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Sanders WB. The disadvantages of current proposals to redefine lichens. THE NEW PHYTOLOGIST 2024; 241:969-971. [PMID: 38031529 DOI: 10.1111/nph.19321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Affiliation(s)
- William B Sanders
- Department of Biological Sciences, Florida Gulf Coast University, Ft Myers, FL, 33965, USA
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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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Nguyen NH, Nguyen PT, Otake H, Nagata A, Hirano N, Imanishi-Shimizu Y, Shimizu K. Biodiversity of Basidiomycetous Yeasts Associated with Cladonia rei Lichen in Japan, with a Description of Microsporomyces cladoniophilus sp. nov. J Fungi (Basel) 2023; 9:jof9040473. [PMID: 37108927 PMCID: PMC10145395 DOI: 10.3390/jof9040473] [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: 12/28/2022] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
For more than a century, lichens have been used as an example of dual-partner symbiosis. Recently, this has been challenged by the discovery of various basidiomycetous yeasts that coexist in multiple lichen species, among which Cladonia lichens from Europe and the United States were discovered to be highly specifically associated with the basidiomycetous yeast of the family Microsporomycetaceae. To verify this highly specific relationship, we investigated the diversity of basidiomycetous yeasts associated with Cladonia rei, a widely distributed lichen in Japan, by applying two approaches: yeast isolation from the lichen thalli and meta-barcoding analysis. We obtained 42 cultures of Cystobasidiomycetous yeast which were grouped into six lineages within the family Microsporomycetaceae. Unexpectedly, although the cystobasidiomycetes-specific primer was used, not only the cystobasidiomycetous yeasts but species from other classes were also detected via the meta-barcoding dataset; in particular, pucciniomycetous yeasts were found at a high frequency in some samples. Further, Halobasidium xiangyangense, which was detected in every sample with high abundance, is highly likely a generalist epiphytic fungus that has the ability to associate with C. rei. In the pucciniomycetous group, most of the detected species belong to the scale insect-associated yeast Septobasidium genus. In conclusion, even though Microsporomyces species are not the only yeast group associated with Cladonia lichen, our study demonstrated that the thalli of Cladonia rei lichen could be a suitable habit for them.
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Affiliation(s)
- Ngoc-Hung Nguyen
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Phuong-Thao Nguyen
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Hitomi Otake
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Ayana Nagata
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Nobuharu Hirano
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Yumi Imanishi-Shimizu
- College of Science and Engineering, Kanto Gakuin University, Mutsuura-higashi 1-50-1, Kanazawa-ku, Yokohama 236-8501, Kanagawa, Japan
| | - Kiminori Shimizu
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
- Medical Mycology Research Center, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8673, Chiba, Japan
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Wijayawardene NN, Dai DQ, Jayasinghe PK, Gunasekara SS, Nagano Y, Tibpromma S, Suwannarach N, Boonyuen N. Ecological and Oceanographic Perspectives in Future Marine Fungal Taxonomy. J Fungi (Basel) 2022; 8:1141. [PMID: 36354908 PMCID: PMC9696965 DOI: 10.3390/jof8111141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2023] Open
Abstract
Marine fungi are an ecological rather than a taxonomic group that has been widely researched. Significant progress has been made in documenting their phylogeny, biodiversity, ultrastructure, ecology, physiology, and capacity for degradation of lignocellulosic compounds. This review (concept paper) summarizes the current knowledge of marine fungal diversity and provides an integrated and comprehensive view of their ecological roles in the world's oceans. Novel terms for 'semi marine fungi' and 'marine fungi' are proposed based on the existence of fungi in various oceanic environments. The major maritime currents and upwelling that affect species diversity are discussed. This paper also forecasts under-explored regions with a greater diversity of marine taxa based on oceanic currents. The prospects for marine and semi-marine mycology are highlighted, notably, technological developments in culture-independent sequencing approaches for strengthening our present understanding of marine fungi's ecological roles.
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Affiliation(s)
- Nalin N. Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Section of Genetics, Institute for Research and Development in Health and Social Care, No: 393/3, Lily Avenue, Off Robert Gunawardane Mawatha, Battaramulla 10120, Sri Lanka
- National Institute of Fundamental Studies, Hantana Road, Kandy 20000, Sri Lanka
| | - Don-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Prabath K. Jayasinghe
- National Aquatic Resources Research and Development Agency (NARA), Crow Island, Colombo 00150, Sri Lanka
| | - Sudheera S. Gunasekara
- National Aquatic Resources Research and Development Agency (NARA), Crow Island, Colombo 00150, Sri Lanka
| | - Yuriko Nagano
- Deep-Sea Biodiversity Research Group, Marine Biodiversity and Environmental Assessment Research Center, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Saowaluck Tibpromma
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nattawut Boonyuen
- Plant Microbe Interaction Research Team (APMT), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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The yeast lichenosphere: High diversity of basidiomycetes from the lichens Tephromela atra and Rhizoplaca melanophthalma. Fungal Biol 2022; 126:587-608. [DOI: 10.1016/j.funbio.2022.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/26/2022] [Accepted: 07/13/2022] [Indexed: 01/03/2023]
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Kumar V, Sarma VV, Thambugala KM, Huang JJ, Li XY, Hao GF. Ecology and Evolution of Marine Fungi With Their Adaptation to Climate Change. Front Microbiol 2021; 12:719000. [PMID: 34512597 PMCID: PMC8430337 DOI: 10.3389/fmicb.2021.719000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/10/2021] [Indexed: 01/04/2023] Open
Abstract
Climate change agitates interactions between organisms and the environment and forces them to adapt, migrate, get replaced by others, or extinct. Marine environments are extremely sensitive to climate change that influences their ecological functions and microbial community including fungi. Fungi from marine habitats are engaged and adapted to perform diverse ecological functions in marine environments. Several studies focus on how complex interactions with the surrounding environment affect fungal evolution and their adaptation. However, a review addressing the adaptation of marine fungi to climate change is still lacking. Here we have discussed the adaptations of fungi in the marine environment with an example of Hortaea werneckii and Aspergillus terreus which may help to reduce the risk of climate change impacts on marine environments and organisms. We address the ecology and evolution of marine fungi and the effects of climate change on them to explain the adaptation mechanism. A review of marine fungal adaptations will show widespread effects on evolutionary biology and the mechanism responsible for it.
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Affiliation(s)
- Vinit Kumar
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | | | - Kasun M. Thambugala
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Jun-Jie Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Xiang-Yang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
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Lücking R, Leavitt SD, Hawksworth DL. Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00477-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AbstractLichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed.
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10
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Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01706-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.
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Shishido TK, Wahlsten M, Laine P, Rikkinen J, Lundell T, Auvinen P. Microbial Communities of Cladonia Lichens and Their Biosynthetic Gene Clusters Potentially Encoding Natural Products. Microorganisms 2021; 9:1347. [PMID: 34206222 PMCID: PMC8304397 DOI: 10.3390/microorganisms9071347] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 01/04/2023] Open
Abstract
Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies.
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Affiliation(s)
- Tânia Keiko Shishido
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (P.L.); (P.A.)
| | - Matti Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (M.W.); (T.L.)
| | - Pia Laine
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (P.L.); (P.A.)
| | - Jouko Rikkinen
- Finnish Museum of Natural History, Botany Unit, University of Helsinki, P.O. Box 7, 00014 Helsinki, Finland;
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (M.W.); (T.L.)
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (P.L.); (P.A.)
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Nazem-Bokaee H, Hom EFY, Warden AC, Mathews S, Gueidan C. Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling. Front Microbiol 2021; 12:667864. [PMID: 34012428 PMCID: PMC8126723 DOI: 10.3389/fmicb.2021.667864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Lichen associations, a classic model for successful and sustainable interactions between micro-organisms, have been studied for many years. However, there are significant gaps in our understanding about how the lichen symbiosis operates at the molecular level. This review addresses opportunities for expanding current knowledge on signalling and metabolic interplays in the lichen symbiosis using the tools and approaches of systems biology, particularly network modelling. The largely unexplored nature of symbiont recognition and metabolic interdependency in lichens could benefit from applying a holistic approach to understand underlying molecular mechanisms and processes. Together with ‘omics’ approaches, the application of signalling and metabolic network modelling could provide predictive means to gain insights into lichen signalling and metabolic pathways. First, we review the major signalling and recognition modalities in the lichen symbioses studied to date, and then describe how modelling signalling networks could enhance our understanding of symbiont recognition, particularly leveraging omics techniques. Next, we highlight the current state of knowledge on lichen metabolism. We also discuss metabolic network modelling as a tool to simulate flux distribution in lichen metabolic pathways and to analyse the co-dependence between symbionts. This is especially important given the growing number of lichen genomes now available and improved computational tools for reconstructing such models. We highlight the benefits and possible bottlenecks for implementing different types of network models as applied to the study of lichens.
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Affiliation(s)
- Hadi Nazem-Bokaee
- CSIRO Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, NCMI, Canberra, ACT, Australia.,CSIRO Land and Water, Canberra, ACT, Australia.,CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, The University of Mississippi, University City, MS, United States
| | | | - Sarah Mathews
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Cécile Gueidan
- CSIRO Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, NCMI, Canberra, ACT, Australia
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Tagirdzhanova G, Saary P, Tingley JP, Díaz-Escandón D, Abbott DW, Finn RD, Spribille T. Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes. Genome Biol Evol 2021; 13:6163286. [PMID: 33693712 PMCID: PMC8355462 DOI: 10.1093/gbe/evab047] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Basidiomycete yeasts have recently been reported as stably associated secondary
fungal symbionts of many lichens, but their role in the symbiosis remains
unknown. Attempts to sequence their genomes have been hampered both by the
inability to culture them and their low abundance in the lichen thallus
alongside two dominant eukaryotes (an ascomycete fungus and chlorophyte alga).
Using the lichen Alectoria sarmentosa, we selectively dissolved
the cortex layer in which secondary fungal symbionts are embedded to enrich
yeast cell abundance and sequenced DNA from the resulting slurries as well as
bulk lichen thallus. In addition to yielding a near-complete genome of the
filamentous ascomycete using both methods, metagenomes from cortex slurries
yielded a 36- to 84-fold increase in coverage and near-complete genomes for two
basidiomycete species, members of the classes Cystobasidiomycetes and
Tremellomycetes. The ascomycete possesses the largest gene repertoire of the
three. It is enriched in proteases often associated with pathogenicity and
harbors the majority of predicted secondary metabolite clusters. The
basidiomycete genomes possess ∼35% fewer predicted genes than the
ascomycete and have reduced secretomes even compared with close relatives, while
exhibiting signs of nutrient limitation and scavenging. Furthermore, both
basidiomycetes are enriched in genes coding for enzymes producing secreted
acidic polysaccharides, representing a potential contribution to the shared
extracellular matrix. All three fungi retain genes involved in dimorphic
switching, despite the ascomycete not being known to possess a yeast stage. The
basidiomycete genomes are an important new resource for exploration of lifestyle
and function in fungal–fungal interactions in lichen symbioses.
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Affiliation(s)
- Gulnara Tagirdzhanova
- Department of Biological Sciences CW405, University of Alberta, Edmonton, Alberta, Canada
| | - Paul Saary
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jeffrey P Tingley
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - David Díaz-Escandón
- Department of Biological Sciences CW405, University of Alberta, Edmonton, Alberta, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Toby Spribille
- Department of Biological Sciences CW405, University of Alberta, Edmonton, Alberta, Canada
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15
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Metagenomic data reveal diverse fungal and algal communities associated with the lichen symbiosis. Symbiosis 2020. [DOI: 10.1007/s13199-020-00699-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Abstract
This article is a Commentary on Mark et al. (2020), 227: 1362–1375.
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Affiliation(s)
- David L. Hawksworth
- Royal Botanic Gardens KewRichmondSurreyTW9 3AEUK
- Natural History MuseumCromwell RoadLondonSW7 5BDUK
- University of SouthamptonSouthamptonSO17 1BJUK
| | - Martin Grube
- Institute of BiologyUniversity of GrazHolteigasse 68010GrazAustria
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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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Nelsen MP, Lücking R, Boyce CK, Lumbsch HT, Ree RH. The macroevolutionary dynamics of symbiotic and phenotypic diversification in lichens. Proc Natl Acad Sci U S A 2020; 117:21495-21503. [PMID: 32796103 PMCID: PMC7474681 DOI: 10.1073/pnas.2001913117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Symbioses are evolutionarily pervasive and play fundamental roles in structuring ecosystems, yet our understanding of their macroevolutionary origins, persistence, and consequences is incomplete. We traced the macroevolutionary history of symbiotic and phenotypic diversification in an iconic symbiosis, lichens. By inferring the most comprehensive time-scaled phylogeny of lichen-forming fungi (LFF) to date (over 3,300 species), we identified shifts among symbiont classes that broadly coincided with the convergent evolution of phylogenetically or functionally similar associations in diverse lineages (plants, fungi, bacteria). While a relatively recent loss of lichenization in Lecanoromycetes was previously identified, our work instead suggests lichenization was abandoned far earlier, interrupting what had previously been considered a direct switch between trebouxiophycean and trentepohlialean algal symbionts. Consequently, some of the most diverse clades of LFF are instead derived from nonlichenized ancestors and re-evolved lichenization with Trentepohliales algae, a clade that also facilitated lichenization in unrelated lineages of LFF. Furthermore, while symbiont identity and symbiotic phenotype influence the ecology and physiology of lichens, they are not correlated with rates of lineage birth and death, suggesting more complex dynamics underly lichen diversification. Finally, diversification patterns of LFF differed from those of wood-rotting and ectomycorrhizal taxa, likely reflecting contrasts in their fundamental biological properties. Together, our work provides a timeline for the ecological contributions of lichens, and reshapes our understanding of symbiotic persistence in a classic model of symbiosis.
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Affiliation(s)
- Matthew P Nelsen
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605;
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, 14195 Berlin, Germany
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University, Stanford, CA 94305
| | - H Thorsten Lumbsch
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
| | - Richard H Ree
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
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