Fungal diversity associated with thirty-eight lichen species revealed a new genus of endolichenic fungi, Intumescentia gen. nov. (Teratosphaeriaceae)

DATA AVAILABILITY STATEMENT : All sequence data are available in NCBI GenBank following the accession numbers in the manuscript.SUPPLEMENTARY MATERIALS : FIGURE S1: Maximum likelihood phylogeny using ITS dataset for Teratosphaeriaceae. The bootstrap support value 75% and posterior probability 0.95 displayed above the node are ML/MP/PP. The isolates of Intumescentia gen. nov. obtained in this study are shown in bold. T = ex-type isolates; FIGURE S2: Maximum likelihood phylogeny using LSU dataset for Teratosphaeriaceae. The bootstrap support value 75% and posterior probability 0.95 displayed above the node are ML/MP/PP. The isolates of Intumescentia gen. nov. obtained in this study are shown in bold. T = ex-type isolates; FIGURE S3: Maximum likelihood phylogeny using TEF dataset for Teratosphaeriaceae. The bootstrap support value 75% and posterior probability 0.95 displayed above the node are ML/MP/PP. The isolates of Intumescentia gen. nov. obtained in this study are shown in bold. T = ex-type isolates; FIGURE S4: Maximum likelihood phylogeny using CAL dataset for Teratosphaeriaceae. The bootstrap support value 75% and posterior probability 0.95 displayed above the node are ML/MP/PP. The isolates of Intumescentia gen. nov. obtained in this study are shown in bold. T = ex-type isolates; FIGURE S5: Maximum likelihood phylogeny using RPB2 dataset for Teratosphaeriaceae. The bootstrap support value 75% and posterior probability 0.95 displayed above the node are ML/MP/PP. The isolates of Intumescentia gen. nov. obtained in this study are shown in bold. T = ex-type isolates; FIGURE S6: Maximum likelihood phylogeny using ACT dataset for Teratosphaeriaceae. The bootstrap support value 75% and posterior probability 0.95 displayed above the node are ML/MP/PP. The isolates of Intumescentia gen. nov. obtained in this study are shown in bold. T = ex-type isolates. TABLE S1: The lichen species sampled in this study, along with their sample numbers, habitat, distribution, and growth type; TABLE S2: Taxa used in the phylogenetic analyses and their corresponding GenBank numbers. T = ex-type isolates; TABLE S3: List of fungal species isolated from 38 lichen species sampled in this study and their respective guilds. Numbers in the cells indicate the number of isolates.Fungi from the Teratosphaeriaceae (Mycosphaerellales; Dothideomycetes; Ascomycota) have a wide range of lifestyles. Among these are a few species that are endolichenic fungi. However, the known diversity of endolichenic fungi from Teratosphaeriaceae is far less understood compared to other lineages of Ascomycota. We conducted five surveys from 2020 to 2021 in Yunnan Province of China, to explore the biodiversity of endolichenic fungi. During these surveys, we collected multiple samples of 38 lichen species. We recovered a total of 205 fungal isolates representing 127 species from the medullary tissues of these lichens. Most of these isolates were from Ascomycota (118 species), and the remaining were from Basidiomycota (8 species) and Mucoromycota (1 species). These endolichenic fungi represented a wide variety of guilds, including saprophytes, plant pathogens, human pathogens, as well as entomopathogenic, endolichenic, and symbiotic fungi. Morphological and molecular data indicated that 16 of the 206 fungal isolates belonged to the family Teratosphaeriaceae. Among these were six isolates that had a low sequence similarity with any of the previously described species of Teratosphaeriaceae. For these six isolates, we amplified additional gene regions and conducted phylogenetic analyses. In both single gene and multi-gene phylogenetic analyses using ITS, LSU, SSU, RPB2, TEF1, ACT, and CAL data, these six isolates emerged as a monophyletic lineage within the family Teratosphaeriaceae and sister to a clade that included fungi from the genera Acidiella and Xenopenidiella. The analyses also indicated that these six isolates represented four species. Therefore, we established a new genus, Intumescentia gen. nov., to describe these species as Intumescentia ceratinae, I. tinctorum, I. pseudolivetorum, and I. vitii. These four species are the first endolichenic fungi representing Teratosphaeriaceae from China.The Shandong Normal University.https://www.mdpi.com/journal/jofam2024BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologySDG-15:Life on lan

The effects of co-culture on the expression of selected PKS genes in the lichenized fungus Xanthoparmelia taractica

DATA AVAILABILITY : All sequence data generated in this study (the genome sequence of X. taractica, Table S1 and S2) are available at NCBI GenBank (https://www.ncbi.nlm.nih.gov/genbank/).Lichens produce diverse secondary metabolites. A diversity of these compounds is synthesized by fungal polyketide synthases (PKSs). In this study, we catalogued the PKS genes from Xanthoparmelia taractica, a lichen with global distribution. To accomplish this, we isolated the symbionts to sequence the whole genome of the mycobiont and established an in vitro co-culture system for this lichen. We also added an endolichenic fungus, Coniochaeta fibrosae, to this co-culture to evaluate its effect on lichen symbiosis. The genome of the mycobiont X. taractica was around 43.1 Mb with 10,730 ORFs. Twenty-eight PKS genes were identified in the genome. These included 27 Type I and one Type III gene. Except for three PKS genes, XTPKS12, XTPKS18, and XTPKS22, the function of the majority of PKS genes remained unknown. We selected these genes for the expression analyses using a co-culture system. The co-culture system that included the mycobiont and the photobiont showed an early stage of lichenization because the fungi produced a hyphal network connecting and penetrating the algal cells. Also, XTPKS12 was down-regulated and XTPKS18 and XTPKS22 were modestly up-regulated. As predicted, C. fibrosae did not participate in the symbiosis. This study reconfirms that Type I is the most dominant PKS gene in lichenized fungi and the function of these genes might be influenced by symbiosis.The National Natural Science Foundation of China and Open Fund for Instruments and Equipment of Shandong Normal University.http://link.springer.com/journal/115572024-04-24hj2024BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyZoology and EntomologyNon

Ophiostomatoid fungi including a new species associated with Asian larch bark beetle Ips subelongatus, in Heilongjiang (Northeast China)

Ips subelongatus (Coleoptera, Scolytinae) is an important bark beetle species that infests Larix spp. in Asia. Individuals of this beetle are vectors of ophiostomatoid fungi, on their exoskeletons, that are transmitted to infested trees. In this study, the symbiotic assemblage of ophiostomatoid fungi associated with I. subelongatus in Northeast China was studied. Fungal isolates were identified based on their morphological characters and sequences of ITS, beta-tubulin, elongation factor 1-alpha and calmodulin gene regions. In total, 48 isolates were collected and identified, residing in six taxa. These included a novel species, described here as Ophiostoma gmelinii sp. nov.Members of Tree Protection and Cooperation Programme (TPCP), the Department of Science and Technology (DST)-National Research Foundations (NRF), Center of Excellence in Plant Health Biotechnology (CPHB), and University of Pretoria, Pretoria, South Africa.https://fuse-journal.orgam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Phylogenetic and morphological analyses of Coniochaeta isolates recovered from Inner Mongolia and Yunnan revealed three new endolichenic fungal species

Lichens are the result of a symbiotic interaction between fungi (mycobionts) and algae (phycobionts). Aside from mycobionts, lichen thalli can also contain non-lichenised fungal species, such as lichenicolous and endolichenic fungi. For this study, three surveys were conducted in China’s Yunnan Province and Inner Mongolia Autonomous Region between 2017 and 2020. Several samples of four lichen species were collected during these surveys: Candelaria fibrosa, Flavoparmelia caperata, Flavopunctelia flaventior and Ramalina sinensis. Six isolates of Coniochaeta were recovered from these four lichen species. The phylogenetic and morphological analyses revealed that two of these isolates were previously identified species, Coniochaeta velutinosa and C. acaciae. Those remaining were from potentially unknown species. We used molecular and morphological data to describe these previously-unknown species as Coniochaeta fibrosae sp. nov., C. mongoliae sp. nov. and C. sinensis sp. nov. The findings of this study significantly improve our understanding of the variety and habitat preferences of Coniochaeta in China and globally.The National Natural Science Foundation of China.https://mycokeys.pensoft.netam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Ophiostomatoid fungi associated with conifer-infesting beetles and their phoretic mites in Yunnan, China

The Ophiostomatales is an Ascomycete order of fungi that accommodates several tree pathogens and many species that degrade wood. These fungi are commonly vectored by Scolytine bark and ambrosia beetles. In recent years it has also been shown that hyperphoretic mites on these beetles can vector some Ophiostomatales. Little is known regarding the Ophiostomatales in China and we have consequently explored the diversity of these fungi associated with conifer-infesting beetles and mites in Yunnan province. Galleries and beetles were collected for 17 beetle species, while 13 mite species were obtained from six of these beetle species. Collectively, 340 fungal isolates were obtained, 45 from beetles, 184 from mites, 56 from galleries and 55 isolates where the specific niche was not clear. DNA sequences for five gene regions (ITS, LSU, BT, EF, and CAL) were determined for fungal isolates representing different morphological groups. Phylogenetic analyses confirmed the presence of 19 fungal taxa, including five novel species described here as Ophiostoma acarorum sp. nov., Ophiostoma brevipilosi sp. nov., Graphilbum kesiyae sp. nov., Graphilbum puerense sp. nov., and Leptographium ningerense sp. nov. Ophiostoma ips was the most frequently isolated species, representing approximately 31% of all isolates. Six of 19 taxa were present on mites, beetles and in the galleries of the beetles, while three species were found on mites and galleries. Two species were found only on mites and one species only on a beetle. Although the numbers of beetles and mites were insufficient to provide statistical inferences, this study confirmed that mites are important vectors of the Ophiostomatales in China. We hypothesize that these mites are most likely responsible for horizontal transfer of fungal species between galleries of different beetle species. The fact that half of the fungal species found were new to science, suggests that the forests of east Asia include many undescribed Ophiostomatales yet to be discovered.Figure S1. Map of Yunnan Province in China showing the sites and tree hosts from which samples were collected during the three surveys in 2001, 2002 and 2010.Figure S2. ML trees of the genus Graphium generated from DNA sequences of the ITS and BT regions. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Figure S3. ML trees of the genus Sporothrix generated from DNA sequences of ITS and BT regions. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Figure S4. ML trees of the O. ips complex generated from DNA sequences of ITS and BT regions. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Figure S5. ML trees of the O. piceae complex generated from DNA sequences of BT and EF regions. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Figure S6. ML tree of the O. quercus complex generated from DNA sequences of ITS region. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Figure S7. ML tree of the O. quercus complex generated from DNA sequences of BT region. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Figure S8. ML tree of the O. quercus complex generated from DNA sequences of EF region. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Figure S9. ML trees of the L. procerum complex generated from DNA sequences of BT, EF and CAL regions. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Figure S10. ML trees of the G. galeiformis complex generated from DNA sequences of BT and EF regions. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Figure S11. ML trees of the L. lundbergii complex generated from DNA sequences of BT and EF regions. Bold branches indicate posterior probabilities values ≥ 0.95. Bootstrap values ≥ 70 % are recorded at nodes as ML/MP. T = ex-type isolates.Table S1. Numbers of ophiostomatoid fungal isolates obtained from different mite species in this study.Table S2. Haplotypes of Ophiostoma quercus.Table S3. Haplotypes of Ophiostoma tsotsi.Members of Tree Protection and Cooperation Programme (TPCP), Center of Excellence in Tree Health Biotechnology (CTHB), the National Research Foundation (NRF), the Department of Science and Technology (DST)/NRF and the University of Pretoria, South Africa.https://mycokeys.pensoft.netam2018Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Ophiostomatoid species associated with pine trees (Pinus spp.) infested by Cryphalus piceae from eastern China, including five new species

Cryphalus piceae attacks various economically important conifers. Similar to other bark beetles, Cr. piceae plays a role as a vector for an assortment of fungi and nematodes. Previously, several ophiostomatoid fungi were isolated from Cr. piceae in Poland and Japan. In the present study, we explored the diversity of ophiostomatoid fungi associated with Cr. piceae infesting pines in the Shandong Province of China. We isolated ophiostomatoid fungi from both galleries and beetles collected from our study sites. These fungal isolates were identified using both molecular and morphological data. In this study, we recovered 175 isolates of ophiostomatoid fungi representing seven species. Ophiostoma ips was the most frequently isolated species. Molecular and morphological data indicated that five ophiostomatoid fungal species recovered were previously undescribed. Thus, we proposed these five novel species as Ceratocystiopsis yantaiensis, C. weihaiensis, Graphilbum translucens, Gr. niveum, and Sporothrix villosa. These new ophiostomatoid fungi add to the increasing number of fungi known from China, and this evidence suggests that numerous novel taxa are awaiting discovery in other forests of China.Shandong Normal University.https://mycokeys.pensoft.netam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Nine new species of black lichenicolous fungi from the genus cladophialophora (chaetothyriales) from two different climatic zones of China

DATA AVAILABILITY STATEMENT : The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.Lichenicolous fungi are parasites of lichens. Many of these fungi are referred to as “black fungi”. A diversity of these black fungi include species that are pathogenic to humans and plants. A majority of black fungi reside in the phylum Ascomycota within the sub-classes Chaetothyriomycetidae and Dothideomycetidae. To explore the diversity of lichenicolous “black fungi” associated with lichens in China, we conducted several field surveys in the Inner Mongolia Autonomous Region and Yunnan Province between 2019 and 2020. We recovered 1,587 fungal isolates from the lichens collected during these surveys. During the preliminary identification of these isolates using the complete internal transcribed spacer (ITS), partial large subunit of nuclear ribosomal RNA gene (LSU), and small subunit of nuclear ribosomal RNA gene (SSU), we identified 15 fungal isolates from the genus Cladophialophora. However, these isolates had low sequence similarities with all known species from the genus. Therefore, we amplified additional gene regions, such as, translation elongation factor (TEF) and partial β-tubulin gene (TUB), and constructed a multi-gene phylogeny using maximum likelihood, maximum parsimony, and Bayesian inference. In our datasets, we included type sequences where available for all Cladophialophora species. Phylogenetic analyses revealed that none of the 15 isolates belonged to any of the previously described species in the genus. Therefore, using both morphological and molecular data, we classified these 15 isolates as nine new species within the genus Cladophialophora: C. flavoparmeliae, C. guttulate, C. heterodermiae, C. holosericea, C. lichenis, C. moniliformis, C. mongoliae, C. olivacea, and C. yunnanensis. The outcome from this study shows that lichens are an important refugia for black lichenicolous fungi, such as those from Chaetothyriales.The Qingchuang Talents Induction Program of Shandong Higher Education Institution in 2021, Open Fund for Instruments and Equipment of Shandong Normal University, the “Startup Fund” by the Shandong Normal University and National College Students Innovative Entrepreneurship Training Programs.http://www.frontiersin.org/Microbiologyam2024BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologySDG-15:Life on lan

Draft genome sequences for Ceratocystis fagacearum, C. harringtonii, Grosmannia penicillata, and Huntiella bhutanensis

Draft genomes for the fungi Ceratocystis fagacearum, C. harringtonii, Grosmannia penicillata, and Huntiella bhutanensis are presented. Ceratocystis fagacearum is a major causal agent of vascular wilt of oaks and other trees in the family Fagaceae. Ceratocystis harringtonii, previously known as C. populicola, causes disease in Populus species in the USA and Canada. Grosmannia penicillata is the causal agent of bluestain of sapwood on various conifers, including Picea spp. and Pinus spp. in Europe. Huntiella bhutanensis is a fungus in Ceratocystidaceae and known only in association with the bark beetle Ips schmutzenhorferi that infests Picea spinulosa in Bhutan. The availability of these genomes will facilitate further studies on these fungi.The Genomics Research Institute (University of Pretoria), the University of Pretoria Research Development Programme, the DST/NRF Center of Excellence in Tree Health Biotechnology (FABI, University of Pretoria), and the National Research Foundation (NRF) (Grant number 87332). Sequencing the genomes of Ceratocystis fagacearum, C. harringtonii, Huntiella bhutanensis was made possible through the Improving Academics Qualifications (IAQ) grant from the NRF.http://www.imafungus.orgam2017Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Ophiostomatoid fungi associated with conifer-infesting beetles and their phoretic mites in Yunnan, China

Volume: 28Start Page: 19End Page: 6

Ophiostomatoid fungi associated with mites phoretic on bark beetles in Qinghai, China

Bark beetle galleries are complex ecosystems where many microbes and other arthropods co-exist with the beetles. Fungi isolated from these galleries are often referred to as ‘beetle associates’, but the nature of these associations are poorly understood. The possibility that many of these fungi might in fact be mite associates is often overlooked. Several recent studies explored the diversity of fungi from conifer-infesting bark beetles and their galleries in China, but only one study considered phoretic mites and their fungi from conifer-infesting bark beetles in Yunnan, southwestern China. We studied the mites and fungi from galleries of four spruce-infesting bark beetle species in the high altitude forests of Qinghai province, western China. Mites were identified based on morphological characteristics, and fungi based on DNA sequences of four gene regions. In total, 173 mite individuals were collected belonging to 18 species in 11 genera. A total of 135 fungal isolates were obtained from the mites, representing 14 taxa from the Ophiostomatales. The most frequently isolated fungus was Ophiostoma nitidum, which represented 23.5% of the total isolates. More fungal species were found from fewer mites and bark beetle species than from the study in Yunnan. Although we could not elucidate the exact nature of interactions between mites and their fungi, our results re-enforce that these organisms should not be ignored in pest risk assessments of bark beetles, that often focus only on the beetles and their fungi. Three new species are described: Grosmannia zekuensis, O. manchongi, and O. kunlunense spp. nov., and our data revealed that O. typographi, recently described from China, is a synonym of O. ainoae.Additional file 1: Fig. S1. Phylogram obtained from ML analyses of the partial BT and EF gene of Ophiostoma clavatum complex. Sequences obtained in this study are printed in bold type. ML and MP bootstrap support values (1000 replicates, normal type) above 75% are indicated at the nodes. Posterior probabilities (above 0.9) obtained from BI are indicated by bold lines at the relevant branching points. T = ex-type cultures. Scale bar = total nucleotide difference between taxa.Additional file 2: Fig. S2. Phylogram obtained from ML analyses of the partial BT and EF gene of Leptographium olivaceum complex. Sequences obtained in this study are printed in bold type. ML bootstrap support values (1000 replicates, normal type) above 75% are indicated at the nodes. Posterior probabilities (above 0.9) obtained from BI are indicated by bold lines at the relevant branching points. T = ex-type cultures. Scale bar = total nucleotide difference between taxa.Additional file 3: Table S1. Ophiostomatoid fungi reported from China.Additional file 4: Table S2. Numbers of mite individuals collected and numbers of mite individuals carring fungi in this study.Additional file 5: Table S3. Numbers of fungal isolates associated with mites from different beetle galleries. Shades of red indicate number of fungal isolates.Members of Tree Protection and Cooperation Programme (TPCP), the Department of Science and Technology (DST)-National Research Foundations (NRF), Center of Excellence in Tree Health Biotechnology (CTHB), and University of Pretoria, Pretoria, South Africa.http://www.imafungus.orgam2020BiochemistryGeneticsMicrobiology and Plant Patholog