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Gacura MD, Zak DR, Blackwood CB. From individual leaves to forest stands: importance of niche, distance decay, and stochasticity vary by ecosystem type and functional group for fungal community composition. FEMS Microbiol Ecol 2024; 100:fiae016. [PMID: 38373845 PMCID: PMC10913062 DOI: 10.1093/femsec/fiae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/26/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024] Open
Abstract
Community assembly is influenced by environmental niche processes as well as stochastic processes that can be spatially dependent (e.g. dispersal limitation) or independent (e.g. priority effects). Here, we sampled senesced tree leaves as unit habitats to investigate fungal community assembly at two spatial scales: (i) small neighborhoods of overlapping leaves from differing tree species and (ii) forest stands of differing ecosystem types. Among forest stands, ecosystem type explained the most variation in community composition. Among adjacent leaves within stands, variability in fungal composition was surprisingly high. Leaf type was more important in stands with high soil fertility and dominated by differing tree mycorrhizal types (sugar maple vs. basswood or red oak), whereas distance decay was more important in oak-dominated forest stands with low soil fertility. Abundance of functional groups was explained by environmental factors, but predictors of taxonomic composition within differing functional groups were highly variable. These results suggest that fungal community assembly processes are clearest for functional group abundances and large spatial scales. Understanding fungal community assembly at smaller spatial scales will benefit from further study focusing on differences in drivers for different ecosystems and functional groups, as well as the importance of spatially independent factors such as priority effects.
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Affiliation(s)
- Matthew D Gacura
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Biology Department, Gannon University, 109 University Square, Erie, PA 16541, United States
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, 440 Church St., Ann Arbor, MI 48109, United States
| | - Christopher B Blackwood
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Department of Plant, Soil, and Microbial Sciences and Department of Plant Biology, Michigan State University, 1066 Bogue St., East Lansing, MI 48842, United States
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Rzehak T, Praeg N, Zink H, Simon A, Geitner C, Illmer P. Microbial perspective of inhibited carbon turnover in Tangel humus of the Northern Limestone Alps. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13215. [PMID: 38062558 PMCID: PMC10866079 DOI: 10.1111/1758-2229.13215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/01/2023] [Indexed: 02/15/2024]
Abstract
Tangel humus primarily occurs in montane and subalpine zones of the calcareous Alps that exhibit low temperatures and high precipitation sums. This humus form is characterized by inhibited carbon turnover and accumulated organic matter, leading to the typical thick organic layers. However, the reason for this accumulation of organic matter is still unclear, and knowledge about the microbial community within Tangel humus is lacking. Therefore, we investigated the prokaryotic and fungal communities along with the physical and chemical properties within a depth gradient (0-10, 10-20, 20-30, 30-40, 40-50 cm) of a Tangel humus located in the Northern Limestone Alps. We hypothesized that humus properties and microbial activity, biomass, and diversity differ along the depth gradient and that microbial key players refer to certain humus depths. Our results give the first comprehensive information about microbiota within the Tangel humus and establish a microbial zonation of the humus. Microbial activity, biomass, as well as microbial alpha diversity significantly decreased with increasing depths. We identified microbial biomarkers for both, the top and the deepest depth, indicating different, microbial habitats. The microbial characterization together with the established nutrient deficiencies in the deeper depths might explain reduced C-turnover and Tangel humus formation.
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Affiliation(s)
- Theresa Rzehak
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| | - Nadine Praeg
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| | - Harald Zink
- Department of GeographyUniversität InnsbruckInnsbruckAustria
| | - Alois Simon
- Department of Forest PlanningOffice of the Tyrolean GovernmentInnsbruckAustria
| | - Clemens Geitner
- Department of GeographyUniversität InnsbruckInnsbruckAustria
| | - Paul Illmer
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
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3
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Li C, Nie H, Zhang S, Jia Z, Ma S, Li T, Zhai L, Zhang B, Liu X, Zhang J, Müller C. Mineral-solubilizing microbial inoculant positively affects the multifunctionality of anthropogenic soils in abandoned mining areas. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118553. [PMID: 37399621 DOI: 10.1016/j.jenvman.2023.118553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
The mining industry has a significant negative impact on ecosystems, and the remediation of abandoned mining sites requires effective strategies. One promising approach is the incorporation of mineral-solubilizing microorganisms into current external soil spray seeding technologies. These microorganisms possess the ability to decrease mineral particle sizes, promote plant growth, and enhance the release of vital soil nutrients. However, most previous studies on mineral-solubilizing microorganisms have been conducted in controlled greenhouse environments, and their practical application in field settings remains uncertain. To address this knowledge gap, we conducted a four-year field experiment at an abandoned mining site to investigate the efficacy of mineral-solubilizing microbial inoculants in restoring derelict mine ecosystems. We assessed soil nutrients, enzyme activities, functional genes, and soil multifunctionality. We also examined microbial compositions, co-occurrence networks, and community assembly processes. Our results demonstrated that the application of mineral-solubilizing microbial inoculants significantly enhanced soil multifunctionality. Interestingly, certain bacterial phyla or class taxa with low relative abundances were found to be key drivers of multifunctionality. Surprisingly, we observed no significant correlation between microbial alpha diversity and soil multifunctionality, but we did identify positive associations between the relative abundance and biodiversity of keystone ecological clusters (Module #1 and #2) and soil multifunctionality. Co-occurrence network analysis revealed that microbial inoculants reduced network complexity while increasing stability. Additionally, we found that stochastic processes played a predominant role in shaping bacterial and fungal communities, and the inoculants increased the stochastic ratio of microbial communities, particularly bacteria. Moreover, microbial inoculants significantly decreased the relative importance of dispersal limitations and increased the relative importance of drift. High relative abundances of certain bacterial and fungal phyla were identified as major drivers of the microbial community assembly process. In conclusion, our findings highlight the crucial role of mineral-solubilizing microorganisms in soil restoration at abandoned mining sites, shedding light on their significance in future research endeavors focused on optimizing the effectiveness of external soil spray seeding techniques.
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Affiliation(s)
- Chong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China; Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Hui Nie
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China
| | - Shuifeng Zhang
- Faculty of Information Technology, Nanjing Forest Police College, Nanjing, 210000, China
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China
| | - Shilin Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China
| | - Tao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China
| | - Lu Zhai
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK, 74078, USA; Department of Integrative Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Bo Zhang
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China.
| | - Christoph Müller
- Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany; School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland; Liebig Centre for Agroecology and Climate Impact Research, Justus Liebig University, Germany
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Li Q, Xiao W, Wu P, Zhang T, Xiang P, Wu Q, Zou L, Gui M. The first two mitochondrial genomes from Apiotrichum reveal mitochondrial evolution and different taxonomic assignment of Trichosporonales. IMA Fungus 2023; 14:7. [PMID: 37004131 PMCID: PMC10064765 DOI: 10.1186/s43008-023-00112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Apiotrichum is a diverse anamorphic basidiomycetous yeast genus, and its mitogenome characterization has not been revealed. In this study, we assembled two Apiotrichum mitogenomes and compared them with mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. The mitogenomes of Apiotrichum gracile and A. gamsii comprised circular DNA molecules, with sizes of 34,648 bp and 38,096 bp, respectively. Intronic regions were found contributed the most to the size expansion of A. gamsii mitogenome. Comparative mitogenomic analysis revealed that 6.85-38.89% of nucleotides varied between tRNAs shared by the two Apiotrichum mitogenomes. The GC content of all core PCGs in A. gamsii was lower than that of A. gracile, with an average low value of 4.97%. The rps3 gene differentiated the most among Agaricomycotina, Pucciniomycotina and Ustilaginomycotina species, while nad4L gene was the most conserved in evolution. The Ka/Ks values for cob and rps3 genes were > 1, indicating the two genes may be subjected to positive selection in Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. Frequent intron loss/gain events and potential intron transfer events have been detected in evolution of Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. We further detected large-scale gene rearrangements between the 19 mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina, and fifteen of the 17 mitochondrial genes shared by Apiotrichum varied in gene arrangements. Phylogenetic analyses based on maximum likelihood and Bayesian inference methods using a combined mitochondrial gene dataset revealed different taxonomic assignment of two Apiotrichum species, wherein A. gamsii had a more closely relationship with Trichosporon asahii. This study served as the first report on mitogenomes from the genus Apiotrichum, which promotes the understanding of evolution, genomics, and phylogeny of Apiotrichum.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenqi Xiao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Wu
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Chengdu, 610106, Sichuan, China.
| | - Mingying Gui
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Chengdu, 610106, Sichuan, China.
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5
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Culturable Diversity of Lichen-Associated Yeasts through Enrichment Strategies. ECOLOGIES 2023. [DOI: 10.3390/ecologies4010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Lichens are symbiotic partnerships between a filamentous fungus and a photosymbiotic “alga”. Studies show that lichens harbor endothallic fungi, but that some taxa have been difficult to isolate from the main filamentous thallus-forming fungus and other faster growing lichenicolous/endothallic fungi. Therefore, we aimed to develop and evaluate liquid yeast-enrichment strategies to (1) isolate lichen-associated yeasts in pure culture, and (2) determine the taxonomic placement and breadth of the diversity of culturable yeasts. Eighty-two lichen samples were collected and washed with distilled water, and healthy thalli were ground up and added to seven different yeast-enrichment broths. Yeast colonies were isolated in pure culture and identified using molecular techniques. Initial isolates were identified using BLASTn analysis, and a taxonomic refinement was completed using PhyML analysis. In total, 215 isolates were obtained. The most prevalently isolated ascomycetous yeasts were within the Dothideomycetes (Aureobasidium, Plowrightia, and Dothiora), while the most frequently isolated basidiomycetous yeasts belonged to the genera Curvibasidium, Sporobolomyces, and Tremella. The generic placements could not be determined for 17 isolates, and in total 25 novel species were recovered. The results of this research indicate that (1) lichen-associated yeasts are diverse, (2) employing liquid enrichment strategies is effective for isolating many of these, and (3) lichen thalli represent a valuable untapped reservoir of diverse and novel yeast species.
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Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
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Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
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7
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Yamada M, Endoh R, Masumoto H, Yoshihashi Y, Ohkuma M, Degawa Y. Taxonomic study of polymorphic basidiomycetous fungi Sirobasidium and Sirotrema: Sirobasidium apiculatum sp. nov., Phaeotremella translucens comb. nov. and rediscovery of Sirobasidium japonicum in Japan. Antonie Van Leeuwenhoek 2022; 115:1421-1436. [DOI: 10.1007/s10482-022-01787-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
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8
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The yeast lichenosphere: High diversity of basidiomycetes from the lichens Tephromela atra and Rhizoplaca melanophthalma. Fungal Biol 2022; 126:587-608. [DOI: 10.1016/j.funbio.2022.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/26/2022] [Accepted: 07/13/2022] [Indexed: 01/03/2023]
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9
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Kutos S, Barnes EM, Bhutada A, Lewis JD. Preferential associations of soil fungal taxa under mixed compositions of eastern American tree species. FEMS Microbiol Ecol 2022; 98:6581587. [PMID: 35521705 DOI: 10.1093/femsec/fiac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/12/2022] [Accepted: 05/04/2022] [Indexed: 11/14/2022] Open
Abstract
Soil fungi are vital to forest ecosystem function, in part through their role mediating tree responses to environmental factors, as well as directly through effects on resource cycling. While the distribution of soil fungi can vary with abiotic factors, plant species identity is also known to affect community composition. However, the particular influence that a plant will have on its soil microbiota remains difficult to predict. Here, we paired amplicon sequencing and enzymatic assays to assess soil fungal composition and function under three tree species, Quercus rubra, Betula nigra, and Acer rubrum, planted individually and in all combinations in a greenhouse. We observed that fungal communities differed between each of the individual planted trees, suggesting at least some fungal taxa may associate preferentially with these tree species. Additionally, fungal community composition under mixed-tree plantings broadly differed from the individual planted trees, suggesting mixing of these distinct soil fungal communities. The data also suggest that there were larger enzymatic activities in the individual plantings as compared to all mixed-tree plantings which may be due to variations in fungal community composition. This study provides further evidence of the importance of tree identity on soil microbiota and functional changes to forest soils.
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Affiliation(s)
- Steve Kutos
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA.,Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Elle M Barnes
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA.,Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Arnav Bhutada
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
| | - J D Lewis
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA.,Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY 10504, USA
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Li Q, Bao Z, Tang K, Feng H, Tu W, Li L, Han Y, Cao M, Zhao C. First two mitochondrial genomes for the order Filobasidiales reveal novel gene rearrangements and intron dynamics of Tremellomycetes. IMA Fungus 2022; 13:7. [PMID: 35501936 PMCID: PMC9059411 DOI: 10.1186/s43008-022-00094-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 04/22/2022] [Indexed: 02/03/2023] Open
Abstract
In the present study, two mitogenomes from the Filobasidium genus were assembled and compared with other Tremellomycetes mitogenomes. The mitogenomes of F. wieringae and F. globisporum both comprised circular DNA molecules, with sizes of 27,861 bp and 71,783 bp, respectively. Comparative mitogenomic analysis revealed that the genetic contents, tRNAs, and codon usages of the two Filobasidium species differed greatly. The sizes of the two Filobasidium mitogenomes varied greatly with the introns being the main factor contributing to mitogenome expansion in F. globisporum. Positive selection was observed in several protein-coding genes (PCGs) in the Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina species, including cob, cox2, nad2, and rps3 genes. Frequent intron loss/gain events were detected to have occurred during the evolution of the Tremellomycetes mitogenomes, and the mitogenomes of 17 species from Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina have undergone large-scale gene rearrangements. Phylogenetic analyses based on Bayesian inference and the maximum likelihood methods using a combined mitochondrial gene set generated identical and well-supported phylogenetic trees, wherein Filobasidium species had close relationships with Trichosporonales species. This study, which is the first report on mitogenomes from the order Filobasidiales, provides a basis for understanding the genomics, evolution, and taxonomy of this important fungal group.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Ke Tang
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China
| | - Huiyu Feng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Yunlei Han
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, Sichuan, China
| | - Mei Cao
- Core Laboratory, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China. .,Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, Sichuan, China.
| | - Changsong Zhao
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China.
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Wolińska A, Podlewski J, Słomczewski A, Grządziel J, Gałązka A, Kuźniar A. Fungal Indicators of Sensitivity and Resistance to Long-Term Maize Monoculture: A Culture-Independent Approach. Front Microbiol 2022; 12:799378. [PMID: 35046921 PMCID: PMC8761758 DOI: 10.3389/fmicb.2021.799378] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/07/2021] [Indexed: 01/04/2023] Open
Abstract
Although fungi are regarded as very important components of soils, the knowledge of their community in agricultural (monocultural) soils is still limited. This indicates that soil fungal communities are investigated less intensively than bacteria. Therefore, the main goal of this paper was to evaluate the fungal mycobiome structure in monoculture soils in a culture-independent approach. Firstly, the study was conducted to identify the core mycobiome composition and its variability at different stages of the maize growing season (spring, summer, and autumn). Secondly, we identified and recommended fungal indicators of both sensitivity and resistance to long-term maize monoculture. Two neighboring fields from the Potulicka Foundation area were selected for the study: K20 sown with a Gorzow mixture (intercropping mixture) to improve soil quality after a maize monoculture in 2020 and K21, where long-term (over 30 years) monoculture cultivation was continued. The basic chemical features [acidity, redox potential, total organic carbon (TOC), and moisture] of soils were determined, fungal genetic diversity was assessed by ITS next generation sequencing (NGS) analyses, and biodiversity indices were calculated. The results of the NGS technique facilitated recognition and classification of the fungal mycobiome to the taxonomic genus level and changes in the fungal structure in the three periods (spring, summer, and autumn) were assessed. It was evidenced that the mycobiome composition was dependent on both the seasons and the agricultural practices. It was also found that even a 1-year break in the monoculture in favor of an intercropping mixture improved soil properties thus contributing to higher biodiversity. Mortierella was recommended as a potential indicator of sensitivity to long-term maize cultivation, whereas Solicoccozyma and Exophiala were proposed as indicators of resistance to long-term maize cultivation. We proved that the precision farming principles applied on the Potulicka Foundation farm had a very positive effect on fungal biodiversity, which was high even in the long-term maize monoculture field. Therefore, the monoculture cultivation carried out in this way does not induce biological degradation of monoculture soils but preserves their good biological quality.
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Affiliation(s)
- Agnieszka Wolińska
- Department of Biology and Biotechnology of Microorganisms, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
| | | | | | - Jarosław Grządziel
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation in Pulawy, Puławy, Poland
| | - Anna Gałązka
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation in Pulawy, Puławy, Poland
| | - Agnieszka Kuźniar
- Department of Biology and Biotechnology of Microorganisms, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
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12
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13
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Cao B, Haelewaters D, Schoutteten N, Begerow D, Boekhout T, Giachini AJ, Gorjón SP, Gunde-Cimerman N, Hyde KD, Kemler M, Li GJ, Liu DM, Liu XZ, Nuytinck J, Papp V, Savchenko A, Savchenko K, Tedersoo L, Theelen B, Thines M, Tomšovský M, Toome-Heller M, Urón JP, Verbeken A, Vizzini A, Yurkov AM, Zamora JC, Zhao RL. Delimiting species in Basidiomycota: a review. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00479-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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14
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Fan LF, Alvarenga RLM, Gibertoni TB, Wu F, Dai YC. Four new species in the Tremellafibulifera complex (Tremellales, Basidiomycota). MycoKeys 2021; 82:33-56. [PMID: 34393591 PMCID: PMC8357700 DOI: 10.3897/mycokeys.82.63241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Samples of species close to Tremellafibulifera from China and Brazil are studied, and T.fibulifera is confirmed as a species complex including nine species. Five known species (T.cheejenii, T.fibulifera s.s., T. “neofibulifera”, T.lloydiae-candidae and T.olens) and four new species (T.australe, T.guangxiensis, T.latispora and T.subfibulifera) in the complex are recognized based on morphological characteristics, molecular evidence, and geographic distribution. Sequences of eight species of the complex were included in the phylogenetic analyses because T.olens lacks molecular data. The phylogenetic analyses were performed by a combined sequence dataset of the internal transcribed spacer (ITS) and the partial nuclear large subunit rDNA (nLSU), and a combined sequence dataset of the ITS, partial nLSU, the small subunit mitochondrial rRNA gene (mtSSU), the translation elongation factor 1-α (TEF1), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). The eight species formed eight independent lineages with robust support in phylogenies based on both datasets. Illustrated description of the six species including Tremellafibulifera s.s., T. “neofibulifera” and four new species, and discussions with their related species, are provided. A table of the comparison of the important characteristics of nine species in the T.fibulifera complex and a key to the whitish species in Tremella s.s. are provided.
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Affiliation(s)
- Long-Fei Fan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.,College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Renato Lúcio Mendes Alvarenga
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Av. da Engenharia s/n, Recife, Pernambuco 50740-570, Brazil
| | - Tatiana Baptista Gibertoni
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Av. da Engenharia s/n, Recife, Pernambuco 50740-570, Brazil
| | - Fang Wu
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yu-Cheng Dai
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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15
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Muneer MA, Huang X, Hou W, Zhang Y, Cai Y, Munir MZ, Wu L, Zheng C. Response of Fungal Diversity, Community Composition, and Functions to Nutrients Management in Red Soil. J Fungi (Basel) 2021; 7:jof7070554. [PMID: 34356933 PMCID: PMC8307627 DOI: 10.3390/jof7070554] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/23/2022] Open
Abstract
Soil fungi play a critical role in plant performance and soil nutrient cycling. However, the understanding of soil fungal community composition and functions in response to different nutrients management practices in red soils remains largely unknown. Here, we investigated the responses of soil fungal communities and functions under conventional farmer fertilization practice (FFP) and different nutrient management practices, i.e., optimization of NPK fertilizer (O) with soil conditioner (O + C), with lime and mushroom residue (O + L + M), and with lime and magnesium fertilizer (O + L + Mg). Illumina high-throughput sequencing was used for fungal identification, while the functional groups were inferred with FUNGuild. Nutrient management practices significantly raised the soil pH to 4.79–5.31 compared with FFP (3.69), and soil pH had the most significant effect (0.989 ***) on fungal communities. Predominant phyla, including Ascomycota, Basidiomycota, and Mortierellomycota were identified in all treatments and accounted for 94% of all fungal communities. The alpha diversity indices significantly increased under nutrients management practices compared with FFP. Co-occurrence network analysis revealed the keystone fungal species in the red soil, i.e., Ascomycota (54.04%), Basidiomycota (7.58%), Rozellomycota (4.55%), and Chytridiomycota (4.04%). FUNGuild showed that the relative abundance of arbuscular mycorrhizal fungi and ectomycorrhizal fungi was higher, while pathogenic fungi were lower under nutrient management practices compared with FFP. Our findings have important implications for the understanding of improvement of acidic soils that could significantly improve the soil fungal diversity and functioning in acidic soils.
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Affiliation(s)
- Muhammad Atif Muneer
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Xiaoman Huang
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Wei Hou
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Yadong Zhang
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Yuanyang Cai
- College of Plant Science, Jilin University, Changchun 130062, China;
| | - Muhammad Zeeshan Munir
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China;
| | - Liangquan Wu
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Chaoyuan Zheng
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
- Correspondence: ; Tel.: +86-177-5020-8499
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16
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Tarin MWK, Fan L, Xie D, Tayyab M, Rong J, Chen L, Muneer MA, Zheng Y. Response of Soil Fungal Diversity and Community Composition to Varying Levels of Bamboo Biochar in Red Soils. Microorganisms 2021; 9:microorganisms9071385. [PMID: 34202337 PMCID: PMC8306102 DOI: 10.3390/microorganisms9071385] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
Soil fungi play a vital role in soil nutrient dynamics, but knowledge of their diversity and community composition in response to biochar addition into red soil is either limited or inconsistent. Therefore, we determined the impact of bamboo biochar (BB) with increasing concentrations (0, 5, 20, and 80 g kg−1 of soil, referred to as B0, BB5, BB20, and BB80, respectively) on soil physicochemical properties and fungal communities (Illumina high-throughput sequencing) in red soil under Fokenia hodginsii (Fujian cypress). We found that increasing BB levels effectively raised the soil pH and soil nutrients, particularly under BB80. BB addition significantly increased the relative abundance of important genera, i.e., Basidiomycota, Mucoromycota, and Chytridiomycota that could play a key role in ecological functioning, e.g., wood degradation and litter decomposition, improvement in plant nutrients uptake, and resistance to several abiotic stress factors. Soil amended with BB exhibited a substantial ability to increase the fungal richness and diversity; BB80 > BB20 > BB5 > B0. Basidiomycota, Mucoromycota, Glomeromycota, Rozellomycota, Aphelidiomycota, Kickxellomycota, and Planctomycetes were positively associated with soil pH, total nitrogen, phosphorous, and carbon, and available potassium and phosphorous. Besides, the correlation analysis between the soil fungal communities and soil properties also showed that soil pH was the most influential factor in shaping the soil fungal communities in the red soil. These findings have significant implications for a comprehensive understanding of how to ameliorate acidic soils with BB addition, as well as for future research on sustainable forest management, which might increase soil fungi richness, diversity, and functionality in acidic soils.
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Affiliation(s)
- Muhammad Waqqas Khan Tarin
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.W.K.T.); (L.C.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.F.); (D.X.); (J.R.)
| | - Lili Fan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.F.); (D.X.); (J.R.)
| | - Dejin Xie
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.F.); (D.X.); (J.R.)
| | - Muhammad Tayyab
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Jundong Rong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.F.); (D.X.); (J.R.)
| | - Lingyan Chen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.W.K.T.); (L.C.)
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yushan Zheng
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.W.K.T.); (L.C.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.F.); (D.X.); (J.R.)
- Correspondence:
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17
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Mack J, Assabgui R, Seifert K. Taxonomy and phylogeny of the basidiomycetous hyphomycete genus Hormomyces. Fungal Syst Evol 2021; 7:177-196. [PMID: 34124623 PMCID: PMC8166209 DOI: 10.3114/fuse.2021.07.09] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/21/2021] [Indexed: 01/08/2023] Open
Abstract
The taxonomy of the genus Hormomyces, typified by Hormomyces aurantiacus, which based on circumstantial evidence was long assumed to be the hyphomycetous asexual morph of Tremella mesenterica (Tremellales, Tremellomycetes) or occasionally Dacrymyces (Dacrymycetales, Dacrymycetes), is revised. Phylogenies based on the three nuc rDNA markers [internal transcribed spacers (ITS), 28S large ribosomal subunit nrDNA (28S) and 18S small ribosomal subunit nrDNA (18S)], based on cultures from Canada and the United States, suggest that the genus is synonymous with Tulasnella (Cantharellales, Agaricomycetes) rather than Tremella or Dacrymyces. Morphological studies of 38 fungarium specimens of Hormomyces, including the type specimens of H. callorioides, H. fragiformis, H. paridiphilus and H. peniophorae and examination of the protologues of H. abieticola, H. aurantiacus and H. pezizoideus suggest that H. callorioides and H. fragiformis are conspecific with H. aurantiacus while the remaining species are unlikely to be related to Tulasnella. The conidial chains produced by H. aurantiacus are similar to monilioid cells of asexual morphs of Tulasnella species formerly referred to the genus Epulorhiza. The new combination Tulasnella aurantiaca is proposed and the species is redescribed, illustrated and compared with similar fungi. The ecological niche of T. aurantiaca and its possible relationship to orchid root endophytes is discussed. A key to asexual genera with similar conidium ontogeny to T. aurantiaca is provided. Citation: Mack J, Assabgui RA, Seifert KA (2021). Taxonomy and phylogeny of the basidiomycetous hyphomycete genus Hormomyces. Fungal Systematics and Evolution 7: 177-196. doi: 10.3114/fuse.2021.07.09.
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Affiliation(s)
- J. Mack
- Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - R.A. Assabgui
- Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
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18
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Tuovinen V, Millanes AM, Freire-Rallo S, Rosling A, Wedin M. Tremella macrobasidiata and Tremella variae have abundant and widespread yeast stages in Lecanora lichens. Environ Microbiol 2021; 23:2484-2498. [PMID: 33684261 DOI: 10.1111/1462-2920.15455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 01/22/2023]
Abstract
Dimorphism is a widespread feature of tremellalean fungi in general, but a little-studied aspect of the biology of lichen-associated Tremella. We show that Tremella macrobasidiata and Tremella variae have an abundant and widespread yeast stage in their life cycles that occurs in Lecanora lichens. Their sexual filamentous stage is restricted to a specific lichen: T. macrobasidiata only forms basidiomata on Lecanora chlarotera hymenia and T. variae only on Lecanora varia thalli. However, the yeast stage of T. macrobasidiata is less specific and can occur in L. varia lichens, whilst all life stages of T. variae may be specific to L. varia. Contrary to the hyphal stages, the yeasts are distributed across the thalli and hymenia of Lecanora lichens, and not limited to specimens with basidiomata. Tremella macrobasidiata was present in all studied L. chlarotera, and in 59% of L. varia specimens. Only in 8% of the L. varia thalli could none of the two Tremella species be detected. Our results indicate that lichen-associated Tremella may be much more abundant and widespread than previously assumed leading to skewed estimations about their distribution ranges and lichen specificity, and raise new questions about their biology, ecology and function in the symbiosis.
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Affiliation(s)
- Veera Tuovinen
- Department of Ecology and Genetics, Uppsala University, Uppsala, Norbyvägen 18D, 752 36, Sweden.,Department of Botany, Swedish Museum of Natural History, Stockholm, P.O. Box 50007, SE-104 05, Sweden
| | - Ana Maria Millanes
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, E-28933, Spain
| | - Sandra Freire-Rallo
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, E-28933, Spain
| | - Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Uppsala, Norbyvägen 18D, 752 36, Sweden
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, Stockholm, P.O. Box 50007, SE-104 05, Sweden
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19
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Tagirdzhanova G, Saary P, Tingley JP, Díaz-Escandón D, Abbott DW, Finn RD, Spribille T. Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes. Genome Biol Evol 2021; 13:6163286. [PMID: 33693712 PMCID: PMC8355462 DOI: 10.1093/gbe/evab047] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Basidiomycete yeasts have recently been reported as stably associated secondary
fungal symbionts of many lichens, but their role in the symbiosis remains
unknown. Attempts to sequence their genomes have been hampered both by the
inability to culture them and their low abundance in the lichen thallus
alongside two dominant eukaryotes (an ascomycete fungus and chlorophyte alga).
Using the lichen Alectoria sarmentosa, we selectively dissolved
the cortex layer in which secondary fungal symbionts are embedded to enrich
yeast cell abundance and sequenced DNA from the resulting slurries as well as
bulk lichen thallus. In addition to yielding a near-complete genome of the
filamentous ascomycete using both methods, metagenomes from cortex slurries
yielded a 36- to 84-fold increase in coverage and near-complete genomes for two
basidiomycete species, members of the classes Cystobasidiomycetes and
Tremellomycetes. The ascomycete possesses the largest gene repertoire of the
three. It is enriched in proteases often associated with pathogenicity and
harbors the majority of predicted secondary metabolite clusters. The
basidiomycete genomes possess ∼35% fewer predicted genes than the
ascomycete and have reduced secretomes even compared with close relatives, while
exhibiting signs of nutrient limitation and scavenging. Furthermore, both
basidiomycetes are enriched in genes coding for enzymes producing secreted
acidic polysaccharides, representing a potential contribution to the shared
extracellular matrix. All three fungi retain genes involved in dimorphic
switching, despite the ascomycete not being known to possess a yeast stage. The
basidiomycete genomes are an important new resource for exploration of lifestyle
and function in fungal–fungal interactions in lichen symbioses.
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Affiliation(s)
- Gulnara Tagirdzhanova
- Department of Biological Sciences CW405, University of Alberta, Edmonton, Alberta, Canada
| | - Paul Saary
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jeffrey P Tingley
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - David Díaz-Escandón
- Department of Biological Sciences CW405, University of Alberta, Edmonton, Alberta, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Toby Spribille
- Department of Biological Sciences CW405, University of Alberta, Edmonton, Alberta, Canada
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20
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: cellular, genomic and metabolic complexity. Biol Rev Camb Philos Soc 2020; 95:1198-1232. [PMID: 32301582 PMCID: PMC7539958 DOI: 10.1111/brv.12605] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental Sciences, Universitat Pompeu Fabra (UPF)Dr. Aiguader 88, 08003BarcelonaSpain
- ICREAPg. Lluís Companys 23, 08010BarcelonaSpain
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21
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Mark K, Laanisto L, Bueno CG, Niinemets Ü, Keller C, Scheidegger C. Contrasting co-occurrence patterns of photobiont and cystobasidiomycete yeast associated with common epiphytic lichen species. THE NEW PHYTOLOGIST 2020; 227:1362-1375. [PMID: 32034954 DOI: 10.1111/nph.16475] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
The popular dual definition of lichen symbiosis is under question with recent findings of additional microbial partners living within the lichen body. Here we compare the distribution and co-occurrence patterns of lichen photobiont and recently described secondary fungus (Cyphobasidiales yeast) to evaluate their dependency on lichen host fungus (mycobiont). We sequenced the nuclear internal transcribed spacer (ITS) strands for mycobiont, photobiont, and yeast from six widespread northern hemisphere epiphytic lichen species collected from 25 sites in Switzerland and Estonia. Interaction network analyses and multivariate analyses were conducted on operational taxonomic units based on ITS sequence data. Our study demonstrates the frequent presence of cystobasidiomycete yeasts in studied lichens and shows that they are much less mycobiont-specific than the photobionts. Individuals of different lichen species growing on the same tree trunk consistently hosted the same or closely related mycobiont-specific Trebouxia lineage over geographic distances while the cystobasidiomycete yeasts were unevenly distributed over the study area - contrasting communities were found between Estonia and Switzerland. These results contradict previous findings of high mycobiont species specificity of Cyphobasidiales yeast at large geographic scales. Our results suggest that the yeast might not be as intimately associated with the symbiosis as is the photobiont.
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Affiliation(s)
- Kristiina Mark
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu, 51006, Estonia
- Department of Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Lauri Laanisto
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu, 51006, Estonia
| | - C Guillermo Bueno
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu, 51006, Estonia
- Estonian Academy of Sciences, Kohtu 6, Tallinn, 10130, Estonia
| | - Christine Keller
- Department of Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Christoph Scheidegger
- Department of Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
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22
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Zhou Y, Jia BS, Zhou YG, Li AH, Xue L. Naganishia floricola sp. nov., a novel basidiomycetous yeast species isolated from flowers of Sorbaria sorbifolia. Int J Syst Evol Microbiol 2020; 70:4496-4501. [DOI: 10.1099/ijsem.0.004304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yeast strains representing a novel species in the basidiomycetous yeast genus Naganishia were isolated from flowers of Sorbaria sorbifolia collected in Beijing Olympic Forest Park, PR China. Results of multi-gene phylogenetic analysis indicated that the two strains were closely related to the type strains of Naganishia bhutanensis (CBS 6294T) and Naganishia antarctica (CBS 7687T). However, the new isolates differed from N. bhutanensis CBS 6294T by 1.79 % sequence divergence in the D1/D2 domain (11 nt substitutions and three indels), and 2.42 % (15 nt differences and one indel) to N. antarctica CBS 7687T. In the ITS region, the new isolates showed 1.15 % divergence (7 nt substitutions and one indel) to N. bhutanensis CBS 6294T and 0.92 % divergence (5 nt substitutions and no indels) to N. antarctica CBS 7687T. A phylogenetic analysis employing the sequences of six genes (D1/D2 domain of large subunit rDNA, ITS, small subunit rDNA, two subunits of the RNA polymerase II and elongation factor-1α) indicated that the novel species belonged to the genus Naganishia and formed a well-supported clade with N. bhutanensis, N. antarctica and N. indica. Moreover, the two strains differed from their closest relatives by the ability to grow on distinct carbon and nitrogen sources and ability to grow at 30 °C. On the basis of these findings, we propose a novel species in the genus Naganishia (Filobasidiales), Naganishia floricola sp. nov. (holotype CGMCC 2.5856).
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Affiliation(s)
- Yu Zhou
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Bi-Si Jia
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
| | - Yu-Guang Zhou
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
| | - Ai-Hua Li
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
| | - Lu Xue
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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23
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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Sun Y, Wang GS, Li AH, Wangmu, Chui XQ, Jiang JH, Wang QM. Phaeotremella camelliae sp. nov. (Phaeotremellaceae, Tremellales), A Novel Yeasts Isolated from Tea-Oil Fruits in Jiangxi Province, China. Curr Microbiol 2020; 77:3168-3173. [PMID: 32514781 DOI: 10.1007/s00284-020-02061-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 05/26/2020] [Indexed: 10/24/2022]
Abstract
Sixty-two isolates among the 65 yeast strains isolated from Jiangxi province, China, were identified into 15 known species based on the sequence analysis of the D1/D2 domains of the LSU rRNA and ITS region. The other three strains, GaoanZ14, GaoanC57, and GaoanC191, isolated from tea-oil fruits, were identified as two undescribed species of Phaeotremella based on the multiple gene sequence analysis, physiological, and biochemical comparisons. Strains GaoanC57 and GaoanC191 had one substitution difference both in the D1/D2 domains of the LSU rRNA and ITS region. They formed a separate branch from the other Phaeotremella species in the D1/D2 and multiple genes trees, and differed from the known species by at least 10 nucleotide substitutions in the D1/D2 domains and more than 6% mismatches in the ITS region. The phylogenetic analysis indicated that those two strains represent a novel species of Phaeotremella, for which the names Phaeotremella camelliae sp. nov. (Holotype CGMCC 2.6141, Mycobank MB832699) is proposed. Only one strain, GaoanZ14, represents the other undescribed species of Phaeotremella, so it will be described in latter when more strains are found.
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Affiliation(s)
- Yong Sun
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Gui-Shuang Wang
- Tibet Agriculture & Animal, Husbandry University, Nyingchi, 860000, Tibet, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Ai-Hua Li
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wangmu
- Tibet Agriculture & Animal, Husbandry University, Nyingchi, 860000, Tibet, China
| | - Xian-Qiu Chui
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China.
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.,College of Life Sciences, Hebei University, Baoding, 071002, Hebei, China
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25
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Aliyu H, Gorte O, Zhou X, Neumann A, Ochsenreither K. In silico Proteomic Analysis Provides Insights Into Phylogenomics and Plant Biomass Deconstruction Potentials of the Tremelalles. Front Bioeng Biotechnol 2020; 8:226. [PMID: 32318549 PMCID: PMC7147457 DOI: 10.3389/fbioe.2020.00226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/05/2020] [Indexed: 01/27/2023] Open
Abstract
Basidiomycetes populate a wide range of ecological niches but unlike ascomycetes, their capabilities to decay plant polymers and their potential for biotechnological approaches receive less attention. Particularly, identification and isolation of CAZymes is of biotechnological relevance and has the potential to improve the cache of currently available commercial enzyme cocktails toward enhanced plant biomass utilization. The order Tremellales comprises phylogenetically diverse fungi living as human pathogens, mycoparasites, saprophytes or associated with insects. Here, we have employed comparative genomics approaches to highlight the phylogenomic relationships among thirty-five Tremellales and to identify putative enzymes of biotechnological interest encoded on their genomes. Evaluation of the predicted proteomes of the thirty-five Tremellales revealed 6,918 putative carbohydrate-active enzymes (CAZYmes) and 7,066 peptidases. Two soil isolates, Saitozyma podzolica DSM 27192 and Cryptococcus sp. JCM 24511, show higher numbers harboring an average of 317 compared to a range of 267-121 CAZYmes for the rest of the strains. Similarly, the proteomes of the two soil isolates along with two plant associated strains contain higher number of peptidases sharing an average of 234 peptidases compared to a range of 226-167 for the rest of the strains. Despite these huge differences and the apparent enrichment of these enzymes among the soil isolates, the data revealed a diversity of the various enzyme families that does not reflect specific habitat type. Growth experiment on various carbohydrates to validate the predictions provides support for this view. Overall, the data indicates that the Tremellales could serve as a rich source of both CAZYmes and peptidases with wide range of potential biotechnological relevance.
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Affiliation(s)
- Habibu Aliyu
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Olga Gorte
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Xinhai Zhou
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Anke Neumann
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Katrin Ochsenreither
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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26
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Shirouzu T, Matsuoka S, Doi H, Nagata N, Ushio M, Hosaka K. Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms. Sci Rep 2020; 10:3057. [PMID: 32080243 PMCID: PMC7033186 DOI: 10.1038/s41598-020-59620-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/03/2020] [Indexed: 11/28/2022] Open
Abstract
Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DNA (eDNA) metabarcoding of decaying branches. Among the 28 operational taxonomic units (OTUs) detected during a three-year investigation, 10 each were from fruiting bodies and cultured mycelia and 27 were detected as eDNA sequences. eDNA metabarcoding revealed various lineages across the Dacrymycetes phylogeny. Alternatively, fruiting-body and culture surveys uncovered only ~50% of the OTUs detected through eDNA metabarcoding, suggesting that several inconspicuous or difficult-to-isolate strains are latent in the environment. Further, eDNA and culture surveys revealed early-diverging clades that were not identified in the fruiting-body survey. Thus, eDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations.
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Affiliation(s)
- Takashi Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan.
| | - Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Nobuaki Nagata
- Collection Center, National Museum of Nature and Science, 4-1-1 Amakubo, Ibaraki, 305-0005, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, 606-8501, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
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27
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Li AH, Yuan FX, Groenewald M, Bensch K, Yurkov AM, Li K, Han PJ, Guo LD, Aime MC, Sampaio JP, Jindamorakot S, Turchetti B, Inacio J, Fungsin B, Wang QM, Bai FY. Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species. Stud Mycol 2020; 96:17-140. [PMID: 32206137 PMCID: PMC7082220 DOI: 10.1016/j.simyco.2020.01.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Nearly 500 basidiomycetous yeast species were accepted in the latest edition of The Yeasts: A Taxonomic Study published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the Tremellomycetes (Agaricomycotina). The other 61 are distributed in 26 genera in the Pucciniomycotina. Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.
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Key Words
- Apiotrichum xylopini S.O. Suh, C.F. Lee, Gujjari & J.J. Zhou ex Kachalkin, Yurkov & Boekhout
- Bannozyma arctica Vishniac & M. Takash. ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Basidiomycetous yeasts
- Begerowomyces Q.M. Wang & F.Y. Bai
- Begerowomyces foliicola Q.M. Wang, F.Y. Bai & A.H. Li
- Bensingtonia pseudorectispora Q.M. Wang, F.Y. Bai & A.H. Li
- Bensingtonia wuzhishanensis Q.M. Wang, F.Y. Bai & A.H. Li
- Boekhoutia Q.M. Wang & F.Y. Bai
- Boekhoutia sterigmata Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium cremeum Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium elongatum Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium panici Fungsin, M. Takash. & Nakase ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bulleribasidium phyllophilum Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium phyllostachydis Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium pseudopanici Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium siamense Fungsin, M. Takash. & Nakase ex Q.M. Wang, F.Y. Bai, Boekhout & Nakase
- Carcinomyces arundinariae Fungsin, M. Takash. & Nakase ex Yurkov
- Carlosrosaea foliicola Q.M. Wang, F.Y. Bai & A.H. Li
- Carlosrosaea simaoensis Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma cylindrica Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma flava Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma fusiformis Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma iridis Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma pseudogriseoflava Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma rhododendri Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma sambuci Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma sorbariae Q.M. Wang, F.Y. Bai & A.H. Li
- Colacogloea aletridis Q.M. Wang, F.Y. Bai & A.H. Li
- Colacogloea hydrangeae Q.M. Wang, F.Y. Bai & A.H. Li
- Colacogloea rhododendri Q.M. Wang, F.Y. Bai & A.H. Li
- Colacogloea subericola (Belloch, Villa-Carv., Á;lv.-Rodríg. & Coque) Q.M. Wang, & F.Y. Bai
- Cystobasidium alpinum Turchetti, Selbmann, Onofri & Buzzini
- Cystobasidium portillonense Laich, Vaca & R. Chávez ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Cystobasidium raffinophilum Q.M. Wang, F.Y. Bai & A.H. Li
- Cystobasidium terricola Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces bifurcus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces cylindricus F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang
- Derxomyces elongatus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces hubeiensis F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang
- Derxomyces longicylindricus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces longiovatus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces melastomatis Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces nakasei F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang
- Derxomyces napiformis Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces ovatus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces polymorphus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces pseudoboekhoutii Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces pseudoyunnanensis Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces taiwanicus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces xingshanicus Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia heilongjiangensis Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia kandeliae Q.M. Wang, F.Y. Bai, L.D. Guo & A.H. Li
- Dioszegia maotaiensis Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia milinica Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia ovata Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia zsoltii F.Y. Bai, M. Takash. & Nakase
- F.Y. Bai, M. Groenew. & Boekhout
- Filobasidium dingjieense Q.M. Wang, F.Y. Bai & A.H. Li
- Filobasidium globosum Q.M. Wang, F.Y. Bai & A.H. Li
- Filobasidium mali Q.M. Wang, F.Y. Bai & A.H. Li
- Filobasidium mucilaginum Q.M. Wang, F.Y. Bai & A.H. Li
- Genolevuria bromeliarum Landell & P. Valente ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Genolevuria pseudoamylolytica Q.M. Wang, F.Y. Bai & A.H. Li
- Glaciozyma Turchetti, Connell, Thomas-Hall & Boekhout ex M. Groenew. & Q.M. Wang
- Glaciozyma antarctica (Fell, Statzell, I.L. Hunter & Phaff) M. Groenew. & Q.M. Wang
- Glaciozyma martinii Turchetti, Connell, Thomas-Hall & Boekhout
- Glaciozyma watsonii Turchetti, Connell, Thomas-Hall & Boekhout
- Heitmania cylindrica Q.M. Wang, F.Y. Bai & A.H. Li
- Heitmania tridentata Q.M. Wang, F.Y. Bai & A.H. Li
- Heitmaniaceae Q.M. Wang & F.Y. Bai
- Heitmaniales Q.M. Wang & F.Y. Bai
- Holtermannia saccardoi Q.M. Wang, F.Y. Bai & A.H. Li
- Jianyuniaceae Q.M. Wang & F.Y. Bai
- Kockovaella haikouensis Q.M. Wang, F.Y. Bai & A.H. Li
- Kockovaella ischaemi Q.M. Wang, F.Y. Bai & A.H. Li
- Kockovaella mexicana Lopandić, O. Molnár & Prillinger ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kockovaella nitrophila Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa arboricola Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa chamaenerii Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa cylindrica Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa daliangziensis Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa foliicola Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa lulangica Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa myxariophila Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa rhododendri Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa ribitophobia Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa thailandica Fungsin, Hamam. & Nakase ex Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- Kwoniella newhampshirensis K. Sylvester, Q.M. Wang & C.T. Hittinger
- Kwoniella ovata Q.M. Wang, F.Y. Bai & A.H. Li
- Kwoniella shandongensis R. Chen, Y.M. Jiang & S.C. Wei ex M. Groenew. & Q.M. Wang
- Leucosporidium creatinivorum (Golubev) M. Groenew. & Q.M. Wang
- Leucosporidium fragarium (J.A. Barnett & Buhagiar) M. Groenew. & Q.M. Wang
- Leucosporidium intermedium (Nakase & M. Suzuki) M. Groenew. & Q.M. Wang
- Leucosporidium muscorum (Di Menna) M. Groenew. & Q.M. Wang
- Leucosporidium yakuticum (Golubev) M. Groenew. & Q.M. Wang
- Meniscomyces Q.M. Wang & F.Y. Bai
- Meniscomyces layueensis Q.M. Wang, F.Y. Bai & A.H. Li
- Microbotryozyma swertiae Q.M. Wang, F.Y. Bai & A.H. Li
- Microsporomyces ellipsoideus Q.M. Wang, F.Y. Bai & A.H. Li
- Microsporomyces pseudomagnisporus Q.M. Wang, F.Y. Bai & A.H. Li
- Microsporomyces rubellus Q.M. Wang, F.Y. Bai & A.H. Li
- Molecular phylogeny
- Naganishia onofrii Turchetti, Selbmann & Zucconi ex Yurkov
- Naganishia vaughanmartiniae Turchetti, Blanchette & Arenz ex Yurkov
- Nielozyma Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nielozyma formosana Nakase, Tsuzuki, F.L. Lee & M. Takash. ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nielozyma melastomatis Nakase, Tsuzuki, F.L. Lee & M. Takash. ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozyma dicranopteridis Q.M. Wang, F.Y. Bai & A.H. Li
- Oberwinklerozyma nepetae Q.M. Wang, F.Y. Bai & A.H. Li
- Oberwinklerozyma silvestris Golubev & Scorzetti ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozyma straminea Golubev & Scorzetti ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotrema aspenensis (Ferreira-Paim, et al.) Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotrema baii Yurkov, M.A. Guerreiro & Á;. Fonseca ex Yurkov
- Papiliotrema frias V. de García, Zalar, Brizzio, Gunde-Cim. & Van Broock ex Yurkov
- Papiliotrema hoabinhensis D.T. Luong, M. Takash., Ty, Dung & Nakase ex Yurkov
- Papiliotrema japonica J.P. Samp., Fonseca & Fell ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotrema terrestris Crestani, Landell, Faganello, Vainstein, Vishniac & P. Valente ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotrema wisconsinensis K. Sylvester, Q.M. Wang & Hittinger ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Phaeotremella lactea Q.M. Wang, F.Y. Bai & A.H. Li
- Phaeotremella ovata Q.M. Wang, F.Y. Bai & A.H. Li
- Phaffia aurantiaca Q.M. Wang, F.Y. Bai & A.H. Li
- Phyllozyma aceris Q.M. Wang, F.Y. Bai & A.H. Li
- Phyllozyma jiayinensis Q.M. Wang, F.Y. Bai & A.H. Li
- Piskurozyma fildesensis T.T. Zhang & Li Y. Yu ex Yurkov
- Piskurozyma taiwanensis Nakase, Tsuzuki & M. Takash. ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pseudobensingtonia fusiformis Q.M. Wang, F.Y. Bai & A.H. Li
- Pseudohyphozyma hydrangeae Q.M. Wang, F.Y. Bai & A.H. Li
- Pseudohyphozyma lulangensis Q.M. Wang, F.Y. Bai & A.H. Li
- Pseudoleucosporidium V. de García, et al. ex M. Groenew. & Q.M. Wang
- Pseudoleucosporidium fasciculatum (Babeva & Lisichk.) M. Groenew. & Q.M. Wang
- Pseudosterigmatospora Q.M. Wang & F.Y. Bai
- Pseudosterigmatospora motuoensis Q.M. Wang, F.Y. Bai & A.H. Li
- Pseudotremella lacticolour Satoh & Makimura ex Yurkov
- Rhodosporidiobolus fuzhouensis Q.M. Wang, F.Y. Bai & A.H. Li
- Rhodosporidiobolus jianfalingensis Q.M. Wang, F.Y. Bai & A.H. Li
- Rhodosporidiobolus platycladi Q.M. Wang, F.Y. Bai & A.H. Li
- Rhynchogastrema complexa (Landell, et al.) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema fermentans (C.F. Lee) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema glucofermentans (S.O. Suh & M. Blackw.) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema nanyangensis F.L. Hui & Q.H. Niu ex Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema tunnelae (Boekhout, Fell, Scorzetti & Theelen) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema visegradensis (G. Péter & Dlauchy) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout &Yurkov
- Robertozyma Q.M. Wang & F.Y. Bai
- Robertozyma ningxiaensis Q.M. Wang, F.Y. Bai & A.H. Li
- Rosettozyma Q.M. Wang & F.Y. Bai
- Rosettozyma cystopteridis Q.M. Wang, F.Y. Bai & A.H. Li
- Rosettozyma motuoensis Q.M. Wang, F.Y. Bai & A.H. Li
- Rosettozyma petaloides Q.M. Wang, F.Y. Bai & A.H. Li
- Rosettozymaceae Q.M. Wang & F.Y. Bai
- Rosettozymales Q.M. Wang & F.Y. Bai
- Ruinenia bangxiensis Q.M. Wang, F.Y. Bai & A.H. Li
- Ruinenia diospyri Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash. ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ruinenia fanjingshanensis Q.M. Wang, F.Y. Bai & A.H. Li
- Ruinenia lunata Q.M. Wang, F.Y. Bai & A.H. Li
- Ruinenia pyrrosiae Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash. ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Saitozyma ninhbinhensis (D.T. Luong, M. Takash., Dung & Nakase)Yurkov
- Saitozyma paraflava Golubev & J.P. Samp. ex Xin Zhan Liu
- Saitozyma pseudoflava Q.M. Wang, F.Y. Bai & A.H. Li
- Sakaguchia melibiophila M. Groenew., Q.M. Wang & F.Y. Bai
- Slooffia globosa Q.M. Wang, F.Y. Bai & A.H. Li
- Solicoccozyma gelidoterrea Q.M. Wang, F.Y. Bai & A.H. Li
- Species diversity
- Sporobolomyces cellobiolyticus Q.M. Wang, F.Y. Bai & A.H. Li
- Sporobolomyces ellipsoideus Q.M. Wang, F.Y. Bai & A.H. Li
- Sporobolomyces primogenomicus Q.M. Wang & F.Y. Bai
- Sporobolomyces reniformis Q.M. Wang, F.Y. Bai & A.H. Li
- Sterigmatospora Q.M. Wang & F.Y. Bai
- Sterigmatospora layueensis Q.M. Wang, F.Y. Bai & A.H. Li
- Symmetrospora oryzicola (Nakase & M. Suzuki) Q.M. Wang & F.Y. Bai
- Symmetrospora rhododendri Q.M. Wang, F.Y. Bai & A.H. Li
- Taxonomy
- Teunia Q.M. Wang & F.Y. Bai
- Teunia betulae K. Sylvester, Q.M. Wang & Hittinger ex Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia cuniculi (K.S. Shin & Y.H. Park) Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia globosa Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia helanensis Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia korlaensis Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia tronadorensis V. de Garcia, Zalar, Brizzio, Gunde-Cim. & van Brook ex Q.M. Wang, F.Y. Bai & A.H. Li
- Tremella basidiomaticola Xin Zhan Liu & F.Y. Bai
- Tremella shuangheensis Q.M. Wang, F.Y. Bai & A.H. Li
- Trimorphomyces sakaeraticus Fungsin, M. Takash. & Nakase ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vanrija meifongana C.F. Lee ex Kachalkin Yurkov & Boekhout
- Vanrija nantouana C.F. Lee ex Kachalkin Yurkov & Boekhout
- Vanrija thermophila Vogelmann, S. Chaves & C. Hertel ex Kachalkin Yurkov & Boekhout
- Vishniacozyma europaea Q.M. Wang, F.Y. Bai & A.H. Li
- Vishniacozyma foliicola Q.M. Wang & F.Y. Bai ex Yurkov
- Vishniacozyma heimaeyensis Vishniac ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vishniacozyma melezitolytica Q.M. Wang, F.Y. Bai & A.H. Li
- Vishniacozyma pseudopenaeus Q.M. Wang, F.Y. Bai & A.H. Li
- Vishniacozyma psychrotolerans V. de García, Zalar, Brizzio, Gunde-Cim. & Van Broock ex Yurkov
- Vishniacozyma taibaiensis Q.M. Wang & F.Y. Bai ex Yurkov
- Vishniacozyma tephrensis Vishniac ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamyces rosulatus Golubev & Scorzetti ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamyces terricola Q.M. Wang, F.Y. Bai & A.H. Li
- Yurkovia longicylindrica Q.M. Wang, F.Y. Bai & A.H. Li
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Affiliation(s)
- A-H Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - F-X Yuan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,North Minzu University, Yinchuan, Ningxia, 750030, China
| | - M Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - K Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - A M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - K Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - P-J Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - L-D Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - M C Aime
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN, 47901, USA
| | - J P Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,PYCC - Portuguese Yeast Culture Collection, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - S Jindamorakot
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - B Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, 74 - I-06121, Italy
| | - J Inacio
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ, UK
| | - B Fungsin
- TISTR Culture Collection, Thailand Institute of Scientific and Technological Research (TISTR), 35 M 3, Technopolis, Khlong Ha, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Q-M Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China
| | - F-Y Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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29
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Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales. Fungal Genet Biol 2019; 130:31-42. [DOI: 10.1016/j.fgb.2019.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/19/2019] [Accepted: 04/20/2019] [Indexed: 02/03/2023]
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Lendemer JC, Keepers KG, Tripp EA, Pogoda CS, McCain CM, Kane NC. A taxonomically broad metagenomic survey of 339 species spanning 57 families suggests cystobasidiomycete yeasts are not ubiquitous across all lichens. AMERICAN JOURNAL OF BOTANY 2019; 106:1090-1095. [PMID: 31397894 DOI: 10.1002/ajb2.1339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/12/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested. METHODS We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America. RESULTS Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results. CONCLUSIONS Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.
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Affiliation(s)
- James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Erin A Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Christy M McCain
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
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31
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Wu D, Zhang M, Peng M, Sui X, Li W, Sun G. Variations in Soil Functional Fungal Community Structure Associated With Pure and Mixed Plantations in Typical Temperate Forests of China. Front Microbiol 2019; 10:1636. [PMID: 31379786 PMCID: PMC6646410 DOI: 10.3389/fmicb.2019.01636] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 07/02/2019] [Indexed: 12/31/2022] Open
Abstract
Forest plants are in constant contact with the soil fungal community, which plays an important role in the circulation of nutrients through forest ecosystems. The objective of this study was to evaluate the fungal diversity in soil and elucidate the ecological role of functional fungal communities in forest ecosystems using soil samples from seven different plantations in northeastern China. Our results showed that the fungal communities were dominated by the phyla Ascomycota, Basidiomycota, and Mortierellomycota, and the mixed plantation of Fraxinus mandshurica and Pinus koraiensis had a soil fungal population clearly divergent from those in the other plantations. Additionally, the mixed plantation of F. mandshurica and P. koraiensis, which was low in soil nutrients, contained a highly diverse and abundant population of ectomycorrhizal fungi, whereas saprophytic fungi were more abundant in plantations with high soil nutrients. Redundancy analysis demonstrated a strong correlation between saprophytic fungi and the level of soil nutrients, whereas ectomycorrhizal fungi were mainly distributed in soils with low nutrient. Our findings provide insights into the importance of functional fungi and the mediation of soil nutrients in mixed plantations and reveal the effect of biodiversity on temperate forests.
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Affiliation(s)
- Di Wu
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Mengmeng Zhang
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Mu Peng
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xin Sui
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Wei Li
- College of Resources and Environmental Science, Northeast Agricultural University, Harbin, China
| | - Guangyu Sun
- College of Life Science, Northeast Forestry University, Harbin, China
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32
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Kachalkin AV, Turchetti B, Inácio J, Carvalho C, Mašínová T, Pontes A, Röhl O, Glushakova AM, Akulov A, Baldrian P, Begerow D, Buzzini P, Sampaio JP, Yurkov AM. Rare and undersampled dimorphic basidiomycetes. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01491-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Černajová I, Škaloud P. The first survey of Cystobasidiomycete yeasts in the lichen genus Cladonia; with the description of Lichenozyma pisutiana gen. nov., sp. nov. Fungal Biol 2019; 123:625-637. [PMID: 31416582 DOI: 10.1016/j.funbio.2019.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 12/31/2022]
Abstract
The view of lichens as a symbiosis only between a mycobiont and a photobiont has been challenged by discoveries of diverse associated organisms. Specific basidiomycete yeasts in the cortex of a range of macrolichens were hypothesized to influence the lichens' phenotype. The present study explores the occurrence and diversity of cystobasidiomycete yeasts in the lichen genus Cladonia. We obtained seven cultures and 56 additional sequences using specific primers from 27 Cladonia species from all over Europe and performed phylogenetic analyses based on ITS, LSU and SSU rDNA loci. We revealed yeast diversity distinct from any previously reported. Representatives of Cyphobasidiales, Microsporomycetaceae and of an unknown group related to Symmetrospora have been found. We present evidence that the Microsporomycetaceae contains mainly lichen-associated yeasts. Lichenozyma pisutiana is circumscribed here as a new genus and species. We report the first known associations between cystobasidiomycete yeasts and Cladonia (both corticate and ecorticate), and find that the association is geographically widespread in various habitats. Our results also suggest that a great diversity of lichen associated yeasts remains to be discovered.
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Affiliation(s)
- Ivana Černajová
- Charles University, Faculty of Science, Department of Botany, Benátská 2, 12800 Praha 2, Czech Republic.
| | - Pavel Škaloud
- Charles University, Faculty of Science, Department of Botany, Benátská 2, 12800 Praha 2, Czech Republic
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34
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Flakus A, Etayo J, Pérez-Ortega S, Kukwa M, Palice Z, Rodriguez-Flakus P. A new genus, Zhurbenkoa, and a novel nutritional mode revealed in the family Malmideaceae (Lecanoromycetes, Ascomycota). Mycologia 2019; 111:593-611. [PMID: 31136256 DOI: 10.1080/00275514.2019.1603500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Lichen-inhabiting fungi are highly specialized mycoparasites, commensals or rarely saprotrophs, that are common components of almost every ecosystem, where they develop obligate associations with lichens. Their relevance, however, contrasts with the relatively small number of these fungi described so far. Recent estimates and ongoing studies indicate that a significant fraction of their diversity remains undiscovered and may be expected in tropical regions, in particular in hyperdiverse fog-exposed montane forests. Here, we introduce the new genus Zhurbenkoa, from South America and Europe, for three lichenicolous fungi growing on thalli of the widespread lichen genus Cladonia (Lecanorales). Phylogenetic analyses based on combined sequence data of mt and nuc rDNA obtained from Andean populations (Bolivia) placed Zhurbenkoa as a member of Malmideaceae, a recently introduced family of lichen-forming fungi in the class Lecanoromycetes. Zhurbenkoa is closely related to the genera Savoronala and Sprucidea. The new genus is characterized by the development of grayish brown to almost black apothecia lacking an evident margin, an epihymenium interspersed with crystals (often seen as pruina), a strongly conglutinated hymenium made of noncapitate and sparsely branched paraphyses, a colorless exciple composed of radially arranged hyphae, a Lecanora/Micarea-like ascus type, and aseptate or 1-septate ellipsoidal colorless ascospores. Zhurbenkoa includes two Neotropical (Z. cladoniarum, Z. latispora) and one widespread (Z. epicladonia) species. The lichenicolous trophic mode is documented for the first time in the Malmideaceae, which until now included only lichen-forming associations between fungi and green algae.
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Affiliation(s)
- Adam Flakus
- a Department of Lichenology, W. Szafer Institute of Botany, Polish Academy of Sciences , Lubicz 46 , PL-31-512 Krakow , Poland
| | - Javier Etayo
- b Navarro Villoslada 16 , 3° dcha ., E-31003 Pamplona , Navarra , Spain
| | | | - Martin Kukwa
- d Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk , Wita Stwosza 59 , PL-80-308 Gdańsk , Poland
| | - Zdeněk Palice
- e Institute of Botany, Czech Academy of Sciences , CZ-25243 Průhonice , Czech Republic
| | - Pamela Rodriguez-Flakus
- f Laboratory of Molecular Analyses, W. Szafer Institute of Botany, Polish Academy of Sciences , Lubicz 46 , PL-31512 Krakow , Poland
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Khunnamwong P, Surussawadee J, Ribeiro JRA, Hagler AN, Limtong S. Tremella saccharicola f.a., sp. nov., a novel tremellaceous yeast species isolated from tropical regions. Int J Syst Evol Microbiol 2019; 69:2010-2016. [PMID: 31063122 DOI: 10.1099/ijsem.0.003420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ten strains representing a single anamorphic novel yeast species were isolated from the external surface (DMKU-SP23 and DMKU-SP40) and tissue (DMKU-SE89, DMKU-SE99, DMKU-SE100 and DMKU-SE147) of sugarcane leaves in Thailand, and phylloplane (IMUFRJR 52034) and rhizoplane (IMUFRJ 52036 and 52037) of sugarcane and associated soil (IMUFRJ 52035) in Brazil. These strains showed zero to two nucleotide substitutions in the sequences of the D1/D2 region of the LSU rRNA gene and zero to three nucleotide substitutions in the internal transcribed spacer (ITS) region. Tremella globispora was the most closely related species, but with 1.7-2.1 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene, and 5.3-6.0 % nucleotide substitutions in the ITS region. Phylogenetic analysis based on the concatenated sequences of the ITS and the D1/D2 regions showed that these 10 strains represented a single species belonging to the genus Tremella (class Tremellomycetes, subphylum Agaricomycotina) that was distinct from related species. They therefore represented a novel species of the genus Tremella although the formation of basidia and basidiocarp were not observed. The name Tremella saccharicola f.a., sp. nov. is proposed. The type strain is DMKU-SP23T (=NBRC 109698T=BCC 61186T).
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Affiliation(s)
- Pannida Khunnamwong
- 1Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Janjira Surussawadee
- 1Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - José R A Ribeiro
- 2Instituto de Microbiologia Prof. Paulo de Goes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,3Postgraduated Program in Biotechnology and Bioprocess, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Allen N Hagler
- 2Instituto de Microbiologia Prof. Paulo de Goes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Savitree Limtong
- 4Academy of Science, The Royal Society of Thailand, Bangkok, Thailand.,1Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
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Zhao Y, Liu XZ, Bai FY. Four new species of Tremella (Tremellales, Basidiomycota) based on morphology and DNA sequence data. MycoKeys 2019:75-95. [PMID: 30853836 PMCID: PMC6403202 DOI: 10.3897/mycokeys.47.29180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 01/16/2019] [Indexed: 12/31/2022] Open
Abstract
In the present study, a total of 33 Tremella specimens in China were collected and examined using molecular phylogenetic analysis based on a combined sequence dataset of the nuc rDNA internal transcribed spacer (ITS) region and nuc 28S rDNA D1/D2 domain in conjunction with the morphological characters. Four new species, namely Tremellabasidiomaticola, T.cheejenii, T.erythrina, and T.salmonea, are newly described based on their distinct phylogenetic relationships and the comparison of morphological characters with known Tremella species. Our results indicate a high species diversity of Tremella waiting to be discovered.
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Affiliation(s)
- Ying Zhao
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China 1 State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China 2 Key Laboratory of Microbiology Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, PR China Beijing China.,Key Laboratory of Microbiology Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China 1 State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China Beijing China
| | - Xin-Zhan Liu
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China 1 State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China 2 Key Laboratory of Microbiology Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, PR China Beijing China
| | - Feng-Yan Bai
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China 1 State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China 2 Key Laboratory of Microbiology Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, PR China Beijing China
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Tuovinen V, Ekman S, Thor G, Vanderpool D, Spribille T, Johannesson H. Two Basidiomycete Fungi in the Cortex of Wolf Lichens. Curr Biol 2019; 29:476-483.e5. [PMID: 30661799 DOI: 10.1016/j.cub.2018.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/04/2018] [Accepted: 12/13/2018] [Indexed: 01/26/2023]
Abstract
Since the late 1800s, mycologists have been detecting fungi above and beyond the assumed single fungus in lichen thalli [1-6]. Over the last century, these fungi have been accorded roles ranging from commensalists to pathogens. Recently, Cyphobasidiales yeasts were shown to be ubiquitous in the cortex layer of many macrolichens [7], but for most species, little is known of their cellular distribution and constancy beyond visible fruiting structures. Here, we demonstrate the occurrence of an additional and distantly related basidiomycete, Tremella, in 95% of studied thalli in a global sample of one of the most intensively studied groups of lichens, the wolf lichens (genus Letharia). Tremella species are reported from a wide range of lichen genera [8], but until now, their biology was deduced from fruiting bodies (basidiomata) formed on lichen thalli. Based on this, they have been thought to be uncommon to rare, to occur exclusively in a hyphal form, and to be parasitic on the dominant fungal partner [9, 10]. We show that, in wolf lichens, Tremella occurs as yeast cells also in thalli that lack basidiomata and infer that this is its dominant stage in nature. We further show that the hyphal stage, when present in Letharia, is in close contact with algal cells, challenging the assumption that lichen-associated Tremella species are uniformly mycoparasites. Our results suggest that extent of occurrence and cellular interactions of known fungi within lichens have historically been underestimated and raise new questions about their function in specific lichen symbioses.
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Affiliation(s)
- Veera Tuovinen
- Department of Biological Sciences CW 405, University of Alberta, Edmonton, AB T6G 2R3, Canada; Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden; Department of Ecology, Swedish University of Agricultural Sciences, PO Box 7044, 750 07 Uppsala, Sweden.
| | - Stefan Ekman
- Museum of Evolution, Uppsala University, Norbyvägen 16, 752 36 Uppsala, Sweden
| | - Göran Thor
- Department of Ecology, Swedish University of Agricultural Sciences, PO Box 7044, 750 07 Uppsala, Sweden
| | - Dan Vanderpool
- Department of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA; Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
| | - Toby Spribille
- Department of Biological Sciences CW 405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
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Studies in the Stypella vermiformis group (Auriculariales, Basidiomycota). Antonie van Leeuwenhoek 2018; 112:753-764. [PMID: 30535961 PMCID: PMC6456474 DOI: 10.1007/s10482-018-01209-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/30/2018] [Indexed: 01/27/2023]
Abstract
Stypella vermiformis is a heterobasidiomycete producing minute gelatinous basidiocarps on rotten wood of conifers in the Northern Hemisphere. In the current literature, Stypella papillata, the genus type of Stypella (described from Brazil), is treated as a taxonomic synonym of S. vermiformis. In the present paper, we revise the type material of S. papillata and a number of specimens addressed to S. vermiformis. As a result, the presumed synonymy of S. papillata and S. vermiformis is rejected and the genus Stypella is restricted to the single species S. papillata. Morphological and molecular phylogenetic studies of specimens from the Northern Hemisphere corresponding to the current concept of S. vermiformis uncovered three species from two newly described genera. S. vermiformis s.str. is distributed in temperate Europe and has small-sized basidia and basidiospores, and it is placed in a new genus, Mycostilla. Another genus, Stypellopsis, is created for two other species, the North American Stypellopsis farlowii, comb. nov., and the North European Stypellopsis hyperborea, sp. nov. Basidia and basidiospores of Stypellopsis spp. are larger than in Mycostilla vermiformis but other morphological characters are very similar. In addition, Spiculogloea minuta (Spiculogloeomycetes, Pucciniomycotina) is reported as new to Norway, parasitising basidiocarps of M. vermiformis and Tulasnella spp.
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Wijayawardene NN, Pawłowska J, Letcher PM, Kirk PM, Humber RA, Schüßler A, Wrzosek M, Muszewska A, Okrasińska A, Istel Ł, Gęsiorska A, Mungai P, Lateef AA, Rajeshkumar KC, Singh RV, Radek R, Walther G, Wagner L, Walker C, Wijesundara DSA, Papizadeh M, Dolatabadi S, Shenoy BD, Tokarev YS, Lumyong S, Hyde KD. Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0409-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Pino-Bodas R, Laakso I, Stenroos S. Genetic variation and factors affecting the genetic structure of the lichenicolous fungus Heterocephalacria bachmannii (Filobasidiales, Basidiomycota). PLoS One 2017; 12:e0189603. [PMID: 29253026 PMCID: PMC5734755 DOI: 10.1371/journal.pone.0189603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/29/2017] [Indexed: 11/26/2022] Open
Abstract
Heterocephalacria bachmannii is a lichenicolous fungus that takes as hosts numerous lichen species of the genus Cladonia. In the present study we analyze whether the geographical distance, the host species or the host secondary metabolites determine the genetic structure of this parasite. To address the question, populations mainly from the Southern Europe, Southern Finland and the Azores were sampled. The specimens were collected from 20 different host species representing ten chemotypes. Three loci, ITS rDNA, LSU rDNA and mtSSU, were sequenced. The genetic structure was assessed by AMOVA, redundance analyses and Bayesian clustering methods. The results indicated that the host species and the host secondary metabolites are the most influential factors over the genetic structure of this lichenicolous fungus. In addition, the genetic structure of H. bachmannii was compared with that of one of its hosts, Cladonia rangiformis. The population structure of parasite and host were discordant. The contents in phenolic compounds and fatty acids of C. rangiformis were quantified in order to test whether it had some influence on the genetic structure of the species. But no correlation was found with the genetic clusters of H. bachmannii.
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Affiliation(s)
| | - Into Laakso
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Soili Stenroos
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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Zhang Z, Zhou X, Tian L, Ma L, Luo S, Zhang J, Li X, Tian C. Fungal communities in ancient peatlands developed from different periods in the Sanjiang Plain, China. PLoS One 2017; 12:e0187575. [PMID: 29236715 PMCID: PMC5728540 DOI: 10.1371/journal.pone.0187575] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/23/2017] [Indexed: 01/08/2023] Open
Abstract
Peatlands in the Sanjiang Plain could be more vulnerable to global warming because they are located at the southernmost boundary of northern peatlands. Unlike bacteria, fungi are often overlooked, even though they play important roles in substance circulation in the peatland ecosystems. Accordingly, it is imperative that we deepen our understanding of fungal community structure and diversity in the peatlands. In this study, high-throughput Illumina sequencing was used to study the fungal communities in three fens in the Sanjiang Plain, located at the southern edge of northern peatlands. Peat soil was collected from the three fens which developed during different periods. A total of 463,198 fungal ITS sequences were obtained, and these sequences were classified into at least six phyla, 21 classes, more than 60 orders and over 200 genera. The fungal community structures were distinct in the three sites and were dominated by Ascomycota and Basidiomycota. However, there were no significant differences between these three fens in any α-diversity index (p > 0.05). Soil age and the carbon (C) accumulation rate, as well as total carbon (TC), total nitrogen (TN), C/N ratio, and bulk density were found to be closely related to the abundance of several dominant fungal taxa. We captured a rich fungal community and confirmed that the dominant taxa were those which were frequently detected in other northern peatlands. Soil age and the C accumulation rate were found to play important roles in shaping the fungal community structure.
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Affiliation(s)
- Zhenqing Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xue Zhou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Shasha Luo
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jianfeng Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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Pontes A, Röhl O, Maldonado C, Yurkov AM, Sampaio JP. Cryptotrichosporon argae sp. nov., Cryptotrichosporon brontae sp. nov. and Cryptotrichosporon steropae sp. nov., isolated from forest soils. Int J Syst Evol Microbiol 2017; 67:3610-3614. [DOI: 10.1099/ijsem.0.002177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ana Pontes
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Oliver Röhl
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Geobotany, Faculty for Biology and Biotechnology, Ruhr-Universität Bochum, Bochum, Germany
| | - Cristina Maldonado
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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44
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Microbial succession dynamics along glacier forefield chronosequences in Tierra del Fuego (Chile). Polar Biol 2017. [DOI: 10.1007/s00300-017-2110-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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45
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Resolving relationships at the animal-fungal divergence: A molecular phylogenetic study of the protist trichomycetes (Ichthyosporea, Eccrinida). Mol Phylogenet Evol 2017; 109:447-464. [PMID: 28219758 DOI: 10.1016/j.ympev.2017.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 11/23/2022]
Abstract
Trichomycetes is a group of microorganisms that was considered a class of fungi comprising four orders of commensal, gut-dwelling endosymbionts obligately associated with arthropods. Since molecular phylogenies revealed two of those orders (Amoebidiales and Eccrinales="protist trichos") to be closely related to members of the protist class Ichthyosporea (=Mesomycetozoea), trichomycetes have been considered an ecological association of both early-diverging fungi and protists. Understanding of the taxonomy, evolution, and diversity of the protist trichos is lacking largely due to the difficulties inherent in species collection that have contributed to undersampling and understudy. The most recent classification divides the protist trichos between two families, Amoebidiidae and Eccrinidae (suborder Trichomycina, order Eccrinida). However, there is no comprehensive molecular phylogeny available for this group and major questions about the systematics of protist trichos remain unanswered. Therefore, we generated 18S and 28S rDNA sequences for 106 protist tricho samples and combined them with publicly available Eccrinida sequences for phylogenetic analyses. We also sequenced a conserved protein-coding gene (heat-shock 70 protein) to obtain a multigene data set. We conducted ancestral state reconstruction (ASR) and Bayesian tip-association significance test (BaTS) analyses by mapping six morphological and ecological characters onto the resulting phylogenetic trees. Our results demonstrate: (1) several ecological and morphological character states (habitat, host type, host stage at time of infestation, location within host, spore production, and growth form) are significantly correlated with the phylogeny, and (2) two additional protist tricho families should be incorporated into the taxonomy to reflect phylogenetic relationships. Our data suggest that an integrated strategy that combines morphological, ecological, and molecular characters is needed to further resolve and clarify the systematics of the Eccrinida.
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Chen H, Kovalchuk A, Keriö S, Asiegbu FO. Distribution and bioinformatic analysis of the cerato-platanin protein family in Dikarya. Mycologia 2017; 105:1479-88. [DOI: 10.3852/13-115] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | | | | | - Fred O. Asiegbu
- Department of Forest Sciences, PO Box 27, Latokartanonkaari 7, 00014 University of Helsinki, Helsinki, Finland
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47
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Guzzon R, Carafa I, Tuohy K, Cervantes G, Vernetti L, Barmaz A, Larcher R, Franciosi E. Exploring the microbiota of the red-brown defect in smear-ripened cheese by 454-pyrosequencing and its prevention using different cleaning systems. Food Microbiol 2016; 62:160-168. [PMID: 27889144 DOI: 10.1016/j.fm.2016.10.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 10/03/2016] [Accepted: 10/08/2016] [Indexed: 11/18/2022]
Abstract
Red-brown pigmentation can occasionally form in smeared-ripened cheese such as Fontina during the ripening process. This reaction is due to over-development of the typical microbiota present on the rind. Previous studies have demonstrated the relationship between red-brown pigmentation and the traditional utilization of wooden shelves during cheese ripening. The first part of the paper focuses on the characterisation of yeast and bacterial microbiota: plate counts and 454-pyrosequencing were performed in spoiled (n = 6) and non-spoiled cheeses (n = 6) and on the wooden shelves used during ripening. The second part shows different systems tested for cleaning the wooden shelves and avoiding the development of the red-brown defect in cheese: washing with hot water and ozone treatment. Actinobacteria, dominated on the wooden shelves, suggesting to be responsible for the red-brown pigmentation; they were also found in traces in the defected cheese samples. Galactomyces and Debaryomyces were the main species characterizing the yeast population, with Debaryomyces being the most dominant species on the shelves used during ripening of the red-brown defective cheese. Hot water treatment reduced the microbial contamination of shelves, whereas only the ozone treatment ensured complete elimination of both yeast and bacteria, resulting in the cheese rind not having the red-brown defect.
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Affiliation(s)
- Raffaele Guzzon
- Technology Transfer Centre, Edmund Mach Foundation, Via E. Mach 1, 38121, San Michele all'Adige, Trento, Italy
| | - Ilaria Carafa
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38121, San Michele all'Adige, Trento, Italy
| | - Kieran Tuohy
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38121, San Michele all'Adige, Trento, Italy
| | - Gonzalo Cervantes
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38121, San Michele all'Adige, Trento, Italy
| | - Luca Vernetti
- Institut Agricole Régional, Strada la Rochere 1, 11100, Aosta, AO, Italy
| | - Andrea Barmaz
- Institut Agricole Régional, Strada la Rochere 1, 11100, Aosta, AO, Italy
| | - Roberto Larcher
- Technology Transfer Centre, Edmund Mach Foundation, Via E. Mach 1, 38121, San Michele all'Adige, Trento, Italy
| | - Elena Franciosi
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38121, San Michele all'Adige, Trento, Italy.
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Phylogenetic evidence places the coralloid jelly fungus Tremellodendropsis tuberosa (Tremellodendropsidales) among early diverging Agaricomycetes. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1220-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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49
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Zamora JC, Millanes AM, Wedin M, Rico VJ, Pérez-Ortega S. Understanding lichenicolous heterobasidiomycetes: new taxa and reproductive innovations in Tremella s.l. Mycologia 2016; 108:381-96. [PMID: 27127212 DOI: 10.3852/15-090] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/02/2015] [Indexed: 11/10/2022]
Abstract
Four new lichenicolous Tremella species are described and characterized morphologically and molecularly. Tremella celata grows on Ramalina fraxinea, inducing the formation of inconspicuous galls, and having hyphae with incomplete clamps. Tremella endosporogena develops intrahymenially in the apothecia of Lecanora carpinea, having single-celled basidia and clampless hyphae. Tremella diederichiana is the name proposed for a species micromorphologically close to T. christiansenii but inducing the formation of small, pale galls on the thallus and apothecia of Lecidea aff. erythrophaea Tremella variae grows on Lecanora varia thallus, instead of on the apothecia, as do the other known Tremella species parasitizing Lecanora s.l. Phylogenetic relationships and host specificity of these species are investigated and compared with other taxa that show morphological resemblances, phylogenetic affinities or similar hosts. The formation of mitotic conidia inside old basidia (endospores), which is a poorly known reproductive strategy in the Basidiomycota, is also a distinctive character of Tremella endosporogena A discussion on the reproductive role and systematic implications of endospores is included.
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Affiliation(s)
- Juan Carlos Zamora
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, E-28040 Madrid, Spain
| | - Ana María Millanes
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405 Stockholm, Sweden
| | - Víctor J Rico
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, E-28040 Madrid, Spain
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Nawaz A, Purahong W, Lehmann R, Herrmann M, Küsel K, Totsche KU, Buscot F, Wubet T. Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities. Front Microbiol 2016; 7:666. [PMID: 27242696 PMCID: PMC4860458 DOI: 10.3389/fmicb.2016.00666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/21/2016] [Indexed: 11/13/2022] Open
Abstract
Fungi are one important group of eukaryotic microorganisms in a diverse range of ecosystems, but their diversity in groundwater ecosystems is largely unknown. We used DNA-based pyro-tag sequencing of the fungal internal transcribed spacer (ITS) rDNA gene to investigate the presence and community structure of fungi at different sampling sites of two superimposed limestone aquifers ranging from 8.5 to 84 m depth in the newly established Hainich Critical Zone Exploratory (Hainich CZE). We detected a diversity of fungal OTUs in groundwater samples of all sampling sites. The relative percentage abundance of Basidiomycota was higher in the upper aquifer assemblage, whilst Ascomycota dominated the lower one. In parallel to differences in the hydrochemistry we found distinct fungal communities at all sampling sites. Classification into functional groups revealed an overwhelming majority of saprotrophs. Finding taxa common to all analyzed groundwater sites, point to a groundwater specific fungal microbiome. The presence of different functional groups and, in particular plant and cattle pathogens that are not typical of subsurface habitats, suggests links between the surface and subsurface biogeosphere due to rapid transportation across the fracture networks typical of karstic regions during recharge episodes. However, further studies including sampling series extended in both time and space are necessary to confirm this hypothesis.
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Affiliation(s)
- Ali Nawaz
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil EcologyHalle (Saale), Germany; Department of Biology, University of LeipzigLeipzig, Germany
| | - Witoon Purahong
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil Ecology Halle (Saale), Germany
| | - Robert Lehmann
- Institute of Geosciences, Friedrich Schiller University Jena Jena, Germany
| | - Martina Herrmann
- Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Kirsten Küsel
- Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Kai U Totsche
- Institute of Geosciences, Friedrich Schiller University Jena Jena, Germany
| | - François Buscot
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil EcologyHalle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Tesfaye Wubet
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil EcologyHalle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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