an ascoma; D peridium wall; E pseudoparaphyses; F–J asci; L–O ascospores; P an ascospore stained with Indian ink; K germinated ascospores; Q culture on PDA from obverse and reverse. Scale bars: 50 μm (C); 20 μm (D, E, K–P); 30 μm (F–J).

Figure 17.

Phylogram generated from the best scoring RAxML tree, based on a combined ITS LSU, SSU, RPB2 and TEF1-α sequence dataset. Ohleria modesta Fuckel, (CBS 141480 and MGC) are selected as the outgroup taxa. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are given above the nodes. All type strains are in bold and newly-generated sequences are in red.

Roussoellaceae J.K. Liu, Phookamsak, D.Q. Dai & K.D. Hyde, Phytotaxa 181 (1): 7 (2014).

Pararoussoella Wanas., E.B.G. Jones & K.D. Hyde, Fungal Diversity 89: 169 (2018).

Notes.

Pararoussoella was proposed by Wanasinghe et al. (2018) with the type species P. rosarum Wanas., E.B.G. Jones & K.D. Hyde. The genus was introduced for the species that are distantly related to the type species of Roussoella Sacc., R. nitidula Sacc. & Paol. (Phukhamsakda et al. 2020). Pararoussoella comprises only five species and is reported as anamorph and teleomorph (Crous et al. 2019, 2020). Pararoussoella coffeae is introduced herein as a new species with anamorph; it was isolated from an Arabica coffee plant in Yunnan Province, China and this is the first report of Pararoussoella from a coffee host.

Pararoussoella coffeae L. Lu & Tibpromma, sp. nov.

Index Fungorum number: IF901006

Facesofungi number: FoF14732

Fig. 18

Etymology.

The species epithet “coffeae” refers to the host plant genus “Coffea” from which the fungus was isolated.

Diagnosis.

Differs from other Pararoussoella species by the subcylindrical to ellipsoid or, sometimes, ovoid conidia.

Holotype.

HKAS 137609.

Description.

Saprobic on decaying branch of C. arabica. Teleomorph: Not observed. Anamorph: Conidiomata 60–120 µm high × 100–160 µm diam. (x− = 92 × 121 µm, n = 15), pycnidial, immersed, globose to subglobose, brown, with central ostioles. Conidiomatal wall 15–25 µm wide (x− = 19 µm, n = 20), hyaline to light brown, thick, 4–6 layers, outer layer composed of brown cells of textura angularis, lined with a hyaline layer bearing conidiogenous cells. Conidiophores inconspicuous or micronematous, often reduced to conidiogenous cells. Conidiogenous cells lining the inner cavity, hyaline, smooth, oval to obpyriform or doliiform, phialidic with periclinal thickening at apex, 3–5 × 2–5 µm (x− = 4 × 3.5 µm, n = 30). Conidia 3.5–5 × 2–3 µm (x− = 4.4 × 2.4 µm, n = 30), aseptate, solitary, guttulate, subcylindrical to ellipsoid or, sometimes, ovoid, smooth, apex bluntly rounded, base truncate, hyaline when young, becoming light brown when mature.

Culture characteristics.

Conidia germinating on PDA within 24 h, colonies reached 2.5–3 cm in diameter after one month at 25 °C, filamentous, with entire margin, flat to raised, with many white aerial mycelia, from above, white at the centre, yellowish at the edge, from below, yellowish.

Materials examined.

China, Yunnan Province, Lincang, on a decaying branch of Coffea arabica (Rubiaceae) (24°17'N, 99°99'E, 960 m alt.), 28 July 2022, LiLu, LC1-C3 (HKAS 137609, holotype), isotype MHZU 23-0061, ex-type living culture KUNCC 24-18355 = KUNCC 24-18356, ex-isotype living culture ZHKUCC 23-0632 = ZHKUCC 23-0633.

Notes.

In the concatenated phylogenetic analysis, Pararoussoella coffeae forms a sister branch basal to P. mangrovei (Phukhams. & K.D. Hyde) Phukhams. & K.D. Hyde (Fig. 19). Since P. mangrovei has only been reported as teleomorph, we performed nucleotide comparisons; P. coffeae (ZHKUCC 23-0632) is different from P. mangrovei (MFLUCC 16-0424) by 20/434 bp (4.6%, without gaps) of the ITS, 14/805 bp (1.7%, without gaps) of the LSU, 99/796 bp (12%, without gaps) of the RPB2 and 28/718 bp (3.8%, without gaps) of the TEF1-α. Based on morphology, our novel taxon in Pararoussoella is similar to the species P. juglandicola Crous & R.K. Schumach. in aseptate and brown conidia, but differs in the shape of conidia. The conidia of our new species are subcylindrical to ellipsoid, sometimes ovoid, while the conidia of P. juglandicola are subcylindrical; besides, the characteristics of guttulate in our species are more distinct than P. juglandicola (Fig. 18; Crous et al. (2019)). In addition, the PHI test results (Fig. 22i) revealed no significant recombination relationships between P. coffeae and its phylogenetically related taxa. Therefore, the morphological differences and phylogenetic analyses support the introduction of P. coffeae as a new species.

Figure 18.

Pararoussoella coffeae (HKAS 137609, holotype). A, B appearance of conidiomata on a decaying branch of C. arabica; C, D longitudinal section of conidiomata; E conidiomata wall; F conidiogenous cells and conidia; G conidia; H germinated conidium; I culture on PDA from the obverse and reverse. Scale bars: 20 μm (C–F); 5 μm (G, H).

Figure 19.

Phylogram generated from the best scoring RAxML tree. based on a combined ITS LSU, SSU, RPB2 and TEF1-α sequence dataset. Torula herbarum (Pers.) Link, (CBS 111855) and T. hollandica Crous, (CBS 220.69) are selected as the outgroup taxa. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are given above the nodes. All type strains are in bold and newly-generated sequences are in red.

Thyridariaceae Q. Tian & K.D. Hyde, Fungal Diversity 63 (1): 254 (2013).

Cycasicola Wanas., E.B.G. Jones & K.D. Hyde, Fungal Diversity 89: 161 (2018).

Notes.

Cycasicola , typified by Cy. goaensis Wanas., E.B.G. Jones & K.D. Hyde, was introduced by Wanasinghe et al. (2018), based on multi-gene phylogenetic analyses. This genus consists of only two species: Cy. goaensis and Cy. leucaenae Jayasiri, E.B.G. Jones & K.D. Hyde; both have been reported as saprobic with an anamorph from Cycas sp. in India and Leucaena sp. in Thailand, respectively (Wanasinghe et al. 2018; Jayasiri et al. 2019). In this study, we provide an updated tree for the family and introduce a new species, Cy. coffeae, from an Arabica coffee plant. This is the first report of Cycasicola from a coffee host.

Cycasicola coffeae L. Lu & Tibpromma, sp. nov.

Index Fungorum number: IF901007

Facesofungi number: FoF14733

Fig. 20

Etymology.

The species epithet “coffeae” refers to the host plant genus “Coffea” from which the fungus was isolated.

Diagnosis.

Differs from Cy. goaensis by the ellipsoid and larger conidia.

Holotype.

HKAS 137613.

Description.

Saprobic on decaying branch of C. arabica. Teleomorph: Not observed. Anamorph: Coelomycetous. Conidiomata 100–180 µm high × 120–200 µm diam. (x− = 132 × 160 µm, n = 20), pycnidial, solitary, gregarious or confluent, immersed, unilocular, globose to subglobose or irregular, brown, with central ostiolar. Conidiomatal wall 15–20 µm wide (x− = 17.5 µm, n = 30), composed of 2–3 brown cells in the outer layers and two hyaline cells in the inner layer, with textura angularis cells. Conidiophores inconspicuous or micronematous, often reduced to conidiogenous cells. Conidiogenous cells 4–6 × 3–5 µm (x− = 5 × 4 µm, n = 30), phialidic, hyaline, cylindrical to ampulliform, smooth-walled. Conidia 4–7 × 2–3 µm (x− = 5.5 × 2.7 µm, n = 30), hyaline to brownish-orange, ellipsoid to cylindrical or some ovoid, continuous, straight or slightly curved, obtuse at apex and base, aseptate, guttulate, smooth-walled.

Culture characteristics.

Conidia germinating on PDA within 24 h, colonies reached 3.5 cm in diameter after one month at 25 °C, circular, radially striated, with a filiform edge, flat, smooth, colonies from above brown at the centre, hyaline to grey at the middle, dark green at the edge, from below, dark green to black.

Materials examined.

China, Yunnan Province, Dali, on a decaying branch of Coffea arabica (Rubiaceae) (26°09'N, 101°91'E, 1415 m alt.), 25 July 2022, LiLu, DL-C4 (HKAS 137613, holotype), isotype MHZU 23-0065, ex-type living culture KUNCC 24-18357 = KUNCC 24-18358, ex-isotype living culture ZHKUCC 23-0640 = ZHKUCC 23-0641.

Notes.

In the concatenated phylogenetic analysis, Cycasicola coffeae forms a distinct allied basal lineage with Cy. goaensis and Cy. leucaenae (Fig. 21). Based on morphology, the conidia of our fungus are very similar to those of Cy. goaensis (type species). However, the conidia of Cy. coffeae (4–7 × 2–3 µm) are larger than Cy. goaensis (3.5–5 × 2.2–2.6 µm) (Fig. 20, Wanasinghe et al. (2018)). Based on nucleotide comparisons, Cy. coffeae (ZHKUCC 23-0640) is different from Cy. goaensis (MFLUCC 17-0754) by 31/485 bp (6.5%, without gaps) of the ITS, 4/850 bp (0.5%, without gaps) of the LSU, 2/1036 bp (0.2%, without gaps) of the SSU and 25/925 bp (2.7%, without gaps) of the TEF1-α. In addition, the PHI test results (Fig. 22j) revealed no significant recombination relationships between Cy. coffeae and its phylogenetically related taxa. Therefore, the morphological differences and phylogenetic analyses support the introduction of Cy. coffeae as a new species.

Figure 20.

Cycasicola coffeae (HKAS 137613, holotype). A, B conidiomata on a decaying branch of C. arabica; C, D longitudinal section of conidiomata; E conidioma wall and conidiogenous cells; F conidia; G germinated conidium; H culture on PDA from the obverse and reverse. Scale bars: 50 μm (C, D); 10 μm (E–G).

Figure 21.

Phylogram generated from the best scoring RAxML tree, based on a combined ITS LSU, SSU and TEF1-α sequence dataset. Occultibambusa bambusae D.Q. Dai & K.D. Hyde, (MFLUCC 13-0855 and MFLUCC 11-0394) are selected as the outgroup taxa. Bootstrap support values for ML equal to or greater than 70% and PP equal to or greater than 0.90 are given above the nodes. All type strains are in bold and newly-generated sequences are in red.

Discussion

So far, 10,233 new fungal species have been reported in China, mainly distributed in southern China, viz. Yunnan (2136), Taiwan (1470), Guangdong (614), Hainan (532), Sichuan (473), Guizhou (451) and Guangxi (404) provinces (Wang and Cai 2023). Yunnan’s unique geographical location enhances its rich natural resources, with the western region supporting a highland cold-resistant biome and the southern and south-western regions featuring a tropical biome (Shen et al. 2022). This diverse ecological landscape makes Yunnan a region of significant importance for fungal discoveries, contributing 1/5 of the total number of new fungal species identified in China (Wang and Cai 2023). This study introduces ten new species associated with Arabica coffee distributed across ten different genera and families in the order Pleosporales, from Yunnan, China. Amongst the ten genera, two genera, viz. Helminthosporium and Montagnula, have been reported from coffee previously. However, eight genera, viz. Cycasicola, Flabellascoma, Leucaenicola, Longiostiolum, Neomassaria, Neooccultibambusa, Pararoussoella and Xenodidymella are reported for the first time from Arabica coffee in this study, marking a significant contribution to the field.

In the previous study, Helminthosporium canephorae Steyaert, H. coffeae Massee, H. glabroides F. Steven, and H. ubangiense Henn. have been reported as pathogens in coffee from Africa (the Democratic Republic of the Congo, Ethiopia and Ghana) and America (Nicaragua) (Lu et al. 2022a). However, most Helminthosporium species are usually found as common saprobic fungi from various hosts worldwide; some can be found as pathogens; for example, H. oryzae Breda de Haan has been reported as an economically important pathogen that causes brown spot disease in various crops with worldwide occurrences (Alcorn 1983; Voglmayr and Jaklitsch 2017; Boonmee et al. 2021) and only a few have been reported as endophytes with the ability to promote plant growth (Diene et al. 2010). Another genus, Montagnula has also been reported from coffee; for example, Montagnula thailandica Mapook & K.D. Hyde has been reported as a saprobe in coffee from China (Lu et al. 2022d). Additionally, Montagnula species are distributed on various hosts (such as Arecaceae Bercht. & J.Presl, Asparagaceae Juss., Cactaceae Juss., Fabaceae Lindl., Poaceae Juss. and Rubiaceae) and across different habitats (freshwater to terrestrial) worldwide (Wanasinghe et al. 2024). It is important to note that most Montagnula species have been found as saprobes with teleomorphs (Sun et al. 2023); however, only M. cylindrospora has been isolated from human skin with its anamorph from culture (Crous et al. 2020). The life modes of those fungi are relatively monotonous, with a notable lack of reports on anamorphs occurring on natural substrates. Further investigation into their life modes and complete morphology is essential to understanding their potential impacts on ecosystems.

In addition, the members of the two genera introduced in this study can be found as pathogens and saprobes. For example, three Leucaenicola species were reported to be associated with leaf lesions from different hosts from China, but their pathogenicity has not been confirmed (Ariyawansa 2020a, b); another two species have been reported as saprobes from Thailand (Jayasiri et al. 2019). Xenodidymella species are notable as pathogens causing cane blight, leaf blight, necrosis, leaf spot or spur blight in different plants and are mainly distributed in Iran and New Zealand (Ahmadpour et al. 2022; Crous et al. 2024; Karimi et al. 2024) and fewer are saprobes and mainly distributed on Germany and Italy (Chen et al. 2015; Hyde et al. 2020). The adaptability of the two genera to diverse niches, with pathogenic members posing significant threats to plant health in certain regions (Lu et al. 2022a), is truly impressive. This highlights the importance of understanding their behaviour and potential impact on plant health. Saprobic counterparts contribute to organic matter decomposition in various ecosystems, which is essential in maintaining nutrient cycling (Karaman et al. 2012). We also hypothesised that Leucaenicola and Xenodidymella might be able to switch their life mode from pathogens to saprobes, as fungi are capable of switching their modes of nutrition; many pathogenic fungi may persist as saprobes once the plant organ on which they reside, senesces (Hyde et al. 2007).

The rest of the members in Cycasicola, Flabellascoma, Longiostiolum, Neomassaria, Neooccultibambusa and Pararoussoella, all consist entirely as only saprobic species, which have been reported from various hosts. Cycasicola species have been reported from India and Thailand (Wanasinghe et al. 2018; Jayasiri et al. 2019), all Flabellascoma species have been reported from China (Hashimoto et al. 2018; Bao et al. 2019; Yu et al. 2022), the monotypic genus Longiostiolum was described from Thailand (Li et al. 2016), both Neomassaria and Neooccultibambusa species have been found in China, Thailand and Italy (Hyde et al. 2016; Ariyawansa et al. 2018; de Silva et al. 2022; Yang et al. 2022) and Pararoussoella species have been identified from China, Germany, Thailand, Ukraine and the UK (Crous et al. 2019, 2020; Phukhamsakda et al. 2020). These genera have only been reported as saprobic fungi, which play a crucial role in decomposing organic matter across various environments, including coffee plantations, facilitating the renewal and recycling of nutrients and carbon through the action of multiple enzymes, thereby maintaining ecosystem balance (Karaman et al. 2012).

Saprobic fungi have recently garnered significant attention as biocontrol agents and resistance inducers due to their potential spectrum of antifungal activity (de Oliveira et al. 2023). They are capable of secreting enzymes and activating plant defence responses (Yedidia et al. 2003), while also releasing metabolites that inhibit the growth of phytopathogenic communities (de Oliveira et al. 2023). All of the new species described in this study were found to be associated with dead coffee plants, a clear indication of these fungi’s crucial role in the decomposition of organic matter in coffee plantation ecosystems. This study significantly enriches the knowledge of the diversity of coffee-associated saprobic fungi in Yunnan Province of China, paving the way for potential applications such as biocontrol of coffee diseases and discoveries in mycology.

Pleosporales , the largest order of Dothideomycetes, was proposed by Luttrell (1955) and formally established by Barr (1990). It comprises a quarter of all dothideomycetous species and contains two major suborders: Massarineae and Pleosporineae M.E. Barr (Zhang et al. 2012). Pleosporales, a significant player in the top 50 fungal operational taxonomic units in plants’ diversity of fungal community composition (Yang et al. 2023) and home to about 91 genera and 700 species (Hyde et al. 2024) has been a subject of our intensive study. Our research, conducted rapidly, has unveiled a significant revelation – the order Pleosporales is notably predominant in the diversity of saprobic fungi associated with coffee, particularly in the Yunnan Province of China. Over a span of just four years, we have documented 31 new species and records, with 24 of these belonging to Pleosporales (See Suppl. material 1: table S1).

Interestingly, this study has expanded the morphological characteristics of Leucaenicola. This genus was previously represented by five species known only from their anamorph, including Leucaenicola aseptata and L. phraeana isolated from decaying pods of Leucaena sp. in Thailand, L. osmanthi associated with leaf lesions of Osmanthus fragrans in Taiwan (China) and L. camelliae and L. taiwanensis Ariyaw., I. Tsai & Thambug., isolated from leaf lesions of Camellia sinensis (L.) Kuntze, in the same areas as L. osmanthi. Herein, Leucaenicola coffeae, supported by combined phylogenetic analysis and morphological evidence from both teleomorph and anamorph stages, is presented as the first teleomorph within the genus (Jayasiri et al. 2019; Ariyawansa et al. 2020a, b). This phenomenon may be attributed to the specific growth conditions in Yunnan, such as the temperature, humidity and nutrient availability, which likely favour the production of the teleomorph. As a result, it offers more comprehensive data for future researchers studying and identifying this genus.

Another fascinating aspect of our research is the adaptability of individual fungal species to different geographical and climatic conditions. For instance, Neooccultibambusa coffeae was observed in subtropical (Pu’er) and tropical regions (Xishuangbanna), highlighting its remarkable capacity to overcome geographical and climatic barriers. This adaptability underscores these fungal species’ resilience and potential to colonise diverse ecosystems, offering valuable insights into their ecological roles and exciting potential applications in mycology and environmental science.

Figure 22.

Split graphs showing the results of the pairwise homoplasy index (PHI) test of the new taxa and closely-related taxa using LogDet transformation and splits decomposition. a Leucaenicola coffeae; b Montagnula coffeae; c Xenodidymella coffeae; d Flabellascoma coffeae; e Longiostiolum coffeae; f Helminthosporium puerensis; g Neomassaria coffeae; h Neooccultibambusa coffeae; i Pararoussoella coffeae; j Cycasicola coffeae. PHI test result P‐value (Φw) ≤ 0.05 indicates that there is significant recombination between the isolates included in the alignment. The new taxa are in red, “T” indicate the type species and each PHI test value and scale bars are given in the bottom right corner.

Conclusion

In conclusion, our research on coffee-associated saprobic fungi across five regions of Yunnan Province (Baoshan, Dali, Lincang, Pu’er and Xishuangbanna), China, revealed a rich diversity and numerous species novelties, with ten new taxa formally described in this study. Compared to other coffee-associated saprobic fungi reported from different regions (1980–2020 vs. 2021–2024), our findings suggest unique fungal community structures that local environmental conditions and agricultural practices may influence. For instance, the high prevalence of saprophytic fungi in our samples may reflect the organic matter decomposition dynamics specific to the study region. These findings, a stepping stone for further research, contribute to understanding coffee-associated fungal ecology and provide a foundation for developing sustainable agricultural practices. This is just the beginning of our journey. We believe that additional potentially new taxonomic taxa, new host records and geographic records are waiting to be discovered in subsequent studies. The taxa with distinctive distributions in this region are yet to be fully explored. Some coffee-associated saprobic fungi may serve as potential biocontrol agents, effectively suppressing the growth of pathogens responsible for coffee plant diseases, while also contributing to the balance of organic matter within coffee ecosystems. However, the full potential of these fungi remains untapped. Urgent and comprehensive research is needed to explore fungi’s diversity, community composition and ecological roles in coffee environments. Research should also investigate the environmental factors influencing their ecological preferences and potential host-specific interactions between pathogenic and saprobic species. Additionally, elucidating the biological functions of coffee-associated saprobic fungi, understanding their host or environmental preferences and studying their interactions with other microorganisms within their habitats are crucial for advancing coffee cultivation and production in China and globally.

Acknowledgements

Li Lu is grateful to Mae Fah Luang University for providing the tuition fee scholarship for her Ph.D. She also thanks Hasith Priyashantha for his help with the Graphical abstract image. The authors thank the Key Laboratory of Yunnan Provincial Department of Education of the Deep-Time Evolution on Biodiversity from the Origin of the Pearl River for their support. The authors extend their appreciation to the researchers supporting project number (RSP2025R56), King Saud University, Riyadh, Saudi Arabia. Nakarin Suwannarach and Jaturong Kumla thank Chiang Mai University for the support. We would like to thank Program of Doctoral Innovation Research Team from Qujing Normal University for suppor.

Additional information

Conflict of interest

The authors have declared that no competing interests exist.

Ethical statement

No ethical statement was reported.

Adherence to national and international regulations

All the fungal strains used in this study have been legally obtained, respecting the Convention on Biological Diversity (Rio Convention).

Funding

This work was supported by the Yunnan Provincial Department of Science and Technology “Zhihui Yunnan” plan (202403AM140023), the High-Level Talent Recruitment Plan of Yunnan Provinces (High-End Foreign Experts Programs and “Young Talents”), the National Natural Science Foundation of China (No. NSFC 32260004 and 32460002). The authors further extend their appreciation to the Meemann Chang Academician Workstation in Yunnan Province (202225AF150002), Yunnan Province Young and Middle-aged Academic and Technical Leaders Reserve Talents Program (202305AC350252) and the researchers supporting project number (RSP2025R56), King Saud University, Riyadh, Saudi Arabia.

Author contributions

Writting original draft: Li Lu. Review and editing: Samantha C. Karunarathna, Kunhiraman C. Rajeshkumar, Abdallah M. Elgorban, Ruvishika S. Jayawardena, Sinang Hongsanan, Nakarin Suwannarach, Jaturong Kumla, Kevin D. Hyde, Qiang Li, Dong-Qin Dai. Software: Yin-Ru Xiong. Data curation: Mei-Yan Han, De-Ge Zheng. Supervision: Saowaluck Tibpromma.

Author ORCIDs

Li Lu https://orcid.org/0000-0003-0977-6414

Samantha C. Karunarathna https://orcid.org/0000-0001-7080-0781

Kunhiraman C. Rajeshkumar https://orcid.org/0000-0003-0401-8294

Abdallah M. Elgorban https://orcid.org/0000-0003-3664-7853

Ruvishika S. Jayawardena https://orcid.org/0000-0001-7702-4885

Sinang Hongsanan https://orcid.org/0000-0003-0550-3152

Nakarin Suwannarach https://orcid.org/0000-0002-2653-1913

Jaturong Kumla https://orcid.org/0000-0002-3673-6541

Yin-Ru Xiong https://orcid.org/0000-0002-4673-606X

Kevin D. Hyde https://orcid.org/0000-0002-2191-0762

Mei-Yan Han https://orcid.org/0009-0004-3705-5408

De-Ge Zheng https://orcid.org/0009-0001-9199-6784

Qiang Li https://orcid.org/0000-0002-9735-8214

Dong-Qin Dai https://orcid.org/0000-0001-8935-8807

Saowaluck Tibpromma https://orcid.org/0000-0002-4706-6547

Data availability

All tree alignments generated and/or analysed during the current study were deposited to Figshare (https://doi.org/10.6084/m9.figshare.28268366).

References

Adhikari M, Isaac EL, Paterson RRM, Maslin MA (2020) A review of potential impacts of climate change on coffee cultivation and mycotoxigenic fungi. Microorganisms 8: 1625. https://doi.org/10.3390/microorganisms8101625

Adugna G (2024) Coffee berry disease: a century-old anthracnose of green berries of Arabica coffee (Coffea arabica L.) in Africa. Journal of Plant Diseases and Protection 131(2): 315–328. https://doi.org/10.1007/s41348-023-00838-1

ALAsmari KM, Zeid IMA, Al-Attar AM (2020) Medicinal properties of Arabica coffee (Coffea arabica) oil: An Overview. Advancements in Life Sciences 8(1): 20–29.

Alcorn J (1983) Generic concepts in Drechslera, Bipolaris and Exserohilum. Mycotaxon 17: 1–86.

Aptroot A (2004) Two new ascomycetes with long gelatinous appendages collected from monocots in the tropics. Studies in Mycology 50: 307–311.

Ariyawansa HA, Jaklitsch WM, Voglmayr H (2018) Additions to Taiwan fungal flora 1: Neomassariaceae fam. nov. Cryptogamie. Mycologie 39(3): 359–372. https://doi.org/10.7872/crym/v39.iss3.2018.359

Ariyawansa HA, Tsai I, Hozzein WN, Thambugala KM (2020a) Leucaenicola osmanthi sp. nov. (Bambusicolaceae, Pleosporales), causing leaf spot of Osmanthus fragrans in Taiwan. Phytotaxa 437(1): 023–031. https://doi.org/10.11646/phytotaxa.437.1.3

Ariyawansa HA, Tsai I, Thambugala KM, Chuang WY, Lin SR, Hozzein WN, Cheewangkoon R (2020b) Species diversity of Pleosporalean taxa associated with Camellia sinensis (L.) Kuntze in Taiwan. Scientific Reports 10: 12762. https://doi.org/10.1038/s41598-020-69718-0

Ahmadpour SA, Mehrabi-Koushki M, Farokhinejad R, Asgari B (2022) Xenodidymella iranica sp. nov. and new hosts of X. glycyrrhizicola in Iran. Tropical Plant Pathology 47(3): 430–441. https://doi.org/10.1007/s40858-022-00491-3

Barr ME (1990) Some dictyosporous genera and species of Pleosporales in North America. New York Botanical Garden, 92 pp.

Berlese AN (1896) Icones Fungorum. Pyrenomycetes, vol 2. Kessinger Publishing, LLC, Whitefish, MT, USA, 216 pp.

Boonmee S, Wanasinghe DN, Calabon MS, Huanraluek N, Chandrasiri SKU, Jones GEB, Rossi W, Leonardi M, Singh SK, Rana S, Singh PN, Maurya DK, Lagashetti AC, Choudhary D, Dai YC, Zhao CL, Mu YH, Yuan HS, He SH, Phookamsak R, Jiang HB, Martín MP, Dueñas M, Telleria MT, Kałucka IL, Jagodziński AM, Liimatainen K, Pereira DS, Phillips AJL, Suwannarach N, Kumla J, Khuna S, Lumyong S, Potter TB, Shivas RG, Sparks AH, Vaghefi N, Abdel-Wahab MA, Abdel-Aziz FA, Li GJ, Lin WF, Singh U, Bhatt RP, Lee HB, Nguyen TTT, Kirk PM, Dutta AK, Acharya K, Sarma VV, Niranjan M, Rajeshkumar KC, Ashtekar N, Lad S, Wijayawardene NN, Bhat DJ, Xu RJ, Wijesinghe SN, Shen HW, Luo ZL, Zhang JY, Sysouphanthong P, Thongklang N, Bao DF, Aluthmuhandiram JVS, Abdollahzadeh J, Javadi A, Dovana F, Usman M, Khalid AN, Dissanayake AJ, Telagathoti A, Probst M, Peintner U, Garrido-Benavent I, Bóna L, Merényi Z, Boros L, Zoltán B, Stielow JB, Jiang N, Tian CM, Shams E, Dehghanizadeh F, Pordel A, Javan-Nikkhah M, Denchev TT, Denchev CM, Kemler M, Begerow D, Deng CY, Harrower E, Bozorov T, Kholmuradova T, Gafforov Y, Abdurazakov A, Xu JC, Mortimer PE, Ren GC, Jeewon R, Maharachchikumbura SSN, Phukhamsakda C, Mapook A, Hyde KD (2021) Fungal diversity notes 1387–1511: Taxonomic and phylogenetic contributions on genera and species of fungal taxa. Fungal Diversity 111: 1–335. https://doi.org/10.1007/s13225-021-00489-3

Bruen TC, Philippe H, Bryant D (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665–2681. https://doi.org/10.1534/genetics.105.048975

Chen Q, Jiang J, Zhang G, Cai L, Crous PW (2015) Resolving the Phoma enigma. Studies in Mycology 82: 137–217. https://doi.org/10.1016/j.simyco.2015.10.003

Chen Y, Tian W, Guo Y, Madrid H, Maharachchikumbura SS (2022) Synhelminthosporium gen. et sp. nov. and two new species of Helminthosporium (Massarinaceae, Pleosporales) from Sichuan Province, China. Journal of Fungi 8: 712. https://doi.org/10.3390/jof8070712

Chethana KT, Manawasinghe IS, Hurdeal V, Bhunjun CS, Appadoo M, Gentekaki E, Raspé O, Promputtha I, Hyde KD (2021) What are fungal species and how to delineate them? Fungal Diversity 109: 1–25. https://doi.org/10.1007/s13225-021-00483-9

Crous PW, Schumacher RK, Akulov A, Thangavel R, Hernández-Restrepo M, Carnegie AJ, Cheewangkoon R, Wingfield MJ, Summerell BA, Quaedvlieg W, Coutinho TA, Roux J, Wood AR, Giraldo A, Groenewald JZ (2019) New and interesting fungi. 2. Fungal Systematics and Evolution 3: 57. https://doi.org/10.3114/fuse.2019.03.06

Crous PW, Wingfield MJ, Chooi YH, Gilchrist CL, Lacey E, Pitt JI, Venzhik AS (2020) Fungal Planet description sheets: 1042–1111. Persoonia: Molecular Phylogeny and Evolution of Fungi 44: 301–459. https://doi.org/10.3767/persoonia.2020.44.11

Crous PW, Wingfield MJ, Jurjević Ž, Balashov S, Osiek ER, Marin-Felix Y, Groenewald JZ (2024) Fungal Planet description sheets: 1697–1780. Fungal Systematics and Evolution 14: 325–577. https://doi.org/10.3114/fuse.2024.14.19

De Bruyn F, Zhang SJ, Pothakos V, Torres J, Lambot C, Moroni AV, Callanan M, Sybesma W, Weckx S, De Vuyst L (2017) Exploring the impacts of postharvest processing on the microbiota and metabolite profiles during green coffee bean production. Applied and Environmental Microbiology 83: e02398-16. https://doi.org/10.1128/AEM.02398-16

De Silva N, Hyde KD, Lumyong S, Phillips AJL, Bhat DJ, Maharachchikumbura SSN, Thambugala KM, Tennakoon DS, Suwannarach N, Karunarathna SC (2022) Morphology, phylogeny, host association and geography of fungi associated with plants of Annonaceae, Apocynaceae and Magnoliaceae. Mycosphere 13: 955–1076. https://doi.org/10.5943/mycosphere/13/1/12

de Oliveira SAB, Barbosa FR, de Andrade EA, Bonaldo SM (2023) Saprobe Fungi from the southern Amazon: in vitro phytopathogen control. Observatório De La Economía Latinoamericana 21(11): 22999–23019. https://doi.org/10.55905/oelv21n11-237

Diene O, Takahashi T, Yonekura A, Nitta Y, Narisawa K (2010) A new fungal endophyte, Helminthosporium velutinum, promoting growth of a bioalcohol plant, sweet sorghum. Microbes and Environments 25(3): 216–219. https://doi.org/10.1264/jsme2.ME09165

Dissanayake A, Bhunjun C, Maharachchikumbura S, Liu J (2020) Applied aspects of methods to infer phylogenetic relationships amongst fungi. Mycosphere 11: 2652–2676. https://doi.org/10.5943/mycosphere/11/1/18

Doilom M, Dissanayake AJ, Wanasinghe DN, Boonmee S, Liu JK, Bhat DJ, Taylor JE, Bahkali AH, McKenzie EHC, Hyde KD (2017) Microfungi on Tectona grandis (teak) in northern Thailand. Fungal Diversity 82: 107–182. https://doi.org/10.1007/s13225-016-0368-7

Du T, Hyde KD, Mapook A, Mortimer PE, Xu J, Karunarathna SC, Tibpromma S (2021) Morphology and phylogenetic analyses reveal Montagnula puerensis sp. nov. (Didymosphaeriaceae, Pleosporales) from southwest China. Phytotaxa 514: 1–25. https://doi.org/10.11646/phytotaxa.514.1.1

Duong B, Marraccini P, Maeght JL, Vaast P, Lebrun M, Duponnois R (2020) Coffee microbiota and its potential use in sustainable crop management. A review. Frontiers in Sustainable Food Systems 4: 607935. https://doi.org/10.3389/fsufs.2020.607935

Freitas VV, Borges LLR, Vidigal MCTR, dos Santos MH, Stringheta PC (2024) Coffee: A comprehensive overview of origin, market, and the quality process. Trends in Food Science & Technology 146: 104411. https://doi.org/10.1016/j.tifs.2024.104411

Gichuru E (2005) Laboratory screening of some saprophytic coffee surface microflora antagonistic to Colletotrichum kahawae. Agronomie Africaine 17: 73–80. https://doi.org/10.4314/aga.v17i2.1659

Gole TW, Seyoum A (2024) The economic values of Coffea arabica biodiversity in Ethiopia. Journal of Earth and Environmental Science Research 6(2): 1–10. https://doi.org/10.47363/JEESR/2024(6)211

Hashimoto A, Hirayama K, Takahashi H, Matsumura M, Okada G, Chen C, Huang J, Kakishima M, Ono T, Tanaka K (2018) Resolving the Lophiostoma bipolare complex: Generic delimitations within Lophiostomataceae. Studies in Mycology 90: 161–189. https://doi.org/10.1016/j.simyco.2018.03.001

Hughes SJ (1953) Conidiophores, conidia, and classification. Canadian Journal of Botany 31: 577–659. https://doi.org/10.1139/b53-046

Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254–267. https://doi.org/10.1093/molbev/msj030

Hyde KD, Bussaban B, Paulus B, Crous PW, Lee S, Mckenzie EH, Lumyong S (2007) Diversity of saprobic microfungi. Biodiversity and Conservation 16: 7–35. https://doi.org/10.1007/s10531-006-9119-5

Hyde KD, Tennakoon DS, Jeewon R, Bhat DJ, Maharachchikumbura SSN, Rossi W, Leonardi M, Lee HB, Mun HY, Houbraken J, Nguyen TTT, Jeon SJ, Frisvad JC, Wanasinghe DN, Lücking R, Aptroot A, Cáceres MES, Karunarathna SC, Hongsanan S, Phookamsak R, de Silva NI, Thambugala KM, Jayawardena RS, Senanayake IC, Boonmee S, Chen J, Luo ZL, Phukhamsakda C, Pereira OL, Abreu VP, Rosado AWC, Bart B, Randrianjohany E, Hofstetter V, Gibertoni TB, Soares AMS, Plautz Jr HL, Sotão HMP, Xavier WKS, Bezerra JDP, Oliveira TGL, de Souza-Motta CM, Magalhães OMC, Bundhun D, Harishchandra D, Manawasinghe IS, Dong W, Zhang SN, Bao DF, Samarakoon MC, Pem D, Karunarathna A, Lin CG, Yang J, Perera RH, Kumar V, Huang SK, Dayarathne MC, Ekanayaka AH, Jayasiri SC, Xiao Y, Konta S, Niskanen T, Liimatainen K, Dai YC, Ji XH, Tian XM, Mešić A, Singh SK, Phutthacharoen K, Cai L, Sorvongxay T, Thiyagaraja V, Norphanphoun C, Chaiwan N, Lu YZ, Jiang HB, Zhang JF, Abeywickrama PD, Aluthmuhandiram JVS, Brahmanage RS, Zeng M, Chethana T, Wei D, Réblová M, Fournier J, Nekvindová J, Barbosa RN, dos Santos JEF, Oliveira NT, Li GJ, Ertz D, Shang QJ, Phillips AJL, Kuo CH, Camporesi E, Bulgakov TS, Lumyong S, Jones EBG, Chomnunti P, Gentekaki E, Bungartz F, Zeng XY, Fryar S, Tkalčec Z, Liang J, Li G, Wen TC, Singh PN, Gafforov Y, Promputtha I, Yasanthika E, Goonasekara ID, Zhao RL, Zhao Q, Kirk PM, Liu JK, Yan J, Mortimer PE, Xu J, Doilom M (2016) Fungal diversity notes 367–490: taxonomic and phylogenetic contributions to fungal taxa. Fungal Diversity 80(1): 1–270. https://doi.org/10.1007/s13225-016-0373-x

Hyde KD, Norphanphoun C, Chen J, Dissanayake AJ, Doilom M, Hongsanan S, Jayawardena RS, Jeewon R, Perera RH, Thongbai B, Wanasinghe DN, Wisitrassameewong K, Tibpromma S, Stadler M (2018) Thailand’s amazing diversity: up to 96% of fungi in northern Thailand may be novel. Fungal Diversity 93: 215–239. https://doi.org/10.1007/s13225-018-0415-7

Hyde KD, Dong Y, Phookamsak R, Jeewon R, Bhat DJ, Jones EBG, Liu NG, Abeywickrama PD, Mapook A, Wei D, Perera RH, Manawasinghe IS, Pem D, Bundhun D, Karunarathna A, Ekanayaka AH, Bao DF, Li J, Samarakoon MC, Chaiwan N, Lin CG, Phutthacharoen K, Zhang SN, Senanayake IC, Goonasekara ID, Thambugala KM, Phukhamsakda C, Tennakoon DS, Jiang HB, Yang J, Zeng M, Huanraluek N, Liu JK, Wijesinghe SN, Tian Q, Tibpromma S, Brahmanage RS, Boonmee S, Huang SK, Thiyagaraja V, Lu YZ, Jayawardena RS, Dong W, Yang EF, Singh SK, Singh SM, Rana S, Lad SS, Anand G, Devadatha B, Niranjan M, Sarma VV, Liimatainen K, Aguirre-Hudson B, Niskanen T, Overall A, Alvarenga RLM, Gibertoni TB, Pfliegler WP, Horváth E, Imre A, Alves AL, Santos AC, Tiago PV, Bulgakov TS, Wanasinghe DN, Bahkali AH, Doilom M, Elgorban AM, Maharachchikumbura SSN, Rajeshkumar KC, Haelewaters D, Mortimer PE, Zhao Q, Lumyong S, Xu J, Sheng (2020) Fungal diversity notes 1151–1276: taxonomic and phylogenetic contributions on genera and species of fungal taxa. Fungal Diversity 100: 5–277. https://doi.org/10.1007/s13225-020-00439-5

Hyde KD, Norphanphoun C, Ma J, Yang HD, Zhang JY, Du TY, Gao Y, Gomes de Farias AR, He SC, He YK, Li CJY, Li JY, Liu XF, Lu L, Su HL, Tang X, Tian XG, Wang SY, Wei DP, Xu RF, Xu RJ, Yang YY, Zhang F, Zhang Q, Bahkali AH, Boonmee S, Chethana KWT, Jayawardena RS, Lu YZ, Karunarathna SC, Tibpromma S, Wang Y, Zhao Q (2023) Mycosphere notes 387–412-novel species of fungal taxa from around the world. Mycosphere 4: 663–744. https://doi.org/10.5943/mycosphere/14/1/8

Hyde KD, Noorabadi MT, Thiyagaraja V, He MQ, Johnston PR, Wijesinghe SN, Armand A, Biketova AY, Chethana KWT, Erdoğdu M, Ge ZW, Groenewald JZ, Hongsanan S, Kušan I, Leontyev DV, Li DW, Lin CG, Liu NG, Maharachchikumbura SSN, Matočec N, May TW, McKenzie EHC, Mešić A, Perera RH, Phukhamsakda C, Piątek M, Samarakoon MC, Selcuk F, Senanayake IC, Tanney JB, Tian Q, Vizzini A, Wanasinghe DN, Wannasawang N, Wijayawardene NN, Zhao RL, Abdel-Wahab MA, Abdollahzadeh J, Abeywickrama PD, Absalan S, Acharya K, Afshari N, Afshan NS, Afzalinia S, Ahmadpour SA, Akulov O, Alizadeh A, Alizadeh M, Al-Sadi AM, Alves A, Alves VCS, Alves-Silva G, Antonín V, Aouali S, Aptroot A, Apurillo CCS, Arias RM, Asgari B, Asghari R, Assis DMA, Assyov B, Atienza V, Aumentado HDR, Avasthi S, Azevedo E, Bakhshi M, Bao DF, Baral HO, Barata M, Barbosa KD, Barbosa RN, Barbosa FR, Baroncelli R, Barreto GG, Baschien C, Bennett RM, Bera I, Bezerra JDP, Bhunjun CS, Bianchinotti MV, Błaszkowski J, Boekhout T, Bonito GM, Boonmee S, Boonyuen N, Bortnikov FM, Bregant C, Bundhun D, Burgaud G, Buyck B, Caeiro MF, Cabarroi-Hernández M, Cai MF, Cai L, Calabon MS, Calaça FJS, Callalli M, Câmara MPS, Cano-Lira J, Cao B, Carlavilla JR, Carvalho A, Carvalho TG, Castañeda-Ruiz RF, Catania MDV, Cazabonne J, Cedeño-Sanchez M, Chaharmiri-Dokhaharani S, Chaiwan N, Chakraborty N, Cheewankoon R, Chen C, Chen J, Chen Q, Chen YP, Chinaglia S, Coelho-Nascimento CCS, Coleine C, Costa-Rezende DH, Cortés-Pérez A, Crouch JA, Crous PW, Cruz RHSF, Czachura P, Damm U, Darmostuk V, Daroodi Z, Das K, Das K, Davoodian N, Davydov EA, da Silva GA, da Silva IR, da Silva RMF, da Silva Santos AC, Dai DQ, Dai YC, de Groot MD, De Kesel A, De Lange R, de Medeiros EV, de Souza CFA, de Souza FA, dela Cruz TEE, Decock C, Delgado G, Denchev CM, Denchev TT, Deng YL, Dentinger BTM, Devadatha B, Dianese JC, Dima B, Doilom M, Dissanayake AJ, Dissanayake DMLS, Dissanayake LS, Diniz AG, Dolatabadi S, Dong JH, Dong W, Dong ZY, Drechsler-Santos ER, Druzhinina IS, Du TY, Dubey MK, Dutta AK, Elliott TF, Elshahed MS, Egidi E, Eisvand P, Fan L, Fan X, Fan XL, Fedosova AG, Ferro LO, Fiuza PO, Flakus A, Fonseca EO, Fryar SC, Gabaldón T, Gajanayake AJ, Gannibal PB, Gao F, García-Sánchez D, García-Sandoval R, Garrido-Benavent I, Garzoli L, Gasca-Pineda J, Gautam AK, Gené J, Ghobad-Nejhad M, Ghosh A, Giachini AJ, Gibertoni TB, Gentekaki E, Gmoshinskiy VI, Góes-Neto A, Gomdola D, Gorjón SP, Goto BT, Granados-Montero MM, Griffith GW, Groenewald M, Grossart HP, Gu ZR, Gueidan C, Gunarathne A, Gunaseelan S, Guo SL, Gusmão LFP, Gutierrez AC, Guzmán-Dávalos L, Haelewaters D, Haituk H, Halling RE, He SC, Heredia G, Hernández-Restrepo M, Hosoya T, Hoog SD, Horak E, Hou CL, Houbraken J, Htet ZH, Huang SK, Huang WJ, Hurdeal VG, Hustad VP, Inácio CA, Janik P, Jayalal RGU, Jayasiri SC, Jayawardena RS, Jeewon R, Jerônimo GH, Jin J, Jones EBG, Joshi Y, Jurjević Ž, Justo A, Kakishima M, Kaliyaperumal M, Kang GP, Kang JC, Karimi O, Karunarathna SC, Karpov SA, Kezo K, Khalid AN, Khan MK, Khuna S, Khyaju S, Kirchmair M, Klawonn I, Kraisitudomsook N, Kukwa M, Kularathnage ND, Kumar S, Lachance MA, Lado C, Latha KPD, Lee HB, Leonardi M, Lestari AS, Li C, Li H, Li J, Li Q, Li Y, Li YC, Li YX, Liao CF, Lima JLR, Lima JMS, Lima NB, Lin L, Linaldeddu BT, Linn MM, Liu F, Liu JK, Liu JW, Liu S, Liu SL, Liu XF, Liu XY, Longcore JE, Luangharn T, Luangsa-ard JJ, Lu L, Lu YZ, Lumbsch HT, Luo L, Luo M, Luo ZL, Ma J, Madagammana AD, Madhushan A, Madrid H, Magurno F, Magyar D, Mahadevakumar S, Malosso E, Malysh JM, Mamarabadi M, Manawasinghe IS, Manfrino RG, Manimohan P, Mao N, Mapook A, Marchese P, Marasinghe DS, Mardones M, Marin-Felix Y, Masigol H, Mehrabi M, Mehrabi-Koushki M, Meiras-Ottoni A de, Melo RFR, Mendes-Alvarenga RL, Mendieta S, Meng QF, Menkis A, Menolli NJ, Mikšík M, Miller SL, Moncada B, Moncalvo JM, Monteiro JS, Monteiro M, Mora-Montes HM, Moroz EL, Moura JC, Muhammad U, Mukhopadhyay S, Nagy GL, Najam ul Sehar A, Najafiniya M, Nanayakkara CM, Naseer A, Nascimento ECR, Nascimento SS, Neuhauser S, Neves MA, Niazi AR, Nie Y, Nilsson RH, Nogueira PTS, Novozhilov YK, Noordeloos M, Norphanphoun C, Nuñez Otaño N, O’Donnell RP, Oehl F, Oliveira Jr JA, Oliveira I, Oliveira NVL, Oliveira PHF, Orihara T, Oset M, Pang KL, Papp V, Pathirana LS, Peintner U, Pem D, Pereira OL, Pérez-Moreno J, Pérez-Ortega S, Péter G, Pires-Zottarelli CLA, Phonemany M, Phongeun S, Pošta A, Prazeres JFSA, Quan Y, Quandt CA, Queiroz MB, Radek R, Rahnama K, Raj KNA, Rajeshkumar KC, Rajwar S, Ralaiveloarisoa AB, Rämä T, Ramírez-Cruz V, Rambold G, Rathnayaka AR, Raza M, Ren GC, Rinaldi AC, Rivas-Ferreiro M, Robledo GL, Ronikier A, Rossi W, Rusevska K, Ryberg M, Safi A, Salimi F, Salvador-Montoya CA, Samant B, Samaradiwakara NP, Sánchez-Castro I, Sandoval-Denis M, Santiago ALCMA, Santos ACDS, Santos LAdos, Sarma VV, Sarwar S, Savchenko A, Savchenko K, Saxena RK, Schoutteten N, Selbmann L, Ševčíková H, Sharma A, Shen HW, Shen YM, Shu YX, Silva HF, Silva-Filho AGS, Silva VSH, Simmons DR, Singh R, Sir EB, Sohrabi M, Souza FA, Souza-Motta CM, Sri-indrasutdhi V, Sruthi OP, Stadler M, Stemler J, Stephenson SL, Stoyneva-Gaertner MP, Strassert JFH, Stryjak-Bogacka M, Su H, Sun YR, Svantesson S, Sysouphanthong P, Takamatsu S, Tan TH, Tanaka K, Tang C, Tang X, Taylor JE, Taylor PWJ, Tennakoon DS, Thakshila SAD, Thambugala KM, Thamodini GK, Thilanga D, Thines M, Tiago PV, Tian XG, Tian WH, Tibpromma S, Tkalčec Z, Tokarev YS, Tomšovský M, Torruella G, Tsurykau A, Udayanga D, Ulukapı M, Untereiner WA, Usman M, Uzunov BA, Vadthanarat S, Valenzuela R, Van den Wyngaert S, Van Vooren N, Velez P, Verma RK, Vieira LC, Vieira WAS, Vinzelj JM, Tang AMC, Walker A, Walker AK, Wang QM, Wang Y, Wang XY, Wang ZY, Wannathes N, Wartchow F, Weerakoon G, Wei DP, Wei X, White JF, Wijesundara DSA, Wisitrassameewong K, Worobiec G, Wu HX, Wu N, Xiong YR, Xu B, Xu JP, Xu R, Xu RF, Xu RJ, Yadav S, Yakovchenko LS, Yang HD, Yang X, Yang YH, Yang YY, Yang YY, Yoshioka R, Youssef Noha H, Yu FM, Yu ZF, Yuan LL, Yuan Q, Zabin DA, Zamora JC, Zapata CV, Zare R, Zeng M, Zeng XY, Zhang JF, Zhang JY, Zhang S, Zhang XC, Zhao CL, Zhao H, Zhao HJ, Zhao Q, Zhou HM, Zhu XY, Zmitrovich IV, Zucconi L, Zvyagina E (2024) The 2024 Outline of Fungi and fungus-like taxa. Mycosphere 15(1): 5146–6239. https://doi.org/10.5943/mycosphere/15/1/25

Janse JM (1897) Les endophytes radicaux de quelques plantes javanaises. Annales du Jardin Botanique de Buitenzorg 14: 53–201.

Jaklitsch W, Voglmayr H (2016) Hidden diversity in Thyridaria and a new circumscription of the Thyridariaceae. Studies in Mycology 85: 35–64. https://doi.org/10.1016/j.simyco.2016.09.002

Jayasiri SC, Hyde KD, Ariyawansa HA, Bhat J, Buyck B, Cai L, Dai YC, Abd-Elsalam KA, Ertz D, Hidayat I, Jeewon R, Jones EBG, Bahkali AH, Karunarathna SC, Liu JK, Luangsa-ard JJ, Lumbsch HT, Maharachchikumbura SSN, McKenzie EHC, Moncalvo J-M, Ghobad-Nejhad M, Nilsson H, Pang KL, Pereira OL, Phillips AJL, Raspé O, Rollins AW, Romero AI, Etayo J, Selçuk F, Stephenson SL, Suetrong S, Taylor JE, Tsui CKM, Vizzini A, Abdel-Wahab MA, Wen TC, Boonmee S, Dai DQ, Daranagama DA, Dissanayake AJ, Ekanayaka AH, Fryar SC, Hongsanan S, Jayawardena RS, Li WJ, Perera RH, Phookamsak R, de Silva NI, Thambugala KM, Tian Q, Wijayawardene NN, Zhao RL, Zhao Q, Kang J-C, Promputtha I (2015) The faces of fungi database: fungal names linked with morphology, phylogeny and human impacts. Fungal Diversity 74: 3–18. https://doi.org/10.1007/s13225-015-0351-8

Jayasiri SC, Hyde KD, Jones EBG, McKenzie EHC, Jeewon R, Phillips AJL, Bhat DJ, Wanasinghe DN, Liu JK, Lu YZ, Kang JC, Xu J, Karunarathna SC (2019) Diversity, morphology and molecular phylogeny of Dothideomycetes on decaying wild seed pods and fruits. Mycosphere 10: 1–186. https://doi.org/10.5943/mycosphere/10/1/1

Karaman M, Novakovic M, Matavuly M (2012) Fundamental fungal strategies in restoration of natural environment. Fungi: Types, environmental impact and role in disease. New York: Nova Science Publishers Inc. [ISBN:978-1-61942-671-9]

Kraisitudomsook N, Ahrendt S, Riley R, LaButti K, Lipzen A, Daum C, Barry K, Grigoriev IV, Rämä T, Martin F, Smith ME (2024) On the origin of bird’s nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota). Molecular Phylogenetics and Evolution 193: 108010. https://doi.org/10.1016/j.ympev.2024.108010

Karimi M, Mehrabi-Koushki M, Farokhinejad R, Beigi S (2024) Additional new species of Xenodidymella from pasture-medicinal plants in Iran. Antonie van Leeuwenhoek 117(1): 110. https://doi.org/10.1007/s10482-024-02007-2

Larsson A (2014) AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30: 3276–3278. https://doi.org/10.1093/bioinformatics/btu531

Li GJ, Hyde KD, Zhao RL, Hongsanan S, Abdel-Aziz FA, Abdel-Wahab MA, Alvarado P, Alves-Silva G, Ammirati JF, Ariyawansa HA, Baghela A, Bahkali AH, Beug M, Bhat DJ, Bojantchev D, Boonpratuang T, Bulgakov TS, Camporesi E, Boro MC, Ceska O, Chakraborty D, Chen JJ, Chethana KWT, Chomnunti P, Consiglio G, Cui BK, Dai DQ, Dai YC, Daranagama DA, Das K, Dayarathne MC, De Crop E, De Oliveira RJV, Fragoso de Souza CA, De Souza JI, Dentinger BTM, Dissanayake AJ, Doilom M, Drechsler-Santos ER, Ghobad-Nejhad M, Gilmore SP, Góes-Neto A (2016) Fungal diversity notes 253–366: taxonomic and phylogenetic contributions to fungal taxa. Fungal Diversity 78: 1–237. https://doi.org/10.1007/s13225-016-0366-9

Liu SL, Zhao P, Cai L, Shen S, Wei HW, Na Q, Han M, Wei RX, Ge YP, Ma HX, Karunarathna SC, Tibpromma S, Zhang B, Dai D, Lin L, Fan XL, Luo ZL, Shen HW, Lu L, Lu WH, Xu RF, Tohtirjap A, Wu F, Zhou LW (2024) Catalogue of fungi in China 1. New taxa of plant-inhabiting fungi. Mycology: 1–58. https://doi.org/10.1080/21501203.2024.2316066

Lu L, Tibpromma S, Karunarathna SC, Jayawardena RS, Lumyong S, Xu J, Hyde KD (2022a) Comprehensive review of fungi on coffee. Pathogens 11: 411. https://doi.org/10.3390/pathogens11040411

Lu L, Karunarathna SC, Hyde KD, Suwannarach N, Elgorban AM, Stephenson SL, Al-Rejaie S, Jayawardena RS, Tibpromma S (2022b) Endophytic fungi associated with coffee leaves in China exhibited in vitro antagonism against fungal and bacterial pathogens. Journal of Fungi 8: 698. https://doi.org/10.3390/jof8070698

Lu L, Karunarathna SC, Hyde KD, Bhat DJ, Dai DQ, Jayawardena RS, Tibpromma S (2022c) Crassiparies yunnanensis sp. nov. (Neohendersoniaceae, Pleosporales) from dead twigs of Coffea arabica in China. Phytotaxa 543(4): 244–254. https://doi.org/10.11646/phytotaxa.543.4.4

Lu L, Karunarathna SC, Dai DQ, Xiong YR, Suwannarach N, Stephenson SL, Elgorban AM, Al-Rejaie S, Jayawardena RS, Tibpromma S (2022d) Description of four novel species in Pleosporales associated with coffee in Yunnan, China. Journal of Fungi 8: 1113. https://doi.org/10.3390/jof8101113

Lu L, Karunarathna SC, Dai DQ, Jayawardena RS, Suwannarach N, Tibpromma S (2022e) Three new species of Nigrograna (Dothideomycetes, Pleosporales) associated with Arabica coffee from Yunnan Province, China. MycoKeys 94: 51. https://doi.org/10.3897/mycokeys.94.95751

Lu L, Karunarathna SC, Liu YN, Elgorban AM, Tibpromma S, Jayawardena RS (2024) Pseudoconiocessia xishuangbannaensis gen. et sp. nov. in Coniocessiaceae, Xylariales from Coffea liberica in China. Phytotaxa 641(2): 125–137. https://doi.org/10.11646/phytotaxa.641.2.4

Luttrell ES (1955) The ascostromatic ascomycetes. Mycologia 47: 511–532. https://doi.org/10.1080/00275514.1955.12024473

Mapook A, Hyde KD, McKenzie EHC, Jones EB Gareth, Bhat DJ, Jeewon R, Stadler M, Samarakoon MC, Malaithong M, Tanunchai B, Buscot F, Wubet T, Purahong W (2020) Taxonomic and phylogenetic contributions to fungi associated with the invasive weed Chromolaena odorata (Siam weed). Fungal Diversity 101: 1–175. https://doi.org/10.1007/s13225-020-00444-8

Masaba DM (1993) The role of saprophytic surface microflora in the development of coffee berry disease (Colletotrichum coffeanum) in Kenya. PhD Thesis, Reading University. Reading, UK.

Monteiro MCP, Tavares DG, Nery EM, Queiroz MVD, Pereira OL, Cardoso PG (2020) Enzyme production by Induratia spp. isolated from coffee plants in Brazil. Brazilian Archives of Biology and Technology 63: e20180673. https://doi.org/10.1590/1678-4324-2020180673

Neilson J, Wang JHZ (2019) China and the changing economic geography of coffee value chains. Singapore Journal of Tropical Geography 40(3): 429–451. https://doi.org/10.1111/sjtg.12279

Niskanen T, Lücking R, Dahlberg A, Gaya E, Suz LM, Mikryukov V, Liimatainen K, Druzhinina I, Westrip JRS, Mueller GM, Martins-Cunha K, Kirk P, Tedersoo L, Antonelli A (2023) Pushing the frontiers of biodiversity research: Unveiling the global diversity, distribution, and conservation of fungi. Annual Review of Environment and Resources 48(1): 149–176. https://doi.org/10.1146/annurev-environ-112621-090937

Pem D, Jeewon R, Chethana KWT, Hongsanan S, Doilom M, Suwannarach N, Hyde KD (2021) Species concepts of Dothideomycetes: classification, phylogenetic inconsistencies and taxonomic standardization. Fungal Diversity 109: 283–319. https://doi.org/10.1007/s13225-021-00485-7

Phukhamsakda C, McKenzie EHC, Phillips AJL, Jones EBG, Bhat DJ, Stadler M, Bhunjun CS, Wanasinghe DN, Thongbai B, Camporesi E, Ertz D, Jayawardena RS, Perera RH, Ekanayake AH, Tibpromma S, Doilom M, Xu J, Hyde KD (2020) Microfungi associated with Clematis (Ranunculaceae) with an integrated approach to delimiting species boundaries. Fungal Diversity 102: 1–203. https://doi.org/10.1007/s13225-020-00448-4

Quesada-Moraga E, Herrero N, Zabalgogeazcoa Í (2014) Entomopathogenic and Nematophagous fungal endophytes. In: Verma V, Gange A (Eds) Advances in endophytic research. Springer, New Delhi, 85–99. https://doi.org/10.1007/978-81-322-1575-2_4

Rambaut A (2014) FigTree 1.4. 2 software. Institute of Evolutionary Biology, Univ. Edinburgh.

Rathnayaka AR, Tennakoon DS, Jones GE, Wanasinghe DN, Bhat DJ, Priyashantha AH, Stephenson SL, Tibprommaa 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: 1–28. https://doi.org/10.1080/0028825X.2024.2381734

Rigal C, Xu J, Hu G, Qiu M, Vaast P (2020) Coffee production during the transition period from monoculture to agroforestry systems in near optimal growing conditions, in Yunnan Province. Agricultural Systems 177: 102696. https://doi.org/10.1016/j.agsy.2019.102696

Senanayake IC, Rathnayaka AR, Marasinghe DS, Calabon MS, Gentekaki E, Lee HB, Hurdeal VG, Pem D, Dissanayake LS, Wijesinghe SN, Bundhun D, Nguyen TT, Goonasekara ID, Abeywickrama PD, Bhunjun CS, Jayawardena RS, Wanasinghe DN, Jeewon R, Bhat DJ, Xiang MM (2020) Morphological approaches in studying fungi: Collection, examination, isolation, sporulation and preservation. Mycosphere 11: 2678–2754. https://doi.org/10.5943/mycosphere/11/1/20

Shen HW, Bao DF, Bhat DJ, Su HY, Luo ZL (2022) Lignicolous freshwater fungi in Yunnan Province, China: an overview. Mycology 13(2): 119–132. https://doi.org/10.1080/21501203.2022.2058638

Subramanian C (1987) Three bitunicate ascomycetes and their anamorphs. Kavaka 15: 87–98.

Tanaka K, Hirayama K, Yonezawa H, Sato G, Toriyabe A, Kudo H, Hashimoto A, Matsumura M, Harada Y, Kurihara Y, Shirouzu T, Hosoya T (2015) Revision of the Massarineae (Pleosporales, Dothideomycetes). Studies in Mycology 82: 75–136. https://doi.org/10.1016/j.simyco.2015.10.002

Tibpromma S, Hyde KD, McKenzie EHC, Bhat DJ, Phillips AJL, Wanasinghe DN, Samarakoon MC, Jayawardena RS, Dissanayake AJ, Tennakoon DS, Doilom M, Phookamsak R, Tang AMC, Xu J, Mortimer PE, Promputtha I, Maharachchikumbura SSN, Khan S, Karunarathna SC (2018) Fungal diversity notes 840–928: micro-fungi associated with Pandanaceae. Fungal Diversity 93: 1–160. https://doi.org/10.1007/s13225-018-0408-6

Vaidya G, Lohman DJ, Meier R (2011) SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information. Cladistics 27: 171–180. https://doi.org/10.1111/j.1096-0031.2010.00329.x

Voglmayr H, Jaklitsch W (2017) Corynespora, Exosporium and Helminthosporium revisited-new species and generic reclassification. Studies in Mycology 87: 43–76. https://doi.org/10.1016/j.simyco.2017.05.001

Wanasinghe DN, Phukhamsakda C, Hyde KD, Jeewon R, Lee HB, Jones EBG, Tibpromma S, Tennakoon DS, Dissanayake AJ, Jayasiri SC, Gafforov Y, Camporesi E, Bulgakov TS, Ekanayake AHE, Perera RH, Samarakoon MC, Goonasekara ID, Mapook A, Li WJ, Senanayake IC, Li J, Norphanphoun C, Doilom M, Bahkali AH, Xu J, Mortimer PE, Tibell L, Tibell S, Karunarathna SC (2018) Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae. Fungal Diversity 89: 1–236. https://doi.org/10.1007/s13225-018-0395-7

Wanasinghe DN, Nimalrathna TS, Xian LQ, Faraj TK, Xu J, Mortimer PE (2024) Taxonomic novelties and global biogeography of Montagnula (Ascomycota, Didymosphaeriaceae). MycoKeys 101: 191–232. https://doi.org/10.3897/mycokeys.101.113259

Wang K, Cai L (2023) Overview of the historical and current status of fungal taxonomy and diversity in China. Mycosystema 42(1): 50–62. https://doi.org/10.13346/j.mycosystema.220497

Yang EF, Tibpromma S, Karunarathna SC, Phookamsak R, Xu JC, Zhao ZX, Karunanayake C, Promputtha I (2022) Taxonomy and phylogeny of novel and extant taxa in Pleosporales associated with Mangifera indica from Yunnan, China (Series I). Journal of Fungi 8: 152. https://doi.org/10.3390/jof8020152

Yang T, Tedersoo L, Soltis PS, Soltis DE, Sun M, Ma Y, Ni Y, Liu X, Fu X, Shi Y, Lin HY, Zhao YP, Fu C, Dai CC, Gilbert JA, Chu H (2023) Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China. Science China-Life Sciences 66: 1134–1150. https://doi.org/10.1007/s11427-022-2174-3

Yedidia I, Shoresh M, Kerem Z, Benhamou N, Kapulnik Y, Chet I (2003) Concomitant induction of systemic resistance to Pseudomonas syringae pv. lachrymans in cucumber by Trichoderma asperellum (T-203) and accumulation of phytoalexins. Applied and Environmental Microbiology 69(12): 7343–7353. https://doi.org/10.1128/AEM.69.12.7343-7353.2003

Yu XD, Zhang SN, Cheewangkoon R, Liu JK (2021) Additions to Occultibambusaceae (Pleosporales, Dothideomycetes): Unrevealing Palmicolous Fungi in China. Diversity 13: 516. https://doi.org/10.3390/d13110516

Yu XD, Zhang SN, Liu JK (2022) Morpho-phylogenetic evidence reveals novel Pleosporalean taxa from Sichuan Province, China. Journal of Fungi 8: 720. https://doi.org/10.3390/jof8070720

Zhang S, Liu X, Li R, Wang X, Cheng J, Yang Q, Kong H (2021) AHP-GIS and MaxEnt for delineation of potential distribution of Arabica coffee plantation under future climate in Yunnan, China. Ecological Indicators 132: 108339. https://doi.org/10.1016/j.ecolind.2021.108339

Zhang Y, Crous PW, Schoch CL, Hyde KD (2012) Pleosporales. Fungal Diversity 53: 1–221. https://doi.org/10.1007/s13225-011-0117-x

Supplementary materials

Supplementary material 1

Supplementary tables 1–14

Li Lu, Samantha C. Karunarathna, Kunhiraman C. Rajeshkumar, Abdallah M. Elgorban, Ruvishika S. Jayawardena, Sinang Hongsanan, Nakarin Suwannarach, Jaturong Kumla, Yin-Ru Xiong, Kevin D. Hyde, Mei-Yan Han, De-Ge Zheng, Qiang Li, Dong-Qin Dai, Saowaluck Tibpromma

Data type: docx

Explanation note: table S1: Checklist of coffee-associated saprobic fungi worldwide. tables S2, S3: Partial gene regions, primers and amplification procedure. tables S4–S13: Names, voucher numbers and corresponding GenBank numbers of the taxa used in the phylogenetic analyses of this study. table S14: Phylogenetic statistics in each tree legend.

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.

https://doi.org/10.3897/imafungus.16.144874.suppl1

Download file (192.91 kb)

Supplementary material 2

Tree alignment

Data type: zip

https://doi.org/10.3897/imafungus.16.144874.suppl2

Download file (138.69 kb)

﻿Abstract

Key words:

﻿Introduction

﻿Methods

﻿Literature survey

﻿Sample collection, morphological observation and isolation

﻿Molecular studies

﻿Phylogenetic analyses

﻿Genealogical concordance phylogenetic species recognition analysis

﻿Results

﻿Global diversity of coffee-associated saprobic fungi

﻿Taxonomy

﻿Fungi

Bambusicolaceae D.Q. Dai & K.D. Hyde, Fungal Diversity 63 (1): 49 (2013).

﻿ Leucaenicola Jayasiri, E.B.G. Jones & K.D. Hyde, Mycosphere 10 (1): 37 (2019).

Notes.

﻿ Leucaenicola coffeae L. Lu & Tibpromma, sp. nov.

Etymology.

Diagnosis.

Holotype.

Description.

Culture characteristics.

Materials examined.

Notes.

Didymosphaeriaceae Munk, Dansk botanisk Arkiv 15 (2): 128 (1953).

﻿ Montagnula Berl., Icones Fungorum. Pyrenomycetes 2: 68 (1896).

Notes.

﻿ Montagnula coffeae L. Lu & Tibpromma, sp. nov.

Etymology.

Diagnosis.

Holotype.

Description.

Culture characteristics.

Materials examined.

Notes.

Didymellaceae Gruyter, Aveskamp & Verkley, Mycological Research 113 (4): 516 (2009).

﻿ Xenodidymella Qian Chen & L. Cai, Stud. Mycol. 82: 205 (2015).

Notes.

﻿ Xenodidymella coffeae L. Lu & Tibpromma, sp. nov.

Etymology.

Diagnosis.

Holotype.

Description.

Culture characteristics.

Materials examined.

Notes.

Lophiostomataceae Sacc., Syll. Fung. 2: 672 (1883).

﻿ Flabellascoma A. Hashim., K. Hiray. & Kaz. Tanaka, Studies in Mycology 90: 167 (2018).

Notes.

﻿ Flabellascoma coffeae L. Lu & Karun., sp. nov.

Etymology.

Diagnosis.

Holotype.

Description.

Culture characteristics.

Materials examined.

Notes.

Longiostiolaceae Phukhams., Doilom & K.D. Hyde, Fungal Diversity 102: 43 (2020).

﻿ Longiostiolum Doilom, Ariyaw. & K.D. Hyde, Fungal Diversity 78: 55 (2016).

Notes.

﻿ Longiostiolum coffeae L. Lu & Tibpromma, sp. nov.

Etymology.

Diagnosis.

Holotype.

Description.

Culture characteristics.

Materials examined.

Notes.

Massarinaceae Munk, Friesia 5 (3–5): 305 (1956).

﻿ Helminthosporium Link, Mag. Ges. Naturf. Freunde Berlin 3 (1): 10 (1809).

Notes.

﻿ Helminthosporium puerensis L. Lu & Tibpromma, sp. nov.

Etymology.

Diagnosis.

Holotype.

Description.

Culture characteristics.

Materials examined.

Notes.

Neomassariaceae H.A. Ariyaw., Jaklitsch & Voglmayr, Cryptogamie, Mycologie 39 (3): 367 (2018).

Abstract

Introduction

Methods

Literature survey

Sample collection, morphological observation and isolation

Molecular studies

Phylogenetic analyses

Genealogical concordance phylogenetic species recognition analysis

Results

Global diversity of coffee-associated saprobic fungi

Taxonomy

Fungi

Leucaenicola Jayasiri, E.B.G. Jones & K.D. Hyde, Mycosphere 10 (1): 37 (2019).

Leucaenicola coffeae L. Lu & Tibpromma, sp. nov.

Montagnula Berl., Icones Fungorum. Pyrenomycetes 2: 68 (1896).

Montagnula coffeae L. Lu & Tibpromma, sp. nov.

Xenodidymella Qian Chen & L. Cai, Stud. Mycol. 82: 205 (2015).

Xenodidymella coffeae L. Lu & Tibpromma, sp. nov.

Flabellascoma A. Hashim., K. Hiray. & Kaz. Tanaka, Studies in Mycology 90: 167 (2018).

Flabellascoma coffeae L. Lu & Karun., sp. nov.

Longiostiolum Doilom, Ariyaw. & K.D. Hyde, Fungal Diversity 78: 55 (2016).

Longiostiolum coffeae L. Lu & Tibpromma, sp. nov.

Helminthosporium Link, Mag. Ges. Naturf. Freunde Berlin 3 (1): 10 (1809).

Helminthosporium puerensis L. Lu & Tibpromma, sp. nov.

Neomassaria Mapook, Camporesi & K.D. Hyde, Fungal Diversity 80: 74 (2016).

Neomassaria coffeae L. Lu & Tibpromma, sp. nov.

Neooccultibambusa Doilom & K.D. Hyde, Fungal Diversity 82: 126 (2016).

Neooccultibambusa coffeae L. Lu & Tibpromma, sp. nov.

Pararoussoella Wanas., E.B.G. Jones & K.D. Hyde, Fungal Diversity 89: 169 (2018).

Pararoussoella coffeae L. Lu & Tibpromma, sp. nov.

Cycasicola Wanas., E.B.G. Jones & K.D. Hyde, Fungal Diversity 89: 161 (2018).

Cycasicola coffeae L. Lu & Tibpromma, sp. nov.

Discussion

Conclusion

Acknowledgements

Additional information

References