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He Z, Naganuma T, Nakai R, Uetake J, Hahn MW. Microbiomic Analysis of Bacteria Associated with Rock Tripe Lichens from Alpine Areas in Eastern Alps and Equatorial Africa. Curr Microbiol 2024; 81:115. [PMID: 38483599 PMCID: PMC10940493 DOI: 10.1007/s00284-024-03626-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/27/2024] [Indexed: 03/17/2024]
Abstract
The diversity of bacteria associated with alpine lichens was profiled. Lichen samples belonging to the Umbilicariaceae family, commonly known as rock tripe lichens, were gathered from two distinct alpine fellfields: one situated on Mt. Brennkogel located in the Eastern European Alps (Austria), and the other on Mt. Stanley located in the Rwenzori mountains of equatorial Africa (Uganda). The primary aim of this research was to undertake a comparative investigation into the bacterial compositions, and diversities, identifying potential indicators and exploring their potential metabolisms, of these lichen samples. Bulk genomic DNA was extracted from the lichen samples, which was used to amplify the 18S rRNA gene by Sanger sequencing and the V3-V4 region of the 16S rRNA gene by Illumina Miseq sequencing. Examination of the fungal partner was carried out through the analysis of 18S rRNA gene sequences, belonging to the genus Umbilicaria (Ascomycota), and the algal partner affiliated with the lineage Trebouxia (Chlorophyta), constituted the symbiotic components. Analyzing the MiSeq datasets by using bioinformatics methods, operational taxonomic units (OTUs) were established based on a predetermined similarity threshold for the V3-V4 sequences, which were assigned to a total of 26 bacterial phyla that were found in both areas. Eight of the 26 phyla, i.e. Acidobacteriota, Actinomycota, Armatimonadota, Bacteroidota, Chloroflexota, Deinococcota, Planctomycetota, and Pseudomonadota, were consistently present in all samples, each accounting for more than 1% of the total read count. Distinct differences in bacterial composition emerged between lichen samples from Austria and Uganda, with the OTU frequency-based regional indicator phyla, Pseudomonadota and Armatimonadota, respectively. Despite the considerable geographic separation of approximately 5430 km between the two regions, the prediction of potential metabolic pathways based on OTU analysis revealed similar relative abundances. This similarity is possibly influenced by comparable alpine climatic conditions prevailing in both areas.
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Affiliation(s)
- Zichen He
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, 062-8517, Japan
| | - Jun Uetake
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, 060-0811, Japan
| | - Martin W Hahn
- Research Department for Limnology, Universität Innsbruck, 5310, Mondsee, Austria
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2
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Sanders WB. The disadvantages of current proposals to redefine lichens. THE NEW PHYTOLOGIST 2024; 241:969-971. [PMID: 38031529 DOI: 10.1111/nph.19321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Affiliation(s)
- William B Sanders
- Department of Biological Sciences, Florida Gulf Coast University, Ft Myers, FL, 33965, USA
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3
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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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4
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Ahmad N, Ritz M, Calchera A, Otte J, Schmitt I, Brueck T, Mehlmer N. Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. Microbiologyopen 2023; 12:e1386. [PMID: 37877655 PMCID: PMC10582450 DOI: 10.1002/mbo3.1386] [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: 08/03/2023] [Revised: 09/15/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus), which together generate a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here, we provide a comparative view of the biosynthetic gene clusters of three lichen mycobionts derived from Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. In addition, we present a high-quality PacBio metagenome of Parmelia sulcata, from which we extracted the mycobiont bin containing 214 biosynthetic gene clusters. Most biosynthetic gene clusters in these genomes were associated with T1PKSs, followed by NRPSs and terpenes. This study focused on biosynthetic gene clusters related to polyketide synthesis. Based on ketosynthase homology, we identified nine highly syntenic clusters present in all three species. Among the four clusters belonging to nonreducing PKSs, two are putatively linked to lichen substances derived from orsellinic acid (orcinol depsides and depsidones, e.g., lecanoric acid, physodic acid, lobaric acid), one to compounds derived from methylated forms of orsellinic acid (beta orcinol depsides, e.g., atranorin), and one to melanins. Five clusters with orthologs in all three species are linked to reducing PKSs. Our study contributes to sorting and dereplicating the vast PKS diversity found in lichenized fungi. High-quality sequences of biosynthetic gene clusters of these three common species provide a foundation for further exploration into biotechnological applications and the molecular evolution of lichen substances.
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Affiliation(s)
- Nadim Ahmad
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
| | - Manfred Ritz
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am MainGermany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am MainGermany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am MainGermany
- Institute of Ecology, Evolution and DiversityGoethe University FrankfurtFrankfurt am MainGermany
| | - Thomas Brueck
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
| | - Norbert Mehlmer
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
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5
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Ahmad N, Ritz M, Calchera A, Otte J, Schmitt I, Brueck T, Mehlmer N. Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways. J Fungi (Basel) 2023; 9:jof9050546. [PMID: 37233257 DOI: 10.3390/jof9050546] [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: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.
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Affiliation(s)
- Nadim Ahmad
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Manfred Ritz
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany
| | - Thomas Brueck
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Norbert Mehlmer
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
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Xu M, Liu Y, Möller E, LaGreca S, Moya P, Wang X, Timdal E, de Boer H, Barreno E, Wang L, Thüs H, Andrésson Ó, Magnússon KP, Ólafsdóttir ES, Heiðmarsson S. Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland. MycoKeys 2023; 96:57-75. [PMID: 37252058 PMCID: PMC10210050 DOI: 10.3897/mycokeys.96.100037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/07/2023] [Indexed: 05/31/2023] Open
Abstract
The fungal mitochondrial small subunit (mtSSU) ribosomal DNA is one of the most commonly used loci for phylogenetic analysis of lichen-forming fungi, but their primer specificity to mycobionts has not been evaluated. The current study aimed to design mycobiont-specific mtSSU primers and highlights their utility with an example from the saxicolous lichen-forming fungal genus Melanelia Essl. in Iceland. The study found a 12.5% success rate (3 out of 24 specimens with good-quality mycobiont mtSSU sequences) using universal primers (i.e. mrSSU1 and mrSSU3R), not including off-target amplification of environmental fungi, e.g. Cladophialophoracarrionii and Lichenotheliaconvexa. New mycobiont-specific primers (mt-SSU-581-5' and mt-SSU-1345-3') were designed by targeting mycobiont-specific nucleotide sites in comparison with environmental fungal sequences, and assessed for mycobiont primer specificity using in silico PCR. The new mycobiont-specific mtSSU primers had a success rate of 91.7% (22 out of 24 specimens with good-quality mycobiont mtSSU sequences) on the studied Melanelia specimens. Additional testing confirmed the specificity and yielded amplicons from 79 specimens of other Parmeliaceae mycobiont lineages. This study highlights the effectiveness of designing mycobiont-specific primers for studies on lichen identification, barcoding and phylogenetics.
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Affiliation(s)
- Maonian Xu
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, IS-107 Reykjavik, Iceland
| | - Yingkui Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, College of Life Sciences, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China
| | - Erik Möller
- Natural History Museum, University of Oslo, NO-0318 Oslo, Norway
| | - Scott LaGreca
- Department of Biology, Duke University, NC 27708-0338 Durham, USA
| | - Patricia Moya
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva (ICBIBE), Dpto. Botánica, Facultat de Ciències Biològiques, Universitat de València, C/ Dr. Moliner 50, 46100-Burjassot, València, Spain
| | - Xinyu Wang
- Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Einar Timdal
- Natural History Museum, University of Oslo, NO-0318 Oslo, Norway
| | - Hugo de Boer
- Natural History Museum, University of Oslo, NO-0318 Oslo, Norway
| | - Eva Barreno
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva (ICBIBE), Dpto. Botánica, Facultat de Ciències Biològiques, Universitat de València, C/ Dr. Moliner 50, 46100-Burjassot, València, Spain
| | - Lisong Wang
- Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Holger Thüs
- Botany Department, State Museum of Natural History Stuttgart, D-70191 Stuttgart, Germany
| | - Ólafur Andrésson
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, IS-107 Reykjavik, Iceland
| | - Kristinn Pétur Magnússon
- Faculty of Life and Environmental Sciences, University of Iceland, IS-102 Reykjavik, Iceland
- Faculty of Natural Resource Sciences, University of Akureyri, IS-600 Akureyri, Iceland
| | - Elín Soffia Ólafsdóttir
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, IS-107 Reykjavik, Iceland
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7
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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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Valim HF, Dal Grande F, Otte J, Singh G, Merges D, Schmitt I. Identification and expression of functionally conserved circadian clock genes in lichen-forming fungi. Sci Rep 2022; 12:15884. [PMID: 36151124 PMCID: PMC9508176 DOI: 10.1038/s41598-022-19646-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Lichen-forming fungi establish stable symbioses with green algae or cyanobacteria. Many species have broad distributions, both in geographic and ecological space, making them ideal subjects to study organism-environment interactions. However, little is known about the specific mechanisms that contribute to environmental adaptation in lichen-forming fungi. The circadian clock provides a well-described mechanism that contributes to regional adaptation across a variety of species, including fungi. Here, we identify the putative circadian clock components in phylogenetically divergent lichen-forming fungi. The core circadian genes (frq, wc-1, wc-2, frh) are present across the Fungi, including 31 lichen-forming species, and their evolutionary trajectories mirror overall fungal evolution. Comparative analyses of the clock genes indicate conserved domain architecture among lichen- and non-lichen-forming taxa. We used RT-qPCR to examine the core circadian loop of two unrelated lichen-forming fungi, Umbilicaria pustulata (Lecanoromycetes) and Dermatocarpon miniatum (Eurotiomycetes), to determine that the putative frq gene is activated in a light-dependent manner similar to the model fungus Neurospora crassa. Together, these results demonstrate that lichen-forming fungi retain functional light-responsive mechanisms, including a functioning circadian clock. Our findings provide a stepping stone into investigating the circadian clock in the lichen symbiosis, e.g. its role in adaptation, and in synchronizing the symbiotic interaction.
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Affiliation(s)
- Henrique F Valim
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Biology, University of Padua, Via U. Bassi 58/B, Padua, Italy
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Garima Singh
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Biology, University of Padua, Via U. Bassi 58/B, Padua, Italy
| | - Dominik Merges
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7070, 750 07, Uppsala, Sweden
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany.
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9
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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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10
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Srimani S, Schmidt CX, Gómez-Serranillos MP, Oster H, Divakar PK. Modulation of Cellular Circadian Rhythms by Secondary Metabolites of Lichens. Front Cell Neurosci 2022; 16:907308. [PMID: 35813500 PMCID: PMC9260025 DOI: 10.3389/fncel.2022.907308] [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: 04/08/2022] [Accepted: 05/20/2022] [Indexed: 12/14/2022] Open
Abstract
Background Most mammalian cells harbor molecular circadian clocks that synchronize physiological functions with the 24-h day-night cycle. Disruption of circadian rhythms, through genetic or environmental changes, promotes the development of disorders like obesity, cardiovascular diseases, and cancer. At the cellular level, circadian, mitotic, and redox cycles are functionally coupled. Evernic (EA) and usnic acid (UA), two lichen secondary metabolites, show various pharmacological activities including anti-oxidative, anti-inflammatory, and neuroprotective action. All these effects have likewise been associated with a functional circadian clock. Hypothesis/Purpose To test, if the lichen compounds EA and UA modulate circadian clock function at the cellular level. Methods We used three different cell lines and two circadian luminescence reporter systems for evaluating dose- and time-dependent effects of EA/UA treatment on cellular clock regulation at high temporal resolution. Output parameters studied were circadian luminescence rhythm period, amplitude, phase, and dampening rate. Results Both compounds had marked effects on clock rhythm amplitudes and dampening independent of cell type, with UA generally showing a higher efficiency than EA. Only in fibroblast cells, significant effects on clock period were observed for UA treated cells showing shorter and EA treated cells showing longer period lengths. Transient treatment of mouse embryonic fibroblasts at different phases had only minor clock resetting effects for both compounds. Conclusion Secondary metabolites of lichen alter cellular circadian clocks through amplitude reduction and increased rhythm dampening.
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Affiliation(s)
- Soumi Srimani
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Cosima Xenia Schmidt
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Maria Pilar Gómez-Serranillos
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Henrik Oster
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Pradeep K. Divakar
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
- *Correspondence: Pradeep K. Divakar
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De Carolis R, Cometto A, Moya P, Barreno E, Grube M, Tretiach M, Leavitt SD, Muggia L. Photobiont Diversity in Lichen Symbioses From Extreme Environments. Front Microbiol 2022; 13:809804. [PMID: 35422771 PMCID: PMC9002315 DOI: 10.3389/fmicb.2022.809804] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/27/2022] [Indexed: 11/19/2022] Open
Abstract
Fungal–algal relationships—both across evolutionary and ecological scales—are finely modulated by the presence of the symbionts in the environments and by the degree of selectivity and specificity that either symbiont develop reciprocally. In lichens, the green algal genus Trebouxia Puymaly is one of the most frequently recovered chlorobionts. Trebouxia species-level lineages have been recognized on the basis of their morphological and phylogenetic diversity, while their ecological preferences and distribution are still only partially unknown. We selected two cosmopolitan species complexes of lichen-forming fungi as reference models, i.e., Rhizoplaca melanophthalma and Tephromela atra, to investigate the diversity of their associated Trebouxia spp. in montane habitats across their distributional range worldwide. The greatest diversity of Trebouxia species-level lineages was recovered in the altitudinal range 1,000–2,500 m a.s.l. A total of 10 distinct Trebouxia species-level lineages were found to associate with either mycobiont, for which new photobionts are reported. One previously unrecognized Trebouxia species-level lineage was identified and is here provisionally named Trebouxia “A52.” Analyses of cell morphology and ultrastructure were performed on axenically isolated strains to fully characterize the new Trebouxia “A52” and three other previously recognized lineages, i.e., Trebouxia “A02,” T. vagua “A04,” and T. vagua “A10,” which were successfully isolated in culture during this study. The species-level diversity of Trebouxia associating with the two lichen-forming fungi in extreme habitats helps elucidate the evolutionary pathways that this lichen photobiont genus traversed to occupy varied climatic and vegetative regimes.
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Affiliation(s)
| | - Agnese Cometto
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Patricia Moya
- Botánica, ICBIBE, Faculty of CC. Biológicas, Universitat de València, Valencia, Spain
| | - Eva Barreno
- Botánica, ICBIBE, Faculty of CC. Biológicas, Universitat de València, Valencia, Spain
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Mauro Tretiach
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Steven D Leavitt
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
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12
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Yeasts Inhabiting Extreme Environments and Their Biotechnological Applications. Microorganisms 2022; 10:microorganisms10040794. [PMID: 35456844 PMCID: PMC9028089 DOI: 10.3390/microorganisms10040794] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
Yeasts are microscopic fungi inhabiting all Earth environments, including those inhospitable for most life forms, considered extreme environments. According to their habitats, yeasts could be extremotolerant or extremophiles. Some are polyextremophiles, depending on their growth capacity, tolerance, and survival in the face of their habitat’s physical and chemical constitution. The extreme yeasts are relevant for the industrial production of value-added compounds, such as biofuels, lipids, carotenoids, recombinant proteins, enzymes, among others. This review calls attention to the importance of yeasts inhabiting extreme environments, including metabolic and adaptive aspects to tolerate conditions of cold, heat, water availability, pH, salinity, osmolarity, UV radiation, and metal toxicity, which are relevant for biotechnological applications. We explore the habitats of extreme yeasts, highlighting key species, physiology, adaptations, and molecular identification. Finally, we summarize several findings related to the industrially-important extremophilic yeasts and describe current trends in biotechnological applications that will impact the bioeconomy.
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13
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14
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Vančurová L, Malíček J, Steinová J, Škaloud P. Choosing the Right Life Partner: Ecological Drivers of Lichen Symbiosis. Front Microbiol 2022; 12:769304. [PMID: 34970234 PMCID: PMC8712729 DOI: 10.3389/fmicb.2021.769304] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 11/24/2022] Open
Abstract
Lichens are an iconic example of symbiotic systems whose ecology is shaped by the requirements of the symbionts. Previous studies suggest that fungal (mycobionts) as well as photosynthesizing (phycobionts or cyanobionts) partners have a specific range of acceptable symbionts that can be chosen according to specific environmental conditions. This study aimed to investigate the effects of climatic conditions and mycobiont identity on phycobiont distribution within the lichen genera Stereocaulon, Cladonia, and Lepraria. The study area comprised the Canary Islands, Madeira, Sicily, and the Aeolian Islands, spanning a wide range of climatic conditions. These islands are known for their unique and diverse fauna and flora; however, lichen phycobionts have remained unstudied in most of these areas. In total, we genetically analyzed 339 lichen samples. The phycobiont pool differed significantly from that outside the studied area. Asterochloris mediterranea was identified as the most abundant phycobiont. However, its distribution was limited by climatic constraints. Other species of Asterochloris and representatives of the genera Chloroidium, Vulcanochloris, and Myrmecia were also recovered as phycobionts. The selection of symbiotic partners from the local phycobiont pool was driven by mycobiont specificity (i.e., the taxonomic range of acceptable partners) and the environmental conditions, mainly temperature. Interestingly, the dominant fungal species responded differently in their selection of algal symbionts along the environmental gradients. Cladonia rangiformis associated with its phycobiont A. mediterranea in a broader range of temperatures than Stereocaulon azoreum, which favors other Asterochloris species along most of the temperature gradient. Stereocaulon vesuvianum associated with Chloroidium spp., which also differed in their temperature optima. Finally, we described Stereocaulon canariense as a new endemic species ecologically distinct from the other Stereocaulon species on the Canary Islands.
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Affiliation(s)
- Lucie Vančurová
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Jiří Malíček
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Jana Steinová
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
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15
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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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16
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Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01706-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.
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17
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Shishido TK, Wahlsten M, Laine P, Rikkinen J, Lundell T, Auvinen P. Microbial Communities of Cladonia Lichens and Their Biosynthetic Gene Clusters Potentially Encoding Natural Products. Microorganisms 2021; 9:1347. [PMID: 34206222 PMCID: PMC8304397 DOI: 10.3390/microorganisms9071347] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 01/04/2023] Open
Abstract
Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies.
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Affiliation(s)
- Tânia Keiko Shishido
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (P.L.); (P.A.)
| | - Matti Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (M.W.); (T.L.)
| | - Pia Laine
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (P.L.); (P.A.)
| | - Jouko Rikkinen
- Finnish Museum of Natural History, Botany Unit, University of Helsinki, P.O. Box 7, 00014 Helsinki, Finland;
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (M.W.); (T.L.)
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (P.L.); (P.A.)
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18
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Molins A, Moya P, Muggia L, Barreno E. Thallus Growth Stage and Geographic Origin Shape Microalgal Diversity in Ramalina farinacea Lichen Holobionts. JOURNAL OF PHYCOLOGY 2021; 57:975-987. [PMID: 33528835 DOI: 10.1111/jpy.13140] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 05/26/2023]
Abstract
Lichen symbioses are microecosystems hosting many other living organisms besides the two major lichen symbionts (i.e., lichenized fungi [the mycobiont] and green microalgae or cyanobacteria [the photobiont]). Recent investigations evidenced that other fungi, non-photosynthetic bacteria, and microalgae co-inhabit within the lichen thalli, but their diversity and their roles are still underinvestigated. Here we present an ad hoc stratified sampling design and in-depth Illumina paired-end metabarcoding approach to explore microalgal diversity in lichen thalli of the model species Ramalina farinacea from different ecologies. Lichen thalli were surveyed according to three different sizes, and different thallus parts were considered for molecular, bioinformatics, and community diversity analyses. The results revealed that microalgal diversity strongly depends on the growth stage of the thalli, the geographic area, and the habitat type. The results also show that microalgal diversity does not vary along the thallus branches (lacinias)-that is, it does not correlate with the apical growth and founder effects-and that there is no balanced co-presence of two main photobionts as previously established in R. farinacea. The sampling design performed here minimizes bias in the assessment of photobiont diversity in lichens and is proposed to be reliable and applicable to further study microalgal diversity in lichen symbioses.
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Affiliation(s)
- Arantzazu Molins
- Instituto "Cavanilles" de Biodiversidad y Biología Evolutiva, Botánica, Fac. CC. Biológicas, Universitat de València, 46100, Burjassot, Valencia, Spain
| | - Patricia Moya
- Instituto "Cavanilles" de Biodiversidad y Biología Evolutiva, Botánica, Fac. CC. Biológicas, Universitat de València, 46100, Burjassot, Valencia, Spain
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via L. Giorgieri 10, 34127, Trieste, Italy
| | - Eva Barreno
- Instituto "Cavanilles" de Biodiversidad y Biología Evolutiva, Botánica, Fac. CC. Biológicas, Universitat de València, 46100, Burjassot, Valencia, Spain
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19
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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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