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Strullu-Derrien C, Goral T, Spencer ART, Kenrick P, Catherine Aime M, Gaya E, Hawksworth DL. A fungal plant pathogen discovered in the Devonian Rhynie Chert. Nat Commun 2023; 14:7932. [PMID: 38040707 PMCID: PMC10692235 DOI: 10.1038/s41467-023-43276-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023] Open
Abstract
Fungi are integral to well-functioning ecosystems, and their broader impact on Earth systems is widely acknowledged. Fossil evidence from the Rhynie Chert (Scotland, UK) shows that Fungi were already diverse in terrestrial ecosystems over 407-million-years-ago, yet evidence for the occurrence of Dikarya (the subkingdom of Fungi that includes the phyla Ascomycota and Basidiomycota) in this site is scant. Here we describe a particularly well-preserved asexual fungus from the Rhynie Chert which we examined using brightfield and confocal microscopy. We document Potteromyces asteroxylicola gen. et sp. nov. that we attribute to Ascomycota incertae sedis (Dikarya). The fungus forms a stroma-like structure with conidiophores arising in tufts outside the cuticle on aerial axes and leaf-like appendages of the lycopsid plant Asteroxylon mackiei. It causes a reaction in the plant that gives rise to dome-shaped surface projections. This suite of features in the fungus together with the plant reaction tissues provides evidence of it being a plant pathogenic fungus. The fungus evidently belongs to an extinct lineage of ascomycetes that could serve as a minimum node age calibration point for the Ascomycota as a whole, or even the Dikarya crown group, along with some other Ascomycota previously documented in the Rhynie Chert.
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Affiliation(s)
- Christine Strullu-Derrien
- Science Group, The Natural History Museum, London, UK.
- Institut Systématique Évolution Biodiversité (UMR 7205), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, Paris, France.
| | - Tomasz Goral
- Imaging and Analysis Centre, The Natural History Museum, London, UK
- Center of New Technologies, University of Warsaw, Warsaw, Poland
| | - Alan R T Spencer
- Science Group, The Natural History Museum, London, UK
- Department of Earth Science & Engineering, Imperial College London, London, UK
| | - Paul Kenrick
- Science Group, The Natural History Museum, London, UK
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Ester Gaya
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - David L Hawksworth
- Science Group, The Natural History Museum, London, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
- Jilin Agricultural University, Changchun, 130118, Jilin Province, China
- Geography and Environmental Science, University of Southampton, Southampton, UK
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Worobiec G, Worobiec E, Gedl P, Kowalski R, Peryt D, Tietz O. Fossil history of fungus host-specificity: Association of conidia of fossil Asterosporium asterospermum with macro- and microremains of Fagus. Fungal Biol 2023; 127:1312-1320. [PMID: 37821153 DOI: 10.1016/j.funbio.2023.07.005] [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: 05/11/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 10/13/2023]
Abstract
Fossil staurosporous conidia almost identical to modern conidia of Asterosporium asterospermum were found from three Central European localities ranging from the Late Oligocene (Germany) to Middle/Late Miocene (Poland). Extant A. asterospermum is strictly host-specific and found only on branches or bark of various Fagus species from Europe, Asia and North America. Conspicuous association of conidia of A. asterospermum with numerous macro- and microremains of Fagus were reported from all the localities where fossil conidia of Asterosporium were found confirming the host-specificity of fossil A. asterospermum to ancient beeches. The host-specific relationship of A. asterospermum and beech was presumably established early in the history of the Fagus genus.
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Affiliation(s)
- Grzegorz Worobiec
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland.
| | - Elżbieta Worobiec
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Przemysław Gedl
- Institute of Geological Sciences, Polish Academy of Sciences, Research Centre in Cracow, Senacka 1, 31-002 Kraków, Poland
| | - Rafał Kowalski
- Museum of the Earth in Warsaw, Polish Academy of Sciences, Al. Na Skarpie 27, 00-488 Warszawa, Poland
| | - Danuta Peryt
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00-818 Warszawa, Poland
| | - Olaf Tietz
- Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826 Görlitz, Germany
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Case NT, Song M, Fulford AH, Graham HV, Orphan VJ, Stajich JE, Casadevall A, Mustard J, Heitman J, Lollar BS, Cowen LE. Exploring Space via Astromycology: A Report on the CIFAR Programs Earth 4D and Fungal Kingdom Inaugural Joint Meeting. ASTROBIOLOGY 2022; 22:637-640. [PMID: 35196462 PMCID: PMC9233531 DOI: 10.1089/ast.2021.0186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/22/2022] [Indexed: 06/03/2023]
Abstract
"Fungi on Mars!": a popular news heading that piques public interest and makes scientists' blood boil. While such a statement is laden with misinformation and light on evidence, the search for past and present extraterrestrial life is an ongoing scientific effort. Moreover, it is one that is increasingly gaining momentum with the recent collection of martian rock cores from Jezero Crater by NASA's Perseverance rover. Despite the increasingly sophisticated approaches guiding the search for microbial life on other planets, fungi remain relatively underexplored compared to their bacterial counterparts, highlighting a gap between the astrobiological and fungal research communities. Through a meeting in April 2021, the CIFAR Earth 4D and Fungal Kingdom research programs worked to bridge this divide by uniting experts in each field. CIFAR is a Canadian-based global research organization that convenes researchers across disciplines to address important questions facing science and humanity. The CIFAR Earth 4D: Subsurface Science & Exploration and Fungal Kingdom: Threats & Opportunities research programs were launched by CIFAR in July 2019, each made up of approximately two dozen international researchers who are experts in their fields. The Earth 4D program, led by co-directors John Mustard (Brown University, USA) and Barbara Sherwood Lollar (University of Toronto, Canada), aims to understand the complex chemical, physical, and biological interactions that occur within and between Earth's surface and subsurface to explore questions on the evolution of planets and life. The Fungal Kingdom program, led by co-directors Leah Cowen (University of Toronto, Canada) and Joseph Heitman (Duke University, USA), seeks to tackle the most pressing threats fungi pose to human health, agriculture, and biodiversity and to harness their extraordinary potential. The programs met to explore areas for synergy within four major themes: (1) the origins of life; (2) the evolution and diversification of life; (3) life in diverse and extreme environments; and (4) extinction: lessons learned and threats. This report covers the research discussed during the meeting across these four themes.
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Affiliation(s)
- Nicola T. Case
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Min Song
- Department of Earth Sciences, University of Toronto, Toronto, Canada
| | | | - Heather V. Graham
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Department of Physics, Catholic University of America, Washington, DC, USA
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - John Mustard
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, Rhode Island, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Strullu-Derrien C, Philippe M, Kenrick P, Blanchette RA. Blue stain fungi infecting an 84-million-year-old conifer from South Africa. THE NEW PHYTOLOGIST 2022; 233:1032-1037. [PMID: 34743346 DOI: 10.1111/nph.17843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Christine Strullu-Derrien
- Institut Systématique Evolution Biodiversité, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, 75005, Paris, France
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Marc Philippe
- CNRS, ENTPE, UMR 5023 LEHNA, Univ Lyon, Université Claude Bernard Lyon 1, F-69622, Villeurbanne, France
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Robert A Blanchette
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55126, USA
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Aghdam SA, Brown AMV. Deep learning approaches for natural product discovery from plant endophytic microbiomes. ENVIRONMENTAL MICROBIOME 2021; 16:6. [PMID: 33758794 PMCID: PMC7972023 DOI: 10.1186/s40793-021-00375-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/21/2021] [Indexed: 05/10/2023]
Abstract
Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely hidden through regulatory silencing of biosynthetic genes. The recent explosion of powerful interdisciplinary approaches, including multi-omics methods to address multi-trophic interactions and artificial intelligence-based computational approaches to infer distribution of function, together present a paradigm shift in high-throughput approaches to natural product discovery from plant-associated microbes. Arguably, the key to characterizing and harnessing this biochemical capacity depends on a novel, systematic approach to characterize the triggers that turn on secondary metabolite biosynthesis through molecular or genetic signals from the host plant, members of the rich 'in planta' community, or from the environment. This review explores breakthrough approaches for natural product discovery from plant microbiomes, emphasizing the promise of deep learning as a tool for endophyte bioprospecting, endophyte biochemical novelty prediction, and endophyte regulatory control. It concludes with a proposed pipeline to harness global databases (genomic, metabolomic, regulomic, and chemical) to uncover and unsilence desirable natural products. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s40793-021-00375-0.
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Affiliation(s)
- Shiva Abdollahi Aghdam
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
| | - Amanda May Vivian Brown
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
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Gan T, Luo T, Pang K, Zhou C, Zhou G, Wan B, Li G, Yi Q, Czaja AD, Xiao S. Cryptic terrestrial fungus-like fossils of the early Ediacaran Period. Nat Commun 2021; 12:641. [PMID: 33510166 PMCID: PMC7843733 DOI: 10.1038/s41467-021-20975-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
The colonization of land by fungi had a significant impact on the terrestrial ecosystem and biogeochemical cycles on Earth surface systems. Although fungi may have diverged ~1500-900 million years ago (Ma) or even as early as 2400 Ma, it is uncertain when fungi first colonized the land. Here we report pyritized fungus-like microfossils preserved in the basal Ediacaran Doushantuo Formation (~635 Ma) in South China. These micro-organisms colonized and were preserved in cryptic karstic cavities formed via meteoric water dissolution related to deglacial isostatic rebound after the terminal Cryogenian snowball Earth event. They are interpreted as eukaryotes and probable fungi, thus providing direct fossil evidence for the colonization of land by fungi and offering a key constraint on fungal terrestrialization.
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Affiliation(s)
- Tian Gan
- State Key Laboratory of Ore Deposit Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Taiyi Luo
- State Key Laboratory of Ore Deposit Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China.
| | - Ke Pang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Chuanming Zhou
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Guanghong Zhou
- School of Geography and Resources, Guizhou Education University, Guiyang, China
| | - Bin Wan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Gang Li
- Institute of High Energy Physics, CAS, Beijing, China
| | - Qiru Yi
- University of Chinese Academy of Sciences, Beijing, China
| | - Andrew D Czaja
- Department of Geology, University of Cincinnati, Cincinnati, OH, USA
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA.
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Harper CJ, Walker C, Schwendemann AB, Kerp H, Krings M. Archaeosporites rhyniensis gen. et sp. nov. (Glomeromycota, Archaeosporaceae) from the Lower Devonian Rhynie chert: a fungal lineage morphologically unchanged for more than 400 million years. ANNALS OF BOTANY 2020; 126:915-928. [PMID: 32577725 PMCID: PMC7539360 DOI: 10.1093/aob/mcaa113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS Structurally preserved arbuscular mycorrhizas from the Lower Devonian Rhynie chert represent core fossil evidence of the evolutionary history of mycorrhizal systems. Moreover, Rhynie chert fossils of glomeromycotan propagules suggest that this lineage of arbuscular fungi was morphologically diverse by the Early Devonian; however, only a small fraction of this diversity has been formally described and critically evaluated. METHODS Thin sections, previously prepared by grinding wafers of chert from the Rhynie beds, were studied by transmitted light microscopy. Fossils corresponding to the description of Archaeospora spp. occurred in 29 slides, and were measured, photographed and compared with modern-day species in that genus. KEY RESULTS Sessile propagules <85 µm in diameter, some still attached to a sporiferous saccule, were found in early land plant axes and the chert matrix; they developed, in a similar manner to extant Archaeospora, laterally or centrally within the saccule neck. Microscopic examination and comparison with extant fungi showed that, morphologically, the fossils share the characters used to circumscribe the genus Archaeospora (Glomeromycota; Archaeosporales; Archaeosporaceae). CONCLUSIONS The fossils can be assigned with confidence to the extant family Archaeosporaceae, but because molecular analysis is necessary to place organisms in these taxa to present-day genera and species, they are placed in a newly proposed fossil taxon, Archaeosporites rhyniensis.
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Affiliation(s)
- Carla J Harper
- Botany Department, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
- Department of Ecology and Evolutionary Biology, and Natural History Museum and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Christopher Walker
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- School of Agriculture and Environment, University of Western Australia, Crawley, WA, Australia
| | | | - Hans Kerp
- Forschungsstelle für Paläobotanik am Geologisch-Paläontologischen Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Michael Krings
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
- Department of Ecology and Evolutionary Biology, and Natural History Museum and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
- Department für Geo- und Umweltwissenschaften, Paläontologie und Geobiologie, Ludwig-Maximilians-Universität, Munich, Germany
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Genomic and fossil windows into the secret lives of the most ancient fungi. Nat Rev Microbiol 2020; 18:717-730. [PMID: 32908302 DOI: 10.1038/s41579-020-0426-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2020] [Indexed: 12/26/2022]
Abstract
Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi.
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Strullu-Derrien C. Fossil filamentous microorganisms associated with plants in early terrestrial environments. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:122-128. [PMID: 29684703 DOI: 10.1016/j.pbi.2018.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 05/16/2023]
Abstract
Microorganisms are ubiquitous in modern environments, where they have a variety of essential functions but little is known about their diversity and roles in early terrestrial environments. The earliest direct evidence of filamentous microorganisms associated with plants occurs around 407 million years ago in landscapes dominated by an herbaceous flora. 100 million years later, forests were well established and associations had increased in diversity. After more than a century since the first descriptions, the need for better understood fossils has renewed interest in their study. New discoveries and advances in imaging methods are beginning to reveal the importance of Cyanobacteria, Fungi and Oomycota and their interactions with plants in early floras.
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Edwards D, Kenrick P, Dolan L. History and contemporary significance of the Rhynie cherts-our earliest preserved terrestrial ecosystem. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2016.0489. [PMID: 29254954 DOI: 10.1098/rstb.2016.0489] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2017] [Indexed: 01/03/2023] Open
Abstract
The Rhynie cherts Unit is a 407 million-year old geological site in Scotland that preserves the most ancient known land plant ecosystem, including associated animals, fungi, algae and bacteria. The quality of preservation is astonishing, and the initial description of several plants 100 years ago had a huge impact on botany. Subsequent discoveries provided unparalleled insights into early life on land. These include the earliest records of plant life cycles and fungal symbioses, the nature of soil microorganisms and the diversity of arthropods. Today the Rhynie chert (here including the Rhynie and Windyfield cherts) takes on new relevance, especially in relation to advances in the fields of developmental genetics and Earth systems science. New methods and analytical techniques also contribute to a better understanding of the environment and its organisms. Key discoveries are reviewed, focusing on the geology of the site, the organisms and the palaeoenvironments. The plants and their symbionts are of particular relevance to understanding the early evolution of the plant life cycle and the origins of fundamental organs and tissue systems. The Rhynie chert provides remarkable insights into the structure and interactions of early terrestrial communities, and it has a significant role to play in developing our understanding of their broader impact on Earth systems.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- Dianne Edwards
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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