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Pino-Bodas R, Blázquez M, de los Ríos A, Pérez-Ortega S. Myrmecia, Not Asterochloris, Is the Main Photobiont of Cladonia subturgida ( Cladoniaceae, Lecanoromycetes). J Fungi (Basel) 2023; 9:1160. [PMID: 38132761 PMCID: PMC10744234 DOI: 10.3390/jof9121160] [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: 11/01/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
This study explores the diversity of photobionts associated with the Mediterranean lichen-forming fungus Cladonia subturgida. For this purpose, we sequenced the whole ITS rDNA region by Sanger using a metabarcoding method for ITS2. A total of 41 specimens from Greece, Italy, France, Portugal, and Spain were studied. Additionally, two specimens from Spain were used to generate four cultures. Our molecular studies showed that the genus Myrmecia is the main photobiont of C. subturgida throughout its geographic distribution. This result contrasts with previous studies, which indicated that the main photobiont for most Cladonia species is Asterochloris. The identity of Myrmecia was also confirmed by ultrastructural studies of photobionts within the lichen thalli and cultures. Photobiont cells showed a parietal chloroplast lacking a pyrenoid, which characterizes the species in this genus. Phylogenetic analyses indicate hidden diversity within this genus. The results of amplicon sequencing showed the presence of multiple ASVs in 58.3% of the specimens studied.
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Affiliation(s)
- Raquel Pino-Bodas
- Biodiversity and Conservation Area, Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, C/Tulipán s/n, 28933 Móstoles, Spain
- Royal Botanic Gardens, Kew, Richmond, London TW9 3DS, UK
| | - Miguel Blázquez
- Department of Mycology, Real Jardín Botánico (CSIC), 28014 Madrid, Spain; (M.B.); (S.P.-O.)
| | | | - Sergio Pérez-Ortega
- Department of Mycology, Real Jardín Botánico (CSIC), 28014 Madrid, Spain; (M.B.); (S.P.-O.)
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La Torre RD, Ramos D, Mejía MD, Neyra E, Loarte E, Orjeda G. Survey of Lichenized Fungi DNA Barcodes on King George Island (Antarctica): An Aid to Species Discovery. J Fungi (Basel) 2023; 9:jof9050552. [PMID: 37233263 DOI: 10.3390/jof9050552] [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: 10/31/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 05/27/2023] Open
Abstract
DNA barcoding is a powerful method for the identification of lichenized fungi groups for which the diversity is already well-represented in nucleotide databases, and an accurate, robust taxonomy has been established. However, the effectiveness of DNA barcoding for identification is expected to be limited for understudied taxa or regions. One such region is Antarctica, where, despite the importance of lichens and lichenized fungi identification, their genetic diversity is far from characterized. The aim of this exploratory study was to survey the lichenized fungi diversity of King George Island using a fungal barcode marker as an initial identification tool. Samples were collected unrestricted to specific taxa in coastal areas near Admiralty Bay. Most samples were identified using the barcode marker and verified up to the species or genus level with a high degree of similarity. A posterior morphological evaluation focused on samples with novel barcodes allowed for the identification of unknown Austrolecia, Buellia, and Lecidea s.l. species. These results contribute to better represent the lichenized fungi diversity in understudied regions such as Antarctica by increasing the richness of the nucleotide databases. Furthermore, the approach used in this study is valuable for exploratory surveys in understudied regions to guide taxonomic efforts towards species recognition and discovery.
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Affiliation(s)
- Renato Daniel La Torre
- Laboratorio de Genómica y Bioinformática para la Biodiversidad, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, German Amezaga 375, Lima 15081, Peru
- Dirección de Investigación en Glaciares, Instituto Nacional de Investigación en Glaciares y Ecosistemas de Montaña, Centenario 2656, Huaraz 02002, Peru
| | - Daniel Ramos
- Herbario Sur Peruano-Instituto Científico Michael Owen Dillon, Jorge Chavez 610, Arequipa 04001, Peru
| | - Mayra Doris Mejía
- Dirección de Investigación en Glaciares, Instituto Nacional de Investigación en Glaciares y Ecosistemas de Montaña, Centenario 2656, Huaraz 02002, Peru
| | - Edgar Neyra
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Honorio Delgado 430, Lima 15102, Peru
- Unidad de Investigación Genómica, Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Honorio Delgado 430, Lima 15102, Peru
| | - Edwin Loarte
- Facultad de Ciencias del Ambiente, Universidad Nacional Santiago Antúnez de Mayolo, Centenario 200, Huaraz 02002, Peru
| | - Gisella Orjeda
- Laboratorio de Genómica y Bioinformática para la Biodiversidad, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, German Amezaga 375, Lima 15081, Peru
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Gunawardana D, Wanigatunge RP, Wewalwela JJ, Vithanage M, Wijeyaratne C. Sulfur is in the Air: Cyanolichen Marriages and Pollution. Acta Biotheor 2023; 71:14. [PMID: 37148405 DOI: 10.1007/s10441-023-09465-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/15/2023] [Indexed: 05/08/2023]
Abstract
Cyanolichens are symbiotic organisms involving cyanobacteria and fungi (bipartite) or with the addition of an algal partner (tripartite). Cyanolichens are known for their heightened susceptibility to environmental pollution. We focus here on the impacts on cyanolichens due to rising air pollution; we are especially interested in the role of sulfur dioxide on cyanolichen biology. Cyanolichens due to air pollution including sulfur dioxide exposure, show symptomatic changes including degradation of chlorophyll, lipid membrane peroxidation, decrease in ATP production, changes in respiration rate, and alteration of endogenous auxins and ethylene production, although symptoms are known to vary with species and genotype. Sulfur dioxide has been shown to be damaging to photosynthesis but is relatively benign on nitrogen fixation which proposes as a hypothesis that the algal partner may be more in harm's way than the cyanobiont. In fact, the Nostoc cyanobiont of sulfur dioxide-susceptible Lobaria pulmonaria carries a magnified set of sulfur (alkane sulfonate) metabolism genes capable of alkane sulfonate transport and assimilation, which were only unraveled by genome sequencing, a technology unavailable in the 1950-2000 epoch, where most physiology- based studies were performed. There is worldwide a growing corpus of evidence that sulfur has an important role to play in biological symbioses including rhizobia-legumes, mycorrhizae-roots and cyanobacteria-host plants. Furthermore, the fungal and algal partners of L. pulmonaria appear not to have the sulfonate transporter genes again providing the roles of ambient-sulfur (alkanesulfonate metabolism etc.) mediated functions primarily to the cyanobacterial partner. In conclusion, we have addressed here the role of the atmospheric pollutant sulfur dioxide to tripartite cyanolichen viability and suggest that the weaker link is likely to be the photosynthetic algal (chlorophyte) partner and not the nitrogen-fixing cyanobiont.
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Affiliation(s)
- Dilantha Gunawardana
- Research Council, University of Sri Jayewardenepura, Nugegoda, Sri Jayewardenepura Kotte, 10250, Sri Lanka.
| | - Rasika P Wanigatunge
- Department of Plant and Molecular Biology, Faculty of Science, University of Kelaniya, Kelaniya, Sri Lanka
| | - Jayani J Wewalwela
- Department of Agricultural Technology, Faculty of Technology, University of Colombo, Colombo, Sri Lanka
| | - Meththika Vithanage
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Jayewardenepura Kotte, 10250, Sri Lanka
| | - Chandrani Wijeyaratne
- Department of Botany, University of Sri Jayewardenepura, Nugegoda, Sri Jayewardenepura Kotte, 10250, Sri Lanka
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Beck A, Casanova-Katny A, Gerasimova J. Metabarcoding of Antarctic Lichens from Areas with Different Deglaciation Times Reveals a High Diversity of Lichen-Associated Communities. Genes (Basel) 2023; 14:genes14051019. [PMID: 37239380 DOI: 10.3390/genes14051019] [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: 12/30/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Lichens have developed numerous adaptations to optimise their survival under harsh abiotic stress, colonise different substrates, and reach substantial population sizes and high coverage in ice-free Antarctic areas, benefiting from a symbiotic lifestyle. As lichen thalli represent consortia with an unknown number of participants, it is important to know about the accessory organisms and their relationships with various environmental conditions. To this end, we analysed lichen-associated communities from Himantormia lugubris, Placopsis antarctica, P. contortuplicata, and Ramalina terebrata, collected from soils with differing deglaciation times, using a metabarcoding approach. In general, many more Ascomycete taxa are associated with the investigated lichens compared to Basidiomycota. Given our sampling, a consistently higher number of lichen-associated eukaryotes are estimated to be present in areas with deglaciation times of longer than 5000 years compared to more recently deglaciated areas. Thus far, members of Dothideomycetes, Leotiomycetes, and Arthoniomycetes have been restricted to the Placopsis specimens from areas with deglaciation times longer than 5000 years. Striking differences between the associated organisms of R. terebrata and H. lugubris have also been discovered. Thus, a species-specific basidiomycete, Tremella, was revealed for R. terebrata, as was a member of Capnodiales for H. lugubris. Our study provides further understanding of the complex terricolous lichen-associated mycobiome using the metabarcoding approach. It also illustrates the necessity to extend our knowledge of complex lichen symbiosis and further improve the coverage of microbial eukaryotes in DNA barcode libraries, including more extended sampling.
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Affiliation(s)
- Andreas Beck
- SNSB-Botanische Staatssammlung München, 80638 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Angélica Casanova-Katny
- Laboratorio de Ecofisiología Vegetal y Cambio Climático, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco 4780000, Chile
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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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Alonso-García M, Pino-Bodas R, Villarreal A JC. Co-dispersal of symbionts in the lichen Cladonia stellaris inferred from genomic data. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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Yang JH, Oh SY, Kim W, Hur JS. Endolichenic Fungal Community Analysis by Pure Culture Isolation and Metabarcoding: A Case Study of Parmotrema tinctorum. MYCOBIOLOGY 2022; 50:55-65. [PMID: 35291596 PMCID: PMC8890557 DOI: 10.1080/12298093.2022.2040112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/03/2022] [Accepted: 02/06/2022] [Indexed: 05/31/2023]
Abstract
Lichen is a symbiotic mutualism of mycobiont and photobiont that harbors diverse organisms including endolichenic fungi (ELF). Despite the taxonomic and ecological significance of ELF, no comparative investigation of an ELF community involving isolation of a pure culture and high-throughput sequencing has been conducted. Thus, we analyzed the ELF community in Parmotrema tinctorum by culture and metabarcoding. Alpha diversity of the ELF community was notably greater in metabarcoding than in culture-based analysis. Taxonomic proportions of the ELF community estimated by metabarcoding and by culture analyses showed remarkable differences: Sordariomycetes was the most dominant fungal class in culture-based analysis, while Dothideomycetes was the most abundant in metabarcoding analysis. Thirty-seven operational taxonomic units (OTUs) were commonly observed by culture- and metabarcoding-based analyses but relative abundances differed: most of common OTUs were underrepresented in metabarcoding. The ELF community differed in lichen segments and thalli in metabarcoding analysis. Dissimilarity of ELF community intra lichen thallus increased with thallus segment distance; inter-thallus ELF community dissimilarity was significantly greater than intra-thallus ELF community dissimilarity. Finally, we tested how many fungal sequence reads would be needed to ELF diversity with relationship assays between numbers of lichen segments and saturation patterns of OTU richness and sample coverage. At least 6000 sequence reads per lichen thallus were sufficient for prediction of overall ELF community diversity and 50,000 reads per thallus were enough to observe rare taxa of ELF.
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Affiliation(s)
- Ji Ho Yang
- Department of Biology, Sunchon National University, Suncheon, Korea
| | - Seung-Yoon Oh
- Department of Biology and Chemistry, Changwon National University, Changwon, South Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
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Vančurová L, Malíček J, Steinová J, Škaloud P. Choosing the Right Life Partner: Ecological Drivers of Lichen Symbiosis. Front Microbiol 2022; 12:769304. [PMID: 34970234 PMCID: PMC8712729 DOI: 10.3389/fmicb.2021.769304] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 11/24/2022] Open
Abstract
Lichens are an iconic example of symbiotic systems whose ecology is shaped by the requirements of the symbionts. Previous studies suggest that fungal (mycobionts) as well as photosynthesizing (phycobionts or cyanobionts) partners have a specific range of acceptable symbionts that can be chosen according to specific environmental conditions. This study aimed to investigate the effects of climatic conditions and mycobiont identity on phycobiont distribution within the lichen genera Stereocaulon, Cladonia, and Lepraria. The study area comprised the Canary Islands, Madeira, Sicily, and the Aeolian Islands, spanning a wide range of climatic conditions. These islands are known for their unique and diverse fauna and flora; however, lichen phycobionts have remained unstudied in most of these areas. In total, we genetically analyzed 339 lichen samples. The phycobiont pool differed significantly from that outside the studied area. Asterochloris mediterranea was identified as the most abundant phycobiont. However, its distribution was limited by climatic constraints. Other species of Asterochloris and representatives of the genera Chloroidium, Vulcanochloris, and Myrmecia were also recovered as phycobionts. The selection of symbiotic partners from the local phycobiont pool was driven by mycobiont specificity (i.e., the taxonomic range of acceptable partners) and the environmental conditions, mainly temperature. Interestingly, the dominant fungal species responded differently in their selection of algal symbionts along the environmental gradients. Cladonia rangiformis associated with its phycobiont A. mediterranea in a broader range of temperatures than Stereocaulon azoreum, which favors other Asterochloris species along most of the temperature gradient. Stereocaulon vesuvianum associated with Chloroidium spp., which also differed in their temperature optima. Finally, we described Stereocaulon canariense as a new endemic species ecologically distinct from the other Stereocaulon species on the Canary Islands.
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Affiliation(s)
- Lucie Vančurová
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Jiří Malíček
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Jana Steinová
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
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Diversity and Physiological Characteristics of Antarctic Lichens-Associated Bacteria. Microorganisms 2021; 9:microorganisms9030607. [PMID: 33804278 PMCID: PMC8001610 DOI: 10.3390/microorganisms9030607] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/23/2022] Open
Abstract
The diversity of lichen-associated bacteria from lichen taxa Cetraria, Cladonia, Megaspora, Pseudephebe, Psoroma, and Sphaerophorus was investigated by sequencing of 16S rRNA gene amplicons. Physiological characteristics of the cultured bacterial isolates were investigated to understand possible roles in the lichen ecosystem. Proteobacteria (with a relative abundance of 69.7–96.7%) were mostly represented by the order Rhodospirillales. The 117 retrieved isolates were grouped into 35 phylotypes of the phyla Actinobacteria (27), Bacteroidetes (6), Deinococcus-Thermus (1), and Proteobacteria (Alphaproteobacteria (53), Betaproteobacteria (18), and Gammaproteobacteria (12)). Hydrolysis of macromolecules such as skim milk, polymer, and (hypo)xanthine, solubilization of inorganic phosphate, production of phytohormone indole-3-acetic acid, and fixation of atmospheric nitrogen were observed in different taxa. The potential phototrophy of the strains of the genus Polymorphobacter which were cultivated from a lichen for the first time was revealed by the presence of genes involved in photosynthesis. Altogether, the physiological characteristics of diverse bacterial taxa from Antarctic lichens are considered to imply significant roles of lichen-associated bacteria to allow lichens to be tolerant or competitive in the harsh Antarctic environment.
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12
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Rola K, Lenart-Boroń A, Boroń P, Osyczka P. Heavy-metal pollution induces changes in the genetic composition and anatomical properties of photobionts in pioneer lichens colonising post-industrial habitats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:141439. [PMID: 32882488 DOI: 10.1016/j.scitotenv.2020.141439] [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: 06/18/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Certain lichens are effective colonisers of polluted sites. However, little is known about the tolerance of photobionts and the degree of mycobiont selectivity to photobionts relative to metal pollution. The present study recognises the genetic and anatomical diversity of Asterochloris photobionts in epigeic lichens, i.e. Cladonia cariosa, C. rei, and Diploschistes muscorum, in relation to a wide spectrum of soil pollution. In accordance with phylogenetic analysis, photobionts were clustered in 7 moderately- to well-supported clades, including 19 haplotypes. The mycobionts of all studied lichens demonstrated a low level of selectivity and were capable of associating with various Asterochloris lineages. This tendency was also expressed by the frequent (~25%) occurrence of multiple algal genotypes in a single thallus. This indicates that identified Asterochloris lineages are generally tolerant to heavy-metal pollution, and the low level of selectivity of mycobionts enables them to select the most suitable and/or available partner. The trend of increasing incidence of certain Asterochloris lineages and decreasing frequency of others along with increasing soil pollution was observed. This proves the superior adaptation of some photobionts to polluted sites. Such symbiotic plasticity constitute an adaptive feature necessary for the successful colonisation. High number of haplotypes at polluted sites could be the result of multiple introduction events from different areas during the initial stages of spontaneous succession. Regardless of the genetic pattern, Asterochloris cells were considerably smaller, and the density and compaction of cells in the algal layer were higher, in lichen specimens from polluted sites, indicating that photobiont characteristics may be closely dependent on heavy-metal pollution.
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Affiliation(s)
- Kaja Rola
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Anna Lenart-Boroń
- Department of Microbiology and Biomonitoring, Faculty of Agriculture and Economics, University of Agriculture in Kraków, Adam Mickiewicz Ave. 24/28, 31-059 Kraków, Poland
| | - Piotr Boroń
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Kraków, 29 Listopada Ave. 46, 31-425 Kraków, Poland
| | - Piotr Osyczka
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland.
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13
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Mark K, Laanisto L, Bueno CG, Niinemets Ü, Keller C, Scheidegger C. Contrasting co-occurrence patterns of photobiont and cystobasidiomycete yeast associated with common epiphytic lichen species. THE NEW PHYTOLOGIST 2020; 227:1362-1375. [PMID: 32034954 DOI: 10.1111/nph.16475] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
The popular dual definition of lichen symbiosis is under question with recent findings of additional microbial partners living within the lichen body. Here we compare the distribution and co-occurrence patterns of lichen photobiont and recently described secondary fungus (Cyphobasidiales yeast) to evaluate their dependency on lichen host fungus (mycobiont). We sequenced the nuclear internal transcribed spacer (ITS) strands for mycobiont, photobiont, and yeast from six widespread northern hemisphere epiphytic lichen species collected from 25 sites in Switzerland and Estonia. Interaction network analyses and multivariate analyses were conducted on operational taxonomic units based on ITS sequence data. Our study demonstrates the frequent presence of cystobasidiomycete yeasts in studied lichens and shows that they are much less mycobiont-specific than the photobionts. Individuals of different lichen species growing on the same tree trunk consistently hosted the same or closely related mycobiont-specific Trebouxia lineage over geographic distances while the cystobasidiomycete yeasts were unevenly distributed over the study area - contrasting communities were found between Estonia and Switzerland. These results contradict previous findings of high mycobiont species specificity of Cyphobasidiales yeast at large geographic scales. Our results suggest that the yeast might not be as intimately associated with the symbiosis as is the photobiont.
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Affiliation(s)
- Kristiina Mark
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu, 51006, Estonia
- Department of Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Lauri Laanisto
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu, 51006, Estonia
| | - C Guillermo Bueno
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu, 51006, Estonia
- Estonian Academy of Sciences, Kohtu 6, Tallinn, 10130, Estonia
| | - Christine Keller
- Department of Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Christoph Scheidegger
- Department of Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
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14
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Batista TM, Hilario HO, de Brito GAM, Moreira RG, Furtado C, de Menezes GCA, Rosa CA, Rosa LH, Franco GR. Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny. Genomics 2020; 112:2915-2921. [DOI: 10.1016/j.ygeno.2020.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022]
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15
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Diversity and Distribution Patterns of Endolichenic Fungi in Jeju Island, South Korea. SUSTAINABILITY 2020. [DOI: 10.3390/su12093769] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lichens are symbiotic organisms containing diverse microorganisms. Endolichenic fungi (ELF) are one of the inhabitants living in lichen thalli, and have potential ecological and industrial applications due to their various secondary metabolites. As the function of endophytic fungi on the plant ecology and ecosystem sustainability, ELF may have an influence on the lichen diversity and the ecosystem, functioning similarly to the influence of endophytic fungi on plant ecology and ecosystem sustainability, which suggests the importance of understanding the diversity and community pattern of ELF. In this study, we investigated the diversity and the factors influencing the community structure of ELF in Jeju Island, South Korea by analyzing 619 fungal isolates from 79 lichen samples in Jeju Island. A total of 112 ELF species was identified and the most common species belonged to Xylariales in Sordariomycetes. The richness and community structure of ELF were significantly influenced by the host taxonomy, together with the photobiont types and environmental factors. Our results suggest that various lichen species in more diverse environments need to be analyzed to expand our knowledge of the diversity and ecology of ELF.
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16
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Noh HJ, Lee YM, Park CH, Lee HK, Cho JC, Hong SG. Microbiome in Cladonia squamosa Is Vertically Stratified According to Microclimatic Conditions. Front Microbiol 2020; 11:268. [PMID: 32161575 PMCID: PMC7053493 DOI: 10.3389/fmicb.2020.00268] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/05/2020] [Indexed: 11/21/2022] Open
Abstract
Lichens are miniature ecosystems that contain fungi, microalgae, and bacteria. It is generally accepted that symbiosis between mycobiont and photobiont and microbial contribution to the ecosystem support the wide distribution of lichens in terrestrial ecosystems, including polar areas. The composition of symbiotic components can be affected by subtle microenvironmental differences within a thallus, as well as large-scale climate differences. In this study, we investigated fine-scale profiles of algal, fungal, and bacterial compositions through horizontal and vertical positions of the Antarctic lichen Cladonia squamosa colonies by next-generation sequencing of the nuclear large subunit rRNA gene (nucLSU) of eukaryotes and the 16S rRNA gene of bacteria. Apical parts of thalli were exposed to strong light, low moisture, and high variability of temperature compared with basal parts. Microbial diversity increased from apical parts to basal parts of thalli. Asterochloris erici was the major photobiont in apical positions of thalli, but other microalgal operational taxonomic units (OTUs) of Trebouxiophyceae and Ulvophyceae were major microalgal components in basal positions. Photochemical responses of algal components from apical and basal parts of thalli were quite different under variable temperature and humidity conditions. Several fungal OTUs that belonged to Arthoniomycetes and Lecanoromycetes, and diverse bacterial OTUs that belonged to Alphaproteobacteria, Acidobacteria_Gp1, and candidate division WPS-2 showed a clear distribution pattern according to their vertical positions within thalli. The overall lichen microbiome was significantly differentiated by the vertical position within a thallus. These results imply that different microclimate are formed at different lichen thallus parts, which can affect microbial compositions and physiological responses according to positions within the thalli.
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Affiliation(s)
- Hyun-Ju Noh
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
- Department of Biological Sciences, Inha University, Incheon, South Korea
| | - Yung Mi Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Chae Haeng Park
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Hong Kum Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, South Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
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17
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Cho SM, Lee H, Hong SG, Lee J. Study of Ecophysiological Responses of the Antarctic Fruticose Lichen Cladonia borealis Using the PAM Fluorescence System under Natural and Laboratory Conditions. PLANTS (BASEL, SWITZERLAND) 2020; 9:E85. [PMID: 31936612 PMCID: PMC7020452 DOI: 10.3390/plants9010085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/20/2019] [Accepted: 01/07/2020] [Indexed: 11/16/2022]
Abstract
Antarctic lichens have been used as indicators of climate change for decades, but only a few species have been studied. We assessed the photosynthetic performance of the fruticose lichen Cladonia borealis under natural and laboratory conditions using the PAM fluorescence system. Compared to that of sun-adapted Usnea sp., the photosynthetic performance of C. borealis exhibits shade-adapted lichen features, and its chlorophyll fluorescence does not occur during dry days without rain. To understand its desiccation-rehydration responses, we measured changes in the PSII photochemistry in C. borealis under the average light intensity of dawn light and daylight and the desiccating conditions of its natural microclimate. Interestingly, samples under daylight and rapid-desiccation conditions showed a delayed reduction in Fv'/Fm' and rETRmax, and an increase in Y(II) and Y(NPQ) levels. These results suggest that the photoprotective mechanism of C. borealis depends on sunlight and becomes more efficient with improved desiccation tolerance. Amplicon sequencing revealed that the major photobiont of C. borealis was Asterochloris irregularis, which has not been reported in Antarctica before. Collectively, these results from both field and laboratory could provide a better understanding of specific ecophysiological responses of shade-adapted lichens in the Antarctic region.
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Affiliation(s)
- Sung Mi Cho
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Korea;
| | - Hyoungseok Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Korea; (H.L.); (S.G.H.)
- Polar Sciences, University of Science and Technology, Daejeon 34114, Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Korea; (H.L.); (S.G.H.)
| | - Jungeun Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Korea;
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18
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Lezcano MÁ, Moreno-Paz M, Carrizo D, Prieto-Ballesteros O, Fernández-Martínez MÁ, Sánchez-García L, Blanco Y, Puente-Sánchez F, de Diego-Castilla G, García-Villadangos M, Fairén AG, Parro V. Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and Cold. ASTROBIOLOGY 2019; 19:1490-1504. [PMID: 31339746 PMCID: PMC6918857 DOI: 10.1089/ast.2018.2004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/15/2019] [Indexed: 05/04/2023]
Abstract
Substrate-atmosphere interfaces in Antarctic geothermal environments are hot-cold regions that constitute thin habitable niches for microorganisms with possible counterparts in ancient Mars. Cerro Caliente hill in Deception Island (active volcano in the South Shetland Islands) is affected by ascending hydrothermal fluids that form a band of warm substrates buffered by low air temperatures. We investigated the influence of temperature on the community structure and metabolism of three microbial mats collected along the geothermal band of Cerro Caliente registering 88°C, 8°C, and 2°C at the time of collection. High-throughput sequencing of small subunit ribosomal ribonucleic acid (SSU rRNA) genes and Life Detector Chip (LDChip) microarray immunoassays revealed different bacterial, archaeal, and eukaryotic composition in the three mats. The mat at 88°C showed the less diverse microbial community and a higher proportion of thermophiles (e.g., Thermales). In contrast, microbial communities in the mats at 2°C and 8°C showed relatively higher diversity and higher proportion of psychrophiles (e.g., Flavobacteriales). Despite this overall association, similar microbial structures at the phylum level (particularly the presence of Cyanobacteria) and certain hot- and cold-tolerant microorganisms were identified in the three mats. Daily thermal oscillations recorded in the substrate over the year (4.5-76°C) may explain the coexistence of microbial fingerprints with different thermal tolerances. Stable isotope composition also revealed metabolic differences among the microbial mats. Carbon isotopic ratios suggested the Calvin-Benson-Bassham cycle as the major pathway for carbon dioxide fixation in the mats at 2°C and 8°C, and the reductive tricarboxylic acid cycle and/or the 3-hydroxypropionate bicycle for the mat at 88°C, indicating different metabolisms as a function of the prevailing temperature of each mat. The comprehensive biomarker profile on the three microbial mats from Cerro Caliente contributes to unravel the diversity, composition, and metabolism in geothermal polar sites and highlights the relevance of geothermal-cold environments to create habitable niches with interest in other planetary environments.
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Affiliation(s)
- María Ángeles Lezcano
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Daniel Carrizo
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Olga Prieto-Ballesteros
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | | | - Laura Sánchez-García
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | | | | | | | - Alberto G. Fairén
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Department of Astronomy, Cornell University, Ithaca, New York, USA
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
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19
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Sayed AM, Hassan MHA, Alhadrami HA, Hassan HM, Goodfellow M, Rateb ME. Extreme environments: microbiology leading to specialized metabolites. J Appl Microbiol 2019; 128:630-657. [PMID: 31310419 DOI: 10.1111/jam.14386] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 07/10/2019] [Indexed: 12/19/2022]
Abstract
The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.
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Affiliation(s)
- A M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - M H A Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - H A Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.,Special Infectious Agent Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - H M Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - M Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, UK
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20
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Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB. The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics 2019; 20:605. [PMID: 31337355 PMCID: PMC6652019 DOI: 10.1186/s12864-019-5629-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution. RESULTS A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting. CONCLUSIONS The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.
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Affiliation(s)
| | - Olaf Müller
- Department of Biology, Duke University, Durham, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | | | - Ólafur S. Andrésson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Guillaume Blanc
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften & Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
| | - Fred Dietrich
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
| | - Suzanne Joneson
- Department of Biology, Duke University, Durham, USA
- College of General Studies, University of Wisconsin - Milwaukee at Waukesha, Waukesha, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
| | - Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | | | | | - Francis Martin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Susan P. May
- Department of Biology, Duke University, Durham, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, USA
| | - Tami R. McDonald
- Department of Biology, Duke University, Durham, USA
- Department of Biology, St. Catherine University, St. Paul, USA
| | - Sabeeha S. Merchant
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, USA
| | - Vivian Miao
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Emmanuelle Morin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California - Santa Barbara, Santa Barbara, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, and DOE Institute for Genomics and Proteomics, University of California, Los Angeles, USA
| | - Nimrod Rubinstein
- National Evolutionary Synthesis Center, Durham, USA
- Calico Life Sciences LLC, South San Francisco, USA
| | | | | | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Fachbereich Biowissenschaften, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jason C. Slot
- College of Food, Agricultural, and Environmental Sciences, Department of Plant Pathology, The Ohio State University, Columbus, USA
| | - Darren Soanes
- College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | | | - Claire Veneault-Fourrey
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
- Université de Lorraine, INRA, Interactions Arbres-Microorganismes, Faculté des Sciences et Technologies, Vandoeuvre les Nancy Cedex, France
| | - Basil B. Xavier
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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21
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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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22
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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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23
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Yu NH, Park SY, Kim JA, Park CH, Jeong MH, Oh SO, Hong SG, Talavera M, Divakar PK, Hur JS. Endophytic and endolichenic fungal diversity in maritime Antarctica based on cultured material and their evolutionary position among Dikarya. Fungal Syst Evol 2018; 2:263-272. [PMID: 32467890 PMCID: PMC7225575 DOI: 10.3114/fuse.2018.02.07] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts. They live asymptomatically within vascular plants, bryophytes and also in close association with algal photobionts inside lichen thalli. While endophytic diversity in land plants has been well studied, their diversity in lichens and bryophytes are poorly understood. Here, we compare the endolichenic and endophytic fungal communities isolated from lichens and bryophytes in the Barton Peninsula, King George Island, Antarctica. A total of 93 fungal isolates were collected from lichens and bryophytes. In order to determine their identities and evolutionary relationships, DNA sequences of the nuclear internal transcribed spacer (ITS), nuclear ribosomal small subunit (nuSSU), nuclear large subunit (nuLSU), and mitochondrial SSU (mtSSU) rDNA were obtained and protein coding markers of the two largest subunit of RNA polymerase II (RPB1 and RPB2) were generated. Multilocus phylogenetic analyses revealed that most of the fungal isolates were distributed in the following six classes in the phylum Ascomycota: Dothideomycetes, Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Pezizomycetes and Sordariomycetes. For the first time we report the presence of subphylum Mortierellomycotina that may belong to an undescribed order in endophytic fungi. Taken together, our results imply that lichens and bryophytes provide similar niches and harbour a selection of these fungi, indicating generalists within the framework of evolutionary adaptation.
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Affiliation(s)
- N H Yu
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea.,Division of Applied Bioscience and Biotechnology, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - S-Y Park
- Department of Plant Medicine, College of Life Science and Natural Resources, Sunchon National University, Suncheon, Korea
| | - J A Kim
- National Institute of Biological Resources, Incheon, South Korea
| | - C-H Park
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - M-H Jeong
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - S-O Oh
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Korea
| | - S G Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - M Talavera
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - P K Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - J-S Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
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24
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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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25
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Vančurová L, Muggia L, Peksa O, Řídká T, Škaloud P. The complexity of symbiotic interactions influences the ecological amplitude of the host: A case study in Stereocaulon (lichenized Ascomycota). Mol Ecol 2018; 27:3016-3033. [PMID: 29900606 DOI: 10.1111/mec.14764] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/03/2018] [Accepted: 06/05/2018] [Indexed: 01/21/2023]
Abstract
Symbiosis plays a fundamental role in nature. Lichens are among the best known, globally distributed symbiotic systems whose ecology is shaped by the requirements of all symbionts forming the holobiont. The widespread lichen-forming fungal genus Stereocaulon provides a suitable model to study the ecology of microscopic green algal symbionts (i.e., phycobionts) within the lichen symbiosis. We analysed 282 Stereocaulon specimens, collected in diverse habitats worldwide, using the algal ITS rDNA and actin gene sequences and fungal ITS rDNA sequences. Phylogenetic analyses revealed a great diversity among the predominant phycobionts. The algal genus Asterochloris (Trebouxiophyceae) was recovered in most sampled thalli, but two additional genera, Vulcanochloris and Chloroidium, were also found. We used variation-partitioning analyses to investigate the effects of climatic conditions, substrate/habitat characteristic, spatial distribution and mycobionts on phycobiont distribution. Based on an analogy, we examined the effects of climate, substrate/habitat, spatial distribution and phycobionts on mycobiont distribution. According to our analyses, the distribution of phycobionts is primarily driven by mycobionts and vice versa. Specificity and selectivity of both partners, as well as their ecological requirements and the width of their niches, vary significantly among the species-level lineages. We demonstrated that species-level lineages, which accept more symbiotic partners, have wider climatic niches, overlapping with the niches of their partners. Furthermore, the survival of lichens on substrates with high concentrations of heavy metals appears to be supported by their association with toxicity-tolerant phycobionts. In general, low specificity towards phycobionts allows the host to associate with ecologically diversified algae, thereby broadening its ecological amplitude.
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Affiliation(s)
- Lucie Vančurová
- Faculty of Science, Department of Botany, Charles University, Prague 2, Czech Republic
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Ondřej Peksa
- The West Bohemian Museum in Pilsen, Plzeň, Czech Republic
| | - Tereza Řídká
- Faculty of Science, Department of Botany, Charles University, Prague 2, Czech Republic
| | - Pavel Škaloud
- Faculty of Science, Department of Botany, Charles University, Prague 2, Czech Republic
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26
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Onuț-Brännström I, Benjamin M, Scofield DG, Heiðmarsson S, Andersson MGI, Lindström ES, Johannesson H. Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing. Sci Rep 2018. [PMID: 29535321 PMCID: PMC5849601 DOI: 10.1038/s41598-018-22470-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this study, we explored the diversity of green algal symbionts (photobionts) in sympatric populations of the cosmopolitan lichen-forming fungi Thamnolia and Cetraria. We sequenced with both Sanger and Ion Torrent High-Throughput Sequencing technologies the photobiont ITS-region of 30 lichen thalli from two islands: Iceland and Öland. While Sanger recovered just one photobiont genotype from each thallus, the Ion Torrent data recovered 10-18 OTUs for each pool of 5 lichen thalli, suggesting that individual lichens can contain heterogeneous photobiont populations. Both methods showed evidence for photobiont sharing between Thamnolia and Cetraria on Iceland. In contrast, our data suggest that on Öland the two mycobionts associate with distinct photobiont communities, with few shared OTUs revealed by Ion Torrent sequencing. Furthermore, by comparing our sequences with public data, we identified closely related photobionts from geographically distant localities. Taken together, we suggest that the photobiont composition in Thamnolia and Cetraria results from both photobiont-mycobiont codispersal and local acquisition during mycobiont establishment and/or lichen growth. We hypothesize that this is a successful strategy for lichens to be flexible in the use of the most adapted photobiont for the environment.
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Affiliation(s)
- Ioana Onuț-Brännström
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mitchell Benjamin
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Douglas G Scofield
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), Uppsala University, Uppsala, Sweden
| | - Starri Heiðmarsson
- Icelandic Institute of Natural History, Akureyri Division, Borgir Nordurslod, Iceland
| | - Martin G I Andersson
- Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Eva S Lindström
- Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
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28
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Dal Grande F, Rolshausen G, Divakar PK, Crespo A, Otte J, Schleuning M, Schmitt I. Environment and host identity structure communities of green algal symbionts in lichens. THE NEW PHYTOLOGIST 2018; 217:277-289. [PMID: 28892165 DOI: 10.1111/nph.14770] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
An understanding of how biotic interactions shape species' distributions is central to predicting host-symbiont responses under climate change. Switches to locally adapted algae have been proposed to be an adaptive strategy of lichen-forming fungi to cope with environmental change. However, it is unclear how lichen photobionts respond to environmental gradients, and whether they play a role in determining the fungal host's upper and lower elevational limits. Deep-coverage Illumina DNA metabarcoding was used to track changes in the community composition of Trebouxia algae associated with two phylogenetically closely related, but ecologically divergent fungal hosts along a steep altitudinal gradient in the Mediterranean region. We detected the presence of multiple Trebouxia species in the majority of thalli. Both altitude and host genetic identity were strong predictors of photobiont community assembly in these two species. The predominantly clonally dispersing fungus showed stronger altitudinal structuring of photobiont communities than the sexually reproducing host. Elevation ranges of the host were not limited by the lack of compatible photobionts. Our study sheds light on the processes guiding the formation and distribution of specific fungal-algal combinations in the lichen symbiosis. The effect of environmental filtering acting on both symbiotic partners appears to shape the distribution of lichens.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Pradeep K Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany
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29
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30
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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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31
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Pivovarova JF, Blagodatnova AG, Bagautdinova ZZ. Specific features of taxonomic organization of cyanobacterial–algal flora in extreme habitats as reflection of different sucfcession models. CONTEMP PROBL ECOL+ 2017. [DOI: 10.1134/s1995425516060093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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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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33
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Diversity and distribution of cultured endolichenic fungi in the Ny-Ålesund Region, Svalbard (High Arctic). Extremophiles 2016; 20:461-70. [DOI: 10.1007/s00792-016-0836-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022]
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34
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Prateeksha P, Paliya BS, Bajpai R, Jadaun V, Kumar J, Kumar S, Upreti DK, Singh BR, Nayaka S, Joshi Y, Singh BN. The genus Usnea: a potent phytomedicine with multifarious ethnobotany, phytochemistry and pharmacology. RSC Adv 2016. [DOI: 10.1039/c5ra24205c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The genusUsneaAdans. (Parmeliaceae; lichenized Ascomycetes) is a typical group of mostly pale grayish-green fruticoselichens that grow as leafless mini-shrubs.
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Affiliation(s)
- Prateeksha Prateeksha
- Pharmacognosy & Ethnopharmacology Division
- CSIR-National Botanical Research Institute
- Lucknow – 226001
- India
| | - B. S. Paliya
- Pharmacognosy & Ethnopharmacology Division
- CSIR-National Botanical Research Institute
- Lucknow – 226001
- India
| | - R. Bajpai
- Lichenology Laboratory
- Plant Biodiversity and Conservation Biology Division
- CSIR-National Botanical Research Institute
- Lucknow – 226001
- India
| | - V. Jadaun
- Pharmacognosy & Ethnopharmacology Division
- CSIR-National Botanical Research Institute
- Lucknow – 226001
- India
| | - J. Kumar
- Pharmacognosy & Ethnopharmacology Division
- CSIR-National Botanical Research Institute
- Lucknow – 226001
- India
| | - S. Kumar
- Pharmacognosy & Ethnopharmacology Division
- CSIR-National Botanical Research Institute
- Lucknow – 226001
- India
| | - D. K. Upreti
- Lichenology Laboratory
- Plant Biodiversity and Conservation Biology Division
- CSIR-National Botanical Research Institute
- Lucknow – 226001
- India
| | - B. R. Singh
- Centre of Excellence in Materials Science (Nanomaterials)
- Z. H. College of Engineering & Technology
- Aligarh Muslim University
- Aligarh-202002
- India
| | - S. Nayaka
- Lichenology Laboratory
- Plant Biodiversity and Conservation Biology Division
- CSIR-National Botanical Research Institute
- Lucknow – 226001
- India
| | | | - Brahma N. Singh
- Pharmacognosy & Ethnopharmacology Division
- CSIR-National Botanical Research Institute
- Lucknow – 226001
- India
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35
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Zhang T, Wei XL, Zhang YQ, Liu HY, Yu LY. Diversity and distribution of lichen-associated fungi in the Ny-Ålesund Region (Svalbard, High Arctic) as revealed by 454 pyrosequencing. Sci Rep 2015; 5:14850. [PMID: 26463847 PMCID: PMC4604449 DOI: 10.1038/srep14850] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/20/2015] [Indexed: 12/02/2022] Open
Abstract
This study assessed the diversity and distribution of fungal communities associated with seven lichen species in the Ny-Ålesund Region (Svalbard, High Arctic) using Roche 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Lichen-associated fungal communities showed high diversity, with a total of 42,259 reads belonging to 370 operational taxonomic units (OTUs) being found. Of these OTUs, 294 belonged to Ascomycota, 54 to Basidiomycota, 2 to Zygomycota, and 20 to unknown fungi. Leotiomycetes, Dothideomycetes, and Eurotiomycetes were the major classes, whereas the dominant orders were Helotiales, Capnodiales, and Chaetothyriales. Interestingly, most fungal OTUs were closely related to fungi from various habitats (e.g., soil, rock, plant tissues) in the Arctic, Antarctic and alpine regions, which suggests that living in association with lichen thalli may be a transient stage of life cycle for these fungi and that long-distance dispersal may be important to the fungi in the Arctic. In addition, host-related factors shaped the lichen-associated fungal communities in this region. Taken together, these results suggest that lichens thalli act as reservoirs of diverse fungi from various niches, which may improve our understanding of fungal evolution and ecology in the Arctic.
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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 100050, PR China
| | - Xin-Li Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Qin Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Hong-Yu Liu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Yan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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