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Worthy FR, Schaefer DA, Wanasinghe D, Xu JC, Wang LS, Wang XY. Acquisition of green algal photobionts enables both chlorolichens and chloro-cyanolichens to activate photosynthesis at low humidity without liquid water. AOB PLANTS 2024; 16:plae025. [PMID: 38770101 PMCID: PMC11102867 DOI: 10.1093/aobpla/plae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 04/23/2024] [Indexed: 05/22/2024]
Abstract
Cyanobacteria require liquid water for photosynthesis, whereas green algae can photosynthesise with water vapour alone. We discovered that several Lobaria spp. which normally have cyanobacteria as the sole photobiont, in some regions of the trans-Himalayas also harboured green algae. We tested whether green algal acquisition was: limited to high elevations; obtained from neighbouring chloro-Lobaria species; enabled photosynthesis at low humidity. Lobaria spp. were collected from 2000 to 4000 m elevation. Spectrophotometry quantified green algal abundance by measuring chlorophyll b (absent in cyanobacteria). Thalli cross-sections visually confirmed green algal presence. We sequenced gene regions: Lobaria (ITS-EF-1α-RPB2), green algae (18S-RBC-L) and Nostoc (16S). Phylogenetic analysis determined myco-photobiont associations. We used a custom closed-circuit gas exchange system with an infrared gas analyser to measure CO2 exchange rates for desiccated specimens at 33%, 76%, 86% and 98% humidity. Cross-sections revealed that the photobiont layers in putative cyano-Lobaria contained both cyanobacteria and green algae, indicating that they should be considered chloro-cyanolichens. Chloro-Lobaria had no visible cephalodia nor cyanobacteria in the photobiont layer. Chloro-Lobaria and chloro-cyano-Lobaria had comparable levels of chlorophyll b. Chloro-Lobaria usually contained Symbiochloris. Chloro-cyano-Lobaria mainly associated with Parachloroidium and Nostoc; infrequently with Symbiochloris, Apatococcus, Chloroidium, Pseudochlorella, Trebouxia. Sequences from two green algal genera were obtained from within some thalli. Desiccated specimens of every Lobaria species could attain net photosynthesis with light exposure and 33% humidity. CO2 exchange dynamics over a five-day period differed between species. At all elevations, chloro-cyano-Lobaria spp. had abundant green algae in the photobiont layer, but green algal strains mostly differed to those of chloro-Lobaria spp. Both chloro-Lobaria and chloro-cyano-Lobaria were capable of conducting photosynthesis without liquid water. The data strongly suggest that they attained positive net photosynthesis.
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Affiliation(s)
- Fiona Ruth Worthy
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
- Honghe Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
| | - Douglas Allen Schaefer
- Honghe Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
| | - Dhanushka Wanasinghe
- Honghe Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
- Department of Soil Science, College of Food and Agriculture Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Jian Chu Xu
- Honghe Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
| | - Li Song Wang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
| | - Xin Yu Wang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
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Iacovelli R, He T, Allen JL, Hackl T, Haslinger K. Genome sequencing and molecular networking analysis of the wild fungus Anthostomella pinea reveal its ability to produce a diverse range of secondary metabolites. Fungal Biol Biotechnol 2024; 11:1. [PMID: 38172933 PMCID: PMC10763133 DOI: 10.1186/s40694-023-00170-1] [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: 10/26/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Filamentous fungi are prolific producers of bioactive molecules and enzymes with important applications in industry. Yet, the vast majority of fungal species remain undiscovered or uncharacterized. Here we focus our attention to a wild fungal isolate that we identified as Anthostomella pinea. The fungus belongs to a complex polyphyletic genus in the family of Xylariaceae, which is known to comprise endophytic and pathogenic fungi that produce a plethora of interesting secondary metabolites. Despite that, Anthostomella is largely understudied and only two species have been fully sequenced and characterized at a genomic level. RESULTS In this work, we used long-read sequencing to obtain the complete 53.7 Mb genome sequence including the full mitochondrial DNA. We performed extensive structural and functional annotation of coding sequences, including genes encoding enzymes with potential applications in biotechnology. Among others, we found that the genome of A. pinea encodes 91 biosynthetic gene clusters, more than 600 CAZymes, and 164 P450s. Furthermore, untargeted metabolomics and molecular networking analysis of the cultivation extracts revealed a rich secondary metabolism, and in particular an abundance of sesquiterpenoids and sesquiterpene lactones. We also identified the polyketide antibiotic xanthoepocin, to which we attribute the anti-Gram-positive effect of the extracts that we observed in antibacterial plate assays. CONCLUSIONS Taken together, our results provide a first glimpse into the potential of Anthstomella pinea to provide new bioactive molecules and biocatalysts and will facilitate future research into these valuable metabolites.
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Affiliation(s)
- R Iacovelli
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - T He
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - J L Allen
- Department of Biology, Eastern Washington University, Cheney, WA, 99004, USA
| | - T Hackl
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - K Haslinger
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands.
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Jung P, Baumann K, Emrich D, Schermer M, Eckhardt KU, Jandl G, Leinweber P, Harion F, Wruck A, Grube M, Büdel B, Lakatos M. The dark side of orange: Multiorganismic continuum dynamics within a lichen of the Atacama Desert. Mycologia 2024; 116:44-58. [PMID: 37955984 DOI: 10.1080/00275514.2023.2263148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/20/2023] [Indexed: 11/15/2023]
Abstract
Over the decades our understanding of lichens has shifted to the fact that they are multiorganismic, symbiotic microecosystems, with their complex interactions coming to the fore due to recent advances in microbiomics. Here, we present a mutualistic-parasitic continuum dynamics scenario between an orange lichen and a lichenicolous fungus from the Atacama Desert leading to the decay of the lichen's photobiont and leaving behind a black lichen thallus. Based on isolation, sequencing, and ecophysiological approaches including metabolic screenings of the symbionts, we depict consequences upon infection with the lichenicolous fungus. This spans from a loss of the lichen's photosynthetic activity and an increased roughness of its surface to an inhibition of the parietin synthesis as a shared pathway between the photobiont and the mycobiont, including a shift of secondary metabolism products. This degree of relations has rarely been documented before, although lichenicolous fungi have been studied for over 200 years, adding an additional level to the view of interactions within lichens.
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Affiliation(s)
- Patrick Jung
- Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Carl-Schurz-Str. 10-16, Pirmasens 66953, Germany
| | - Karen Baumann
- Soil Science, Faculty of Agricultural and Environmental Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Dina Emrich
- Applied Vegetation Ecology, Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Str. 4, Freiburg 79106, Germany
| | - Michael Schermer
- Biology, Rhineland-Palatinate Technical University Kaiserslautern Landau, Erwin-Schrödinger Str. 52, Kaiserslautern 67663, Germany
| | - Kai-Uwe Eckhardt
- Soil Science, Faculty of Agricultural and Environmental Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Gerald Jandl
- Soil Science, Faculty of Agricultural and Environmental Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Peter Leinweber
- Soil Science, Faculty of Agricultural and Environmental Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Felix Harion
- Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Carl-Schurz-Str. 10-16, Pirmasens 66953, Germany
| | - Andreas Wruck
- Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Carl-Schurz-Str. 10-16, Pirmasens 66953, Germany
| | - Martin Grube
- Institute of Biology, University of Graz, Holteigasse 6, Graz 8010, Austria
| | - Burkhard Büdel
- Department of Biology, Rhineland-Palatinate Technical University Kaiserslautern Landau, Erwin-Schrödinger Str. 52, Kaiserslautern 67663, Germany
| | - Michael Lakatos
- Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Carl-Schurz-Str. 10-16, Pirmasens 66953, Germany
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Khakhar A. A roadmap for the creation of synthetic lichen. Biochem Biophys Res Commun 2023; 654:87-93. [PMID: 36898228 DOI: 10.1016/j.bbrc.2023.02.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Lichens represent a charismatic corner of biology that has a rich history of scientific exploration, but to which modern biological techniques have been sparsely applied. This has limited our understanding of phenomena unique to lichen, such as the emergent development of physically coupled microbial consortia or distributed metabolisms. The experimental intractability of natural lichens has prevented studies of the mechanistic underpinnings of their biology. Creating synthetic lichen from experimentally tractable, free-living microbes has the potential to overcome these challenges. They could also serve as powerful new chassis for sustainable biotechnology. In this review we will first briefly introduce what lichen are, what remains mysterious about their biology, and why. We will then articulate the scientific insights that creating a synthetic lichen will generate and lay out a roadmap for how this could be achieved using synthetic biology. Finally, we will explore the translational applications of synthetic lichen and detail what is needed to advance the pursuit of their creation.
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Affiliation(s)
- Arjun Khakhar
- Biology Department, Colorado State University, 251 West Pitkin Drive, Fort Collins, CO, 80525, 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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7
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Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
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Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
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8
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Fruticose Lichen Communities at the Edge: Distribution and Diversity in a Desert Sky Island on the Colorado Plateau. CONSERVATION 2022. [DOI: 10.3390/conservation2040037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Subalpine habitats in sky islands in the Southwestern USA are currently facing large-scale transformations. Lichens have widely been used as bioindicators of environmental change. On the Colorado Plateau, fruticose lichens occur in patchy, disconnected populations, including unique lichen-draped conifer sites in subalpine forests in the La Sal Mountains in southeastern Utah. Here, we document the distribution and fungal diversity within these lichen communities. We find that lichen-draped conifer sites in the La Sal Mountains are restricted to only three known, small areas in Picea englemannii forests above 3000 m above sea level, two of which have recently been impacted by wildfire. We document 30 different species of lichen-forming fungi in these communities, several which represent the first reports from the Colorado Plateau. We also characterize mycobiont haplotype diversity for the fruticose lichens Evernia divaricata, Ramalina sinensis, and multiple Usnea species. We also report a range of diverse fungi associated with these lichens, including genetic clusters representing 22 orders spanning seven classes of Ascomycetes and fewer clusters representing Basidiomycetes. Our results provide a baseline for ongoing monitoring and help to raise awareness of unique lichen communities and other biodiversity in the region.
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9
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Furmanek Ł, Czarnota P, Seaward MRD. A review of the potential of lichen substances as antifungal agents: the effects of extracts and lichen secondary metabolites on Fusarium fungi. Arch Microbiol 2022; 204:523. [PMID: 35881248 PMCID: PMC9325835 DOI: 10.1007/s00203-022-03104-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/06/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022]
Abstract
The present meta-analysis provides literature data on the effect of lichen extracts and single secondary metabolites used against Fusarium spp. moulds. Lichen extracts were obtained from 51 corticolous, 17 terricolous and 18 saxicolous lichen species and 37 secondary compounds were tested against eight fungal species, i.e., Fusarium acuminatum, F. avenaceum, F. culmorum, F. fujikuroi, F. oxysporum, F. roseum, F. solani and F. udum. The researchers used several test methods, mostly to determine MIC and IZ. Extracts were obtained using several solvents, mainly organic ones with use of the Soxhlet apparatus. The most frequently tested species was F. oxysporum, against which lichen substances from Alectoria sarmentosa, Cladonia mitis, C. rangiferina, Flavoparmelia caperata, Hypotrachyna cirrhata, Leucodermia leucomelos, Parmotrema austrosinense, P. reticulatum, Physcia aipolia, Pseudevernia furfuracea, Roccella montagnei and Umbilicaria nylanderiana and secondary metabolites such as 2-hydroxy-4-methoxy-3,6-dimethylbenzoic acid, atranorin, lecanoric and (+)-usnic acids showed the highest antifungal potential. These agencies could compete with the potential of fungicides, such as flucytosine and fluconazole. Other species have been poorly investigated. Statistical analysis of literature data showed that the fungistatic potential of lichen extracts is significantly different from individual secondary metabolites. Similarly, the potential of secondary metabolites often differs significantly from that of non-lichen substances. This meta-analysis indicates the potential of lichen substances as future anti-fusarial agents.
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Affiliation(s)
- Łukasz Furmanek
- Department of Ecology and Environmental Protection, University of Rzeszów, ul. Zelwerowicza 4, 35-601, Rzeszow, Poland.
| | - Paweł Czarnota
- Department of Ecology and Environmental Protection, University of Rzeszów, ul. Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Mark R D Seaward
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, BD7 1DP, UK
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10
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Allen JL, Lendemer JC. A call to reconceptualize lichen symbioses. Trends Ecol Evol 2022; 37:582-589. [PMID: 35397954 DOI: 10.1016/j.tree.2022.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/23/2022]
Abstract
Several decades of research across disciplines have overturned historical perspectives of symbioses dominated by binary characterizations of highly specific species-species interactions. This paradigm shift has unlocked the previously underappreciated and overlooked dynamism of fungal mutualisms such as mycorrhizae. Lichens are another example of important fungal mutualisms where reconceptualization is urgently needed to realize their potential as model systems. This reconceptualization requires both an objective synthesis of new data and envisioning a revised integrative approach that unifies the spectrum of ecology and evolution. We propose a ten-theme framework that if pursued would propel lichens to the vanguard of symbiotic theory.
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Affiliation(s)
- Jessica L Allen
- Eastern Washington University, Biology Department, Cheney, WA 99004, USA.
| | - James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458-5126, USA.
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11
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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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12
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A comparative genomic analysis of lichen-forming fungi reveals new insights into fungal lifestyles. Sci Rep 2022; 12:10724. [PMID: 35750715 PMCID: PMC9232553 DOI: 10.1038/s41598-022-14340-5] [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: 03/23/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Lichen-forming fungi are mutualistic symbionts of green algae or cyanobacteria. We report the comparative analysis of six genomes of lichen-forming fungi in classes Eurotiomycetes and Lecanoromycetes to identify genomic information related to their symbiotic lifestyle. The lichen-forming fungi exhibited genome reduction via the loss of dispensable genes encoding plant-cell-wall-degrading enzymes, sugar transporters, and transcription factors. The loss of these genes reflects the symbiotic biology of lichens, such as the absence of pectin in the algal cell wall and obtaining specific sugars from photosynthetic partners. The lichens also gained many lineage- and species-specific genes, including those encoding small secreted proteins. These genes are primarily induced during the early stage of lichen symbiosis, indicating their significant roles in the establishment of lichen symbiosis.Our findings provide comprehensive genomic information for six lichen-forming fungi and novel insights into lichen biology and the evolution of symbiosis.
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13
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Spribille T, Resl P, Stanton DE, Tagirdzhanova G. Evolutionary biology of lichen symbioses. THE NEW PHYTOLOGIST 2022; 234:1566-1582. [PMID: 35302240 DOI: 10.1111/nph.18048] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/21/2021] [Indexed: 05/28/2023]
Abstract
Lichens are the symbiotic outcomes of open, interspecies relationships, central to which are a fungus and a phototroph, typically an alga and/or cyanobacterium. The evolutionary processes that led to the global success of lichens are poorly understood. In this review, we explore the goods and services exchange between fungus and phototroph and how this propelled the success of both symbiont and symbiosis. Lichen fungal symbionts count among the only filamentous fungi that expose most of their mycelium to an aerial environment. Phototrophs export carbohydrates to the fungus, which converts them to specific polyols. Experimental evidence suggests that polyols are not only growth and respiratory substrates but also play a role in anhydrobiosis, the capacity to survive desiccation. We propose that this dual functionality is pivotal to the evolution of fungal symbionts, enabling persistence in environments otherwise hostile to fungi while simultaneously imposing costs on growth. Phototrophs, in turn, benefit from fungal protection from herbivory and light stress, while appearing to exert leverage over fungal sex and morphogenesis. Combined with the recently recognized habit of symbionts to occur in multiple symbioses, this creates the conditions for a multiplayer marketplace of rewards and penalties that could drive symbiont selection and lichen diversification.
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Affiliation(s)
- Toby Spribille
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Philipp Resl
- Institute of Biology, University of Graz, Universitätsplatz 3, Graz, 8010, Austria
| | - Daniel E Stanton
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB, T6G 2R3, Canada
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Zhang Y, Clancy J, Jensen J, McMullin RT, Wang L, Leavitt SD. Providing Scale to a Known Taxonomic Unknown—At Least a 70-Fold Increase in Species Diversity in a Cosmopolitan Nominal Taxon of Lichen-Forming Fungi. J Fungi (Basel) 2022; 8:jof8050490. [PMID: 35628746 PMCID: PMC9146994 DOI: 10.3390/jof8050490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/06/2023] Open
Abstract
Robust species delimitations provide a foundation for investigating speciation, phylogeography, and conservation. Here we attempted to elucidate species boundaries in the cosmopolitan lichen-forming fungal taxon Lecanora polytropa. This nominal taxon is morphologically variable, with distinct populations occurring on all seven continents. To delimit candidate species, we compiled ITS sequence data from populations worldwide. For a subset of the samples, we also generated alignments for 1209 single-copy nuclear genes and an alignment spanning most of the mitochondrial genome to assess concordance among the ITS, nuclear, and mitochondrial inferences. Species partitions were empirically delimited from the ITS alignment using ASAP and bPTP. We also inferred a phylogeny for the L. polytropa clade using a four-marker dataset. ASAP species delimitations revealed up to 103 species in the L. polytropa clade, with 75 corresponding to the nominal taxon L. polytropa. Inferences from phylogenomic alignments generally supported that these represent evolutionarily independent lineages or species. Less than 10% of the candidate species were comprised of specimens from multiple continents. High levels of candidate species were recovered at local scales but generally with limited overlap across regions. Lecanora polytropa likely ranks as one of the largest species complexes of lichen-forming fungi known to date.
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Affiliation(s)
- Yanyun Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
- College of Life Science, Anhui Normal University, Wuhu 241000, China
| | - Jeffrey Clancy
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA; (J.C.); (J.J.)
| | - Jacob Jensen
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA; (J.C.); (J.J.)
| | | | - Lisong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
- Correspondence: (L.W.); (S.D.L.)
| | - Steven D. Leavitt
- Department of Biology, M. L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA
- Correspondence: (L.W.); (S.D.L.)
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15
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Mitchell G, Wilson PJ, Manseau M, Redquest B, Patterson BR, Rutledge LY. DNA metabarcoding of faecal pellets reveals high consumption of yew ( Taxus spp.) by caribou ( Rangifer tarandus) in a lichen-poor environment. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Woodland caribou ( Rangifer tarandus caribou) are threatened in Canada because of the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast trnL region, which was only successful on island samples, revealed primary consumption of yew ( Taxus spp.) based on relative read abundance (83.68%) with dogwood ( Cornus spp.; 9.67%) and maple ( Acer spp.; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.
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Affiliation(s)
- Greniqueca Mitchell
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| | - Paul J. Wilson
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| | - Micheline Manseau
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
- Landscape Science and Technology Division, Environment and Climate Change Canada, 1125 Colonel By Drive, Ottawa, ON K1S 5R1, Canada
| | - Bridgett Redquest
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| | - Brent R. Patterson
- Ontario Ministry of Natural Resources and Forestry, Trent University, DNA Building, Peterborough, ON K9L 1Z8, Canada
| | - Linda Y. Rutledge
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
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DA SILVA MAYANNEKARLA, DA SILVA AVERLANEV, FERNANDEZ PAULAM, MONTONE ROSALINDAC, ALVES RODRIGOP, DE QUEIROZ ALINEC, DE OLIVEIRA VALÉRIAM, DOS SANTOS VIVIANEP, PUTZKE JAIR, ROSA LUIZHENRIQUE, DUARTE ALYSSONW. Extracellular hydrolytic enzymes produced by yeasts from Antarctic lichens. AN ACAD BRAS CIENC 2022; 94:e20210540. [DOI: 10.1590/0001-3765202220210540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/21/2021] [Indexed: 11/22/2022] Open
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Kyriatzi A, Tzivras G, Pirintsos S, Kotzabasis K. Biotechnology under extreme conditions: Lichens after extreme UVB radiation and extreme temperatures produce large amounts of hydrogen. J Biotechnol 2021; 342:128-138. [PMID: 34743006 DOI: 10.1016/j.jbiotec.2021.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/04/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
The present study demonstrates biotechnological applications of the lichen Pleurosticta acetabulum, specifically the production of large amounts of hydrogen even after the lichen exposure to extreme conditions such as a) extreme UVB radiation (1.7 mW/cm2 = 1000 J m-2 min-1) over different time periods (4, 20 & 70 h) and b) combined exposure of the lichen to high intensity UVB radiation and extreme low (-196 °C) or extreme high temperatures (+70 °C). The results highlight that the extremophilic and polyextremophilic behavior of lichens both in dehydrated and in regenerated form, under extreme conditions not necessarily recorded on earth, is compatible with their biotechnological uses. The lichen viability was measured using fluorescence induction techniques (OJIP-test), which record changes in the molecular structure and function of the photosynthetic mechanism, while its ability to produce molecular hydrogen was measured through thermal conductivity gas chromatography (GC-TCD) analysis. Hydrogen is a promising fuel for the future. The exciting result of a lichen micro-ecosystem is its ability to expel its moisture and remain in an inactive state, protecting itself from extreme conditions and maintaining its ability to high yield hydrogen production in a closed system, with the sole addition of water and without the need for additional energy. Our results expand the potential use of lichens for future biotechnological applications in extreme Earth environments, but also in environments on other planets, such as Mars, thus paving the way for astrobiotechnological applications.
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Affiliation(s)
- Anastasia Kyriatzi
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
| | - Gerasimos Tzivras
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
| | - Stergios Pirintsos
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR-74100 Rethymnon, Crete, Greece
| | - Kiriakos Kotzabasis
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR-74100 Rethymnon, Crete, Greece.
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Lofgren LA, Stajich JE. Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes. Curr Biol 2021; 31:R1312-R1325. [PMID: 34637742 PMCID: PMC8516061 DOI: 10.1016/j.cub.2021.06.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.
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Affiliation(s)
- Lotus A Lofgren
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA
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20
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Drew GC, Stevens EJ, King KC. Microbial evolution and transitions along the parasite-mutualist continuum. Nat Rev Microbiol 2021; 19:623-638. [PMID: 33875863 PMCID: PMC8054256 DOI: 10.1038/s41579-021-00550-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Virtually all plants and animals, including humans, are home to symbiotic microorganisms. Symbiotic interactions can be neutral, harmful or have beneficial effects on the host organism. However, growing evidence suggests that microbial symbionts can evolve rapidly, resulting in drastic transitions along the parasite-mutualist continuum. In this Review, we integrate theoretical and empirical findings to discuss the mechanisms underpinning these evolutionary shifts, as well as the ecological drivers and why some host-microorganism interactions may be stuck at the end of the continuum. In addition to having biomedical consequences, understanding the dynamic life of microorganisms reveals how symbioses can shape an organism's biology and the entire community, particularly in a changing world.
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Affiliation(s)
| | | | - Kayla C King
- Department of Zoology, University of Oxford, Oxford, UK.
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23
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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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Ament-Velásquez SL, Tuovinen V, Bergström L, Spribille T, Vanderpool D, Nascimbene J, Yamamoto Y, Thor G, Johannesson H. The Plot Thickens: Haploid and Triploid-Like Thalli, Hybridization, and Biased Mating Type Ratios in Letharia. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:656386. [PMID: 37744149 PMCID: PMC10512270 DOI: 10.3389/ffunb.2021.656386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/24/2021] [Indexed: 09/26/2023]
Abstract
The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we infer the genome organization and reproduction in Letharia by analyzing genomic data from a pure culture and from thalli, and performing a PCR survey of the MAT locus in natural populations. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations.
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Affiliation(s)
| | - Veera Tuovinen
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Linnea Bergström
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Toby Spribille
- Biological Sciences CW 405, University of Alberta, Edmonton, AB, Canada
| | - Dan Vanderpool
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Juri Nascimbene
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Yoshikazu Yamamoto
- Department of Bioproduction Science, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Göran Thor
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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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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Carr EC, Harris SD, Herr JR, Riekhof WR. Lichens and biofilms: Common collective growth imparts similar developmental strategies. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Grimm M, Grube M, Schiefelbein U, Zühlke D, Bernhardt J, Riedel K. The Lichens' Microbiota, Still a Mystery? Front Microbiol 2021; 12:623839. [PMID: 33859626 PMCID: PMC8042158 DOI: 10.3389/fmicb.2021.623839] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/10/2021] [Indexed: 01/03/2023] Open
Abstract
Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont's contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.
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Affiliation(s)
- Maria Grimm
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University Graz, Graz, Austria
| | | | - Daniela Zühlke
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University Greifswald, Greifswald, Germany
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Tuovinen V, Millanes AM, Freire-Rallo S, Rosling A, Wedin M. Tremella macrobasidiata and Tremella variae have abundant and widespread yeast stages in Lecanora lichens. Environ Microbiol 2021; 23:2484-2498. [PMID: 33684261 DOI: 10.1111/1462-2920.15455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 01/22/2023]
Abstract
Dimorphism is a widespread feature of tremellalean fungi in general, but a little-studied aspect of the biology of lichen-associated Tremella. We show that Tremella macrobasidiata and Tremella variae have an abundant and widespread yeast stage in their life cycles that occurs in Lecanora lichens. Their sexual filamentous stage is restricted to a specific lichen: T. macrobasidiata only forms basidiomata on Lecanora chlarotera hymenia and T. variae only on Lecanora varia thalli. However, the yeast stage of T. macrobasidiata is less specific and can occur in L. varia lichens, whilst all life stages of T. variae may be specific to L. varia. Contrary to the hyphal stages, the yeasts are distributed across the thalli and hymenia of Lecanora lichens, and not limited to specimens with basidiomata. Tremella macrobasidiata was present in all studied L. chlarotera, and in 59% of L. varia specimens. Only in 8% of the L. varia thalli could none of the two Tremella species be detected. Our results indicate that lichen-associated Tremella may be much more abundant and widespread than previously assumed leading to skewed estimations about their distribution ranges and lichen specificity, and raise new questions about their biology, ecology and function in the symbiosis.
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Affiliation(s)
- Veera Tuovinen
- Department of Ecology and Genetics, Uppsala University, Uppsala, Norbyvägen 18D, 752 36, Sweden.,Department of Botany, Swedish Museum of Natural History, Stockholm, P.O. Box 50007, SE-104 05, Sweden
| | - Ana Maria Millanes
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, E-28933, Spain
| | - Sandra Freire-Rallo
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, E-28933, Spain
| | - Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Uppsala, Norbyvägen 18D, 752 36, Sweden
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, Stockholm, P.O. Box 50007, SE-104 05, Sweden
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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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Antarctic lichens as a source of phosphate-solubilizing bacteria. Extremophiles 2021; 25:181-191. [PMID: 33635427 DOI: 10.1007/s00792-021-01220-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
In association with lichens, bacteria can play key roles in solubilizing sources of inorganic phosphates that are available in the environment. In this study, the potential of bacteria isolated from 15 Antarctic lichen samples for phosphate solubilization was investigated. From 124 bacteria tested, 66 (53%) were positive for phosphate solubilization in solid NBRIP medium, with a higher prevalence of Pseudomonas, followed by Caballeronia and Chryseobacterium. Most of the phosphate-solubilizing bacteria were isolated from Usnea auratiacoatra, followed by Caloplaca regalis and Xanthoria candelaria. Two isolates showed outstanding performance, Pseudomonas sp. 11.LB15 and Pseudomonas sp. 1.LB34, since they presented solubilization in the temperature range from 15.0 to 30.0 °C, and maximum quantification of soluble phosphate at 25.0 °C was 511.21 and 532.07 mg/L for Pseudomonas sp. 11.LB15 and Pseudomonas sp. 1.LB34, respectively. At 30.0 °C soluble phosphate yield was 639.43 and 518.95 mg/L with pH of 3.74 and 3.87 for Pseudomonas sp. 11.LB15 and Pseudomonas sp. 1.LB34, respectively. Fumaric and tartaric acids were released during the solubilization process. Finally, bacteria isolated from Antarctic lichens were shown to have the potential for phosphate solubilization, opening perspectives for future application in the agricultural sector and contributing to reduce the use of chemical fertilizers.
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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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33
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Kono M, Kon Y, Ohmura Y, Satta Y, Terai Y. In vitro resynthesis of lichenization reveals the genetic background of symbiosis-specific fungal-algal interaction in Usnea hakonensis. BMC Genomics 2020; 21:671. [PMID: 32993496 PMCID: PMC7526373 DOI: 10.1186/s12864-020-07086-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Symbiosis is central to ecosystems and has been an important driving force of the diversity of life. Close and long-term interactions are known to develop cooperative molecular mechanisms between the symbiotic partners and have often given them new functions as symbiotic entities. In lichen symbiosis, mutualistic relationships between lichen-forming fungi and algae and/or cyanobacteria produce unique features that make lichens adaptive to a wide range of environments. Although the morphological, physiological, and ecological uniqueness of lichens has been described for more than a century, the genetic mechanisms underlying this symbiosis are still poorly known. RESULTS This study investigated the fungal-algal interaction specific to the lichen symbiosis using Usnea hakonensis as a model system. The whole genome of U. hakonensis, the fungal partner, was sequenced by using a culture isolated from a natural lichen thallus. Isolated cultures of the fungal and the algal partners were co-cultured in vitro for 3 months, and thalli were successfully resynthesized as visible protrusions. Transcriptomes of resynthesized and natural thalli (symbiotic states) were compared to that of isolated cultures (non-symbiotic state). Sets of fungal and algal genes up-regulated in both symbiotic states were identified as symbiosis-related genes. CONCLUSION From predicted functions of these genes, we identified genetic association with two key features fundamental to the symbiotic lifestyle in lichens. The first is establishment of a fungal symbiotic interface: (a) modification of cell walls at fungal-algal contact sites; and (b) production of a hydrophobic layer that ensheaths fungal and algal cells;. The second is symbiosis-specific nutrient flow: (a) the algal supply of photosynthetic product to the fungus; and (b) the fungal supply of phosphorous and nitrogen compounds to the alga. Since both features are widespread among lichens, our result may indicate important facets of the genetic basis of the lichen symbiosis.
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Affiliation(s)
- Mieko Kono
- SOKENDAI (The Graduate University for Advanced Studies), Department of Evolutionary Studies of Biosystems, Shonan Village, Hayama, Kanagawa, 240-0193, Japan.
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden.
| | - Yoshiaki Kon
- Tokyo Metropolitan Hitotsubashi High School, 1-12-13 Higashikanda, Chiyoda-ku, Tokyo, 101-0031, Japan
| | - Yoshihito Ohmura
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
| | - Yoko Satta
- SOKENDAI (The Graduate University for Advanced Studies), Department of Evolutionary Studies of Biosystems, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Yohey Terai
- SOKENDAI (The Graduate University for Advanced Studies), Department of Evolutionary Studies of Biosystems, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
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Spribille T, Tagirdzhanova G, Goyette S, Tuovinen V, Case R, Zandberg WF. 3D biofilms: in search of the polysaccharides holding together lichen symbioses. FEMS Microbiol Lett 2020; 367:5731805. [PMID: 32037451 PMCID: PMC7164778 DOI: 10.1093/femsle/fnaa023] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
Stable, long-term interactions between fungi and algae or cyanobacteria, collectively known as lichens, have repeatedly evolved complex architectures with little resemblance to their component parts. Lacking any central scaffold, the shapes they assume are casts of secreted polymers that cement cells into place, determine the angle of phototropic exposure and regulate water relations. A growing body of evidence suggests that many lichen extracellular polymer matrices harbor unicellular, non-photosynthesizing organisms (UNPOs) not traditionally recognized as lichen symbionts. Understanding organismal input and uptake in this layer is key to interpreting the role UNPOs play in lichen biology. Here, we review both polysaccharide composition determined from whole, pulverized lichens and UNPOs reported from lichens to date. Most reported polysaccharides are thought to be structural cell wall components. The composition of the extracellular matrix is not definitively known. Several lines of evidence suggest some acidic polysaccharides have evaded detection in routine analysis of neutral sugars and may be involved in the extracellular matrix. UNPOs reported from lichens include diverse bacteria and yeasts for which secreted polysaccharides play important biological roles. We conclude by proposing testable hypotheses on the role that symbiont give-and-take in this layer could play in determining or modifying lichen symbiotic outcomes.
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Affiliation(s)
- Toby Spribille
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Spencer Goyette
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Veera Tuovinen
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Rebecca Case
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Wesley F Zandberg
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3427 University Way, Kelowna, BC V1V 1V7, Canada
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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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36
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Abstract
Mutualistic symbiosis can be regarded as interspecific division of labour, which can improve the productivity of metabolites and services but deteriorate the ability to live without partners. Interestingly, even in environmentally acquired symbiosis, involved species often rely exclusively on the partners despite the lethal risk of missing partners. To examine this paradoxical evolution, we explored the coevolutionary dynamics in symbiotic species for the amount of investment in producing their essential metabolites, which symbiotic species can share. Our study has shown that, even if obtaining partners is difficult, 'perfect division of labour' (PDL) can be maintained evolutionarily, where each species perfectly specializes in producing one of the essential metabolites so that every member entirely depends on the others for survival, i.e. in exchange for losing the ability of living alone. Moreover, the coevolutionary dynamics shows multistability with other states including a state without any specialization. It can cause evolutionary hysteresis: once PDL has been achieved evolutionarily when obtaining partners was relatively easy, it is not reverted even if obtaining partners becomes difficult later. Our study suggests that obligate mutualism with a high degree of mutual specialization can evolve and be maintained easier than previously thought.
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Affiliation(s)
- Yu Uchiumi
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Kanagawa 240-0193, Japan
| | - Akira Sasaki
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Kanagawa 240-0193, Japan.,Evolution and Ecology Program, International Institute for Applied Systems Analysis, Schlosplatz 1, 2361, Laxenburg, Austria
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37
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Skejo J, Franjević D. Eukaryotes Are a Holophyletic Group of Polyphyletic Origin. Front Microbiol 2020; 11:1380. [PMID: 32714303 PMCID: PMC7343848 DOI: 10.3389/fmicb.2020.01380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/28/2020] [Indexed: 12/02/2022] Open
Affiliation(s)
- Josip Skejo
- Institute of Molecular Evolution, Heinrich–Heine University Düsseldorf, Düsseldorf, Germany
- Evolution Lab, Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Damjan Franjević
- Evolution Lab, Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- *Correspondence: Damjan Franjević
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McKenzie SK, Walston RF, Allen JL. Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture. Genomics 2020; 112:3150-3156. [PMID: 32504651 DOI: 10.1016/j.ygeno.2020.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/20/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023]
Abstract
Fungal genomes display incredible levels of complexity and diversity, and are exceptional study systems for genome evolution. Here we used the Oxford Nanopore MinION sequencing platform to generate high-quality fungal genomes from complex metagenomic samples of lichen thalli. We sequenced two wolf lichens using one flow cell per sample, generating 17.1 Gbps for Letharia lupina and 14.3 Gbps for Letharia columbiana. The resulting L. lupina genome is one of the most contiguous lichen genomes available to date, with 49.2 Mbp contained on 31 contigs. The L. columbiana genome, while less contiguous, is still relatively high quality, with 52.3 Mbp on a total of 161 contigs. Each thallus for both species contained multiple distinct haplotypes, a phenomenon that has rarely been empirically demonstrated. The Oxford Nanopore sequencing technologies are robust and effective when applied to complex symbioses, and have the potential to fundamentally transform our understanding of fungal genetics.
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Affiliation(s)
- Sean K McKenzie
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland; Current affiliation: Emory Integrated Computational Core, Emory University, Atlanta, GA, USA.
| | - Ridge F Walston
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Jessica L Allen
- Department of Biology, Eastern Washington University, Cheney, WA, USA
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Tomáška Ľ, Nosek J. Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends. J Mol Evol 2020; 88:293-318. [PMID: 32157325 DOI: 10.1007/s00239-020-09935-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
Abstract
Biological entities are multicomponent systems where each part is directly or indirectly dependent on the others. In effect, a change in a single component might have a consequence on the functioning of its partners, thus affecting the fitness of the entire system. In this article, we provide a few examples of such complex biological systems, ranging from ant colonies to a population of amino acids within a single-polypeptide chain. Based on these examples, we discuss one of the central and still challenging questions in biology: how do such multicomponent consortia co-evolve? More specifically, we ask how telomeres, nucleo-protein complexes protecting the integrity of linear DNA chromosomes, originated from the ancestral organisms having circular genomes and thus not dealing with end-replication and end-protection problems. Using the examples of rapidly evolving topologies of mitochondrial genomes in eukaryotic microorganisms, we show what means of co-evolution were employed to accommodate various types of telomere-maintenance mechanisms in mitochondria. We also describe an unprecedented runaway evolution of telomeric repeats in nuclei of ascomycetous yeasts accompanied by co-evolution of telomere-associated proteins. We propose several scenarios derived from research on telomeres and supported by other studies from various fields of biology, while emphasizing that the relevant answers are still not in sight. It is this uncertainty and a lack of a detailed roadmap that makes the journey through the jungle of biological systems still exciting and worth undertaking.
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Affiliation(s)
- Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia
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40
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Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei. Sci Rep 2020; 10:1303. [PMID: 31992756 PMCID: PMC6987183 DOI: 10.1038/s41598-020-58025-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/16/2019] [Indexed: 01/24/2023] Open
Abstract
The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.
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41
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Lendemer JC, Keepers KG, Tripp EA, Pogoda CS, McCain CM, Kane NC. A taxonomically broad metagenomic survey of 339 species spanning 57 families suggests cystobasidiomycete yeasts are not ubiquitous across all lichens. AMERICAN JOURNAL OF BOTANY 2019; 106:1090-1095. [PMID: 31397894 DOI: 10.1002/ajb2.1339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/12/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested. METHODS We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America. RESULTS Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results. CONCLUSIONS Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.
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Affiliation(s)
- James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Erin A Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Christy M McCain
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
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42
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Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica. Microorganisms 2019; 7:microorganisms7070203. [PMID: 31323808 PMCID: PMC6681027 DOI: 10.3390/microorganisms7070203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/13/2019] [Accepted: 07/16/2019] [Indexed: 01/26/2023] Open
Abstract
Saxicolous rock ripe lichens that grow on rocks in the East Antarctic fellfields were sampled for phylotypic characterization of its constituent mycobionts (fungi) and photobionts (algae and cyanobacteria). The rock tripe lichen-forming fungal and algal phylotypes were classified under the common lichen-forming genera of ascomycetes, namely, Umbilicaria, and green algae, namely, Trebouxia and Coccomyxa. However, phylotypes of the green algal chloroplasts and the lichen-associated cyanobacteria showed unexpectedly high diversity. The detected chloroplast phylotypes were not fully affiliated with the green algal genera Trebouxia or Coccomyxa. The predominant chloroplast phylotype demonstrated maximum resemblance to Neglectella solitaria, which is neither a known Antarctic species nor a typical lichen photobiont. Another dominant chloroplast phylotype belonged to the atypical Antarctic green algae family. Cyanobacterial phylotypes were dominated by those affiliated with the Microcoleus species rather than the well-known lichen-associates, Nostoc species. The occurrences of these Microcoleus-affiliated cyanobacterial phylotypes were specifically abundant within the Yukidori Valley site, one of the Antarctic Specially Protected Areas (ASPA). The ASPA site, along with another 50 km-distant site, yielded most of the cryptic diversity in the phylotypes of chloroplasts and cyanobacteria, which may contribute to the phenotypic variability within the rock tripe lichen photobionts.
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43
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Jung P, Emrich D, Briegel-Williams L, Schermer M, Weber L, Baumann K, Colesie C, Clerc P, Lehnert LW, Achilles S, Bendix J, Büdel B. Ecophysiology and phylogeny of new terricolous and epiphytic chlorolichens in a fog oasis of the Atacama Desert. Microbiologyopen 2019; 8:e894. [PMID: 31276321 PMCID: PMC6813448 DOI: 10.1002/mbo3.894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 11/24/2022] Open
Abstract
The Atacama Desert is one of the driest and probably oldest deserts on Earth where only a few extremophile organisms are able to survive. This study investigated two terricolous and two epiphytic lichens from the fog oasis “Las Lomitas” within the National Park Pan de Azúcar which represents a refugium for a few vascular desert plants and many lichens that can thrive on fog and dew alone. Ecophysiological measurements and climate records were combined with molecular data of the mycobiont, their green algal photobionts and lichenicolous fungi to gain information about the ecology of lichens within the fog oasis. Phylogenetic and morphological investigations led to the identification and description of the new lichen species Acarospora conafii sp. nov. as well as the lichenicolous fungi that accompanied them and revealed the trebouxioid character of all lichen photobionts. Their photosynthetic responses were compared during natural scenarios such as reactivation by high air humidity and in situ fog events to elucidate the activation strategies of this lichen community. Epiphytic lichens showed photosynthetic activity that was rapidly induced by fog and high relative air humidity whereas terricolous lichens were only activated by fog.
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Affiliation(s)
- Patrick Jung
- Plant Ecology and Systematics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Dina Emrich
- Plant Ecology and Systematics, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Michael Schermer
- Plant Ecology and Systematics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Lena Weber
- Plant Ecology and Systematics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Karen Baumann
- Faculty of Agricultural and Environmental Science, University of Rostock, Rostock, Germany
| | - Claudia Colesie
- Edinburgh Global Change Institute, School of GeoSciences, University of Edinburgh, Edinburgh, Scotland
| | - Philippe Clerc
- Conservatoire et Jardin botaniques de la Ville de Genève, Chambésy, Switzerland
| | - Lukas W Lehnert
- Department of Geography, Ludwig-Maximilians-University Munich, Munich, Germany
| | | | - Jörg Bendix
- Faculty of Geography, Philipps University of Marburg, Marburg, Germany
| | - Burkhard Büdel
- Plant Ecology and Systematics, University of Kaiserslautern, Kaiserslautern, Germany
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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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Abstract
Identification of the fungus Tremella as a consistent fourth component of wolf lichens further challenges the conventional view of lichen symbiosis as a mutualistic interaction between two players.
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Affiliation(s)
- Benjamin Jenkins
- Living Systems Institute, Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, UK
| | - Thomas A Richards
- Living Systems Institute, Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, UK.
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