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Wei J, Yuan X, Geng Y, Bi W, Wang Y. Draft genome sequence of endolichenic fungus Dothichiza sp. strain YAFEF048, isolated from Usnea longissima on Haba Snow Mountain. Microbiol Resour Announc 2023; 12:e0101123. [PMID: 37971261 PMCID: PMC10720515 DOI: 10.1128/mra.01011-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
In this study, we report a draft genome sequence of the endolichenic fungus Dothichiza sp. strain YAFEF048, isolated from the lichen Usnea longissima on Haba Snow Mountain. The genome resource will support future research into the endolichenic lifestyle and potential secondary metabolite diversity of this fungus.
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Affiliation(s)
- Jiansheng Wei
- Haba Snow Mountain Provincial Nature Reserve Management and Protection Bureau, Diqing, China
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming Yunnan, China
| | - Xiaolong Yuan
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming Yunnan, China
| | - Yunfen Geng
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming Yunnan, China
| | - Wei Bi
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming Yunnan, China
| | - Yi Wang
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming Yunnan, China
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Chen X, Yan D, Yu L, Zhang T. An Integrative Study of Mycobiome in Different Habitats from a High Arctic Region: Diversity, Distribution, and Functional Role. J Fungi (Basel) 2023; 9:jof9040437. [PMID: 37108892 PMCID: PMC10144742 DOI: 10.3390/jof9040437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
In the Arctic ecosystems, fungi are crucial for interactions between soil and plants, the cycling of nutrients, and the transport of carbon. To date, no studies have been conducted to thoroughly examine the mycobiome and its functional role in various habitats of the High Arctic region. The aim was to unravel the mycobiome in the nine habitats (i.e., soil, lichen, vascular plant, moss, freshwater, seawater, marine sediment, dung, and marine alga) in the Ny-Ålesund Region (Svalbard, High Arctic) using a high-throughput sequencing approach. A total of 10,419 ASVs were detected. Among them, 7535 ASVs were assigned to unidentified phyla, while the remaining 2884 ASVs were assigned to 11 phyla, 33 classes, 81 orders, 151 families, 278 genera, and 261 species that were known. The distribution of the mycobiome was driven by habitat specificity, indicating that habitat filtering is a crucial factor influencing the fungal assemblages at a local scale in this High Arctic region. Six growth forms and 19 fungal guilds were found. The ecological guild (e.g., lichenized, ectomycorrhizal) and growth form (e.g., yeast, thallus photosynthetic) varied significantly among various habitats. In addition, the occurrence of 31 fungal species that are considered to be potential pathogens was determined. These results will increase our understanding of fungal diversity and its functional significance in this distinctive High Arctic area and thereby establish the groundwork for prediction about how the mycobiome will alter in various environments as a result of anticipated climate change.
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Affiliation(s)
- Xiufei Chen
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Dong Yan
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Liyan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Si H, Wang Y, Liu Y, Li S, Bose T, Chang R. Fungal Diversity Associated with Thirty-Eight Lichen Species Revealed a New Genus of Endolichenic Fungi, Intumescentia gen. nov. (Teratosphaeriaceae). J Fungi (Basel) 2023; 9:jof9040423. [PMID: 37108878 PMCID: PMC10143819 DOI: 10.3390/jof9040423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Fungi from the Teratosphaeriaceae (Mycosphaerellales; Dothideomycetes; Ascomycota) have a wide range of lifestyles. Among these are a few species that are endolichenic fungi. However, the known diversity of endolichenic fungi from Teratosphaeriaceae is far less understood compared to other lineages of Ascomycota. We conducted five surveys from 2020 to 2021 in Yunnan Province of China, to explore the biodiversity of endolichenic fungi. During these surveys, we collected multiple samples of 38 lichen species. We recovered a total of 205 fungal isolates representing 127 species from the medullary tissues of these lichens. Most of these isolates were from Ascomycota (118 species), and the remaining were from Basidiomycota (8 species) and Mucoromycota (1 species). These endolichenic fungi represented a wide variety of guilds, including saprophytes, plant pathogens, human pathogens, as well as entomopathogenic, endolichenic, and symbiotic fungi. Morphological and molecular data indicated that 16 of the 206 fungal isolates belonged to the family Teratosphaeriaceae. Among these were six isolates that had a low sequence similarity with any of the previously described species of Teratosphaeriaceae. For these six isolates, we amplified additional gene regions and conducted phylogenetic analyses. In both single gene and multi-gene phylogenetic analyses using ITS, LSU, SSU, RPB2, TEF1, ACT, and CAL data, these six isolates emerged as a monophyletic lineage within the family Teratosphaeriaceae and sister to a clade that included fungi from the genera Acidiella and Xenopenidiella. The analyses also indicated that these six isolates represented four species. Therefore, we established a new genus, Intumescentia gen. nov., to describe these species as Intumescentia ceratinae, I. tinctorum, I. pseudolivetorum, and I. vitii. These four species are the first endolichenic fungi representing Teratosphaeriaceae from China.
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Affiliation(s)
- Hongli Si
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yichen Wang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yanyu Liu
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Shiguo Li
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Tanay Bose
- Department of Biochemistry, Genetics & Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
- Correspondence: (T.B.); (R.C.)
| | - Runlei Chang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
- Correspondence: (T.B.); (R.C.)
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4
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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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Rojas-Gätjens D, Avey-Arroyo J, Chaverri P, Rojas-Jimenez K, Chavarría M. Differences in fungal communities in the fur of two- and three-toed sloths revealed by ITS metabarcoding. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36848210 DOI: 10.1099/mic.0.001309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Sloths have dense fur on which insects, algae, bacteria and fungi coexist. Previous studies using cultivation-dependent methods and 18S rRNA sequencing revealed that the fungal communities in their furs comprise members of the phyla Ascomycota and Basidiomycota. In this note, we increase the resolution and knowledge of the mycobiome inhabiting the fur of the two- (Choloepus hoffmanni) and three-toed (Bradypus variegatus) sloths. Targeted amplicon metagenomic analysis of ITS2 nrDNA sequences obtained from 10 individuals of each species inhabiting the same site revealed significant differences in the structure of their fungal communities and also in the alpha-diversity estimators. The results suggest a specialization by host species and that the host effect is stronger than that of sex, age and animal weight. Capnodiales were the dominant order in sloths' fur and Cladosporium and Neodevriesia were the most abundant genera in Bradypus and Choloepus, respectively. The fungal communities suggest that the green algae that inhabit the fur of sloths possibly live lichenized with Ascomycota fungal species. The data shown in this note offer a more detailed view of the fungal content in the fur of these extraordinary animals and could help explain other mutualistic relationships in this complex ecosystem.
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Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Priscila Chaverri
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
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Zhang T, Yan D, Ji Z, Chen X, Yu L. A comprehensive assessment of fungal communities in various habitats from an ice-free area of maritime Antarctica: diversity, distribution, and ecological trait. ENVIRONMENTAL MICROBIOME 2022; 17:54. [PMID: 36380397 PMCID: PMC9667611 DOI: 10.1186/s40793-022-00450-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/04/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND In the ice-free area of maritime Antarctica, fungi are the essential functioning group in terrestrial and marine ecosystems. Until now, no study has been conducted to comprehensively assess fungal communities in various habitats in Antarctica. We aimed to characterize fungal communities in the eleven habitats (i.e., soil, seawater, vascular plant, dung, moss, marine alga, lichen, green alga, freshwater, feather) in the Fildes Region (maritime Antarctica) using next-generation sequencing. RESULTS A total of 12 known phyla, 37 known classes, 85 known orders, 164 known families, 313 known genera, and 320 known species were detected. Habitat specificity rather than habitat overlap determined the composition of fungal communities, suggesting that, although fungal communities were connected by dispersal at the local scale, the environmental filter is a key factor driving fungal assemblages in the ice-free Antarctica. Furthermore, 20 fungal guilds and 6 growth forms were detected. Many significant differences in the functional guild (e.g., lichenized, algal parasite, litter saprotroph) and growth form (e.g., yeast, filamentous mycelium, thallus photosynthetic) existed among different habitat types. CONCLUSION The present study reveals the high diversity of fungal communities in the eleven ice-free Antarctic habitats and elucidates the ecological traits of fungal communities in this unique ice-free area of maritime Antarctica. The findings will help advance our understanding of fungal diversity and their ecological roles with respect to habitats on a neighbourhood scale in the ice-free area of maritime Antarctica.
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Affiliation(s)
- Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
| | - Dong Yan
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, People's Republic of China
| | - Zhongqiang Ji
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, People's Republic of China
| | - Xiufei Chen
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Liyan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
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Wang Q, Li J, Yang J, Zou Y, Zhao XQ. Diversity of endophytic bacterial and fungal microbiota associated with the medicinal lichen Usnea longissima at high altitudes. Front Microbiol 2022; 13:958917. [PMID: 36118246 PMCID: PMC9479685 DOI: 10.3389/fmicb.2022.958917] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Endophytic microbial communities of lichen are emerging as novel microbial resources and for exploration of potential biotechnological applications. Here, we focused on a medicinal lichen Usnea longissima, and investigated its bacterial and fungal endophytes. Using PacBio 16S rRNA and ITS amplicon sequencing, we explored the diversity and composition of endophytic bacteria and fungi in U. longissima collected from Tibet at five altitudes ranging from 2,989 to 4,048 m. A total of 6 phyla, 12 classes, 44 genera, and 13 species of the bacterial community have been identified in U. longissima. Most members belong to Alphaproteobacteria (42.59%), Betaproteobacteria (33.84%), Clostridia (13.59%), Acidobacteria (7%), and Bacilli (1.69%). As for the fungal community, excluding the obligate fungus sequences, we identified 2 phyla, 15 classes, 65 genera, and 19 species. Lichen-related fungi of U. longissima mainly came from Ascomycota (95%), Basidiomycota (2.69%), and unidentified phyla (2.5%). The presence of the sequences that have not been characterized before suggests the novelty of the microbiota. Of particular interest is the detection of sequences related to lactic acid bacteria and budding yeast. In addition, the possible existence of harmful bacteria was also discussed. To our best knowledge, this is the first relatively detailed study on the endophytic microbiota associated with U. longissima. The results here provide the basis for further exploration of the microbial diversity in lichen and promote biotechnological applications of lichen-associated microbial strains.
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Affiliation(s)
- Qi Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Li
- R&D Center, JALA Group Co., Ltd., Shanghai, China
| | - Jie Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zou
- R&D Center, JALA Group Co., Ltd., Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Xin-Qing Zhao,
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Xu H, Wang L, Feng X, Gong X. Core taxa and photobiont-microbial interaction within the lichen Heterodermia obscurata (Physcsiaceae, Heterodermia). Symbiosis 2022. [DOI: 10.1007/s13199-022-00832-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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9
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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates. J Fungi (Basel) 2022; 8:jof8030226. [PMID: 35330228 PMCID: PMC8955040 DOI: 10.3390/jof8030226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/19/2022] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
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Yang Z, Zhang Y, Xie Z, Wang J, Li Z, Li Y, Du J, Sun L. Potential influence of rapid climate change on elemental geochemistry distributions in lacustrine sediments-A case study at a high Arctic site in Ny-Ålesund, Svalbard. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149784. [PMID: 34428654 DOI: 10.1016/j.scitotenv.2021.149784] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/28/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Metal contamination has become an increasingly severe environmental issue due to intense anthropogenic activities in recent decades. Many studies have reported a rapidly increasing trend of heavy metal contents in sedimentary records. In this study, two lacustrine sediment cores (LDL and YL) far away from scientific research stations were collected in Ny-Ålesund and analyzed for the vertical distributions of 17 elemental concentrations (Cu, Zn, Pb, Co, Ni, Cr, Sr, Ba, Mn, P, Ti, K2O, Na2O, CaO, MgO, Fe2O3, Al2O3), CIA and TOC contents. The results indicated that only the proxies Pb, P, CaO, TOC, and CIA showed an increasing trend in the upper 7 cm section of the sediment cores, while most of the elements' concentrations decreased towards the surface. The rapid increase of TOC contents is likely related to the climate warming over the past 200 years, which promotes the prosperity of vegetation and thus leads to more input of organic matter into the lakes. Moreover, a large number of seabirds live around the sampling position and the seabird guano contains high concentrations of P, which could be regarded as an important nutrient source for vegetation. Additionally, the rapid climate warming could accelerate the chemical weathering rates, and thus lead to increased CaO contents in the sediment profiles according to its geological background. Therefore, the concentrations of other elements are very likely diluted by the high contents of organic matter and CaO in the upper part of the sediment cores. It is noteworthy that the rapidly increasing trend of Pb contents are related to the gas-oil powered generators in Ny-Ålesund and long-range atmospheric transport from Europe. This study highlighted the nonnegligible influence of climate warming on the inorganic elemental geochemistry distributions in remote lakes.
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Affiliation(s)
- Zhongkang Yang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271000, China; Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Youai Zhang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271000, China
| | - Zhouqing Xie
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271000, China.
| | - Zhaolei Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271000, China
| | - Yanqiang Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271000, China
| | - Jinlong Du
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Liguang Sun
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
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Ndinga-Muniania C, Mueller RC, Kuske CR, Porras-Alfaro A. Seasonal variation and potential roles of dark septate fungi in an arid grassland. Mycologia 2021; 113:1181-1198. [PMID: 34686124 DOI: 10.1080/00275514.2021.1965852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
High temperatures and extended drought in temperate and tropical arid ecosystems promote the colonization of diverse microenvironments by dark septate fungi (DSF). These fungi contribute to soil nutrient cycling, soil stabilization, and plant survival, but the roles of individual DSF species, their distributions, and their community diversity are poorly understood. The objective of this study was to evaluate the distribution, seasonal variation, and potential roles of DSF on plant growth. We collected biocrust (lichen-, moss-, and cyanobacterium-dominated biocrusts) soils at different depths and rhizosphere soils from two grasses, Bromus tectorum and Pleuraphis jamesii, in an arid grassland near Moab, Utah, USA. Seasonal variation of DSF was evaluated using culture-based approaches and compared with fungal community profiles from next-generation sequencing (NGS). Culturing showed that DSF were 30% more abundant in biocrusts compared with the focal rhizospheres. The abundance of DSF varied seasonally in belowground samples (rhizosphere and below-biocrust), with a significant increase during the summer months. Pleosporales was the dominant order (35%) in both biocrust and rhizosphere soils out of 817 isolated fungi. Dominant DSF genera in culture included Alternaria, Preussia, Cladosporium, Phoma, and an unknown Pleosporales. Similar results were observed in biocrust and rhizosphere soils NGS. Further, seed germination experiments using dominant taxa were conducted to determine their potential roles on germination and seedling growth using maize as a model plant. Cladosporium and unknown Pleosporales isolates showed plant growth-promoting ability. The variation in abundance of DSF, their differential occurrence in different microenvironments, and their ability to grow in a xerotolerant medium reflect adaptations to summer environmental conditions and to changes in the abundance of organic matter, as well as a potential increase in plant investment in these fungi when heat and drought stresses are more severe.
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Affiliation(s)
- Cedric Ndinga-Muniania
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455.,Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, 55108, Minnesota
| | - Rebecca C Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana 59717
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Andrea Porras-Alfaro
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455.,Division of Environmental Biology, National Science Foundation, Alexandria, Virginia 22314
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12
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Zhang T, Wang NF, Yu LY. Geographic Distance and Habitat Type Influence Fungal Communities in the Arctic and Antarctic Sites. MICROBIAL ECOLOGY 2021; 82:224-232. [PMID: 34081147 DOI: 10.1007/s00248-021-01742-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
The Antarctic and Arctic regions are collectively referred to as the "Two Poles" of the earth and have extremely harsh climate conditions and fragile ecosystems. Until now, the biogeography of the fungal communities in the bipolar regions is not well known. In this study, we focused on the fungal communities in 110 samples collected from four habitat types (i.e., soil, vascular plant, freshwater, moss) in the Antarctic and Arctic sites using high-throughput sequencing. The data showed that the diversity and composition of fungal communities were both geographically patterned and habitat-patterned. ANOSIM tests revealed statistically significant differences among fungal communities in the eight sample types (R = 0.5035, p < 0.001) and those in the bipolar regions (R = 0.32859, p < 0.001). Only 396 OTUs (14.8%) were shared between the bipolar sites. Fungal communities in the four habitat types clustered together in the Arctic site but were separate from those of the Antarctic site, indicating that geographic distance was a more important determinant of fungal communities in the bipolar sites. These findings offer insights into the present-day biogeography of fungal communities in the bipolar sites.
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Affiliation(s)
- Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
| | - Neng-Fei Wang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, People's Republic of China
| | - Li-Yan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
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13
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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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14
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Metagenomic data reveal diverse fungal and algal communities associated with the lichen symbiosis. Symbiosis 2020. [DOI: 10.1007/s13199-020-00699-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Rajulu MBG, Thirunavukkarasu N, Kumar SS, Kaur T, Reddy MS, Suryanarayanan TS. Endolichenic fungal diversity associated with some lichens of the Western Ghats. PLANTA MEDICA 2020; 86:960-966. [PMID: 31766071 DOI: 10.1055/a-1045-1989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A total of 389 strains of fungi belonging to 38 species were isolated from 10 lichen species of the Western Ghats, southern India. All the lichens screened, irrespective of their growth forms or location, harboured endolichenic fungi. Most of the fungi belonged to the Ascomycotina. Chaetomium sp. 1, Hypoxylon investiens, Nemania bipapillata, Nodulisporium sp., Paecilomyces sp., and Sporormiella intermedia were the most common ones and were present in 5 or more lichen species. Of the 28 sporulating fungi, 7 belonged to Xylariales, and their total colonization frequency in all the lichens was also high. This observation further substantiates the high ecological amplitude of Xylariales, possibly due to overlapping ecological niches and their ability to inhibit co-occurring endolichenic fungi.
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Affiliation(s)
| | | | - Subramanya Shravan Kumar
- Divecha Centre for Climate Change & Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Tanveer Kaur
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Mondem Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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16
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Comparative Genomic Study of Polar Lichen-Associated Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 Reveals the Presence of Polysaccharide-Degrading Ability Based on Habitat. Curr Microbiol 2020; 77:2940-2952. [PMID: 32681312 DOI: 10.1007/s00284-020-02120-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022]
Abstract
The genus Hymenobacter is classified in the family Hymenobacteraceae under the phylum Bacteroidetes. They have been isolated from diverse environments, such as air, soil, and lichen, along with extreme polar environments, including the Arctic and Antarctic regions. The polar regions have attracted intense research interest for the discovery of novel microorganisms and their functions. Analysis of the polysaccharide utilization-related carbohydrate-active enzyme among the two lichen-associated polar organisms Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 was performed, along with its comparison with the complete genome of the same genus available in the NCBI database. The study was conducted relying on the AZCL screening data for the two polar lichen-associated species. While comparing with eight other complete genomes, differences in polysaccharide preferences based on the isolation environment and biosample source were discovered. All the species showed almost similar percentage of cellulose synthesis and degradation genes. However, the polar lichen-associated microorganism was found to have a high percentage of hemicellulose degradation genes, and less starch and laminarin degradation. The Hymenobacter species with higher number of hemicellulose degradation genes was found to have a lower number of starch and laminarin degradation genes and vice versa, highlighting the differences in polysaccharide utilization among the species.
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Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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González-Hourcade M, Braga MR, del Campo EM, Ascaso C, Patiño C, Casano LM. Ultrastructural and biochemical analyses reveal cell wall remodelling in lichen-forming microalgae submitted to cyclic desiccation-rehydration. ANNALS OF BOTANY 2020; 125:459-469. [PMID: 31679006 PMCID: PMC7061176 DOI: 10.1093/aob/mcz181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/29/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS One of the most distinctive features of desiccation-tolerant plants is their high cell wall (CW) flexibility. Most lichen microalgae can tolerate drastic dehydration-rehydration (D/R) conditions; however, their mechanisms of D/R tolerance are scarcely understood. We tested the hypothesis that D/R-tolerant microalgae would have flexible CWs due to species-specific CW ultrastructure and biochemical composition, which could be remodelled by exposure to cyclic D/R. METHODS Two lichen microalgae, Trebouxia sp. TR9 (TR9, adapted to rapid D/R cycles) and Coccomyxa simplex (Csol, adapted to seasonal dry periods) were exposed to no or four cycles of desiccation [25-30 % RH (TR9) or 55-60 % RH (Csol)] and 16 h of rehydration (100 % RH). Low-temperature SEM, environmental SEM and freeze-substitution TEM were employed to visualize structural alterations induced by D/R. In addition, CWs were extracted and sequentially fractionated with hot water and KOH, and the gel permeation profile of polysaccharides was analysed in each fraction. The glycosyl composition and linkage of the main polysaccharides of each CW fraction were analysed by GC-MS. KEY RESULTS All ultrastructural analyses consistently showed that desiccation caused progressive cell shrinkage and deformation in both microalgae, which could be rapidly reversed when water availability increased. Notably, the plasma membrane of TR9 and Csol remained in close contact with the deformed CW. Exposure to D/R strongly altered the size distribution of TR9 hot-water-soluble polysaccharides, composed mainly of a β-3-linked rhamnogalactofuranan and Csol KOH-soluble β-glucans. CONCLUSIONS Cyclic D/R induces biochemical remodelling of the CW that could increase CW flexibility, allowing regulated shrinkage and expansion of D/R-tolerant microalgae.
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Affiliation(s)
| | - Marcia R Braga
- Institute of Botany, Department of Plant Physiology and Biochemistry, São Paulo, SP, Brazil
| | - Eva M del Campo
- University of Alcalá, Department of Life Sciences, Alcalá de Henares, Madrid, Spain
| | - Carmen Ascaso
- Museo Nacional de Ciencias Naturales, CSIC, Department of Biogeochemistry and Microbial Ecology, Madrid, Spain
| | | | - Leonardo M Casano
- University of Alcalá, Department of Life Sciences, Alcalá de Henares, Madrid, Spain
- For correspondence. E-mail
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19
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Łubek A, Kukwa M, Czortek P, Jaroszewicz B. Lichenicolous fungi are more specialized than their lichen hosts in primeval forest ecosystems, Białowieża Forest, northeast Poland. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.100866] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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20
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Yurkov AM, Sannino C, Turchetti B. Mrakia fibulata sp. nov., a psychrotolerant yeast from temperate and cold habitats. Antonie van Leeuwenhoek 2019; 113:499-510. [PMID: 31754948 DOI: 10.1007/s10482-019-01359-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/08/2019] [Indexed: 01/21/2023]
Abstract
Tree fluxes are sugar-rich, sometimes ephemeral, substrates occurring on sites where tree sap (xylem or phloem) is leaking through damages of tree bark. Tree sap infested with microorganisms has been the source of isolation of many species, including the biotechnologically relevant carotenoid yeast Phaffia rhodozyma. Tree fluxes recently sampled in Germany yielded 19 species, including several psychrophilic yeasts of the genus Mrakia. Four strains from tree fluxes represented a potential novel Mrakia species previously known from two isolates from superficial glacial melting water of Calderone Glacier (Italy). The Italian isolates, originally identified as Mrakia aquatica, and two strains from Germany did not show any sexual structures. But another culture collected in Germany produced clamped hyphae with teliospores. A detailed examination of the five isolates (three from Germany and two from Italy) proved them to be a novel yeast species, which is described in this manuscript as Mrakia fibulata sp. nov. (MB 830398), holotype DSM 103931 and isotype DBVPG 8059. In contrast to other sexually reproducing Mrakia species, M. fibulata produces true hyphae with clamp connections. Also, this is the first psychrotolerant Mrakia species which grows above 20 °C. Spring tree fluxes are widespread and can be recognized and sampled by amateurs in a Citizen Science project. This substrate is a prominent source of yeasts, and may harbor unknown species, as demonstrated in the present work. The description of Mrakia fibulata is dedicated to our volunteer helpers and amateurs, like Anna Yurkova (9-years-old daughter of Andrey Yurkov), who collected the sample which yielded the type strain of this species.
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Affiliation(s)
- A M Yurkov
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Brunswick, Germany.
| | - C Sannino
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - B Turchetti
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
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21
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Masumoto H, Degawa Y. The effect of surface sterilization and the type of sterilizer on the genus composition of lichen-inhabiting fungi with notes on some frequently isolated genera. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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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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23
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Lagarde A, Millot M, Pinon A, Liagre B, Girardot M, Imbert C, Ouk T, Jargeat P, Mambu L. Antiproliferative and antibiofilm potentials of endolichenic fungi associated with the lichen
Nephroma laevigatum. J Appl Microbiol 2019; 126:1044-1058. [DOI: 10.1111/jam.14188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/21/2018] [Accepted: 12/26/2018] [Indexed: 12/17/2022]
Affiliation(s)
- A. Lagarde
- Département de Pharmacognosie Laboratoire PEIRENE – EA 7500 Université de Limoges Limoges France
| | - M. Millot
- Département de Pharmacognosie Laboratoire PEIRENE – EA 7500 Université de Limoges Limoges France
| | - A. Pinon
- Laboratoire PEIRENE – EA 7500 Université de Limoges Limoges France
| | - B. Liagre
- Laboratoire PEIRENE – EA 7500 Université de Limoges Limoges France
| | - M. Girardot
- UMR CNRS 7267, Laboratoire Écologie et biologie des interactions Université de Poitiers Poitiers France
| | - C. Imbert
- UMR CNRS 7267, Laboratoire Écologie et biologie des interactions Université de Poitiers Poitiers France
| | - T.S. Ouk
- Laboratoire PEIRENE – EA 7500 Université de Limoges Limoges France
| | - P. Jargeat
- UMR 5174 UPS‐CNRS‐IRD, Laboratoire Évolution et Diversité Biologique Université de Toulouse 3 Toulouse France
| | - L. Mambu
- Département de Pharmacognosie Laboratoire PEIRENE – EA 7500 Université de Limoges Limoges France
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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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Molins A, Moya P, García-Breijo FJ, Reig-Armiñana J, Barreno E. Molecular and morphological diversity of Trebouxia microalgae in sphaerothallioid Circinaria spp. lichens 1. JOURNAL OF PHYCOLOGY 2018; 54:494-504. [PMID: 29791719 DOI: 10.1111/jpy.12751] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Three vagrant (Circinaria hispida, Circinaria gyrosa, and Circinaria sp. 'paramerae') and one crustose (semi-vagrant, Circinaria sp. 'oromediterranea') lichens growing in very continental areas in the Iberian Peninsula were selected to study the phycobiont diversity. Mycobiont identification was checked using nrITS DNA barcoding: Circinaria sp. 'oromediterranea' and Circinaria sp. 'paramerae' formed a new clade. Phycobiont diversity was analyzed in 50 thalli of Circinaria spp. using nrITS DNA and LSU rDNA, with microalgae coexistence being found in all the species analyzed by Sanger sequencing. The survey of phycobiont diversity showed up to four different Trebouxia spp. as the primary phycobiont in 20 thalli of C. hispida, in comparison with the remaining Circinaria spp., where only one Trebouxia was the primary microalga. In lichen species showing coexistence, some complementary approaches are needed (454 pyrosequencing and/or ultrastructural analyses). Five specimens were selected for high-throughput screening (HTS) analyses: 22 Trebouxia OTUs were detected, 10 of them not previously known. TEM analyses showed three different cell morphotypes (Trebouxia sp. OTU A12, OTU S51, and T. cretacea) whose ultrastructure is described here in detail for the first time. HTS revealed a different microalgae pool in each species studied, and we cannot assume a specific pattern between these pools and the ecological and/or morphological characteristics. The mechanisms involved in the selection of the primary phycobiont and the other microalgae by the mycobiont are unknown, and require complex experimental designs. The systematics of the genus Circinaria is not yet well resolved, and more analyses are needed to establish a precise delimitation of the species.
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Affiliation(s)
- Arántzazu Molins
- Botánica, ICBIBE and Jardí Botànic. Fac. CC. Biológicas, Universitat de València, C/Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
| | - Patricia Moya
- Botánica, ICBIBE and Jardí Botànic. Fac. CC. Biológicas, Universitat de València, C/Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
| | - Francisco J García-Breijo
- Dpto. Ecosistemas Agroforestales, Universitat Politècnica de València, Camino de Vera s/n. 46022, Valencia, Spain
| | - José Reig-Armiñana
- Botánica, ICBIBE and Jardí Botànic. Fac. CC. Biológicas, Universitat de València, C/Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
| | - Eva Barreno
- Botánica, ICBIBE and Jardí Botànic. Fac. CC. Biológicas, Universitat de València, C/Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
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Banchi E, Stankovic D, Fernández-Mendoza F, Gionechetti F, Pallavicini A, Muggia L. ITS2 metabarcoding analysis complements lichen mycobiome diversity data. Mycol Prog 2018; 17:1049-1066. [PMID: 30956650 PMCID: PMC6428334 DOI: 10.1007/s11557-018-1415-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/12/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023]
Abstract
Lichen thalli harbor complex fungal communities (mycobiomes) of species with divergent trophic and ecological strategies. The complexity and diversity of lichen mycobiomes are still largely unknown, despite surveys combining culture-based methods and high-throughput sequencing (HTS). The results of such surveys are strongly influenced by the barcode locus chosen, its sensitivity in discriminating taxa, and the depth to which public sequence repositories cover the phylogenetic spectrum of fungi. Here, we use HTS of the internal transcribed spacer 2 (ITS2) to assess the taxonomic composition and diversity of a well-characterized, alpine rock lichen community that includes thalli symptomatically infected by lichenicolous fungi as well as asymptomatic thalli. Taxa belonging to the order Chaetothyriales are the major components of the observed lichen mycobiomes. We predict sequences representative of lichenicolous fungi characterized morphologically and assess their asymptomatic presence in lichen thalli. We demonstrated the limitations of metabarcoding in fungi and show how the estimation of species diversity widely differs when ITS1 or ITS2 are used as barcode, and particularly biases the detection of Basidiomycota. The complementary analysis of both ITS1 and ITS2 loci is therefore required to reliably estimate the diversity of lichen mycobiomes.
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Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - David Stankovic
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
- National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia
| | | | - Fabrizia Gionechetti
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
- Institute of Plant Sciences, Karl-Franzens University of Graz, Holteigasse 6, 8010 Graz, Austria
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Fungal Diversity in Lichens: From Extremotolerance to Interactions with Algae. Life (Basel) 2018; 8:life8020015. [PMID: 29789469 PMCID: PMC6027233 DOI: 10.3390/life8020015] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 12/15/2022] Open
Abstract
Lichen symbioses develop long-living thallus structures even in the harshest environments on Earth. These structures are also habitats for many other microscopic organisms, including other fungi, which vary in their specificity and interaction with the whole symbiotic system. This contribution reviews the recent progress regarding the understanding of the lichen-inhabiting fungi that are achieved by multiphasic approaches (culturing, microscopy, and sequencing). The lichen mycobiome comprises a more or less specific pool of species that can develop symptoms on their hosts, a generalist environmental pool, and a pool of transient species. Typically, the fungal classes Dothideomycetes, Eurotiomycetes, Leotiomycetes, Sordariomycetes, and Tremellomycetes predominate the associated fungal communities. While symptomatic lichenicolous fungi belong to lichen-forming lineages, many of the other fungi that are found have close relatives that are known from different ecological niches, including both plant and animal pathogens, and rock colonizers. A significant fraction of yet unnamed melanized (‘black’) fungi belong to the classes Chaethothyriomycetes and Dothideomycetes. These lineages tolerate the stressful conditions and harsh environments that affect their hosts, and therefore are interpreted as extremotolerant fungi. Some of these taxa can also form lichen-like associations with the algae of the lichen system when they are enforced to symbiosis by co-culturing assays.
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Lagarde A, Jargeat P, Roy M, Girardot M, Imbert C, Millot M, Mambu L. Fungal communities associated with Evernia prunastri, Ramalina fastigiata and Pleurosticta acetabulum: Three epiphytic lichens potentially active against Candida biofilms. Microbiol Res 2018; 211:1-12. [PMID: 29705201 DOI: 10.1016/j.micres.2018.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/07/2018] [Accepted: 03/17/2018] [Indexed: 11/26/2022]
Abstract
Fungal communities associated to three epiphytic lichens active against Candida, were investigated using culture-based methods We hypothetized that associated fungi would contribute to lichens activities. The ability of specific fungi to grow inside or outside lichens was investigated. To detect biogenesis pathways involved in the production of secondary metabolites, genes coding for nonribosomal peptide synthetase (NRPS) and polyketide synthase I (PKS I) were screened by PCR from fungal DNA extracts. Both endo and epilichenic communities were isolated from two fructicose (Evernia prunastri and Ramalina fastigiata) and one foliose (Pleurosticta acetabulum) lichens. A total of 86 endolichenic and 114 epilichenic isolates were obtained, corresponding to 18 and 24 phylogenetic groups respectively suggesting a wide diversity of fungi. The communities and the species richness were distinct between the three lichens which hosted potentially new fungal species. Additionally, the endo- and epilichenic communities differed in their composition: Sordariomycetes were particularly abundant among endolichenic fungi and Dothideomycetes among epilichenic fungi. Only a few fungi colonized both habitats, such as S. fimicola, Cladosporium sp1 and Botrytis cinerea. Interestingly, Nemania serpens (with several genotypes) was the most abundant endolichenic fungus (53% of isolates) and was shared by the three lichens. Finally, 12 out of 36 phylogenetic groups revealed the presence of genes coding for nonribosomal peptide synthetase (NRPs) and polyketide synthase I (PKS I). This study shows that common lichens are reservoirs of diverse fungal communities, which could potentially contribute to global activity of the lichen and, therefore, deserve to be isolated for further chemical studies.
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Affiliation(s)
- Aurélie Lagarde
- EA 1069 Laboratoire de Chimie des Substances Naturelles, Faculté de Pharmacie, Université de Limoges, 2 rue du Dr Marcland, 87025 Limoges Cedex, France
| | - Patricia Jargeat
- UMR5174 UPS-CNRS-IRD Laboratoire Evolution et Diversité Biologique, EDB, Université Toulouse, 3, Bât 4R1, 118 route de Narbonne, 31062 Toulouse, France
| | - Mélanie Roy
- UMR5174 UPS-CNRS-IRD Laboratoire Evolution et Diversité Biologique, EDB, Université Toulouse, 3, Bât 4R1, 118 route de Narbonne, 31062 Toulouse, France
| | - Marion Girardot
- Laboratoire Ecologie et Biologie des Interactions, Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, F-86073 Poitiers, France
| | - Christine Imbert
- Laboratoire Ecologie et Biologie des Interactions, Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, F-86073 Poitiers, France
| | - Marion Millot
- EA 1069 Laboratoire de Chimie des Substances Naturelles, Faculté de Pharmacie, Université de Limoges, 2 rue du Dr Marcland, 87025 Limoges Cedex, France
| | - Lengo Mambu
- EA 1069 Laboratoire de Chimie des Substances Naturelles, Faculté de Pharmacie, Université de Limoges, 2 rue du Dr Marcland, 87025 Limoges Cedex, France.
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Gonzalez-Martinez A, Sihvonen M, Muñoz-Palazon B, Rodriguez-Sanchez A, Mikola A, Vahala R. Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi. Sci Rep 2018; 8:2208. [PMID: 29396546 PMCID: PMC5797233 DOI: 10.1038/s41598-018-20633-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/21/2018] [Indexed: 01/06/2023] Open
Abstract
Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.
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Affiliation(s)
- Alejandro Gonzalez-Martinez
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland.
| | - Maija Sihvonen
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
| | - Barbara Muñoz-Palazon
- Institute of Water Research, University of Granada, C/Ramón y Cajal, 4, 18071, Granada, Spain
| | | | - Anna Mikola
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
| | - Riku Vahala
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
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Wang M, Chen M, Yang Z, Chen N, Chi X, Pan L, Wang T, Yu S, Guo X. Influence of Peanut Cultivars and Environmental Conditions on the Diversity and Community Composition of Pod Rot Soil Fungi in China. MYCOBIOLOGY 2017; 45:392-400. [PMID: 29371808 PMCID: PMC5780372 DOI: 10.5941/myco.2017.45.4.392] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/09/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
Peanut yield and quality are seriously affected by pod rot pathogens worldwide, especially in China in recent years. The goals of this study are to analyze the structure of fungal communities of peanut pod rot in soil in three peanut cultivars and the correlation of pod rot with environmental variables using 454 pyrosequencing. A total of 46,723 internal transcribed spacer high-quality sequences were obtained and grouped into 1,706 operational taxonomic units at the 97% similarity cut-off level. The coverage, rank abundance, and the Chao 1 and Shannon diversity indices of the operational taxonomic units were analyzed. Members of the phylum Ascomycota were dominant, such as Fusarium, Chaetomium, Alternaria, and Sordariomycetes, followed by Basidiomycota. The results of the heatmap and redundancy analysis revealed significant variation in the composition of the fungal community among the three cultivar samples. The environmental conditions in different peanut cultivars may also influence on the structure of the fungal community. The results of this study suggest that the causal agent of peanut pod rot may be more complex, and cultivars and environmental conditions are both important contributors to the community structure of peanut pod rot fungi.
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Affiliation(s)
- Mian Wang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Mingna Chen
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Zhen Yang
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Na Chen
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Xiaoyuan Chi
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Lijuan Pan
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Tong Wang
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Shanlin Yu
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China
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31
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Xu F, Cai T, Yang X, Sui W. Soil fungal community variation by large-scale reclamation in Sanjiang plain, China. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1296-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Fernández-Mendoza F, Fleischhacker A, Kopun T, Grube M, Muggia L. ITS1 metabarcoding highlights low specificity of lichen mycobiomes at a local scale. Mol Ecol 2017; 26:4811-4830. [PMID: 28771869 DOI: 10.1111/mec.14244] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 05/22/2017] [Accepted: 07/06/2017] [Indexed: 01/21/2023]
Abstract
As self-supporting and long-living symbiotic structures, lichens provide a habitat for many other organisms beside the traditionally considered lichen symbionts-the myco- and the photobionts. The lichen-inhabiting fungi either develop diagnostic phenotypes or occur asymptomatically. Because the degree of specificity towards the lichen host is poorly known, we studied the diversity of these fungi among neighbouring lichens on rocks in an alpine habitat. Using a sequencing metabarcoding approach, we show that lichen mycobiomes clearly reflect the overlap of multiple ecological sets of taxa, which differ in their trophic association with lichen thalli. The lack of specificity to the lichen mycobiome is further supported by the lack of community structure observed using clustering and ordination methods. The communities encountered across samples largely result from the subsampling of a shared species pool, in which we identify three major ecological components: (i) a generalist environmental pool, (ii) a lichenicolous/endolichenic pool and (iii) a pool of transient species. These taxa majorly belong to the fungal classes Dothideomycetes, Eurotiomycetes and Tremellomycetes with close relatives in adjacent ecological niches. We found no significant evidence that the phenotypically recognized lichenicolous fungi influence the occurrence of the other asymptomatic fungi in the host thalli. We claim that lichens work as suboptimal habitats or as a complex spore and mycelium bank, which modulate and allow the regeneration of local fungal communities. By performing an approach that minimizes ambiguities in the taxonomic assignments of fungi, we present how lichen mycobiomes are also suitable targets for improving bioinformatic analyses of fungal metabarcoding.
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Affiliation(s)
| | | | - Theodora Kopun
- Institute of Plant Sciences, Karl-Franzens-University Graz, Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University Graz, Graz, Austria
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
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Suryanarayanan TS, Thirunavukkarasu N. Endolichenic fungi: the lesser known fungal associates of lichens. Mycology 2017; 8:189-196. [PMID: 30123639 PMCID: PMC6059131 DOI: 10.1080/21501203.2017.1352048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
Lichens are the result of a stable mutualism between a fungal and a photosynthesising partner (alga or cyanobacterium). In addition to the fungal partner in this mutualism, lichens are associated with endolichenic fungi which reside inside their thalli. The endolichenic fungi appear to have evolved with the lichen and many of them are a source of novel metabolites vested with unique bioactivities. There is very little information on the biology of endolichenic fungi and their interactions with the other components of a lichen microbiome. There is an urgent need to understand these aspects of endolichenic fungi such that their ecology and economic potential are known more completely. The current knowledge on endolichenic fungi is reviewed here.
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Moya P, Molins A, Martínez-Alberola F, Muggia L, Barreno E. Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses. PLoS One 2017; 12:e0175091. [PMID: 28410402 PMCID: PMC5392050 DOI: 10.1371/journal.pone.0175091] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 03/20/2017] [Indexed: 12/20/2022] Open
Abstract
The current literature reveals that the intrathalline coexistence of multiple microalgal taxa in lichens is more common than previously thought, and additional complexity is supported by the coexistence of bacteria and basidiomycete yeasts in lichen thalli. This replaces the old paradigm that lichen symbiosis occurs between a fungus and a single photobiont. The lichen Ramalina farinacea has proven to be a suitable model to study the multiplicity of microalgae in lichen thalli due to the constant coexistence of Trebouxia sp. TR9 and T. jamesii in long-distance populations. To date, studies involving phycobiont diversity within entire thalli are based on Sanger sequencing, but this method seems to underestimate the diversity. Here, we aim to analyze both the microalgal diversity and its community structure in a single thallus of the lichen R. farinacea by applying a 454 pyrosequencing approach coupled with a careful ad hoc-performed protocol for lichen sample processing prior to DNA extraction. To ascertain the reliability of the pyrosequencing results and the applied bioinformatics pipeline results, the thalli were divided into three sections (apical, middle and basal zones), and a mock community sample was used. The developed methodology allowed 40448 filtered algal reads to be obtained from a single lichen thallus, which encompassed 31 OTUs representative of different microalgae genera. In addition to corroborating the coexistence of the two Trebouxia sp. TR9 and T. jamesii taxa in the same thallus, this study showed a much higher microalgal diversity associated with the lichen. Along the thallus ramifications, we also detected variations in phycobiont distribution that might correlate with different microenvironmental conditions. These results highlight R. farinacea as a suitable material for studying microalgal diversity and further strengthen the concept of lichens as multispecies microecosystems. Future analyses will be relevant to ecophysiological and evolutionary studies to understand the roles of the multiple photobionts in lichen symbioses.
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Affiliation(s)
- Patricia Moya
- Dpto. Botánica, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Fac. CC. Biológicas, Universitat de València, Burjassot, Valencia, Spain
- * E-mail:
| | - Arántzazu Molins
- Dpto. Botánica, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Fac. CC. Biológicas, Universitat de València, Burjassot, Valencia, Spain
| | - Fernando Martínez-Alberola
- Dpto. Botánica, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Fac. CC. Biológicas, Universitat de València, Burjassot, Valencia, Spain
| | - Lucia Muggia
- University of Trieste, Department of Life Sciences, Trieste, Italy
| | - Eva Barreno
- Dpto. Botánica, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Fac. CC. Biológicas, Universitat de València, Burjassot, Valencia, Spain
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Abstract
ABSTRACT
Lichen symbioses comprise a fascinating relationship between algae and fungi. The lichen symbiotic lifestyle evolved early in the evolution of ascomycetes and is also known from a few basidiomycetes. The ascomycete lineages have diversified in the lichenized stage to give rise to a tremendous variety of morphologies. Their thalli are often internally complex and stratified for optimized integration of algal and fungal metabolisms. Thalli are frequently colonized by specific nonlichenized fungi and occasionally also by other lichens. Microscopy has revealed various ways these fungi interact with their hosts. Besides the morphologically recognizable diversity of the lichen mycobionts and lichenicolous (lichen-inhabiting) fungi, many other microorganisms including other fungi and bacterial communities are now detected in lichens by culture-dependent and culture-independent approaches. The application of multi-omics approaches, refined microscopic techniques, and physiological studies has added to our knowledge of lichens, not only about the taxa involved in the lichen interactions, but also about their functions.
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Ivanova AA, Kulichevskaya IS, Merkel AY, Toshchakov SV, Dedysh SN. High Diversity of Planctomycetes in Soils of Two Lichen-Dominated Sub-Arctic Ecosystems of Northwestern Siberia. Front Microbiol 2016; 7:2065. [PMID: 28066382 PMCID: PMC5177623 DOI: 10.3389/fmicb.2016.02065] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/07/2016] [Indexed: 11/13/2022] Open
Abstract
A wide variety of terrestrial ecosystems in tundra have a ground vegetation cover composed of reindeer lichens (genera Cladonia and Cetraria). The microbial communities of two lichen-dominated ecosystems typical of the sub-arctic zone of northwestern Siberia, that is a forested tundra soil and a shallow acidic peatland, were examined in our study. As revealed by molecular analyses, soil and peat layers just beneath the lichen cover were abundantly colonized by bacteria from the phylum Planctomycetes. Highest abundance of planctomycetes detected by fluorescence in situ hybridization was in the range 2.2-2.7 × 107 cells per gram of wet weight. 16S rRNA gene fragments from the Planctomycetes comprised 8-13% of total 16S rRNA gene reads retrieved using Illumina pair-end sequencing from the soil and peat samples. Lichen-associated assemblages of planctomycetes displayed unexpectedly high diversity, with a total of 89,662 reads representing 1723 operational taxonomic units determined at 97% sequence identity. The soil of forested tundra was dominated by uncultivated members of the family Planctomycetaceae (53-71% of total Planctomycetes-like reads), while sequences affiliated with the Phycisphaera-related group WD2101 (recently assigned to the order Tepidisphaerales) were most abundant in peat (28-51% of total reads). Representatives of the Isosphaera-Singulisphaera group (14-28% of total reads) and the lineages defined by the genera Gemmata (1-4%) and Planctopirus-Rubinisphaera (1-3%) were present in both habitats. Two strains of Singulisphaera-like bacteria were isolated from studied soil and peat samples. These planctomycetes displayed good tolerance of low temperatures (4-15°C) and were capable of growth on a number of polysaccharides, including lichenan, a characteristic component of lichen-derived phytomass.
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Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia
| | - Irina S. Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia
| | | | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia
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Blanchette RA, Held BW, Hellmann L, Millman L, Büntgen U. Arctic driftwood reveals unexpectedly rich fungal diversity. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.06.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Wang Y, Zheng Y, Wang X, Wei X, Wei J. Lichen-Associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude. Front Microbiol 2016; 7:1231. [PMID: 27547204 PMCID: PMC4975045 DOI: 10.3389/fmicb.2016.01231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/25/2016] [Indexed: 11/13/2022] Open
Abstract
Lichen-associated fungal species have already been investigated in almost all the main growth forms of lichens, however, whether or not they are homogeneous and constant within each lichen species are still inconclusive. Moreover, the related ecological factors to affect and structure the fungal composition have been poorly studied. In order to answer these questions, we took Hypogymnia hypotrypa as a model to study the relationship between the lichen-associated fungal composition and two ecological factors, i.e., site and altitude, using the method of IlluminaMiSeq sequencing. Four different sites and two levels of altitude were included in this study, and the effects of site and altitude on fungal community composition were assessed at three levels, i.e., operational taxonomic unit (OTU), class and phylum. The results showed that a total of 50 OTUs were identified and distributed in 4 phyla, 13 classes, and 20 orders. The lichen-associated fungal composition within H. hypotrypa were significantly affected by both site and altitude at OTU and class levels, while at the phylum level, it was only affected by altitude. While the lichen associated fungal communities were reported to be similar with endophytic fungi of the moss, our results indicated the opposite results in some degree. But whether there exist specific OTUs within this lichen species corresponding to different sites and altitudes is still open. More lichen species and ecological factors would be taken into the integrated analyses to address these knowledge gaps in the near future.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology - Chinese Academy of Sciences Beijing, China
| | - Yong Zheng
- State Key Laboratory of Mycology, Institute of Microbiology - Chinese Academy of Sciences Beijing, China
| | - Xinyu Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany - Chinese Academy of Sciences Kunming, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology - Chinese Academy of Sciences Beijing, China
| | - Jiangchun Wei
- State Key Laboratory of Mycology, Institute of Microbiology - Chinese Academy of Sciences Beijing, China
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