1
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Anderson RP, Mughal S, Wedlake GO. Proterozoic microfossils continue to provide new insights into the rise of complex eukaryotic life. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240154. [PMID: 39170929 PMCID: PMC11336685 DOI: 10.1098/rsos.240154] [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: 01/26/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 08/23/2024]
Abstract
Eukaryotes have evolved to dominate the biosphere today, accounting for most documented living species and the vast majority of the Earth's biomass. Consequently, understanding how these biologically complex organisms initially diversified in the Proterozoic Eon over 539 million years ago is a foundational question in evolutionary biology. Over the last 70 years, palaeontologists have sought to document the rise of eukaryotes with fossil evidence. However, the delicate and microscopic nature of their sub-cellular features affords early eukaryotes diminished preservation potential. Chemical biomarker signatures of eukaryotes and the genetics of living eukaryotes have emerged as complementary tools for reconstructing eukaryote ancestry. In this review, we argue that exceptionally preserved Proterozoic microfossils are critical to interpreting these complementary tools, providing crucial calibrations to molecular clocks and testing hypotheses of palaeoecology. We highlight recent research on their preservation and biomolecular composition that offers new ways to enhance their utility.
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Affiliation(s)
- Ross P. Anderson
- Museum of Natural History, University of Oxford, OxfordOX1 3PW, UK
- All Souls College, University of Oxford, OxfordOX1 4AL, UK
| | - Sanaa Mughal
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AlbertaT6G 2E3, Canada
| | - George O. Wedlake
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
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2
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Baluška F, Miller WB, Reber AS. Sentient cells as basic units of tissues, organs and organismal physiology. J Physiol 2024; 602:2491-2501. [PMID: 37847422 DOI: 10.1113/jp284419] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
Cells evolved some 4 billion years ago, and since then the integrity of the structural and functional continuity of cellular life has been maintained via highly conserved and ancient processes of cell reproduction and division. The plasma membrane as well as all the cytoplasmic structures are reproduced and inherited uninterruptedly by each of the two daughter cells resulting from every cell division. Although our understanding of the evolutionary emergence of the very first cells is obscured by the extremely long timeline since that revolutionary event, the generally accepted position is that the de novo formation of cells is not possible; all present cells are products of other prior cells. This essential biological principle was first discovered by Robert Remak and then effectively coined as Omnis Cellula e Cellula (every cell of the cell) by Rudolf Virchow: all currently living cells have direct structural and functional connections to the very first cells. Based on our previous theoretical analysis, all cells are endowed with individual sentient cognition that guides their individual agency, behaviour and evolution. There is a vital consequence of this new sentient and cognitive view of cells: when cells assemble as functional tissue ecologies and organs within multicellular organisms, including plants, animals and humans, these cellular aggregates display derivative versions of aggregate tissue- and organ-specific sentience and consciousness. This innovative view of the evolution and physiology of all currently living organisms supports a singular principle: all organismal physiology is based on cellular physiology that extends from unicellular roots.
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Affiliation(s)
- František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - William B Miller
- Banner Health Systems - Medicine, Paradise Valley, Phoneix, Arizona, USA
| | - Arthur S Reber
- Department of Psychology, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Kliska N, Nehaniv CL. Autocatalysis, Autopoiesis, and the Opportunity Cost of Individuality. Biomimetics (Basel) 2024; 9:328. [PMID: 38921211 PMCID: PMC11201707 DOI: 10.3390/biomimetics9060328] [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: 04/11/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Ever since Varela and Maturana proposed the concept of autopoiesis as the minimal requirement for life, there has been a focus on cellular systems that erect topological boundaries to separate themselves from their surrounding environment. Here, we reconsider whether the existence of such a spatial boundary is strictly necessary for self-producing entities. This work presents a novel computational model of a minimal autopoietic system inspired by dendrites and molecular dynamic simulations in three-dimensional space. A series of simulation experiments where the metabolic pathways of a particular autocatalytic set are successively inhibited until autocatalytic entities that could be considered autopoietic are produced. These entities maintain their distinctness in an environment containing multiple identical instances of the entities without the existence of a topological boundary. This gives rise to the concept of a metabolic boundary which manifests as emergent self-selection criteria for the processes of self-production without any need for unique identifiers. However, the adoption of such a boundary comes at a cost, as these autopoietic entities are less suited to their simulated environment than their autocatalytic counterparts. Finally, this work showcases a generalized metabolism-centered approach to the study of autopoiesis that can be applied to both physical and abstract systems alike.
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Affiliation(s)
- Nemanja Kliska
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Chrystopher L. Nehaniv
- Departments of Systems Design Engineering and of Electrical & Computer Engineering, Waterloo Institute for Complexity and Innovation, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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4
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Barlow EV, House CH, Liu MC, Wetherington MT, Van Kranendonk MJ. Distinctive microfossil supports early Paleoproterozoic rise in complex cellular organisation. GEOBIOLOGY 2024; 22:e12576. [PMID: 37803496 DOI: 10.1111/gbi.12576] [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: 12/23/2022] [Revised: 08/14/2023] [Accepted: 09/07/2023] [Indexed: 10/08/2023]
Abstract
The great oxidation event (GOE), ~2.4 billion years ago, caused fundamental changes to the chemistry of Earth's surface environments. However, the effect of these changes on the biosphere is unknown, due to a worldwide lack of well-preserved fossils from this time. Here, we investigate exceptionally preserved, large spherical aggregate (SA) microfossils permineralised in chert from the c. 2.4 Ga Turee Creek Group in Western Australia. Field and petrographic observations, Raman spectroscopic mapping, and in situ carbon isotopic analyses uncover insights into the morphology, habitat, reproduction and metabolism of this unusual form, whose distinctive, SA morphology has no known counterpart in the fossil record. Comparative analysis with microfossils from before the GOE reveals the large SA microfossils represent a step-up in cellular organisation. Morphological comparison to extant micro-organisms indicates the SAs have more in common with coenobial algae than coccoidal bacteria, emphasising the complexity of this microfossil form. The remarkable preservation here provides a unique window into the biosphere, revealing an increase in the complexity of life coinciding with the GOE.
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Affiliation(s)
- Erica V Barlow
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Australian Research Council Centre of Excellence for Core to Crust Fluid Systems (CCFS), Macquarie University, Sydney, New South Wales, Australia
- Department of Geosciences and the Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Christopher H House
- Department of Geosciences and the Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ming-Chang Liu
- Department of Earth, Planetary, and Space Sciences, University of California at Los Angeles, Los Angeles, California, USA
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Maxwell T Wetherington
- Materials Research Institute and Department of Materials Science & Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Australian Research Council Centre of Excellence for Core to Crust Fluid Systems (CCFS), Macquarie University, Sydney, New South Wales, Australia
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5
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Del Mouro L, Becker-Kerber B, Janasi VA, de Araújo Carvalho M, Waichel BL, Lima EF, Rossetti LMM, Cruz V, Silva MS, Famelli N, Ortega-Hernández J. Organic walled microfossils in wet peperites from the early Cretaceous Paraná-Etendeka volcanism of Brazil. Sci Rep 2023; 13:15362. [PMID: 37717103 PMCID: PMC10505181 DOI: 10.1038/s41598-023-42483-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023] Open
Abstract
Large igneous provinces (LIPs) are major magmatic events that have a significant impact on the global environment and the biosphere, for example as triggers of mass extinctions. LIPs provide an excellent sedimentological and geochemical record of short but intense periods of geological activity in the past, but their contribution towards understanding ancient life is much more restricted due to the destructive nature of their igneous origin. Here, we provide the first paleontological evidence for organic walled microfossils extracted from wet peperites from the Early Cretaceous Paraná-Etendeka intertrappean deposits of the Paraná basin in Brazil. Wet peperites are a volcaniclastic rock formed by the interaction of lava and subaqueous sediments.The Paraná-Etendeka was formed during the Valanginian (ca. 132 Ma) as a continental flood basalt in present day South America and Namibia, and released enormous amounts of carbon dioxide, sulfur dioxide, methane and hydrogen fluoride into the atmosphere. The organic walled microfossils recovered from the Paraná-Etendeka peperites include pollen grains, spores, acritarchs, and other remains of unidentifiable organic matter. In addition to the peperites, organic walled microfossils were also found in heterolithic sandstones and interpillow sandstones. Our findings represent the first insight into the biodiversity of the Paraná Basin during the Early Cretaceous during a period of intense magmatism, and the microfossil assemblages corroborate a regional paleoclimatic transition from arid to more humid conditions that were likely induced by the volcanic activity. We corroborate the potential of wet peperite rocks as a valuable source of paleobiological data and emphasize the importance of sampling volcaniclastic units that have been traditionally considered with lower fossiliferous potential due to their igneous origin.
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Affiliation(s)
- Lucas Del Mouro
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
- Institute of Geosciences, University of São Paulo, São Paulo, Brazil.
| | | | - Valdecir A Janasi
- Institute of Geosciences, University of São Paulo, São Paulo, Brazil
| | | | - Breno L Waichel
- Espepetro, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Evandro F Lima
- Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | | | - Vinicius Cruz
- CODES - Centre for Ore Deposits and Earth Sciences, University of Tasmania, Hobart, 7001, Australia
| | | | - Natália Famelli
- Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Mello - CENPES/PETROBRAS, Rio de Janeiro, Brazil
| | - Javier Ortega-Hernández
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
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Hidalgo-Arias A, Muñoz-Hisado V, Valles P, Geyer A, Garcia-Lopez E, Cid C. Adaptation of the Endolithic Biome in Antarctic Volcanic Rocks. Int J Mol Sci 2023; 24:13824. [PMID: 37762127 PMCID: PMC10530270 DOI: 10.3390/ijms241813824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Endolithic microorganisms, ranging from microeukaryotes to bacteria and archaea, live within the cracks and crevices of rocks. Deception Island in Antarctica constitutes an extreme environment in which endoliths face environmental threats such as intense cold, lack of light in winter, high solar radiation in summer, and heat emitted as the result of volcanic eruptions. In addition, the endolithic biome is considered the harshest one on Earth, since it suffers added threats such as dryness or lack of nutrients. Even so, samples from this hostile environment, collected at various points throughout the island, hosted diverse and numerous microorganisms such as bacteria, fungi, diatoms, ciliates, flagellates and unicellular algae. These endoliths were first identified by Scanning Electron Microscopy (SEM). To understand the molecular mechanisms of adaptation of these endoliths to their environment, genomics techniques were used, and prokaryotic and eukaryotic microorganisms were identified by metabarcoding, sequencing the V3-V4 and V4-V5 regions of the 16S and 18S rRNA genes, respectively. Subsequently, the sequences were analyzed by bioinformatic methods that allow their metabolism to be deduced from the taxonomy. The results obtained concluded that some of these microorganisms have activated the biosynthesis routes of pigments such as prodigiosin or flavonoids. These adaptation studies also revealed that microorganisms defend themselves against environmental toxins by activating metabolic pathways for the degradation of compounds such as ethylbenzene, xylene and dioxins and for the biosynthesis of antioxidant molecules such as glutathione. Finally, these Antarctic endolithic microorganisms are of great interest in astrobiology since endolithic settings are environmentally analogous to the primitive Earth or the surfaces of extraterrestrial bodies.
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Affiliation(s)
- Andrea Hidalgo-Arias
- Center for Astrobiology (CAB), CSIC-INTA, Torrejón de Ardoz, 28850 Madrid, Spain; (A.H.-A.); (V.M.-H.); (E.G.-L.)
| | - Víctor Muñoz-Hisado
- Center for Astrobiology (CAB), CSIC-INTA, Torrejón de Ardoz, 28850 Madrid, Spain; (A.H.-A.); (V.M.-H.); (E.G.-L.)
| | - Pilar Valles
- Materials and Structures Department, National Institute of Aerospace Technology (INTA), Torrejón de Ardoz, 28850 Madrid, Spain;
| | - Adelina Geyer
- Geosciences Barcelona (GEO3BCN), CSIC, Lluís Solé Sabarís s/n, 08028 Barcelona, Spain;
| | - Eva Garcia-Lopez
- Center for Astrobiology (CAB), CSIC-INTA, Torrejón de Ardoz, 28850 Madrid, Spain; (A.H.-A.); (V.M.-H.); (E.G.-L.)
| | - Cristina Cid
- Center for Astrobiology (CAB), CSIC-INTA, Torrejón de Ardoz, 28850 Madrid, Spain; (A.H.-A.); (V.M.-H.); (E.G.-L.)
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7
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Kinneberg VB, Lü DS, Peris D, Ravinet M, Skrede I. Introgression between highly divergent fungal sister species. J Evol Biol 2023; 36:1133-1149. [PMID: 37363874 DOI: 10.1111/jeb.14190] [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: 11/24/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA-BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations.
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Affiliation(s)
- Vilde Bruhn Kinneberg
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Evolution and Paleobiology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Dabao Sun Lü
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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8
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Hoque E, Fritscher J. Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment? Crit Rev Microbiol 2023:1-24. [PMID: 37452612 DOI: 10.1080/1040841x.2023.2224425] [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: 12/31/2021] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 07/18/2023]
Abstract
Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.
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Affiliation(s)
- Enamul Hoque
- Department of Biotechnology, University of Science and Technology, Foy's Lake, Chittagong, Bangladesh
- International Virtual Institute for Advanced Science and Technology (IVAST), Section Microbial Technology, Munich, Germany
- Department of Environmental Science, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Fritscher
- Department of Biotechnology, University of Science and Technology, Foy's Lake, Chittagong, Bangladesh
- International Virtual Institute for Advanced Science and Technology (IVAST), Section Microbial Technology, Munich, Germany
- Department of Environmental Science, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
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9
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Qu Y, Yin Z, Kustatscher E, Nützel A, Peckmann J, Vajda V, Ivarsson M. Traces of Ancient Life in Oceanic Basalt Preserved as Iron-Mineralized Ultrastructures: Implications for Detecting Extraterrestrial Biosignatures. ASTROBIOLOGY 2023; 23:769-785. [PMID: 37222732 DOI: 10.1089/ast.2022.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Benefiting from their adaptability to extreme environments, subsurface microorganisms have been discovered in sedimentary and igneous rock environments on Earth and have been advocated as candidates in the search for extraterrestrial life. In this article, we study iron-mineralized microstructures in calcite-filled veins within basaltic pillows of the late Ladinian Fernazza group (Middle Triassic, 239 Ma) in Italy. These microstructures represent diverse morphologies, including filaments, globules, nodules, and micro-digitate stromatolites, which are similar to extant iron-oxidizing bacterial communities. In situ analyses including Raman spectroscopy have been used to investigate the morphological, elemental, mineralogical, and bond-vibrational modes of the microstructures. According to the Raman spectral parameters, iron minerals preserve heterogeneous ultrastructures and crystallinities, coinciding with the morphologies and precursor microbial activities. The degree of crystallinity usually represents a microscale gradient decreasing toward previously existing microbial cells, revealing a decline of mineralization due to microbial activities. This study provides an analog of possible rock-dwelling subsurface life on Mars or icy moons and advocates Raman spectroscopy as an efficient tool for in situ analyses. We put forward the concept that ultrastructural characteristics of minerals described by Raman spectral parameters corresponding to microscale morphologies could be employed as carbon-lean biosignatures in future space missions.
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Affiliation(s)
- Yuangao Qu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Evelyn Kustatscher
- Museum of Nature South Tyrol, Bozen/Bolzano, Italy
- Department für Geo- und Umweltwissenschaften, Paläontologie und Geobiologie, Ludwig-Maximilians-Universität, München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geobiologie, München, Germany
| | - Alexander Nützel
- Department für Geo- und Umweltwissenschaften, Paläontologie und Geobiologie, Ludwig-Maximilians-Universität, München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geobiologie, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Jörn Peckmann
- Institute für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
| | - Vivi Vajda
- Department of Paleobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Magnus Ivarsson
- Department of Paleobiology, Swedish Museum of Natural History, Stockholm, Sweden
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10
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Luo M, Li Z, Su M, Gadd GM, Yin Z, Benton MJ, Pan Y, Zheng D, Zhao T, Li Z, Chen Y. Fungal-induced fossil biomineralization. Curr Biol 2023:S0960-9822(23)00548-1. [PMID: 37230078 DOI: 10.1016/j.cub.2023.04.067] [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: 01/25/2023] [Revised: 04/10/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023]
Abstract
Exceptional preservation of fossils has often been attributed to the actions of bacteria that aid in the preservation of soft tissues that normally decay rapidly. However, it is well known that fungi play a major role in organic matter decomposition, biogeochemical cycling of elements, and metal-mineral transformations in modern ecosystems. Although the fungal fossil record can be traced back over a billion years, there are only a few recorded examples of fungal roles in fossilization. In this research, we have carried out a detailed geobiological investigation on early Pleistocene hyena coprolites (fossilized dung) in an attempt to ascertain possible fungal involvement in their formation. Using an advanced microscopic and mineralogical approach, we found that numerous hydroxyapatite nanofibers (25-34 nm on average), interwoven to form spheroidal structures, constituted the matrix of the coprolites in addition to food remains. These structures were found to be extremely similar in texture and mineral composition to biominerals produced during laboratory culture of a common saprophytic and geoactive fungus, Aspergillus niger, in the presence of a solid source of calcium (Ca) and phosphorus (P). This observation, and our other data obtained, strongly suggests that fungal metabolism can provide a mechanism that can result in fossil biomineralization, and we hypothesize, therefore, that this may have contributed to the formation of well-preserved fossils (Lagerstätten) in the geological record. The characteristic polycrystalline nanofibers may also have served as a potential biosignature for fungal life in early Earth and extraterrestrial environments.
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Affiliation(s)
- Mao Luo
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Nanjing 211135, China.
| | - Zhen Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Mu Su
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK; State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, College of Chemical Engineering and Environment, China University of Petroleum, 18 Fuxue Road, Changping District, Beijing 102249, China.
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Michael J Benton
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
| | - Yanhong Pan
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Centre for Research and Education on Biological Evolution and Environment and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing 210093, China
| | - Daran Zheng
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Tao Zhao
- Institute of Palaeontology, Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming 650500, Yunnan, China
| | - Zibo Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing 210008, China
| | - Yuxuan Chen
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing 210008, China
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11
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Sobol MS, Hoshino T, Delgado V, Futagami T, Kadooka C, Inagaki F, Kiel Reese B. Genome characterization of two novel deep-sea sediment fungi, Penicillium pacificagyrus sp. nov. and Penicillium pacificasedimenti sp. nov., from South Pacific Gyre subseafloor sediments, highlights survivability. BMC Genomics 2023; 24:249. [PMID: 37165355 PMCID: PMC10173653 DOI: 10.1186/s12864-023-09320-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/18/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Marine deep subsurface sediments were once thought to be devoid of eukaryotic life, but advances in molecular technology have unlocked the presence and activity of well-known closely related terrestrial and marine fungi. Commonly detected fungi in deep marine sediment environments includes Penicillium, Aspergillus, Cladosporium, Fusarium, and Schizophyllum, which could have important implications in carbon and nitrogen cycling in this isolated environment. In order to determine the diversity and unknown metabolic capabilities of fungi in deep-sea sediments, their genomes need to be fully analyzed. In this study, two Penicillium species were isolated from South Pacific Gyre sediment enrichments during Integrated Ocean Drilling Program Expedition 329. The inner gyre has very limited productivity, organic carbon, and nutrients. RESULTS Here, we present high-quality genomes of two proposed novel Penicillium species using Illumina HiSeq and PacBio sequencing technologies. Single-copy homologues within the genomes were compared to other closely related genomes using OrthoMCL and maximum-likelihood estimation, which showed that these genomes were novel species within the genus Penicillium. We propose to name isolate SPG-F1 as Penicillium pacificasedimenti sp. nov. and SPG-F15 as Penicillium pacificagyrus sp. nov. The resulting genome sizes were 32.6 Mbp and 36.4 Mbp, respectively, and both genomes were greater than 98% complete as determined by the presence of complete single-copy orthologs. The transposable elements for each genome were 4.87% for P. pacificasedimenti and 10.68% for P. pacificagyrus. A total of 12,271 genes were predicted in the P. pacificasedimenti genome and 12,568 genes in P. pacificagyrus. Both isolates contained genes known to be involved in the degradation of recalcitrant carbon, amino acids, and lignin-derived carbon. CONCLUSIONS Our results provide the first constructed genomes of novel Penicillium isolates from deep marine sediments, which will be useful for future studies of marine subsurface fungal diversity and function. Furthermore, these genomes shed light on the potential impact fungi in marine sediments and the subseafloor could have on global carbon and nitrogen biogeochemical cycles and how they may be persisting in the most energy-limited sedimentary biosphere.
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Affiliation(s)
- Morgan S Sobol
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Baden-Württemberg, Germany
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, 783-8502, Japan
| | - Victor Delgado
- Department of Life Sciences, TX A&M University, Corpus Christi, Texas, USA
| | - Taiki Futagami
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, 890-0065, Japan
| | - Chihiro Kadooka
- Department of Biotechnology and Life Science, Faculty of Biotechnology and Life Science, Sojo University, Ikeda, Nishiku, Kumamoto, 860-0082, Japan
| | - Fumio Inagaki
- Mantle Drilling Promotion Office, Institute for Marine Earth Exploration and Engineering (MarE3), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, 236- 0001, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, 980-8574, Japan
| | - Brandi Kiel Reese
- Dauphin Island Sea Lab, Dauphin Island, Alabama, USA.
- Stokes School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL, USA.
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12
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Rasmussen B, Muhling JR. Organic carbon generation in 3.5-billion-year-old basalt-hosted seafloor hydrothermal vent systems. SCIENCE ADVANCES 2023; 9:eadd7925. [PMID: 36724225 PMCID: PMC9891697 DOI: 10.1126/sciadv.add7925] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Carbon is the key element of life, and its origin in ancient sedimentary rocks is central to questions about the emergence and early evolution of life. The oldest well-preserved carbon occurs with fossil-like structures in 3.5-billion-year-old black chert. The carbonaceous matter, which is associated with hydrothermal chert-barite vent systems originating in underlying basaltic-komatiitic lavas, is thought to be derived from microbial life. Here, we show that 3.5-billion-year-old black chert vein systems from the Pilbara Craton, Australia contain abundant residues of migrated organic carbon. Using younger analogs, we argue that the black cherts formed during precipitation from silica-rich, carbon-bearing hydrothermal fluids in vein systems and vent-proximal seafloor sediments. Given the volcanic setting and lack of organic-rich sediments, we speculate that the vent-mound systems contain carbon derived from rock-powered organic synthesis in the underlying mafic-ultramafic lavas, providing a glimpse of a prebiotic world awash in terrestrial organic compounds.
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13
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Huld S, McMahon S, Sjöberg S, Huang P, Neubeck A. Chemical Gardens Mimic Electron Paramagnetic Resonance Spectra and Morphology of Biogenic Mn Oxides. ASTROBIOLOGY 2023; 23:24-32. [PMID: 36450112 PMCID: PMC9810355 DOI: 10.1089/ast.2021.0194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 08/01/2022] [Indexed: 06/17/2023]
Abstract
Manganese (Mn) oxides are ubiquitous in nature and occur as both biological and abiotic minerals, but empirically distinguishing between the two remains a problem. Recently, electron paramagnetic resonance (EPR) spectroscopy has been proposed for this purpose. It has been reported that biogenic Mn oxides display a characteristic narrow linewidth in contrast to their pure abiotic counterparts, which is explained in part by the large number of cation vacancies that form within the layers of biogenic Mn oxides. It was, therefore, proposed that natural samples that display a narrow EPR linewidth, ΔHpp < 580G, could be assigned to a biogenic origin. However, in poorly crystalline or amorphous solids, both dipolar broadening and exchange narrowing simultaneously determine the linewidth. Considering that the spectral linewidth is governed by several mechanisms, this approach might be questioned. In this study, we report synthetic chemical garden Mn oxide biomorphs that exhibit both morphologically life-like structures and narrow EPR linewidths, suggesting that a narrow EPR line may be unsuitable as reliable evidence in assessment of biogenicity.
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Affiliation(s)
- Sigrid Huld
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - Sean McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Susanne Sjöberg
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | - Ping Huang
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Neubeck
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
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14
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Ayuso-Fernández I, Molpeceres G, Camarero S, Ruiz-Dueñas FJ, Martínez AT. Ancestral sequence reconstruction as a tool to study the evolution of wood decaying fungi. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1003489. [PMID: 37746217 PMCID: PMC10512382 DOI: 10.3389/ffunb.2022.1003489] [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: 07/26/2022] [Accepted: 09/22/2022] [Indexed: 09/26/2023]
Abstract
The study of evolution is limited by the techniques available to do so. Aside from the use of the fossil record, molecular phylogenetics can provide a detailed characterization of evolutionary histories using genes, genomes and proteins. However, these tools provide scarce biochemical information of the organisms and systems of interest and are therefore very limited when they come to explain protein evolution. In the past decade, this limitation has been overcome by the development of ancestral sequence reconstruction (ASR) methods. ASR allows the subsequent resurrection in the laboratory of inferred proteins from now extinct organisms, becoming an outstanding tool to study enzyme evolution. Here we review the recent advances in ASR methods and their application to study fungal evolution, with special focus on wood-decay fungi as essential organisms in the global carbon cycling.
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Affiliation(s)
- Iván Ayuso-Fernández
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gonzalo Molpeceres
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB), CSIC, Madrid, Spain
| | - Susana Camarero
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB), CSIC, Madrid, Spain
| | | | - Angel T. Martínez
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB), CSIC, Madrid, Spain
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15
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Eukaryogenesis and oxygen in Earth history. Nat Ecol Evol 2022; 6:520-532. [PMID: 35449457 DOI: 10.1038/s41559-022-01733-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/15/2022] [Indexed: 02/07/2023]
Abstract
The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth's surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and life sciences. While the permanent oxygenation of the atmosphere above trace concentrations is now thought to have occurred 2.2 billion years ago, large parts of the deep ocean remained anoxic until less than 0.5 billion years ago. Neither fossils nor molecular clocks correlate the origin of mitochondria, or eukaryogenesis more broadly, to either of these planetary redox transitions. Instead, mitochondria-bearing eukaryotes are consistently dated to between these two oxygenation events, during an interval of pervasive deep-sea anoxia and variable surface-water oxygenation. The discovery and cultivation of the Asgard archaea has reinforced metabolic evidence that eukaryogenesis was initially mediated by syntrophic H2 exchange between an archaeal host and an α-proteobacterial symbiont living under anoxia. Together, these results temporally, spatially and metabolically decouple the earliest stages of eukaryogenesis from the oxygen content of the surface ocean and atmosphere. Rather than reflecting the ancestral metabolic state, obligate aerobiosis in eukaryotes is most probably derived, having only become globally widespread over the past 1 billion years as atmospheric oxygen approached modern levels.
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16
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Kulkarni P, Bhattacharya S, Achuthan S, Behal A, Jolly MK, Kotnala S, Mohanty A, Rangarajan G, Salgia R, Uversky V. Intrinsically Disordered Proteins: Critical Components of the Wetware. Chem Rev 2022; 122:6614-6633. [PMID: 35170314 PMCID: PMC9250291 DOI: 10.1021/acs.chemrev.1c00848] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the wealth of knowledge gained about intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and, hence, poorly understood. A living cell is a complex adaptive system that can be described as a wetware─a metaphor used to describe the cell as a computer comprising both hardware and software and attuned to logic gates─capable of "making" decisions. In this focused Review, we discuss how IDPs, as critical components of the wetware, influence cell-fate decisions by wiring protein interaction networks to keep them minimally frustrated. Because IDPs lie between order and chaos, we explore the possibility that they can be modeled as attractors. Further, we discuss how the conformational dynamics of IDPs manifests itself as conformational noise, which can potentially amplify transcriptional noise to stochastically switch cellular phenotypes. Finally, we explore the potential role of IDPs in prebiotic evolution, in forming proteinaceous membrane-less organelles, in the origin of multicellularity, and in protein conformation-based transgenerational inheritance of acquired characteristics. Together, these ideas provide a new conceptual framework to discern how IDPs may perform critical biological functions despite their lack of structure.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, USA
| | - Srisairam Achuthan
- Division of Research Informatics, Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Amita Behal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sourabh Kotnala
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
- Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow region 141700, Russia
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17
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Dou K, Pang G, Cai F, Chenthamara K, Zhang J, Liu H, Druzhinina IS, Chen J. Functional Genetics of Trichoderma Mycoparasitism. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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McMahon S, Ivarsson M, Wacey D, Saunders M, Belivanova V, Muirhead D, Knoll P, Steinbock O, Frost DA. Dubiofossils from a Mars-analogue subsurface palaeoenvironment: The limits of biogenicity criteria. GEOBIOLOGY 2021; 19:473-488. [PMID: 33951268 DOI: 10.1111/gbi.12445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/12/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
The search for a fossil record of Earth's deep biosphere, partly motivated by potential analogies with subsurface habitats on Mars, has uncovered numerous assemblages of inorganic microfilaments and tubules inside ancient pores and fractures. Although these enigmatic objects are morphologically similar to mineralized microorganisms (and some contain organic carbon), they also resemble some abiotic structures. Palaeobiologists have responded to this ambiguity by evaluating problematic filaments against checklists of "biogenicity criteria". Here, we describe material that tests the limits of this approach. We sampled Jurassic calcite veins formed through subseafloor serpentinization, a water-rock reaction that can fuel the deep biosphere and is known to have occurred widely on Mars. At two localities ~4 km apart, veins contained curving, branched microfilaments composed of Mg-silicate and Fe-oxide minerals. Using a wide range of analytical techniques including synchrotron X-ray microtomography and scanning transmission electron microscopy, we show that these features meet many published criteria for biogenicity and are comparable to fossilized cryptoendolithic fungi or bacteria. However, we argue that abiotic processes driven by serpentinization could account for the same set of lifelike features, and report a chemical garden experiment that supports this view. These filaments are, therefore, most objectively described as dubiofossils, a designation we here defend from criticism and recommend over alternative approaches, but which nevertheless signifies an impasse. Similar impasses can be anticipated in the future exploration of subsurface palaeo-habitats on Earth and Mars. To avoid them, further studies are required in biomimetic geochemical self-organization, microbial taphonomy and micro-analytical techniques, with a focus on subsurface habitats.
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Affiliation(s)
- Sean McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- School of Geosciences, Grant Institute, University of Edinburgh, Edinburgh, UK
| | - Magnus Ivarsson
- Department of Paleobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Wacey
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Martin Saunders
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Veneta Belivanova
- Department of Paleobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Muirhead
- School of Geosciences, King's College, University of Aberdeen, Aberdeen, UK
| | - Pamela Knoll
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Oliver Steinbock
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Daniel A Frost
- Department of Earth & Planetary Science, University of California, Berkeley, CA, USA
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19
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Rasmussen B, Muhling JR, Fischer WW. Ancient Oil as a Source of Carbonaceous Matter in 1.88-Billion-Year-Old Gunflint Stromatolites and Microfossils. ASTROBIOLOGY 2021; 21:655-672. [PMID: 33684328 DOI: 10.1089/ast.2020.2376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The 1.88-billion-year-old Gunflint carbonaceous microfossils are renowned for their exceptional morphological and chemical preservation, attributed to early and rapid entombment in amorphous silica. The carbonaceous matter lining and partly filling filamentous and spherical structures is interpreted to be indigenous, representing thermally altered relicts of cellular material (i.e., kerogen). Here we show that stromatolitic black cherts from the Gunflint Formation, Schreiber Beach, Ontario, Canada, were saturated in syn-sedimentary oil. The thermally altered oil (pyrobitumen), which occurs in the stromatolites and intercolumn sediments, fills pores and fractures, and coats detrital and diagenetic grain surfaces. The occurrence of detrital bitumen grains in the stromatolites points to the proximity of shallow seafloor oil seeps and hence the possible existence of chemosynthetic microbes degrading hydrocarbons. We suggest that hydrocarbons that migrated through the silicifying stromatolites infiltrated semi-hollow microbial molds that formed following silica nucleation on the walls or sheaths of decayed cells. Upon heating, the hydrocarbons were transformed to nanoporous pyrobitumen, retarding silica recrystallization and enhancing detailed preservation of the carbon-rich microfossils. Hydrocarbon infiltration of silicified microbes offers a new explanation for the preservation of the Gunflint microfossils and may have played a role in the formation of some of Earth's oldest microfossils.
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Affiliation(s)
- B Rasmussen
- School of Earth Sciences, The University of Western Australia, Perth, Australia
| | - J R Muhling
- School of Earth Sciences, The University of Western Australia, Perth, Australia
| | - W W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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20
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Phylogenomic Analyses of Nucleotide-Sugar Biosynthetic and Interconverting Enzymes Illuminate Cell Wall Composition in Fungi. mBio 2021; 12:mBio.03540-20. [PMID: 33849982 PMCID: PMC8092308 DOI: 10.1128/mbio.03540-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fungi are an enormously successful eukaryotic lineage that has colonized every aerobic habitat on Earth. This spectacular expansion is reflected in the dynamism and diversity of the fungal cell wall, a matrix of polysaccharides and glycoproteins pivotal to fungal life history strategies and a major target in the development of antifungal compounds. Cell wall polysaccharides are typically synthesized by Leloir glycosyltransferases, enzymes that are notoriously difficult to characterize, but their nucleotide-sugar substrates are well known and provide the opportunity to inspect the monosaccharides available for incorporation into cell wall polysaccharides and glycoproteins. In this work, we have used phylogenomic analyses of the enzymatic pathways that synthesize and interconvert nucleotide-sugars to predict potential cell wall monosaccharide composition across 491 fungal taxa. The results show a complex evolutionary history of these cell wall enzyme pathways and, by association, of the fungal cell wall. In particular, we see a significant reduction in monosaccharide diversity during fungal evolution, most notably in the colonization of terrestrial habitats. However, monosaccharide distribution is also shown to be varied across later-diverging fungal lineages.IMPORTANCE This study provides new insights into the complex evolutionary history of the fungal cell wall. We analyzed fungal enzymes that convert sugars acquired from the environment into the diverse sugars that make up the fundamental building blocks of the cell wall. Species-specific profiles of these nucleotide-sugar interconverting (NSI) enzymes for 491 fungi demonstrated multiple losses and gains of NSI proteins, revealing the rich diversity of cell wall architecture across the kingdom. Pragmatically, because cell walls are essential to fungi, our observations of variation in sugar diversity have important implications for the development of antifungal compounds that target the sugar profiles of specific pathogens.
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21
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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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22
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Tsurkan MV, Voronkina A, Khrunyk Y, Wysokowski M, Petrenko I, Ehrlich H. Progress in chitin analytics. Carbohydr Polym 2021; 252:117204. [DOI: 10.1016/j.carbpol.2020.117204] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 12/25/2022]
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23
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Bell PJ. Evidence supporting a viral origin of the eukaryotic nucleus. Virus Res 2020; 289:198168. [DOI: 10.1016/j.virusres.2020.198168] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022]
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24
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Yanni D, Jacobeen S, Márquez-Zacarías P, Weitz JS, Ratcliff WC, Yunker PJ. Topological constraints in early multicellularity favor reproductive division of labor. eLife 2020; 9:e54348. [PMID: 32940598 PMCID: PMC7609046 DOI: 10.7554/elife.54348] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 09/17/2020] [Indexed: 12/23/2022] Open
Abstract
Reproductive division of labor (e.g. germ-soma specialization) is a hallmark of the evolution of multicellularity, signifying the emergence of a new type of individual and facilitating the evolution of increased organismal complexity. A large body of work from evolutionary biology, economics, and ecology has shown that specialization is beneficial when further division of labor produces an accelerating increase in absolute productivity (i.e. productivity is a convex function of specialization). Here we show that reproductive specialization is qualitatively different from classical models of resource sharing, and can evolve even when the benefits of specialization are saturating (i.e. productivity is a concave function of specialization). Through analytical theory and evolutionary individual-based simulations, we demonstrate that reproductive specialization is strongly favored in sparse networks of cellular interactions that reflect the morphology of early, simple multicellular organisms, highlighting the importance of restricted social interactions in the evolution of reproductive specialization.
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Affiliation(s)
- David Yanni
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Shane Jacobeen
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Pedro Márquez-Zacarías
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Joshua S Weitz
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Peter J Yunker
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
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25
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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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McLoughlin N, Wacey D, Phunguphungu S, Saunders M, Grosch EG. Deconstructing Earth's oldest ichnofossil record from the Pilbara Craton, West Australia: Implications for seeking life in the Archean subseafloor. GEOBIOLOGY 2020; 18:525-543. [PMID: 32542902 DOI: 10.1111/gbi.12399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/30/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Microtextures of titanite (CaTiSiO5 ) in exceptionally preserved Archean pillow lavas have been proposed as the earliest examples of microbial ichnofossils. An origin from microbial tunneling of seafloor volcanic glass that is subsequently chloritized and the tunnels infilled by titanite has been argued to record the activities of subseafloor microbes. We investigate the evidence in pillow lavas of the 3.35 Ga Euro Basalt from the Pilbara Craton, Western Australia, to evaluate the biogenicity of the microtextures. We employ a combination of light microscopy and chlorite mineral chemical analysis by EPMA (electron probe micro-analysis) to document the environment of formation and analyze their ultrastructure using FIB-TEM (focussed ion beam combined with transmission electron microscopy) to investigate their mode of growth. Petrographic study of the original and re-collected material identified an expanded range of titanite morphotypes along with early anatase growth forming chains and aggregates of coalesced crystallites in a sub-greenschist facies assemblage. High-sensitivity mapping of FIB lamellae cut across the microtextures confirm that they are discontinuous chains of coalesced crystallites that are highly variable in cross section and contain abundant chlorite inclusions, excluding an origin from the mineralization of previously hollow microtunnels. Comparison of chlorite mineral compositions to DSDP/IODP data reveals that the Euro Basalt chlorites are similar to recent seafloor chlorites. We advance an abiotic origin for the Euro Basalt microtextures formed by spontaneous nucleation and growth of titanite and/anatase during seafloor-hydrothermal metamorphism. Our findings reveal that the Euro Basalt microtextures are not comparable to microbial ichnofossils from the recent oceanic crust, and we question the evidence for life in these Archean lavas. The metamorphic reactions that give rise to the growth of the Euro Basalt microtextures could be commonplace in Archean pillow lavas and need to be excluded when seeking traces of life in the subseafloor on the early Earth.
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Affiliation(s)
| | - David Wacey
- Centre for Microscopy, Characterization and Analysis (CMCA), The University of Western Australia (UWA), Perth, WA, Australia
| | | | - Martin Saunders
- Centre for Microscopy, Characterization and Analysis (CMCA), The University of Western Australia (UWA), Perth, WA, Australia
| | - Eugene G Grosch
- Department of Geology, Rhodes University, Grahamstown, South Africa
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27
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Quemener M, Mara P, Schubotz F, Beaudoin D, Li W, Pachiadaki M, Sehein TR, Sylvan JB, Li J, Barbier G, Edgcomb V, Burgaud G. Meta-omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust. Environ Microbiol 2020; 22:3950-3967. [PMID: 32743889 DOI: 10.1111/1462-2920.15181] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/23/2020] [Accepted: 07/31/2020] [Indexed: 02/03/2023]
Abstract
The lithified oceanic crust, lower crust gabbros in particular, has remained largely unexplored by microbiologists. Recently, evidence for heterogeneously distributed viable and transcriptionally active autotrophic and heterotrophic microbial populations within low-biomass communities was found down to 750 m below the seafloor at the Atlantis Bank Gabbro Massif, Indian Ocean. Here, we report on the diversity, activity and adaptations of fungal communities in the deep oceanic crust from ~10 to 780 mbsf by combining metabarcoding analyses with mid/high-throughput culturing approaches. Metabarcoding along with culturing indicate a low diversity of viable fungi, mostly affiliated to ubiquitous (terrestrial and aquatic environments) taxa. Ecophysiological analyses coupled with metatranscriptomics point to viable and transcriptionally active fungal populations engaged in cell division, translation, protein modifications and other vital cellular processes. Transcript data suggest possible adaptations for surviving in the nutrient-poor, lithified deep biosphere that include the recycling of organic matter. These active communities appear strongly influenced by the presence of cracks and veins in the rocks where fluids and resulting rock alteration create micro-niches.
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Affiliation(s)
- Maxence Quemener
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Florence Schubotz
- MARUM-Center for Marine Environmental Sciences, University Bremen, Leobener Strasse 8, Bremen, 28359, Germany
| | - David Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Maria Pachiadaki
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Taylor R Sehein
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, TX, 77845, USA
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Georges Barbier
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Gaëtan Burgaud
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
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28
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Cullings K, Stott MB, Marinkovich N, DeSimone J, Bhardwaj S. Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert. Microbiologyopen 2020; 9:e1062. [PMID: 32478485 PMCID: PMC7424252 DOI: 10.1002/mbo3.1062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.
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Affiliation(s)
- Ken Cullings
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Julia DeSimone
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Shilpa Bhardwaj
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
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Chuang WY, Hsieh YC, Lee TT. The Effects of Fungal Feed Additives in Animals: A Review. Animals (Basel) 2020; 10:E805. [PMID: 32384791 PMCID: PMC7278461 DOI: 10.3390/ani10050805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 01/01/2023] Open
Abstract
As probiotics, fungi enhance animal health and are suitable animal feed additives. In addition to brewing fungi, there are also edible and medicinal fungi. Common fungi utilized in feeding programs include Saccharomyces cerevisiae, Aspergillus oryzae, Pleurotus spp., Antrodia cinnamomea, and Cordyceps militaris. These fungi are rich in glucans, polysaccharides, polyphenols, triterpenes, ergosterol, adenosine, and laccases. These functional components play important roles in antioxidant, anti-inflammatory, anti-obesity, and immune system regulation. As such, fungal feed additives could be of potential use when breeding livestock. In previous studies, fungal feed additives enhanced body weight and egg production in poultry and improved the feed conversion rate. Several mycotoxins can be produced by hazardous fungi but fortunately, the cell walls constituents and enzymes of fungal probiotics can also act to decrease the toxicity of mycotoxins. Overall, fungal feed additives are of value, but their safety and usage must be studied further, including cost-benefit economic analyses.
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Affiliation(s)
- Wen Yang Chuang
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan; (W.Y.C.); (Y.C.H.)
| | - Yun Chen Hsieh
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan; (W.Y.C.); (Y.C.H.)
| | - Tzu-Tai Lee
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan; (W.Y.C.); (Y.C.H.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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30
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Ivarsson M, Drake H, Bengtson S, Rasmussen B. A Cryptic Alternative for the Evolution of Hyphae. Bioessays 2020; 42:e1900183. [DOI: 10.1002/bies.201900183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/03/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Magnus Ivarsson
- Department of BiologyUniversity of Southern Denmark Campusvej 55 Odense M DK 5230 Denmark
- Department of PaleobiologySwedish Museum of Natural History Box 50007 Stockholm SE‐104 05 Sweden
| | - Henrik Drake
- Department of Biology and Environmental ScienceLinnaeus University Kalmar 391 82 Sweden
| | - Stefan Bengtson
- Department of PaleobiologySwedish Museum of Natural History Box 50007 Stockholm SE‐104 05 Sweden
| | - Birger Rasmussen
- School of Earth SciencesThe University of Western Australia Nedlands WA 6009 Australia
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31
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Bonneville S, Delpomdor F, Préat A, Chevalier C, Araki T, Kazemian M, Steele A, Schreiber A, Wirth R, Benning LG. Molecular identification of fungi microfossils in a Neoproterozoic shale rock. SCIENCE ADVANCES 2020; 6:eaax7599. [PMID: 32010783 PMCID: PMC6976295 DOI: 10.1126/sciadv.aax7599] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/20/2019] [Indexed: 05/26/2023]
Abstract
Precambrian fossils of fungi are sparse, and the knowledge of their early evolution and the role they played in the colonization of land surface are limited. Here, we report the discovery of fungi fossils in a 810 to 715 million year old dolomitic shale from the Mbuji-Mayi Supergroup, Democratic Republic of Congo. Syngenetically preserved in a transitional, subaerially exposed paleoenvironment, these carbonaceous filaments of ~5 μm in width exhibit low-frequency septation (pseudosepta) and high-angle branching that can form dense interconnected mycelium-like structures. Using an array of microscopic (SEM, TEM, and confocal laser scanning fluorescence microscopy) and spectroscopic techniques (Raman, FTIR, and XANES), we demonstrated the presence of vestigial chitin in these fossil filaments and document the eukaryotic nature of their precursor. Based on those combined evidences, these fossil filaments and mycelium-like structures are identified as remnants of fungal networks and represent the oldest, molecularly identified remains of Fungi.
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Affiliation(s)
- S. Bonneville
- Biogéochimie et Modélisation du Système Terre, Département Géosciences, Environnement et Société, Université Libre de Bruxelles, 50 Av. F. D. Roosevelt, 1050 Brussels, Belgium
| | - F. Delpomdor
- Illinois State Geological Survey, University of Illinois at Urbana-Champaign, 615 E. Peabody Dr., Champaign, IL 61820, USA
| | - A. Préat
- Biogéochimie et Modélisation du Système Terre, Département Géosciences, Environnement et Société, Université Libre de Bruxelles, 50 Av. F. D. Roosevelt, 1050 Brussels, Belgium
| | - C. Chevalier
- Center for Microscopy and Molecular Imaging, Université Libre de Bruxelles, 12 rue des professeurs Jeener et Brachet, Charleroi 6041, Belgium
| | - T. Araki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - M. Kazemian
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - A. Steele
- Geophysical Laboratory, Carnegie Institution of Washington, 1530 P St NW, Washington, DC 20005, USA
| | - A. Schreiber
- German Research Centre for Geosciences, GFZ, Telegrafenberg, 14473 Potsdam, Germany
| | - R. Wirth
- German Research Centre for Geosciences, GFZ, Telegrafenberg, 14473 Potsdam, Germany
| | - L. G. Benning
- German Research Centre for Geosciences, GFZ, Telegrafenberg, 14473 Potsdam, Germany
- Department of Earth Sciences, Free University of Berlin, 12249 Berlin, Germany
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32
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Exceptional Preservation of Fungi as H2-Bearing Fluid Inclusions in an Early Quaternary Paleo-Hydrothermal System at Cape Vani, Milos, Greece. MINERALS 2019. [DOI: 10.3390/min9120749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The production of H2 in hydrothermal systems and subsurface settings is almost exclusively assumed a result of abiotic processes, particularly serpentinization of ultramafic rocks. The origin of H2 in environments not hosted in ultramafic rocks is, as a rule, unjustifiably linked to abiotic processes. Additionally, multiple microbiological processes among both prokaryotes and eukaryotes are known to involve H2-production, of which anaerobic fungi have been put forward as a potential source of H2 in subsurface environments, which is still unconfirmed. Here, we report fungal remains exceptionally preserved as fluid inclusions in hydrothermal quartz from feeder quartz-barite veins from the Cape Vani Fe-Ba-Mn ore on the Greek island of Milos. The inclusions possess filamentous or near-spheroidal morphologies interpreted as remains of fungal hyphae and spores, respectively. They were characterized by microthermometry, Raman spectroscopy, and staining of exposed inclusions with WGA-FITC under fluorescence microscopy. The spheroidal aqueous inclusions interpreted as fungal spores are unique by their coating of Mn-oxide birnessite, and gas phase H2. A biological origin of the H2 resulting from anaerobic fungal respiration is suggested. We propose that biologically produced H2 by micro-eukaryotes is an unrecognized source of H2 in hydrothermal systems that may support communities of H2-dependent prokaryotes.
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33
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McMahon S. Earth's earliest and deepest purported fossils may be iron-mineralized chemical gardens. Proc Biol Sci 2019; 286:20192410. [PMID: 31771469 PMCID: PMC6939263 DOI: 10.1098/rspb.2019.2410] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Recognizing fossil microorganisms is essential to the study of life's origin and evolution and to the ongoing search for life on Mars. Purported fossil microbes in ancient rocks include common assemblages of iron-mineral filaments and tubes. Recently, such assemblages have been interpreted to represent Earth's oldest body fossils, Earth's oldest fossil fungi, and Earth's best analogues for fossils that might form in the basaltic Martian subsurface. Many of these putative fossils exhibit hollow circular cross-sections, lifelike (non-crystallographic, constant-thickness, and bifurcate) branching, anastomosis, nestedness within ‘sheaths’, and other features interpreted as strong evidence for a biological origin, since no abiotic process consistent with the composition of the filaments has been shown to produce these specific lifelike features either in nature or in the laboratory. Here, I show experimentally that abiotic chemical gardening can mimic such purported fossils in both morphology and composition. In particular, chemical gardens meet morphological criteria previously proposed to establish biogenicity, while also producing the precursors to the iron minerals most commonly constitutive of filaments in the rock record. Chemical gardening is likely to occur in nature. Such microstructures should therefore not be assumed to represent fossil microbes without independent corroborating evidence.
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Affiliation(s)
- Sean McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.,School of Geosciences, Grant Institute, University of Edinburgh, James Hutton Road, Edinburgh EH9 3FE, UK
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34
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Onstott T, Ehlmann B, Sapers H, Coleman M, Ivarsson M, Marlow J, Neubeck A, Niles P. Paleo-Rock-Hosted Life on Earth and the Search on Mars: A Review and Strategy for Exploration. ASTROBIOLOGY 2019; 19:1230-1262. [PMID: 31237436 PMCID: PMC6786346 DOI: 10.1089/ast.2018.1960] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/25/2019] [Indexed: 05/19/2023]
Abstract
Here we review published studies on the abundance and diversity of terrestrial rock-hosted life, the environments it inhabits, the evolution of its metabolisms, and its fossil biomarkers to provide guidance in the search for life on Mars. Key findings are (1) much terrestrial deep subsurface metabolic activity relies on abiotic energy-yielding fluxes and in situ abiotic and biotic recycling of metabolic waste products rather than on buried organic products of photosynthesis; (2) subsurface microbial cell concentrations are highest at interfaces with pronounced chemical redox gradients or permeability variations and do not correlate with bulk host rock organic carbon; (3) metabolic pathways for chemolithoautotrophic microorganisms evolved earlier in Earth's history than those of surface-dwelling phototrophic microorganisms; (4) the emergence of the former occurred at a time when Mars was habitable, whereas the emergence of the latter occurred at a time when the martian surface was not continually habitable; (5) the terrestrial rock record has biomarkers of subsurface life at least back hundreds of millions of years and likely to 3.45 Ga with several examples of excellent preservation in rock types that are quite different from those preserving the photosphere-supported biosphere. These findings suggest that rock-hosted life would have been more likely to emerge and be preserved in a martian context. Consequently, we outline a Mars exploration strategy that targets subsurface life and scales spatially, focusing initially on identifying rocks with evidence for groundwater flow and low-temperature mineralization, then identifying redox and permeability interfaces preserved within rock outcrops, and finally focusing on finding minerals associated with redox reactions and associated traces of carbon and diagnostic chemical and isotopic biosignatures. Using this strategy on Earth yields ancient rock-hosted life, preserved in the fossil record and confirmable via a suite of morphologic, organic, mineralogical, and isotopic fingerprints at micrometer scale. We expect an emphasis on rock-hosted life and this scale-dependent strategy to be crucial in the search for life on Mars.
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Affiliation(s)
- T.C. Onstott
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Address correspondence to: T.C. Onstott, Department of Geosciences, Princeton University,, Princeton, NJ 008544
| | - B.L. Ehlmann
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- B.L. Ehlmann, Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - H. Sapers
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - M. Coleman
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- NASA Astrobiology Institute, Pasadena, California, USA
| | - M. Ivarsson
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - J.J. Marlow
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - A. Neubeck
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - P. Niles
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, Texas, USA
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35
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Abstract
Clay authigenesis associated with the activity of microorganisms is an important process for biofilm preservation and may provide clues to the formation of biominerals on the ancient Earth. Fossilization of fungal biofilms attached to vesicles or cracks in igneous rock, is characterized by fungal-induced clay mineralization and can be tracked in deep rock and deep time, from late Paleoproterozoic (2.4 Ga), to the present. Here we briefly review the current data on clay mineralization by fossil fungal biofilms from oceanic and continental subsurface igneous rock. The aim of this study was to compare the nature of subsurface fungal clays from different igneous settings to evaluate the importance of host rock and ambient redox conditions for clay speciation related to fossil microorganisms. Our study suggests that the most common type of authigenic clay associated with pristine fossil fungal biofilms in both oxic (basaltic) and anoxic (granitic) settings are montmorillonite-like smectites and confirms a significant role of fungal biofilms in the cycling of elements between host rock, ocean and secondary precipitates. The presence of life in the deep subsurface may thus prove more significant than host rock geochemistry in directing the precipitation of authigenic clays in the igneous crust, the extent of which remains to be fully understood.
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36
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Bomberg M, Claesson Liljedahl L, Lamminmäki T, Kontula A. Highly Diverse Aquatic Microbial Communities Separated by Permafrost in Greenland Show Distinct Features According to Environmental Niches. Front Microbiol 2019; 10:1583. [PMID: 31354674 PMCID: PMC6637822 DOI: 10.3389/fmicb.2019.01583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/25/2019] [Indexed: 11/13/2022] Open
Abstract
The Greenland Analog Project (GAP) study area in the vicinity of Kangarlussuaq, Western Greenland, was sampled for surface water and deep groundwater in order to determine the composition and estimate the metabolic features of the microbial communities in water bodies separated by permafrost. The sampling sites comprised a freshwater pond, talik lake, deep anoxic groundwater, glacier ice and supraglacial river, meltwater river and melting permafrost active layer. The microbial communities were characterized by amplicon sequencing of the bacterial and archaeal 16S rRNA genes and fungal ITS1 spacer. In addition, bacterial, archaeal and fungal numbers were determined by qPCR and plate counts, and the utilization pattern of carbon and nitrogen substrates was determined with Biolog AN plates and metabolic functions were predicted with FAPROTAX. Different sample types were clearly distinguishable from each other based on community composition, microbial numbers, and substrate utilization patterns, forming four groups, (1) pond/lake, (2) deep groundwater, (3) glacial ice, and (4) meltwater. Bacteria were the most abundant microbial domain, ranging from 0.2–1.4 × 107 16S rRNA gene copies mL-1 in pond/lake and meltwater, 0.1-7.8 × 106 copies mL-1 in groundwater and less than 104 copies mL-1 in ice. The number of archaeal 16S and fungal 5.8S rRNA genes was generally less than 6.0 × 103 and 1.5 × 103, respectively. N2-fixing and methane-oxidizing Actinomycetes, Bacteroidetes and Verrucomicrobia were the dominant microorganisms in the pond/lake samples, whereas iron reducing Desulfosporosinus sp. dominated the deep anaerobic groundwater. The glacial ice was inhabited by Cyanobacteria, which were mostly Chloroplast-like. The meltwater contained methano- and methylotrophic Proteobacteria, but had also high relative abundances of the nano-sized Parcubacteria. The archaea composed approximately 1% of the 16S rRNA gene pool in the pond/lake samples with nano-sized Woesearchaeota as the dominating taxon, while in the other sample types archaea were almost negligent. Fungi were also most common in the pond/lake communities, were zoospore-forming Chytridiomycetes dominated. Our results show highly diverse microbial communities inhabiting the different cold Greenlandic aqueous environments and show clear segregation of the microbial communities according to habitat, with distinctive dominating metabolic features specifically inhabiting defined environmental niches and a high relative abundance of putatively parasitic or symbiotic nano-sized taxa.
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Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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37
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McMahon S, Ivarsson M. A New Frontier for Palaeobiology: Earth's Vast Deep Biosphere. Bioessays 2019; 41:e1900052. [PMID: 31241200 DOI: 10.1002/bies.201900052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/29/2019] [Indexed: 11/11/2022]
Abstract
Diverse micro-organisms populate a global deep biosphere hosted by rocks and sediments beneath land and sea, containing more biomass than any other biome except forests. This paper reviews an emerging palaeobiological archive of these dark habitats: microfossils preserved in ancient pores and fractures in the crust. This archive, seemingly dominated by mineralized filaments (although rods and coccoids are also reported), is presently far too sparsely sampled and poorly understood to reveal trends in the abundance, distribution, or diversity of deep life through time. New research is called for to establish the nature and extent of the fossil record of Earth's deep biosphere by combining systematic exploration, rigorous microanalysis, and experimental studies of both microbial preservation and the formation of abiotic pseudofossils within the crust. It is concluded that the fossil record of Earth's largest microbial habitat may still have much to tell us about the history of life, the evolution of biogeochemical cycles, and the search for life on Mars.
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Affiliation(s)
- Sean McMahon
- School of Geosciences, University of Edinburgh, Edinburgh, EH8 9XP, UK.,UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Magnus Ivarsson
- Department of Biology, University of Southern Denmark, DK-5230, Odense, Denmark.,Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, SE-104 05, Sweden
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38
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Purkamo L, Kietäväinen R, Miettinen H, Sohlberg E, Kukkonen I, Itävaara M, Bomberg M. Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater. FEMS Microbiol Ecol 2019; 94:5035813. [PMID: 29893836 DOI: 10.1093/femsec/fiy116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/08/2018] [Indexed: 01/19/2023] Open
Abstract
The diversity and metabolic functions of deep subsurface ecosystems remain relatively unexplored. Microbial communities in previously studied deep subsurface sites of the Fennoscandian Shield are distinctive to each site. Thus, we hypothesized that the microbial communities of the deep Archaean bedrock fracture aquifer in Romuvaara, northern Finland, differ both in community composition and metabolic functionality from the other sites in the Fennoscandian Shield. We characterized the composition, functionality and substrate preferences of the microbial communities at different depths in a 600 m deep borehole. In contrast to other Fennoscandian deep biosphere communities studied to date, iron-oxidizing Gallionella dominated the bacterial communities, while methanogenic and ammonia-oxidizing archaea were the most prominent archaea, and a diverse fungal community was also detected. Potential for methane cycling and sulfate and nitrate reduction was confirmed by detection of the functional genes of these metabolic pathways. Organotrophs were less abundant, although carbohydrates were the most preferred of the tested substrates. The microbial communities shared features with those detected from other deep groundwaters with similar geochemistry, but the majority of taxa distinctive to Romuvaara are different from the taxa previously detected in saline deep groundwater in the Fennoscandian Shield, most likely because of the differences in water chemistry.
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Affiliation(s)
- Lotta Purkamo
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Riikka Kietäväinen
- Geological Survey of Finland (GTK), Betonimiehenkuja 4, 02151 Espoo, Finland
| | - Hanna Miettinen
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Elina Sohlberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Ilmo Kukkonen
- Geological Survey of Finland (GTK), Betonimiehenkuja 4, 02151 Espoo, Finland
| | - Merja Itävaara
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
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Shaala LA, Asfour HZ, Youssef DTA, Żółtowska-Aksamitowska S, Wysokowski M, Tsurkan M, Galli R, Meissner H, Petrenko I, Tabachnick K, Ivanenko VN, Bechmann N, Muzychka LV, Smolii OB, Martinović R, Joseph Y, Jesionowski T, Ehrlich H. New Source of 3D Chitin Scaffolds: The Red Sea Demosponge Pseudoceratina arabica (Pseudoceratinidae, Verongiida). Mar Drugs 2019; 17:E92. [PMID: 30717221 PMCID: PMC6410331 DOI: 10.3390/md17020092] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 01/10/2023] Open
Abstract
The bioactive bromotyrosine-derived alkaloids and unique morphologically-defined fibrous skeleton of chitin origin have been found recently in marine demosponges of the order Verongiida. The sophisticated three-dimensional (3D) structure of skeletal chitinous scaffolds supported their use in biomedicine, tissue engineering as well as in diverse modern technologies. The goal of this study was the screening of new species of the order Verongiida to find another renewable source of naturally prefabricated 3D chitinous scaffolds. Special attention was paid to demosponge species, which could be farmed on large scale using marine aquaculture methods. In this study, the demosponge Pseudoceratina arabica collected in the coastal waters of the Egyptian Red Sea was examined as a potential source of chitin for the first time. Various bioanalytical tools including scanning electron microscopy (SEM), fluorescence microscopy, FTIR analysis, Calcofluor white staining, electrospray ionization mass spectrometry (ESI-MS), as well as a chitinase digestion assay were successfully used to confirm the discovery of α-chitin within the skeleton of P. arabica. The current finding should make an important contribution to the field of application of this verongiid sponge as a novel renewable source of biologically-active metabolites and chitin, which are important for development of the blue biotechnology especially in marine oriented biomedicine.
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Affiliation(s)
- Lamiaa A Shaala
- Natural Products Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
- Suez Canal University Hospital, Suez Canal University, Ismailia 41522, Egypt.
| | - Hani Z Asfour
- Department of Medical Parasitology, Faculty of Medicine, Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Diaa T A Youssef
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt.
| | - Sonia Żółtowska-Aksamitowska
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Poznan 60965, Poland.
- Institute of Electronics and Sensor Materials, Technische Universität Bergakademie-Freiberg, Freiberg 09599, Germany.
| | - Marcin Wysokowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Poznan 60965, Poland.
- Institute of Electronics and Sensor Materials, Technische Universität Bergakademie-Freiberg, Freiberg 09599, Germany.
| | - Mikhail Tsurkan
- Leibniz Institute of Polymer Research Dresden, Dresden 01069, Germany.
| | - Roberta Galli
- Clinical Sensoring and Monitoring, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden 01307, Germany.
| | - Heike Meissner
- Department of Prosthetic Dentistry, Faculty of Medicine, Technische Universität Dresden, Dresden 01307, Germany.
| | - Iaroslav Petrenko
- Institute of Electronics and Sensor Materials, Technische Universität Bergakademie-Freiberg, Freiberg 09599, Germany.
| | - Konstantin Tabachnick
- P.P. Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia.
| | - Viatcheslav N Ivanenko
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Nicole Bechmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden 01307, Germany.
| | - Lyubov V Muzychka
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, Kiev 02094, Ukraine.
| | - Oleg B Smolii
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, Kiev 02094, Ukraine.
| | - Rajko Martinović
- Institute of Marine Biology, University of Montenegro, Kotor 85330, Montenegro.
| | - Yvonne Joseph
- Institute of Electronics and Sensor Materials, Technische Universität Bergakademie-Freiberg, Freiberg 09599, Germany.
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Poznan 60965, Poland.
| | - Hermann Ehrlich
- Institute of Electronics and Sensor Materials, Technische Universität Bergakademie-Freiberg, Freiberg 09599, Germany.
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Reduction spheroids preserve a uranium isotope record of the ancient deep continental biosphere. Nat Commun 2018; 9:4505. [PMID: 30374101 PMCID: PMC6206012 DOI: 10.1038/s41467-018-06974-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 10/03/2018] [Indexed: 11/22/2022] Open
Abstract
Life on Earth extends to several kilometres below the land surface and seafloor. This deep biosphere is second only to plants in its total biomass, is metabolically active and diverse, and is likely to have played critical roles over geological time in the evolution of microbial diversity, diagenetic processes and biogeochemical cycles. However, these roles are obscured by a paucity of fossil and geochemical evidence. Here we apply the recently developed uranium-isotope proxy for biological uranium reduction to reduction spheroids in continental rocks (red beds). Although these common palaeo-redox features have previously been suggested to reflect deep bacterial activity, unequivocal evidence for biogenicity has been lacking. Our analyses reveal that the uranium present in reduction spheroids is isotopically heavy, which is most parsimoniously explained as a signal of ancient bacterial uranium reduction, revealing a compelling record of Earth’s deep biosphere. Red beds contain reduction spheroids that formed underground millions of years ago and whose origin remains poorly constrained. Here the authors use uranium isotopes to identify ancient fingerprints of bacteria in these features, confirming that they were produced by subsurface life in the geological past.
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Lee SJ, Kong M, Harrison P, Hijri M. Conserved Proteins of the RNA Interference System in the Arbuscular Mycorrhizal Fungus Rhizoglomus irregulare Provide New Insight into the Evolutionary History of Glomeromycota. Genome Biol Evol 2018; 10:328-343. [PMID: 29329439 PMCID: PMC5786227 DOI: 10.1093/gbe/evy002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 11/26/2022] Open
Abstract
Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 Ma. However, Glomeromycota are estimated to have emerged much earlier than land plants. In this study, we surveyed genomic and transcriptomic data of the model arbuscular mycorrhizal fungus Rhizoglomus irregulare (synonym Rhizophagus irregularis) and its relatives to search for evidence of HGT that occurred during AMF evolution. Surprisingly, we found a signature of putative HGT of class I ribonuclease III protein-coding genes that occurred from autotrophic cyanobacteria genomes to R. irregulare. At least one of two HGTs was conserved among AMF species with high levels of sequence similarity. Previously, an example of intimate symbiosis between AM fungus and cyanobacteria was reported in the literature. Ribonuclease III family enzymes are important in small RNA regulation in Fungi together with two additional core proteins (Argonaute/piwi and RdRP). The eukaryotic RNA interference system found in AMF was conserved and showed homology with high sequence similarity in Mucoromycotina, a group of fungi closely related to Glomeromycota. Prior to this analysis, class I ribonuclease III has not been identified in any eukaryotes. Our results indicate that a unique acquisition of class I ribonuclease III in AMF is due to a HGT event that occurred from cyanobacteria to Glomeromycota, at the latest before the divergence of the two Glomeromycota orders Diversisporales and Glomerales.
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Affiliation(s)
- Soon-Jae Lee
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Mengxuan Kong
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Paul Harrison
- Department of Biology, McGill University, Montréal, Quebec, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
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42
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Ancient Microbial Activity in Deep Hydraulically Conductive Fracture Zones within the Forsmark Target Area for Geological Nuclear Waste Disposal, Sweden. GEOSCIENCES 2018. [DOI: 10.3390/geosciences8060211] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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43
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Kauko A, Lehto K. Eukaryote specific folds: Part of the whole. Proteins 2018; 86:868-881. [PMID: 29675831 DOI: 10.1002/prot.25517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 01/07/2023]
Abstract
The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life. The most accepted scenarios suggest the endosymbiosis of a mitochondrial ancestor with a complex archaeon, even though the details regarding the host and the triggering factors are still being discussed. Accordingly, phylogenetic analyses have demonstrated archaeal affiliations with key informational systems, while metabolic genes are often related to bacteria, mostly to the mitochondrial ancestor. Despite of this, there exists a large number of protein families and folds found only in eukaryotes. In this study, we have analyzed structural superfamilies and folds that probably appeared during eukaryogenesis. These folds typically represent relatively small binding domains of larger multidomain proteins. They are commonly involved in biological processes that are particularly complex in eukaryotes, such as signaling, trafficking/cytoskeleton, ubiquitination, transcription and RNA processing, but according to recent studies, these processes also have prokaryotic roots. Thus the folds originating from an eukaryotic stem seem to represent accessory parts that have contributed in the expansion of several prokaryotic processes to a new level of complexity. This might have taken place as a co-evolutionary process where increasing complexity and fold innovations have supported each other.
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Affiliation(s)
- Anni Kauko
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Kirsi Lehto
- Department of Biochemistry, University of Turku, Turku, Finland
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McMahon S, Bosak T, Grotzinger JP, Milliken RE, Summons RE, Daye M, Newman SA, Fraeman A, Williford KH, Briggs DEG. A Field Guide to Finding Fossils on Mars. JOURNAL OF GEOPHYSICAL RESEARCH. PLANETS 2018; 123:1012-1040. [PMID: 30034979 PMCID: PMC6049883 DOI: 10.1029/2017je005478] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 03/28/2018] [Accepted: 04/23/2018] [Indexed: 05/05/2023]
Abstract
The Martian surface is cold, dry, exposed to biologically harmful radiation and apparently barren today. Nevertheless, there is clear geological evidence for warmer, wetter intervals in the past that could have supported life at or near the surface. This evidence has motivated National Aeronautics and Space Administration and European Space Agency to prioritize the search for any remains or traces of organisms from early Mars in forthcoming missions. Informed by (1) stratigraphic, mineralogical and geochemical data collected by previous and current missions, (2) Earth's fossil record, and (3) experimental studies of organic decay and preservation, we here consider whether, how, and where fossils and isotopic biosignatures could have been preserved in the depositional environments and mineralizing media thought to have been present in habitable settings on early Mars. We conclude that Noachian-Hesperian Fe-bearing clay-rich fluvio-lacustrine siliciclastic deposits, especially where enriched in silica, currently represent the most promising and best understood astropaleontological targets. Siliceous sinters would also be an excellent target, but their presence on Mars awaits confirmation. More work is needed to improve our understanding of fossil preservation in the context of other environments specific to Mars, particularly within evaporative salts and pore/fracture-filling subsurface minerals.
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Affiliation(s)
- S. McMahon
- Department of Geology and GeophysicsYale UniversityNew HavenCTUSA
- UK Centre for Astrobiology, School of Physics and AstronomyUniversity of EdinburghEdinburghUK
| | - T. Bosak
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - J. P. Grotzinger
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - R. E. Milliken
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRIUSA
| | - R. E. Summons
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - M. Daye
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - S. A. Newman
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - A. Fraeman
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - K. H. Williford
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - D. E. G. Briggs
- Department of Geology and GeophysicsYale UniversityNew HavenCTUSA
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45
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Muscente AD, Czaja AD, Tuggle J, Winkler C, Xiao S. Manganese Oxides Resembling Microbial Fabrics and Their Implications for Recognizing Inorganically Preserved Microfossils. ASTROBIOLOGY 2018; 18:249-258. [PMID: 29570411 DOI: 10.1089/ast.2017.1699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In the search for microfossils of early life on Earth, the demonstration of biogenicity is paramount. Traditionally, only syngenetic structures with cellular elaboration, hollow sheaths/cell walls, and indigenous kerogen have been considered bona fide fossils. Recent reports of inorganically preserved microfossils represent a shift from this practice. Such a shift, if accompanied by a robust set of biogenicity criteria, could have profound implications for the identification of biosignatures on early Earth and extraterrestrial bodies. Here, we reaffirm the conventional criteria by examining aggregates of inorganic filaments from the Pilbara region of Western Australia. These aggregates are preserved in bedded chert, and the filaments measure up to 1 μm in diameter and 100 μm in length. The aggregates superficially resemble kerogenous microbial fabrics and mycelial organisms. However, the filaments consist of manganese oxide, lack cellular elaboration, and show no evidence for hollow sheaths or cell walls. We conclude that the filaments are fibrous minerals of abiotic origin. The similarities between these pseudofossils and some filamentous fossils highlight the need for strict application of the conventional criteria for recognizing microfossils. In the absence of kerogen, morphologically simple structures should, at least, show evidence of cellular features to be considered bona fide fossils. Key Words: Fossil-Manganese oxide-Pilbara-Precambrian-Pseudofossil. Astrobiology 18, 249-258.
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Affiliation(s)
- A D Muscente
- 1 Department of Earth and Planetary Sciences, Harvard , Cambridge, Massachusetts
| | - Andrew D Czaja
- 2 Department of Geology, University of Cincinnati , Cincinnati, Ohio
| | - James Tuggle
- 3 Nanoscale Characterization and Fabrication Laboratory, Institute for Critical Technology and Applied Science , Virginia Tech, Blacksburg, Virginia
| | - Christopher Winkler
- 3 Nanoscale Characterization and Fabrication Laboratory, Institute for Critical Technology and Applied Science , Virginia Tech, Blacksburg, Virginia
| | - Shuhai Xiao
- 4 Department of Geosciences, Virginia Tech , Blacksburg, Virginia
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Ivarsson M, Bengtson S, Drake H, Francis W. Fungi in Deep Subsurface Environments. ADVANCES IN APPLIED MICROBIOLOGY 2018; 102:83-116. [PMID: 29680127 DOI: 10.1016/bs.aambs.2017.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The igneous crust of the oceans and the continents represents the major part of Earth's lithosphere and has recently been recognized as a substantial, yet underexplored, microbial habitat. While prokaryotes have been the focus of most investigations, microeukaryotes have been surprisingly neglected. However, recent work acknowledges eukaryotes, and in particular fungi, as common inhabitants of the deep biosphere, including the deep igneous provinces. The fossil record of the subseafloor igneous crust, and to some extent the continental bedrock, establishes fungi or fungus-like organisms as inhabitants of deep rock since at least the Paleoproterozoic, which challenges the present notion of early fungal evolution. Additionally, deep fungi have been shown to play an important ecological role engaging in symbiosis-like relationships with prokaryotes, decomposing organic matter, and being responsible for mineral weathering and formation, thus mediating mobilization of biogeochemically important elements. In this review, we aim at covering the abundance and diversity of fungi in the various igneous rock provinces on Earth as well as describing the ecological impact of deep fungi. We further discuss what consequences recent findings might have for the understanding of the fungal distribution in extensive anoxic environments and for early fungal evolution.
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Affiliation(s)
- Magnus Ivarsson
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark; Swedish Museum of Natural History, Stockholm, Sweden.
| | | | | | - Warren Francis
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark
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48
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Berbee ML, James TY, Strullu-Derrien C. Early Diverging Fungi: Diversity and Impact at the Dawn of Terrestrial Life. Annu Rev Microbiol 2017; 71:41-60. [DOI: 10.1146/annurev-micro-030117-020324] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mary L. Berbee
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
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49
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Hawksworth DL. Research News. IMA Fungus 2017. [DOI: 10.1007/bf03449431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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50
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Affiliation(s)
- Nicola McLoughlin
- Department of Geology and Albany Museum, Rhodes University, Grahamstown, 6140, South Africa
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