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Erdmann EA, Brandhorst AKM, Gorbushina AA, Schumacher J. The Tet-on system for controllable gene expression in the rock-inhabiting black fungus Knufia petricola. Extremophiles 2024; 28:38. [PMID: 39105933 PMCID: PMC11303440 DOI: 10.1007/s00792-024-01354-2] [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: 03/05/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024]
Abstract
Knufia petricola is a black fungus that colonizes sun-exposed surfaces as extreme and oligotrophic environments. As ecologically important heterotrophs and biofilm-formers on human-made surfaces, black fungi form one of the most resistant groups of biodeteriorating organisms. Due to its moderate growth rate in axenic culture and available protocols for its transformation and CRISPR/Cas9-mediated genome editing, K. petricola is used for studying the morpho-physiological adaptations shared by extremophilic and extremotolerant black fungi. In this study, the bacteria-derived tetracycline (TET)-dependent promoter (Tet-on) system was implemented to enable controllable gene expression in K. petricola. The functionality i.e., the dose-dependent inducibility of TET-regulated constructs was investigated by using GFP fluorescence, pigment synthesis (melanin and carotenoids) and restored uracil prototrophy as reporters. The newly generated cloning vectors containing the Tet-on construct, and the validated sites in the K. petricola genome for color-selectable or neutral insertion of expression constructs complete the reverse genetics toolbox. One or multiple genes can be expressed on demand from different genomic loci or from a single construct by using 2A self-cleaving peptides, e.g., for localizing proteins and protein complexes in the K. petricola cell or for using K. petricola as host for the expression of heterologous genes.
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Affiliation(s)
- Eileen A Erdmann
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Antonia K M Brandhorst
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Anna A Gorbushina
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Julia Schumacher
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany.
- Freie Universität Berlin, Berlin, Germany.
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2
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Alessia C, Federica DA, Claudia P, Barbara C, Laura Z, Silvano O. A preliminary survey of the cellular responses of the black fungus Cryomyces antarcticus to long and short-term dehydration. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13309. [PMID: 39075848 PMCID: PMC11286975 DOI: 10.1111/1758-2229.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/08/2024] [Indexed: 07/31/2024]
Abstract
The McMurdo Dry Valleys in Southern Victoria Land, Antarctica, are known for their extreme aridity, cold, and nutrient-poor conditions. These valleys provide a valuable comparison to environments on Mars. The survival of microorganisms in these areas hinges on their ability to withstand dehydration due to the limited availability of liquid water. Some microorganisms have adapted to survive extended periods of metabolic inactivity and dehydration, a physiological response to the harsh conditions in which they exist. This adaptation is significant for astrobiology studies as it allows for testing the resilience of microorganisms under extraterrestrial conditions, exploring the boundaries and potential for life beyond Earth. In this study, we examined the survivability, metabolic activity, cellular membrane integrity, and ultrastructural damage of Cryomyces antarcticus, a eukaryotic organism used for astrobiological studies, following two dehydration processes. We conducted a fast dehydration process, simulating what happens on the surface of Antarctic rocks under typical environmental conditions, and a slow dehydration process, which is commonly used in astrobiological experiments. Our findings revealed a higher percentage of damaged cells following slow dehydration treatments, confirming that rapid dehydration reflects the adaptability of microorganisms to respond to sudden and drastic changes in the Antarctic environment.
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Affiliation(s)
- Cassaro Alessia
- Department of Ecological and Biological SciencesUniversity of TusciaViterboItaly
- Department of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - D' Alò Federica
- Department of Ecological and Biological SciencesUniversity of TusciaViterboItaly
- Institute of Research on Terrestrial EcosystemsNational Research CouncilPorano (TR)Italy
| | - Pacelli Claudia
- Department of Ecological and Biological SciencesUniversity of TusciaViterboItaly
- Human Spaceflight and Scientific Research UnitItalian Space AgencyRomeItaly
| | - Cavalazzi Barbara
- Department of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
- LE STUDIUM Institute for Advanced StudiesOrléansFrance
| | - Zucconi Laura
- Department of Ecological and Biological SciencesUniversity of TusciaViterboItaly
- Institute of Polar SciencesNational Research Council of Italy (CNR‐ISP)MessinaItaly
| | - Onofri Silvano
- Department of Ecological and Biological SciencesUniversity of TusciaViterboItaly
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Catanzaro I, Gerrits R, Feldmann I, Gorbushina AA, Onofri S, Schumacher J. Deletion of the polyketide synthase-encoding gene pks1 prevents melanization in the extremophilic fungus Cryomyces antarcticus. IUBMB Life 2024. [PMID: 39011777 DOI: 10.1002/iub.2895] [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: 02/05/2024] [Accepted: 05/15/2024] [Indexed: 07/17/2024]
Abstract
Cryomyces antarcticus, a melanized cryptoendolithic fungus endemic to Antarctica, can tolerate environmental conditions as severe as those in space. Particularly, its ability to withstand ionizing radiation has been attributed to the presence of thick and highly melanized cell walls, which-according to a previous investigation-may contain both 1,8-dihydroxynaphthalene (DHN) and L-3,4 dihydroxyphenylalanine (L-DOPA) melanin. The genes putatively involved in the synthesis of DHN melanin were identified in the genome of C. antarcticus. Most important is capks1 encoding a non-reducing polyketide synthase (PKS) and being the ortholog of the functionally characterized kppks1 from the rock-inhabiting fungus Knufia petricola. The co-expression of CaPKS1 or KpPKS1 with a 4'-phosphopantetheinyl transferase in Saccharomyces cerevisiae resulted in the formation of a yellowish pigment, suggesting that CaPKS1 is the enzyme providing the precursor for DHN melanin. To dissect the composition and function of the melanin layer in the outer cell wall of C. antarcticus, non-melanized mutants were generated by CRISPR/Cas9-mediated genome editing. Notwithstanding its slow growth (up to months), three independent non-melanized Δcapks1 mutants were obtained. The mutants exhibited growth similar to the wild type and a light pinkish pigmentation, which is presumably due to carotenoids. Interestingly, visible light had an adverse effect on growth of both melanized wild-type and non-melanized Δcapks1 strains. Further evidence that light can pass the melanized cell walls derives from a mutant expressing a H2B-GFP fusion protein, which can be detected by fluorescence microscopy. In conclusion, the study reports on the first genetic manipulation of C. antarcticus, resulting in non-melanized mutants and demonstrating that the melanin is rather of the DHN type. These mutants will allow to elucidate the relevance of melanization for surviving extreme conditions found in the natural habitat as well as in space.
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Affiliation(s)
- Ilaria Catanzaro
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Ecological and Biological Sciences (DEB), Università degli Studi della Tuscia, Viterbo, Italy
| | - Ruben Gerrits
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
| | - Ines Feldmann
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
| | - Anna A Gorbushina
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Silvano Onofri
- Department of Ecological and Biological Sciences (DEB), Università degli Studi della Tuscia, Viterbo, Italy
| | - Julia Schumacher
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
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Paiva DS, Fernandes L, Portugal A, Trovão J. First Genome Sequence of the Microcolonial Black Fungus Saxispiralis lemnorum MUM 23.14: Insights into the Unique Genomic Traits of the Aeminiaceae Family. Microorganisms 2024; 12:104. [PMID: 38257931 PMCID: PMC10820743 DOI: 10.3390/microorganisms12010104] [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: 11/16/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Saxispiralis lemnorum MUM 23.14 is an extremotolerant microcolonial black fungus, originally isolated from a biodeteriorated limestone artwork in Portugal. This recently introduced species belongs to the Aeminiaceae family, representing the second member of this monophyletic clade. This fungus exhibits a unique set of characteristics, including xerophily, cold tolerance, high UV radiation tolerance, and an exceptional ability to thrive in NaCl concentrations of up to 30% while also enduring pH levels ranging from 5 to 11. To gain insights into its genomic traits associated with stress resistance mechanisms, specialization, and their potential implications in stone biodeterioration, we conducted a comprehensive genome sequencing and analysis. This draft genome not only marks the first for the Saxispiralis genus but also the second for the Aeminiaceae family. Furthermore, we performed two comparative genomic analyses: one focusing on the closest relative within the Aeminiaceae family, Aeminium ludgeri, and another encompassing the genome of different extremotolerant black fungi. In this study, we successfully achieved high genome completeness for S. lemnorum and confirmed its close phylogenetic relationship to A. ludgeri. Our findings revealed traits contributing to its extremophilic nature and provided insights into potential mechanisms contributing to stone biodeterioration. Many traits are common to both Aeminiaceae species and are shared with other black fungi, while numerous unique traits may be attributed to species-specific characteristics.
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Affiliation(s)
- Diana S. Paiva
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal (J.T.)
| | - Luís Fernandes
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal (J.T.)
| | - António Portugal
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal (J.T.)
- FitoLab—Laboratory for Phytopathology, Instituto Pedro Nunes (IPN), Rua Pedro Nunes, 3030-199 Coimbra, Portugal
- TERRA—Associate Laboratory for Sustainable Land Use and Ecosystem Services, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - João Trovão
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal (J.T.)
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Paiva DS, Trovão J, Fernandes L, Mesquita N, Tiago I, Portugal A. Expanding the Microcolonial Black Fungi Aeminiaceae Family: Saxispiralis lemnorum gen. et sp. nov. ( Mycosphaerellales), Isolated from Deteriorated Limestone in the Lemos Pantheon, Portugal. J Fungi (Basel) 2023; 9:916. [PMID: 37755024 PMCID: PMC10533162 DOI: 10.3390/jof9090916] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023] Open
Abstract
With an impressive ability to survive in harsh environments, black fungi are an ecological group of melanized fungi that are widely recognized as a major contributor to the biodeterioration of stone cultural heritage materials. As part of the ongoing efforts to study the fungal diversity thriving in a deteriorated limestone funerary art piece at the Lemos Pantheon, a national monument located in Águeda, Portugal, two isolates of an unknown microcolonial black fungus were retrieved. These isolates were thoroughly studied through a comprehensive analysis based on a multi-locus phylogeny of a combined dataset of ITS rDNA, LSU, and rpb2, along with morphological, physiological, and ecological characteristics. Based on the data obtained from this integrative analysis, we propose a new genus, Saxispiralis gen. nov., and a new species, Saxispiralis lemnorum sp. nov., in the recently described Aeminiaceae family (order Mycosphaerellales). Prior to this discovery, this family only had one known genus and species, Aeminium ludgeri, also isolated from deteriorated limestone. Additionally, considering the isolation source of the fungus and to better understand its potential contribution to the overall stone monument biodeterioration, its in vitro biodeteriorative potential was also evaluated. This work represents a significant contribution to the understanding of the fungal diversity involved in the biodeterioration of limestone heritage.
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Affiliation(s)
- Diana S. Paiva
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - João Trovão
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Luís Fernandes
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Nuno Mesquita
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Igor Tiago
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - António Portugal
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab—Laboratory for Phytopathology, Instituto Pedro Nunes (IPN), Rua Pedro Nunes, 3030-199 Coimbra, Portugal
- TERRA—Associate Laboratory for Sustainable Land Use and Ecosystem Services, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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Paiva DS, Fernandes L, Pereira E, Trovão J, Mesquita N, Tiago I, Portugal A. Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation-A Case Study in the Limestones of Lemos Pantheon (Portugal). J Fungi (Basel) 2023; 9:jof9040501. [PMID: 37108954 PMCID: PMC10143818 DOI: 10.3390/jof9040501] [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: 03/20/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, we explored the biodiversity and abundance of culturable fungi in four samples associated with different biodeterioration outlines collected from the Lemos Pantheon, a limestone-built artwork in Portugal. We compared the results from prolonged standard freezing with those previously obtained from fresh samples to analyze differences in the obtained community and assess the effectiveness of the standard freezing incubation protocol in uncovering a different segment of culturable fungal diversity. Our results showed a slight decrease in culturable diversity, but over 70% of the obtained isolates were not present in the previously studied fresh samples. We also identified a high number of potential new species with this procedure. Moreover, the use of a wide variety of selective culture media positively influenced the diversity of the cultivable fungi obtained in this study. These findings highlight the importance of developing new protocols under varying conditions to accurately characterize the culturable fraction in a given sample. The identification and study of these communities and their possible contribution to the biodeterioration process is crucial knowledge for formulating effective conservation and restoration plans to prevent further damage to valuable cultural heritage assets.
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Affiliation(s)
- Diana S Paiva
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Luís Fernandes
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Emília Pereira
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - João Trovão
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab-Laboratory for Phytopathology, Instituto Pedro Nunes, Rua Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Nuno Mesquita
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Igor Tiago
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - António Portugal
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab-Laboratory for Phytopathology, Instituto Pedro Nunes, Rua Pedro Nunes, 3030-199 Coimbra, Portugal
- TERRA-Associate Laboratory for Sustainable Land Use and Ecosystem Services, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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Coleine C, Delgado-Baquerizo M, Zerboni A, Turchetti B, Buzzini P, Franceschi P, Selbmann L. Rock Traits Drive Complex Microbial Communities at the Edge of Life. ASTROBIOLOGY 2023; 23:395-406. [PMID: 36812458 DOI: 10.1089/ast.2022.0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Antarctic deserts are among the driest and coldest ecosystems of the planet; there, some microbes survive under these extreme conditions inside porous rocks, forming the so-called endolithic communities. Yet the contribution of distinct rock traits to support complex microbial assemblies remains poorly determined. Here, we combined an extensive Antarctic rock survey with rock microbiome sequencing and ecological networks and found that contrasting combinations of microclimatic and rock traits such as thermal inertia, porosity, iron concentration, and quartz cement can help explain the multiple complex microbial assemblies found in Antarctic rocks. Our work highlights the pivotal role of rocky substrate heterogeneity in sustaining contrasting groups of microorganisms, which is essential to understand life at the edge on Earth and for the search for life on other rocky planets such as Mars.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "A. Desio", Università degli Studi di Milano, Milano, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Pietro Franceschi
- Research and Innovation Center, Fondazione Edmund Mach, Trento, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
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Lin L, Xu J. Production of Fungal Pigments: Molecular Processes and Their Applications. J Fungi (Basel) 2022; 9:44. [PMID: 36675865 PMCID: PMC9866555 DOI: 10.3390/jof9010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/24/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022] Open
Abstract
Due to the negative environmental and health effects of synthetic colorants, pigments of natural origins of plants and microbes constitute an abundant source for the food, cosmetic, textile, and pharmaceutical industries. The demands for natural alternatives, which involve natural colorants and natural biological processes for their production, have been growing rapidly in recent decades. Fungi contain some of the most prolific pigment producers, and they excel in bioavailability, yield, cost-effectiveness, and ease of large-scale cell culture as well as downstream processing. In contrast, pigments from plants are often limited by seasonal and geographic factors. Here, we delineate the taxonomy of pigmented fungi and fungal pigments, with a focus on the biosynthesis of four major categories of pigments: carotenoids, melanins, polyketides, and azaphilones. The molecular mechanisms and metabolic bases governing fungal pigment biosynthesis are discussed. Furthermore, we summarize the environmental factors that are known to impact the synthesis of different fungal pigments. Most of the environmental factors that enhance fungal pigment production are related to stresses. Finally, we highlight the challenges facing fungal pigment utilization and future trends of fungal pigment development. This integrated review will facilitate further exploitations of pigmented fungi and fungal pigments for broad applications.
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Affiliation(s)
- Lan Lin
- Medical School, School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Diseases (MOE), Southeast University, Nanjing 210009, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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Villa F, Wu YL, Zerboni A, Cappitelli F. In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface. Bioscience 2022; 72:1156-1175. [PMID: 36451971 PMCID: PMC9699719 DOI: 10.1093/biosci/biac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.
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Juncheed K, Tanunchai B, Wahdan SFM, Thongsuk K, Schädler M, Noll M, Purahong W. Dark side of a bio-based and biodegradable plastic? Assessment of pathogenic microbes associated with poly(butylene succinate-co-adipate) under ambient and future climates using next-generation sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:966363. [PMID: 36311114 PMCID: PMC9610124 DOI: 10.3389/fpls.2022.966363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Bio-based and biodegradable plastic mulching films have been proposed to replace the non-biodegradable plastic mulch films to solve plastic pollution problems in agricultural soils. However, the impact of bio-based and biodegradable plastics on plant and human health remains largely unexplored. Here, we aimed to assess the risk under field conditions of a bio-based and biodegradable poly(butylene succinate-co-adipate; PBSA), a widely used mulching film as carrier of potential pathogenic microorganisms (bacteria and fungi) at ambient and future climate conditions. Overall, we affiliated 64 fungal and 11 bacterial operational taxonomic units (OTUs) as pathogens by using Next-Generation Sequencing approach. Our results revealed that PBSA hosted at least 53 plant pathogens, of which 51 were classified as fungi, while the other two were bacteria. Most fungal plant pathogens were able to withstand the anticipated future climate changes. We detected 13 fungal and eight bacterial OTUs, which were classified as opportunistic human pathogens. Only one bacterial OTU (Enterococcus faecium) was assigned to a human pathogen. While future climate conditions only significantly impacted on the presence and frequency of detection of few pathogens, incubation time was found to significantly impacted on nine pathogens. This result demonstrates the temporal dynamics of pathogens associated with PBSA. The threats to plant and human health were discussed. We emphasize that the risks to human health are relatively low because we mainly found opportunistic pathogens associated with PBSA and the amount are comparable to the plant debris. However, the risks to plant health may be considered as moderate because many plant pathogens were discovered and/or enriched in PBSA. Furthermore, in soil environments, the pathogenic risk of plastic is highly depending on the surrounding soil pathobiome where plastic is being decomposed.
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Affiliation(s)
- Kantida Juncheed
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
| | - Benjawan Tanunchai
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Sara Fareed Mohamed Wahdan
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Katikarn Thongsuk
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
| | - Martin Schädler
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
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Erdmann EA, Nitsche S, Gorbushina AA, Schumacher J. Genetic Engineering of the Rock Inhabitant Knufia petricola Provides Insight Into the Biology of Extremotolerant Black Fungi. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:862429. [PMID: 37746170 PMCID: PMC10512386 DOI: 10.3389/ffunb.2022.862429] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/02/2022] [Indexed: 09/26/2023]
Abstract
Black microcolonial fungi (Ascomycetes from Arthonio-, Dothideo-, and Eurotiomycetes) are stress-tolerant and persistent dwellers of natural and anthropogenic extreme habitats. They exhibit slow yeast-like or meristematic growth, do not form specialized reproduction structures and accumulate the black pigment 1,8-dihydroxynaphthalene (DHN) melanin in the multilayered cell walls. To understand how black fungi live, survive, colonize mineral substrates, and interact with phototrophs genetic methods are needed to test these functions and interactions. We chose the rock inhabitant Knufia petricola of the Chaetothyriales as a model for developing methods for genetic manipulation. Here, we report on the expansion of the genetic toolkit by more efficient multiplex CRISPR/Cas9 using a plasmid-based system for expression of Cas9 and multiple sgRNAs and the implementation of the three resistance selection markers genR (geneticin/nptII), baR (glufosinate/bar), and suR (chlorimuron ethyl/sur). The targeted integration of expression constructs by replacement of essential genes for pigment synthesis allows for an additional color screening of the transformants. The black-pink screening due to the elimination of pks1 (melanin) was applied for promoter studies using GFP fluorescence as reporter. The black-white screening due to the concurrent elimination of pks1 and phs1 (carotenoids) allows to identify transformants that contain the two expression constructs for co-localization or bimolecular fluorescence complementation (BiFC) studies. The co-localization and interaction of the two K. petricola White Collar orthologs were demonstrated. Two intergenic regions (igr1, igr2) were identified in which expression constructs can be inserted without causing obvious phenotypes. Plasmids of the pNXR-XXX series and new compatible entry plasmids were used for fast and easy generation of expression constructs and are suitable for a broad implementation in other fungi. This variety of genetic tools is opening a completely new perspective for mechanistic and very detailed study of expression, functioning and regulation of the genes/proteins encoded by the genomes of black fungi.
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Affiliation(s)
- Eileen A. Erdmann
- Department of Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Biology Chemistry Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Sarah Nitsche
- Department of Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Biology Chemistry Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Anna A. Gorbushina
- Department of Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Biology Chemistry Pharmacy, Freie Universität Berlin, Berlin, Germany
- Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Julia Schumacher
- Department of Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Biology Chemistry Pharmacy, Freie Universität Berlin, Berlin, Germany
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12
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Jiang X, Van Horn DJ, Okie JG, Buelow HN, Schwartz E, Colman DR, Feeser KL, Takacs-Vesbach CD. Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient. Extremophiles 2022; 26:15. [PMID: 35296937 DOI: 10.1007/s00792-022-01262-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/10/2022] [Indexed: 02/01/2023]
Abstract
Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.
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Affiliation(s)
- Xiaoben Jiang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - David J Van Horn
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jordan G Okie
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - Heather N Buelow
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Daniel R Colman
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kelli L Feeser
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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Liu B, Fu R, Wu B, Liu X, Xiang M. Rock-inhabiting fungi: terminology, diversity, evolution and adaptation mechanisms. Mycology 2022; 13:1-31. [PMID: 35186410 PMCID: PMC8856086 DOI: 10.1080/21501203.2021.2002452] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rock-inhabiting fungi (RIF) constitute an ecological group associated with terrestrial rocks. This association is generally restricted to the persistent colonisation of rocks and peculiar morphological features based on melanisation and slow growth, which endow RIF with significance in eukaryotic biology, special status in ecology, and exotic potential in biotechnology. There is a need to achieve a better understanding of the hidden biodiversity, antistress biology, origin and convergent evolution of RIF, which will facilitate cultural relic preservation, exploitation of the biogeochemical cycle of rock elements and biotechnology applications. This review focuses on summarising the current knowledge of rock-inhabiting fungi, with particular reference to terminology, biodiversity and geographic distribution, origin and evolution, and stress adaptation mechanisms. We especially teased out the definition through summing up the terms related to rock-inhabting fungi, and also provided a checklist of rock-inhabiting fungal taxa recorded following updated classification schemes.
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Affiliation(s)
- Bingjie Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rong Fu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Raman Characterization of Fungal DHN and DOPA Melanin Biosynthesis Pathways. J Fungi (Basel) 2021; 7:jof7100841. [PMID: 34682262 PMCID: PMC8540899 DOI: 10.3390/jof7100841] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/16/2022] Open
Abstract
Fungal melanins represent a resource for important breakthroughs in industry and medicine, but the characterization of their composition, synthesis, and structure is not well understood. Raman spectroscopy is a powerful tool for the elucidation of molecular composition and structure. In this work, we characterize the Raman spectra of wild-type Aspergillus fumigatus and Cryptococcus neoformans and their melanin biosynthetic mutants and provide a rough “map” of the DHN (A. fumigatus) and DOPA (C. neoformans) melanin biosynthetic pathways. We compare this map to the Raman spectral data of Aspergillus nidulans wild-type and melanin biosynthetic mutants obtained from a previous study. We find that the fully polymerized A. nidulans melanin cannot be classified according to the DOPA pathway; nor can it be solely classified according to the DHN pathway, consistent with mutational analysis and chemical inhibition studies. Our approach points the way forward for an increased understanding of, and methodology for, investigating fungal melanins.
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Fungal Melanins and Applications in Healthcare, Bioremediation and Industry. J Fungi (Basel) 2021; 7:jof7060488. [PMID: 34207260 PMCID: PMC8235761 DOI: 10.3390/jof7060488] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/13/2021] [Accepted: 06/13/2021] [Indexed: 01/01/2023] Open
Abstract
Melanin is a complex multifunctional pigment found in all kingdoms of life, including fungi. The complex chemical structure of fungal melanins, yet to be fully elucidated, lends them multiple unique functions ranging from radioprotection and antioxidant activity to heavy metal chelation and organic compound absorption. Given their many biological functions, fungal melanins present many possibilities as natural compounds that could be exploited for human use. This review summarizes the current discourse and attempts to apply fungal melanin to enhance human health, remove pollutants from ecosystems, and streamline industrial processes. While the potential applications of fungal melanins are often discussed in the scientific community, they are successfully executed less often. Some of the challenges in the applications of fungal melanin to technology include the knowledge gap about their detailed structure, difficulties in isolating melanotic fungi, challenges in extracting melanin from isolated species, and the pathogenicity concerns that accompany working with live melanotic fungi. With proper acknowledgment of these challenges, fungal melanin holds great potential for societal benefit in the coming years.
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Tesei D, Chiang AJ, Kalkum M, Stajich JE, Mohan GBM, Sterflinger K, Venkateswaran K. Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos. Front Genet 2021; 12:638708. [PMID: 33815472 PMCID: PMC8012687 DOI: 10.3389/fgene.2021.638708] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Black fungi are a group of melanotic microfungi characterized by remarkable polyextremotolerance. Due to a broad ecological plasticity and adaptations at the cellular level, it is predicted that they may survive in a variety of extreme environments, including harsh niches on Earth and Mars, and in outer space. However, the molecular mechanisms aiding survival, especially in space, are yet to be fully elucidated. Based on these premises, the rock-inhabiting black fungus Knufia chersonesos (Wt) and its non-melanized mutant (Mut) were exposed to simulated microgravity-one of the prevalent features characterizing space conditions-by growing the cultures in high-aspect-ratio vessels (HARVs). Qualitative and quantitative proteomic analyses were performed on the mycelia and supernatant of culture medium (secretome) to assess alterations in cell physiology in response to low-shear simulated microgravity (LSSMG) and to ultimately evaluate the role of cell-wall melanization in stress survival. Differential expression was observed for proteins involved in carbohydrate and lipid metabolic processes, transport, and ribosome biogenesis and translation via ribosomal translational machinery. However, no evidence of significant activation of stress components or starvation response was detected, except for the scytalone dehydratase, enzyme involved in the synthesis of dihydroxynaphthalene (DNH) melanin, which was found to be upregulated in the secretome of the wild type and downregulated in the mutant. Differences in protein modulation were observed between K. chersonesos Wt and Mut, with several proteins being downregulated under LSSMG in the Mut when compared to the Wt. Lastly, no major morphological alterations were observed following exposure to LSSMG. Similarly, the strains' survivability was not negatively affected. This study is the first to characterize the response to simulated microgravity in black fungi, which might have implications on future astrobiological missions.
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Affiliation(s)
- Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Abby J. Chiang
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Ganesh Babu Malli Mohan
- Department of Biotechnology, Centre for Research and Infectious Diseases, SASTRA Deemed University, Thanjavur, India
| | - Katja Sterflinger
- Institute for Natural Sciences and Technology in the Arts, Academy of Fine Arts Vienna, Vienna, Austria
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Geraldes V, Pinto E. Mycosporine-Like Amino Acids (MAAs): Biology, Chemistry and Identification Features. Pharmaceuticals (Basel) 2021; 14:63. [PMID: 33466685 PMCID: PMC7828830 DOI: 10.3390/ph14010063] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 01/16/2023] Open
Abstract
Mycosporines and mycosporine-like amino acids are ultra-violet-absorbing compounds produced by several organisms such as lichens, fungi, algae and cyanobacteria, especially upon exposure to solar ultraviolet radiation. These compounds have photoprotective and antioxidant functions. Mycosporine-like amino acids have been used as a natural bioactive ingredient in cosmetic products. Several reviews have already been developed on these photoprotective compounds, but they focus on specific features. Herein, an extremely complete database on mycosporines and mycosporine-like amino acids, covering the whole class of these natural sunscreen compounds known to date, is presented. Currently, this database has 74 compounds and provides information about the chemistry, absorption maxima, protonated mass, fragments and molecular structure of these UV-absorbing compounds as well as their presence in organisms. This platform completes the previous reviews and is available online for free and in the public domain. This database is a useful tool for natural product data mining, dereplication studies, research working in the field of UV-absorbing compounds mycosporines and being integrated in mass spectrometry library software.
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Affiliation(s)
- Vanessa Geraldes
- School of Pharmaceutical Sciences, University of São Paulo, Avenida Prof. Lineu Prestes, 580, Butantã, São Paulo-SP CEP 05508-000, Brazil;
- Centre for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Piracicaba-SP CEP 13400-970, Brazil
| | - Ernani Pinto
- Centre for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Piracicaba-SP CEP 13400-970, Brazil
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18
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Selbmann L, Benkő Z, Coleine C, de Hoog S, Donati C, Druzhinina I, Emri T, Ettinger CL, Gladfelter AS, Gorbushina AA, Grigoriev IV, Grube M, Gunde-Cimerman N, Karányi ZÁ, Kocsis B, Kubressoian T, Miklós I, Miskei M, Muggia L, Northen T, Novak-Babič M, Pennacchio C, Pfliegler WP, Pòcsi I, Prigione V, Riquelme M, Segata N, Schumacher J, Shelest E, Sterflinger K, Tesei D, U’Ren JM, Varese GC, Vázquez-Campos X, Vicente VA, Souza EM, Zalar P, Walker AK, Stajich JE. Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES. Life (Basel) 2020; 10:life10120362. [PMID: 33352712 PMCID: PMC7767062 DOI: 10.3390/life10120362] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 01/01/2023] Open
Abstract
The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the “Shed light in The daRk lineagES of the fungal tree of life” (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments.
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Affiliation(s)
- Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy;
- Section of Mycology, Italian National Antarctic Museum (MNA), 16121 Genoa, Italy
- Correspondence: (L.S.); (J.E.S.); Tel.: +39-0761-357012 (L.S.); +1-951-827-2363 (J.E.S.)
| | - Zsigmond Benkő
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy;
| | - Sybren de Hoog
- Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, 6532 Nijmegen, The Netherlands;
| | - Claudio Donati
- Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy;
| | - Irina Druzhinina
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China;
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Cassie L. Ettinger
- Genome Center, University of California, Davis, CA 95616, USA;
- Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA;
| | - Amy S. Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA;
| | - Anna A. Gorbushina
- Department of Materials and Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), 10115 Berlin, Germany; (A.A.G.); (J.S.)
- Department of Earth Sciences & Department of Biology, Chemistry, Pharmacy, Freie Universität, Berlin 10115 Berlin, Germany
| | - Igor V. Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; (I.V.G.); (T.N.); (C.P.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Martin Grube
- Institute of Biology, University of Graz, Graz A-8010, Austria;
| | - Nina Gunde-Cimerman
- Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (N.G.-C.); (M.N.-B.); (P.Z.)
| | - Zsolt Ákos Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Beatrix Kocsis
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Tania Kubressoian
- Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA;
| | - Ida Miklós
- Department of Genetics and Applied Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary;
| | - Márton Miskei
- Department of Biochemistry and Molecular Biology, Faculty of Medicine University of Debrecen, 4032 Debrecen, Hungary;
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, 34121 Trieste, Italy;
| | - Trent Northen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; (I.V.G.); (T.N.); (C.P.)
| | - Monika Novak-Babič
- Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (N.G.-C.); (M.N.-B.); (P.Z.)
| | - Christa Pennacchio
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; (I.V.G.); (T.N.); (C.P.)
| | - Walter P. Pfliegler
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Istvàn Pòcsi
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Valeria Prigione
- Mycotheca Universitatis Taurinensis, University of Torino, 10125 Torino, Italy; (V.P.); (G.C.V.)
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Baja California 22980, Mexico;
| | - Nicola Segata
- Department CIBIO, University of Trento, 38123 Trento, Italy;
| | - Julia Schumacher
- Department of Materials and Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), 10115 Berlin, Germany; (A.A.G.); (J.S.)
| | - Ekaterina Shelest
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2UP, UK;
| | - Katja Sterflinger
- Institute of Natural Sciences and Technology in the Arts, Academy of Fine Arts Vienna, Vienna 22180, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 22180, Austria;
| | - Jana M. U’Ren
- Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA;
| | - Giovanna C. Varese
- Mycotheca Universitatis Taurinensis, University of Torino, 10125 Torino, Italy; (V.P.); (G.C.V.)
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2006, Australia;
| | - Vania A. Vicente
- Department of Biochemistry, Federal University of Paraná, Paraná E3100, Brazil; (V.A.V.); (E.M.S.)
| | - Emanuel M. Souza
- Department of Biochemistry, Federal University of Paraná, Paraná E3100, Brazil; (V.A.V.); (E.M.S.)
| | - Polona Zalar
- Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (N.G.-C.); (M.N.-B.); (P.Z.)
| | - Allison K. Walker
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada;
| | - Jason E. Stajich
- Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA;
- Correspondence: (L.S.); (J.E.S.); Tel.: +39-0761-357012 (L.S.); +1-951-827-2363 (J.E.S.)
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An advanced genetic toolkit for exploring the biology of the rock-inhabiting black fungus Knufia petricola. Sci Rep 2020; 10:22021. [PMID: 33328531 PMCID: PMC7745021 DOI: 10.1038/s41598-020-79120-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/03/2020] [Indexed: 01/09/2023] Open
Abstract
Microcolonial black fungi are a group of ascomycetes that exhibit high stress tolerance, yeast-like growth and constitutive melanin formation. They dominate a range of hostile natural and man-made environments, from desert rocks and salterns to dishwashers, roofs and solar panels. Due to their slow growth and a lack of genetic tools, the underlying mechanisms of black fungi’s phenotypic traits have remained largely unexplored. We chose to address this gap by genetically engineering the rock-inhabiting fungus Knufia petricola (Eurotiomycetes, Chaetothyriales), a species that exhibits all characteristics of black fungi. A cell biological approach was taken by generating K. petricola strains expressing green or red fluorescent protein variants. By applying: (1) traditional gene replacement; (2) gene editing and replacement via plasmid-based or ribonucleoprotein (RNP)-based CRISPR/Cas9, and (3) silencing by RNA interference (RNAi), we constructed mutants in the pathways leading to melanin, carotenoids, uracil and adenine. Stable single and double mutants were generated with homologous recombination (HR) rates up to 100%. Efficient, partially cloning-free strategies to mutate multiple genes with or without resistance cassettes were developed. This state-of-the-art genetic toolkit, together with the annotated genome sequence of strain A95, firmly established K. petricola as a model for exploring microcolonial black fungi.
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Coleine C, Stajich JE, de Los Ríos A, Selbmann L. Beyond the extremes: Rocks as ultimate refuge for fungi in drylands. Mycologia 2020; 113:108-133. [PMID: 33232202 DOI: 10.1080/00275514.2020.1816761] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In an era of rapid climate change and expansion of desertification, the extremely harsh conditions of drylands are a true challenge for microbial life. Under drought conditions, where most life forms cannot survive, rocks represent the main refuge for life. Indeed, the endolithic habitat provides thermal buffering, physical stability, and protection against incident ultraviolet (UV) radiation and solar radiation and, to some extent, ensures water retention to microorganisms. The study of these highly specialized extreme-tolerant and extremophiles may provide tools for understanding microbial interactions and processes that allow them to keep their metabolic machinery active under conditions of dryness and oligotrophy that are typically incompatible with active life, up to the dry limits for life. Despite lithobiontic communities being studied all over the world, a comprehensive understanding of their ecology, evolution, and adaptation is still nascent. Herein, we survey the fungal component of these microbial ecosystems. We first provide an overview of the main defined groups (i.e., lichen-forming fungi, black fungi, and yeasts) of the most known and studied Antarctic endolithic communities that are almost the only life forms ensuring ecosystem functionality in the ice-free areas of the continent. For each group, we discuss their main traits and their diversity. Then, we focus on the fungal taxonomy and ecology of other worldwide endolithic communities. Finally, we highlight the utmost importance of a global rock survey in order to have a comprehensive view of the diversity, distribution, and functionality of these fungi in drylands, to obtain tools in desert area management, and as early alarm systems to climate change.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia , Largo dell'Università snc, 01100, Viterbo, Italy
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, 900 University Ave , Riverside, California 92521
| | - Asunción de Los Ríos
- Department of Biogeochemistry and Microbial Ecology, Museo Nacional de Ciencias Naturales, Spanish National Resource Council, Madrid, Spain
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia , Largo dell'Università snc, 01100, Viterbo, Italy.,Italian National Antarctic Museum, Mycological Section, Genoa, Italy
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21
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Unveiling the Hidden Diversity of Rock-Inhabiting Fungi: Chaetothyriales from China. J Fungi (Basel) 2020; 6:jof6040187. [PMID: 32987844 PMCID: PMC7711927 DOI: 10.3390/jof6040187] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022] Open
Abstract
Rock-inhabiting fungi (RIF) are nonlichenized fungi that naturally colonize rock surfaces and subsurfaces. The extremely slow growth rate and lack of distinguishing morphological characteristics of RIF resulted in a poor understanding on their biodiversity. In this study, we surveyed RIF colonizing historical stone monuments and natural rock formations from throughout China. Among over 1000 isolates, after preliminary delimitation using the internal transcribed spacer region (ITS) sequences, representative isolates belonging to Trichomeriaceae and Herpotrichiellaceae were selected for a combined analysis of ITS and the nuclear ribosomal large subunit (nucLSU) to determine the generic placements. Eight clades representing seven known genera and one new genus herein named as Anthracina were placed in Trichomeriaceae. While, for Herpotrichiellaceae, two clades corresponded to two genera: Cladophialophora and Exophiala. Fine-scale phylogenetic analyses using combined sequences of the partial actin gene (ACT), ITS, mitochondrial small subunit ribosomal DNA (mtSSU), nucLSU, the largest subunit of RNA polymerase II (RPB1), small subunit of nuclear ribosomal RNA gene (SSU), translation elongation factor (TEF), and β-tubulin gene (TUB) revealed that these strains represented 11 and 6 new species, respectively, in Trichomeriaceae and Herpotrichiellaceae. The 17 new species were described, illustrated for their morphologies and compared with similar taxa. Our study demonstrated that the diversity of RIF is surprisingly high and still poorly understood. In addition, a rapid strategy for classifying RIF was proposed to determine the generic and familial placements through preliminary ITS and nucLSU analyses, followed by combined analyses of five loci selected from ACT, ITS, mtSSU, nucLSU, RPB1, and/or the second subunit of RNA polymerase II gene (RPB2), SSU, TEF, and TUB regions to classify RIF to the species level.
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22
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Pinek L, Mansour I, Lakovic M, Ryo M, Rillig MC. Rate of environmental change across scales in ecology. Biol Rev Camb Philos Soc 2020; 95:1798-1811. [PMID: 32761787 DOI: 10.1111/brv.12639] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 12/27/2022]
Abstract
The rate of change (RoC) of environmental drivers matters: biotic and abiotic components respond differently when faced with a fast or slow change in their environment. This phenomenon occurs across spatial scales and thus levels of ecological organization. We investigated the RoC of environmental drivers in the ecological literature and examined publication trends across ecological levels, including prevalent types of evidence and drivers. Research interest in environmental driver RoC has increased over time (particularly in the last decade), however, the amount of research and type of studies were not equally distributed across levels of organization and different subfields of ecology use temporal terminology (e.g. 'abrupt' and 'gradual') differently, making it difficult to compare studies. At the level of individual organisms, evidence indicates that responses and underlying mechanisms are different when environmental driver treatments are applied at different rates, thus we propose including a time dimension into reaction norms. There is much less experimental evidence at higher levels of ecological organization (i.e. population, community, ecosystem), although theoretical work at the population level indicates the importance of RoC for evolutionary responses. We identified very few studies at the community and ecosystem levels, although existing evidence indicates that driver RoC is important at these scales and potentially could be particularly important for some processes, such as community stability and cascade effects. We recommend shifting from a categorical (e.g. abrupt versus gradual) to a quantitative and continuous (e.g. °C/h) RoC framework and explicit reporting of RoC parameters, including magnitude, duration and start and end points to ease cross-scale synthesis and alleviate ambiguity. Understanding how driver RoC affects individuals, populations, communities and ecosystems, and furthermore how these effects can feed back between levels is critical to making improved predictions about ecological responses to global change drivers. The application of a unified quantitative RoC framework for ecological studies investigating environmental driver RoC will both allow cross-scale synthesis to be accomplished more easily and has the potential for the generation of novel hypotheses.
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Affiliation(s)
- Liliana Pinek
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, D-14195, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - India Mansour
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, D-14195, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Milica Lakovic
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, D-14195, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Masahiro Ryo
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, D-14195, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Matthias C Rillig
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, D-14195, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
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23
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Schumacher J, Gorbushina AA. Light sensing in plant- and rock-associated black fungi. Fungal Biol 2020; 124:407-417. [DOI: 10.1016/j.funbio.2020.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/09/2020] [Accepted: 01/17/2020] [Indexed: 01/24/2023]
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24
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Coleine C, Pombubpa N, Zucconi L, Onofri S, Stajich JE, Selbmann L. Endolithic Fungal Species Markers for Harshest Conditions in the McMurdo Dry Valleys, Antarctica. Life (Basel) 2020; 10:E13. [PMID: 32041249 PMCID: PMC7175349 DOI: 10.3390/life10020013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/24/2020] [Accepted: 02/04/2020] [Indexed: 02/03/2023] Open
Abstract
The microbial communities that inhabit lithic niches inside sandstone in the Antarctic McMurdo Dry Valleys of life's limits on Earth. The cryptoendolithic communities survive in these ice-free areas that have the lowest temperatures on Earth coupled with strong thermal fluctuations, extreme aridity, oligotrophy and high levels of solar and UV radiation. In this study, based on DNA metabarcoding, targeting the fungal Internal Transcribed Spacer region 1 (ITS1) and multivariate statistical analyses, we supply the first comprehensive overview onto the fungal diversity and composition of these communities sampled over a broad geographic area of the Antarctic hyper-arid cold desert. Six locations with surfaces that experience variable sun exposure were sampled to compare communities from a common area across a gradient of environmental pressure. The Operational Taxonomic Units (OTUs) identified were primarily members of the Ascomycota phylum, comprised mostly of the Lecanoromycetes and Dothideomycetes classes. The fungal species Friedmanniomyces endolithicus, endemic to Antarctica, was found to be a marker species to the harshest conditions occurring in the shady, south exposed rock surfaces. Analysis of community composition showed that sun exposure was an environmental property that explained community diversity and structured endolithic colonization.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (C.C.); (L.Z.); (S.O.)
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA;
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (C.C.); (L.Z.); (S.O.)
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (C.C.); (L.Z.); (S.O.)
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA;
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (C.C.); (L.Z.); (S.O.)
- Italian National Antarctic Museum (MNA), Mycological Section, 16166 Genoa, Italy
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25
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Looby CI, Hollenbeck EC, Treseder KK. Fungi in the Canopy: How Soil Fungi and Extracellular Enzymes Differ Between Canopy and Ground Soils. Ecosystems 2019. [DOI: 10.1007/s10021-019-00439-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Abstract
Tropical montane cloud forests contain a large abundance and diversity of canopy epiphytes, which depend on canopy soil to retain water and nutrients. We lack an in depth understanding of how these soils contribute to ecosystem processes and soil diversity and how sensitive they may be to projected climate change. We compared canopy and ground soils in Monteverde, Costa Rica, to determine how these two soil types differ in their extracellular enzyme activity (EEA) and fungal communities. Samples were also collected along two elevation gradients to reveal if canopy soils differed in how EEA and fungal communities responded to elevation compared to ground soils. We found that canopy soils had higher EEA than ground soils. Fungal communities were less diverse and differed significantly between the two soil types. These differences were associated with higher relative abundances of yeasts and endophytes in canopy soils. The relative abundances of free-living filamentous fungi and yeasts shifted more dramatically with elevation in canopy soils compared to ground soils. Our study suggests that canopy soils may be a reservoir for endophytes. Epiphytes may invest in symbionts that promote stress tolerance over mycorrhizal fungi whose high resource demands are costly and less beneficial. Overall, soils harbor distinct fungal communities that may be altered under projected climate change.
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26
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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27
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Kirchhoff L, Olsowski M, Rath PM, Steinmann J. Exophiala dermatitidis: Key issues of an opportunistic fungal pathogen. Virulence 2019; 10:984-998. [PMID: 30887863 PMCID: PMC8647849 DOI: 10.1080/21505594.2019.1596504] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The black yeast Exophiala dermatitidis is an opportunistic pathogen, causing phaeohyphomycosis in immunosuppressed patients, chromoblastomycosis and fatal infections of the central nervous system in otherwise healthy Asian patients. In addition, it is also regularly isolated from respiratory samples from cystic fibrosis patients, with rates varying between 1% and 19%.Melanin, as part of the cell wall of black yeasts, is one major factor known contributing to the pathogenicity of E. dermatitidis and increased resistance against host defense and anti-infective therapeutics. Further virulence factors, e.g. the capability to adhere to surfaces and to form biofilm were reported. A better understanding of the pathogenicity of E. dermatitidis is essential for the development of novel preventive and therapeutic strategies. In this review, the current knowledge of E. dermatitidis prevalence, clinical importance, diagnosis, microbiological characteristics, virulence attributes, susceptibility, and resistances as well as therapeutically strategies are discussed.
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Affiliation(s)
- Lisa Kirchhoff
- Institute of Medical Microbiology, Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Maike Olsowski
- Institute of Medical Microbiology, Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Klinikum Nürnberg, Paracelsus Medical University, Nuremberg, Germany
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28
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Giauque H, Connor EW, Hawkes CV. Endophyte traits relevant to stress tolerance, resource use and habitat of origin predict effects on host plants. THE NEW PHYTOLOGIST 2019; 221:2239-2249. [PMID: 30276818 DOI: 10.1111/nph.15504] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/19/2018] [Indexed: 05/16/2023]
Abstract
All terrestrial plants are colonized by foliar endophytic fungi that can affect plant growth and physiology, but the prediction of these effects on the plant host remains a challenge. Here, we examined three paradigms that potentially control how endophytes affect plant hosts: habitat adaptation, evolutionary history and functional traits. We screened 35 plant-endophyte pairings in a microcosm experiment under well-watered and drought conditions with Panicum virgatum as the host. We related the measured plant responses to fungal phylogenetic relatedness, characteristics of fungal habitats across a rainfall gradient and functional traits of the fungi related to stress tolerance and resource use. The functional traits and habitat characteristics of the fungi predicted 26-53% of endophyte-mediated effects on measures of plant growth, physiology and survival. Overall, survival was higher for plants grown with more stress-tolerant fungi, and aboveground biomass was enhanced by fungi from warmer and drier habitats. Plant growth and physiology were also dependent on fungal resource use indicators; however, specific predictors were dependent on water availability. Simple ecological traits of foliar endophytic fungi observed in culture can translate to symbiotic lifestyles. These findings offer new insights and key testable predictions for likely pathways by which endophytes benefit the plant host.
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Affiliation(s)
- Hannah Giauque
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Elise W Connor
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Christine V Hawkes
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27965, USA
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29
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Trovão J, Tiago I, Soares F, Paiva DS, Mesquita N, Coelho C, Catarino L, Gil F, Portugal A. Description of Aeminiaceae fam. nov., Aeminium gen. nov. and Aeminiumludgeri sp. nov. (Capnodiales), isolated from a biodeteriorated art-piece in the Old Cathedral of Coimbra, Portugal. MycoKeys 2019:57-73. [PMID: 30728746 PMCID: PMC6361875 DOI: 10.3897/mycokeys.45.31799] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/06/2019] [Indexed: 11/12/2022] Open
Abstract
When colonizing stone monuments, microcolonial black fungi are considered one of the most severe and resistant groups of biodeteriorating organisms, posing a very difficult challenge to conservators and biologists working with cultural heritage preservation. During an experimental survey aimed to isolate fungi from a biodeteriorated limestone art piece in the Old Cathedral of Coimbra, Portugal (a UNESCO World Heritage Site), an unknown microcolonial black fungus was retrieved. The isolated fungus was studied through a complete examination based on multilocus phylogeny of a combined dataset of ITS rDNA, LSU and rpb2, in conjunction with morphological, physiological, and ecological characteristics. This integrative analysis allows for the description of a new family, Aeminiaceae fam. nov., a new genus Aeminium gen. nov., and a new species, Aeminiumludgeri sp. nov., in the order Capnodiales.
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Affiliation(s)
- João Trovão
- Centre for Functional Ecology, Science for People and the Planet, University of Coimbra, Coimbra, Portugal University of Coimbra Coimbra Portugal
| | - Igor Tiago
- Centre for Functional Ecology, Science for People and the Planet, University of Coimbra, Coimbra, Portugal University of Coimbra Coimbra Portugal
| | - Fabiana Soares
- Centre for Functional Ecology, Science for People and the Planet, University of Coimbra, Coimbra, Portugal University of Coimbra Coimbra Portugal
| | - Diana Sofia Paiva
- Laboratory for Plant Health (Fitolab), Instituto Pedro Nunes, Coimbra, Portugal Instituto Pedro Nunes Coimbra Portugal
| | - Nuno Mesquita
- Centre for Functional Ecology, Science for People and the Planet, University of Coimbra, Coimbra, Portugal University of Coimbra Coimbra Portugal
| | - Catarina Coelho
- Centre for Functional Ecology, Science for People and the Planet, University of Coimbra, Coimbra, Portugal University of Coimbra Coimbra Portugal
| | - Lídia Catarino
- Geosciences Center, University of Coimbra, Coimbra, Portugal University of Coimbra Coimbra Portugal
| | - Francisco Gil
- Center for Physics of the University of Coimbra (CfisUC), Coimbra, Portugal Instituto Pedro Nunes Coimbra Portugal
| | - António Portugal
- Centre for Functional Ecology, Science for People and the Planet, University of Coimbra, Coimbra, Portugal University of Coimbra Coimbra Portugal
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30
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Pacelli C, Selbmann L, Zucconi L, Coleine C, de Vera JP, Rabbow E, Böttger U, Dadachova E, Onofri S. Responses of the Black Fungus Cryomyces antarcticus to Simulated Mars and Space Conditions on Rock Analogs. ASTROBIOLOGY 2019; 19:209-220. [PMID: 30067087 DOI: 10.1089/ast.2016.1631] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The BIOMEX (BIOlogy and Mars Experiment) is part of the European Space Agency (ESA) space mission EXPOSE-R2 in Low-Earth Orbit, devoted to exposing microorganisms for 1.5 years to space and simulated Mars conditions on the International Space Station. In preparing this mission, dried colonies of the Antarctic cryptoendolithic black fungus Cryomyces antarcticus CCFEE 515, grown on martian and lunar analog regolith pellets, were subjected to several ground-based preflight tests, Experiment Verification Tests, and Science Verification Tests (SVTs) that were performed to verify (i) the resistance of our model organism to space stressors when grown on extraterrestrial rock analogs and (ii) the possibility of detecting biomolecules as potential biosignatures. Here, the results of the SVTs, the last set of experiments, which were performed in ultraviolet radiation combined with simulated space vacuum or simulated martian conditions, are reported. The results demonstrate that C. antarcticus was able to tolerate the conditions of the SVT experiment, regardless of the substratum in which it was grown. DNA maintained high integrity after treatments and was confirmed as a possible biosignature; melanin, which was chosen to be a target for biosignature detection, was unambiguously detected by Raman spectroscopy.
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Affiliation(s)
- Claudia Pacelli
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Laura Selbmann
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
- 2 Section of Mycology, Italian Antarctic National Museum (MNA), Genoa, Italy
| | - Laura Zucconi
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Claudia Coleine
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Jean-Pierre de Vera
- 3 Institute of Planetary Research, German Aerospace Center (DLR) Berlin, Berlin, Germany
| | - Elke Rabbow
- 4 German Aerospace Centre, Institute of Aerospace Medicine (DLR), Köln, Germany
| | - Ute Böttger
- 5 Institute of Optical Sensor Systems, German Aerospace Center (DLR) Berlin, Berlin, Germany
| | - Ekaterina Dadachova
- 6 College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Silvano Onofri
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
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31
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Bao R, Gao N, Lv J, Ji C, Liang H, Li S, Yu C, Wang Z, Lin X. Enhancement of Torularhodin Production in Rhodosporidium toruloides by Agrobacterium tumefaciens-Mediated Transformation and Culture Condition Optimization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1156-1164. [PMID: 30607946 DOI: 10.1021/acs.jafc.8b04667] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nine transformants of Rhodosporidium toruloides with significant changes in the carotenoid profile were obtained by Agrobacterium tumefaciens-mediated transformation, including a white, three red, and four yellow mutants. A red mutant A1-15-BRQ that showed a high torularhodin production was selected for culture condition optimization. Results indicated that the torularhodin yield was boosted with glucose as the carbon source, at a carbon/nitrogen ratio of 22, a loading volume of 75 mL, and 28 °C. The torularhodin yield of 21.3 mg/L consisting of 94.4% total carotenoids was obtained by Box-Behnken design experiments. The torularhodin yield was 17.0-fold higher than that of the wild type, with time shortened from 9 to 3 days. This study reports an effective strategy for improving torularhodin production and provides a candidate R. toruloides strain for highly selective production of torularhodin.
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Affiliation(s)
- Ruiqi Bao
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , 1 Qinggongyuan , Dalian , Liaoning 116034 , People's Republic of China
| | - Ning Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , 457 Zhongshan Road , Dalian , Liaoning 116023 , People's Republic of China
| | - Jing Lv
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , 1 Qinggongyuan , Dalian , Liaoning 116034 , People's Republic of China
| | - Chaofan Ji
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , 1 Qinggongyuan , Dalian , Liaoning 116034 , People's Republic of China
| | - Huipeng Liang
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , 1 Qinggongyuan , Dalian , Liaoning 116034 , People's Republic of China
| | - Shengjie Li
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , 1 Qinggongyuan , Dalian , Liaoning 116034 , People's Republic of China
| | - Chenxu Yu
- Department of Agricultural and Biosystems Engineering , Iowa State University , Ames , Iowa 50011 , United States
| | - Zhenyu Wang
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , 1 Qinggongyuan , Dalian , Liaoning 116034 , People's Republic of China
| | - Xinping Lin
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , 1 Qinggongyuan , Dalian , Liaoning 116034 , People's Republic of China
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32
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Flieger K, Knabe N, Toepel J. Development of an Improved Carotenoid Extraction Method to Characterize the Carotenoid Composition under Oxidative Stress and Cold Temperature in the Rock Inhabiting Fungus Knufia petricola A95. J Fungi (Basel) 2018; 4:E124. [PMID: 30424015 PMCID: PMC6308947 DOI: 10.3390/jof4040124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 11/21/2022] Open
Abstract
Black yeasts are a highly specified group of fungi, which are characterized by a high resistance against stress factors. There are several factors enabling the cells to survive harsh environmental conditions. One aspect is the pigmentation, the melanin black yeasts often display a highly diverse carotenoid spectrum. Determination and characterization of carotenoids depend on an efficient extraction and separation, especially for black yeast, which is characterized by thick cell walls. Therefore, specific protocols are needed to ensure reliable analyses regarding stress responses in these fungi. Here we present both. First, we present a method to extract and analyze carotenoids and secondly we present the unusual carotenoid composition of the black yeast Knufia petricola A95. Mechanical treatment combined with an acetonitrile extraction gave us very good extraction rates with a high reproducibility. The presented extraction and elution protocol separates the main carotenoids (7) in K. petricola A95 and can be extended for the detection of additional carotenoids in other species. K. petricola A95 displays an unusual carotenoid composition, with mainly didehydrolycopene, torulene, and lycopene. The pigment composition varied in dependency to oxidative stress but remained relatively constant if the cells were cultivated under low temperature. Future experiments have to be carried out to determine if didehydrolycopene functions as a protective agent itself or if it serves as a precursor for antioxidative pigments like torulene and torularhodin, which could be produced after induction under stress conditions. Black yeasts are a promising source for carotenoid production and other substances. To unravel the potential of these fungi, new methods and studies are needed. The established protocol allows the determination of carotenoid composition in black yeasts.
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Affiliation(s)
- Kerstin Flieger
- Department of Plant Physiology, Institute of Biology, Leipzig University, Johannisallee 21-23, 04103 Leipzig, Germany.
| | - Nicole Knabe
- Department of Materials & Environment, Bundesanstalt für Material-forschung und-prüfung, BAM, Unter den Eichen 87, 12205 Berlin, Germany.
| | - Jörg Toepel
- Department of Solar Materials, Applied Biocatalytics, Helmholtz Centre for Environmental Research, Permoser Strasse 15, 04318 Leipzig, Germany.
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Breierová E, Čertík M, Márová I, Vadkertiová R. The Effect of Zn(II) Ions and Reactive Oxygen on the Uptake of Zinc and Production of Carotenoids by Selected Red Yeasts. Chem Biodivers 2018; 15:e1800069. [DOI: 10.1002/cbdv.201800069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/05/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Emília Breierová
- Culture Collection of Yeasts; Institute of Chemistry; Slovak Academy of Sciences; Dúbravská cesta 9 845 38 Bratislava Slovakia
| | - Milan Čertík
- Institute of Biotechnology; Faculty of Chemical and Food Technology; Slovak University of Technology; Radlinského 9 812 37 Bratislava Slovakia
| | - Ivana Márová
- Institute of Food Chemistry and Biotechnology; Faculty of Chemistry; University of Technology; Purkyňova 118 612 00 Brno Czech Republic
| | - Renáta Vadkertiová
- Culture Collection of Yeasts; Institute of Chemistry; Slovak Academy of Sciences; Dúbravská cesta 9 845 38 Bratislava Slovakia
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Knabe N, Gorbushina AA. Territories of Rock-Inhabiting Fungi: Survival on and Alteration of Solid Air-Exposed Surfaces. J Microbiol Methods 2018. [DOI: 10.1016/bs.mim.2018.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Breitenbach R, Silbernagl D, Toepel J, Sturm H, Broughton WJ, Sassaki GL, Gorbushina AA. Corrosive extracellular polysaccharides of the rock-inhabiting model fungus Knufia petricola. Extremophiles 2017; 22:165-175. [PMID: 29275441 PMCID: PMC5847175 DOI: 10.1007/s00792-017-0984-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/08/2017] [Indexed: 01/24/2023]
Abstract
Melanised cell walls and extracellular polymeric matrices protect rock-inhabiting microcolonial fungi from hostile environmental conditions. How extracellular polymeric substances (EPS) perform this protective role was investigated by following development of the model microcolonial black fungus Knufia petricola A95 grown as a sub-aerial biofilm. Extracellular substances were extracted with NaOH/formaldehyde and the structures of two excreted polymers studied by methylation as well as NMR analyses. The main polysaccharide (~ 80%) was pullulan, also known as α-1,4-; α-1,6-glucan, with different degrees of polymerisation. Αlpha-(1,4)-linked-Glcp and α-(1,6)-linked-Glcp were present in the molar ratios of 2:1. A branched galactofuromannan with an α-(1,2)-linked Manp main chain and a β-(1,6)-linked Galf side chain formed a minor fraction (~ 20%). To further understand the roles of EPS in the weathering of minerals and rocks, viscosity along with corrosive properties were studied using atomic force microscopy (AFM). The kinetic viscosity of extracellular K. petricola A95 polysaccharides (≈ 0.97 × 10−6 m2 s−1) ranged from the equivalent of 2% (w/v) to 5% glycerine, and could thus profoundly affect diffusion-dominated processes. The corrosive nature of rock-inhabiting fungal EPS was also demonstrated by its effects on the aluminium coating of the AFM cantilever and the silicon layer below.
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Affiliation(s)
- Romy Breitenbach
- Department 4 (Materials and Environment), Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - Dorothee Silbernagl
- Division 6.6 (Nanotribology and Nano-Structuring), Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205, Berlin, Germany
| | - Jörg Toepel
- Department of Solar Materials, Applied Biocatalytics, Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318, Leipzig, Germany
| | - Heinz Sturm
- Division 6.6 (Nanotribology and Nano-Structuring), Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205, Berlin, Germany
- Institute of Machine Tools and Factory Management, TU Berlin, Pascalstr. 8-9, 10587, Berlin, Germany
| | - William J Broughton
- Department 4 (Materials and Environment), Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205, Berlin, Germany
- Department of Biochemistry and Molecular Biology, Federal University of Parana, Curitiba, PR, CP 19046, Brazil
| | - Guilherme L Sassaki
- Department of Biochemistry and Molecular Biology, Federal University of Parana, Curitiba, PR, CP 19046, Brazil
| | - Anna A Gorbushina
- Department 4 (Materials and Environment), Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205, Berlin, Germany.
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany.
- Department of Earth Sciences, Freie Universität Berlin, Malteserstraße 74-100, 12249, Berlin, Germany.
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Draft Genome Sequences of the Black Rock Fungus Knufia petricola and Its Spontaneous Nonmelanized Mutant. GENOME ANNOUNCEMENTS 2017; 5:5/44/e01242-17. [PMID: 29097475 PMCID: PMC5668551 DOI: 10.1128/genomea.01242-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The fungal genus Knufia mostly comprises extremotolerant species from environmental sources, especially rock surfaces. The draft genome sequence of the rock fungus Knufia petricola presented here is the first whole-genome sequence of the only species among black fungi known to have a nonmelanized spontaneous mutant.
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Pokharel R, Gerrits R, Schuessler JA, Floor GH, Gorbushina AA, von Blanckenburg F. Mg Isotope Fractionation during Uptake by a Rock-Inhabiting, Model Microcolonial Fungus Knufia petricola at Acidic and Neutral pH. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:9691-9699. [PMID: 28758385 DOI: 10.1021/acs.est.7b01798] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The model rock-inhabiting microcolonial fungus Knufia petricola fractionates stable Mg isotopes in a time- and pH-dependent manner. During growth, the increase of 26Mg/24Mg in the fungal cells relative to the growth media amounted to 0.65 ± 0.14‰ at pH 6 and 1.11 ± 0.35‰ at pH 3. We suggest a constant equilibrium fractionation factor during incorporation of Mg into ribosomes and ATP as a cause of enrichment of 26Mg in the cells. We suggest too that the proton gradient across the cell wall and cytoplasmic membrane controls Mg2+ transport into the fungal cell. As the strength of this gradient is a function of extracellular solution pH, the pH-dependence on Mg isotope fractionation is thus due to differences in fungal cell mass fluxes. Through a mass balance model we show that Mg uptake into the fungal cell is not associated with a unique Mg isotope fractionation factor. This Mg isotope fractionation dependence on pH might also be observed in any organism with cells that follow similar Mg uptake and metabolic pathways and serves to reveal Mg cycling in ecosystems.
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Affiliation(s)
- Rasesh Pokharel
- Section 3.3, Earth Surface Geochemistry, GFZ German Research Centre for Geosciences , Telegrafenberg, 14473 Potsdam, Germany
- Institute of Geological Sciences, Freie Universität Berlin , 12249 Berlin, Germany
| | - Ruben Gerrits
- Department 4, Materials & Environment, BAM Federal Institute for Materials Research & Testing , 12205 Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin , 14195 Berlin, Germany
| | - Jan A Schuessler
- Section 3.3, Earth Surface Geochemistry, GFZ German Research Centre for Geosciences , Telegrafenberg, 14473 Potsdam, Germany
| | - Geerke H Floor
- Section 3.3, Earth Surface Geochemistry, GFZ German Research Centre for Geosciences , Telegrafenberg, 14473 Potsdam, Germany
| | - Anna A Gorbushina
- Institute of Geological Sciences, Freie Universität Berlin , 12249 Berlin, Germany
- Department 4, Materials & Environment, BAM Federal Institute for Materials Research & Testing , 12205 Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin , 14195 Berlin, Germany
| | - Friedhelm von Blanckenburg
- Section 3.3, Earth Surface Geochemistry, GFZ German Research Centre for Geosciences , Telegrafenberg, 14473 Potsdam, Germany
- Institute of Geological Sciences, Freie Universität Berlin , 12249 Berlin, Germany
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Ogawa A, Celikkol-Aydin S, Gaylarde C, Baptista-Neto JA, Beech I. Microbiomes of Biofilms on Decorative Siliceous Stone: Drawbacks and Advantages of Next Generation Sequencing. Curr Microbiol 2017; 74:848-853. [PMID: 28466090 DOI: 10.1007/s00284-017-1257-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/25/2017] [Indexed: 11/30/2022]
Abstract
Next Generation Sequencing (NGS), using the Illumina® metabarcoding system, showed differences between biofilm communities on three degraded siliceous stone church façades in central Rio de Janeiro. Two church biofilms (on granite and augen gneiss) were dominated by Actinobacteria; the third (granite), surrounded by trees and further from intense vehicular traffic, by Gammaproteobacteria. Yeast-like forms of Basidiomycetes and Ascomycetes were major fungi on all facades, but 22.8% of Operational Taxonomic Units could not be assigned to any fungal taxon after DNA amplification with ITS primers and analysis with the UNITE database, indicating the need for more fungal NGS studies. The pipeline used in analysis of the V4 region of rRNA bacterial gene sequences influenced the taxa detected, with two major classes and many genera identified only by the pipeline using the Greengenes, and not the Silva, database. Principal Components Analysis separated façade biofilms into the appropriate three groups and indicated greater dissimilarity of the tree-surrounded church biofilm from the others, confirmed by Jaccard Similarity coefficients, suggesting that local environment influences community composition more than stone type. NGS allows rapid and detailed analysis of microbiomes, but results must be carefully assessed and must not be used as the sole indication of community composition.
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Affiliation(s)
- Akiko Ogawa
- Department Microbiology and Plant Biology, University of Oklahoma, Norman, USA
- Department Chemistry and Biochemistry, Suzuka College, National Institute of Technology, Suzuka, Japan
| | | | - Christine Gaylarde
- Department Microbiology and Plant Biology, University of Oklahoma, Norman, USA.
| | | | - Iwona Beech
- Department Microbiology and Plant Biology, University of Oklahoma, Norman, USA
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Mohammadian E, Arzanlou M, Babai-Ahari A. Diversity of culturable fungi inhabiting petroleum-contaminated soils in Southern Iran. Antonie van Leeuwenhoek 2017; 110:903-923. [DOI: 10.1007/s10482-017-0863-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/20/2017] [Indexed: 10/19/2022]
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Melanin production by a yeast strain XJ5-1 of Aureobasidium melanogenum isolated from the Taklimakan desert and its role in the yeast survival in stress environments. Extremophiles 2016; 20:567-77. [DOI: 10.1007/s00792-016-0843-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 06/05/2016] [Indexed: 11/27/2022]
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Abstract
Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance-β-glucan synthesis, trehalose production, and cold-induced RNA helicases-were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter-lignin peroxidases, cellobiohydrolases, and crystalline cellulases-were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming.
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Affiliation(s)
- Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Jacobson K, van Diepeningen A, Evans S, Fritts R, Gemmel P, Marsho C, Seely M, Wenndt A, Yang X, Jacobson P. Non-rainfall moisture activates fungal decomposition of surface litter in the Namib Sand Sea. PLoS One 2015; 10:e0126977. [PMID: 25978429 PMCID: PMC4433119 DOI: 10.1371/journal.pone.0126977] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/09/2015] [Indexed: 11/24/2022] Open
Abstract
The hyper-arid western Namib Sand Sea (mean annual rainfall 0-17 mm) is a detritus-based ecosystem in which primary production is driven by large, but infrequent rainfall events. A diverse Namib detritivore community is sustained by minimal moisture inputs from rain and fog. The decomposition of plant material in the Namib Sand Sea (NSS) has long been assumed to be the province of these detritivores, with beetles and termites alone accounting for the majority of litter losses. We have found that a mesophilic Ascomycete community, which responds within minutes to moisture availability, is present on litter of the perennial Namib dune grass Stipagrostis sabulicola. Important fungal traits that allow survival and decomposition in this hyper-arid environment with intense desiccation, temperature and UV radiation stress are darkly-pigmented hyphae, a thermal range that includes the relatively low temperature experienced during fog and dew, and an ability to survive daily thermal and desiccation stress at temperatures as high as 50°C for five hours. While rainfall is very limited in this area, fog and high humidity provide regular periods (≥ 1 hour) of sufficient moisture that can wet substrates and hence allow fungal growth on average every 3 days. Furthermore, these fungi reduce the C/N ratio of the litter by a factor of two and thus detritivores, like the termite Psammotermes allocerus, favor fungal-infected litter parts. Our studies show that despite the hyper-aridity of the NSS, fungi are a key component of energy flow and biogeochemical cycling that should be accounted for in models addressing how the NSS ecosystem will respond to projected climate changes which may alter precipitation, dew and fog regimes.
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Affiliation(s)
- Kathryn Jacobson
- Biology Department, Grinnell College, Grinnell, Iowa, United States of America
| | | | - Sarah Evans
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
| | - Rachel Fritts
- Biology Department, Grinnell College, Grinnell, Iowa, United States of America
| | - Philipp Gemmel
- Biology Department, Grinnell College, Grinnell, Iowa, United States of America
| | - Chris Marsho
- Biology Department, Grinnell College, Grinnell, Iowa, United States of America
| | - Mary Seely
- Gobabeb Research and Training Centre, Gobabeb, Namibia
| | - Anthony Wenndt
- Biology Department, Grinnell College, Grinnell, Iowa, United States of America
| | - Xiaoxuan Yang
- Biology Department, Grinnell College, Grinnell, Iowa, United States of America
| | - Peter Jacobson
- Biology Department, Grinnell College, Grinnell, Iowa, United States of America
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Su L, Guo L, Hao Y, Xiang M, Cai L, Liu X. Rupestriomyces and Spissiomyces, two new genera of rock-inhabiting fungi from China. Mycologia 2015; 107:831-44. [PMID: 25911702 DOI: 10.3852/14-305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 01/03/2015] [Indexed: 02/01/2023]
Abstract
Bare rocks in arid and semi-arid climates may harbor a bewildering biodiversity of fungi that are overlooked in China. During a survey of rock-inhibiting fungi in China, more than 1000 were isolated and 14 belonging to Dothideomycetes (Ascomycota) were selected for detailed study. Phylogenetic trees based on combined sequence datasets of mt 16S rDNA, partial nuc rDNA 18S and 28S indicated that these strains clustered in two distinct, well supported and previously unknown lineages within the class Dothideomycetes. Therefore two new genera were established corresponding to those two clades. Spissiomyces gen. nov. is characterized by thick-walled, yellowish brown hyphae and globose or subglobose conidia, if present. Rupestriomyces gen. nov. is characterized by globose, barrel-shaped, ampulliform or ovoidal conidia formed from acropetal, catenate hyphae. Further phylogenetic analyses using combined sequence datasets of the rDNA internal transcribed spacer (ITS) region and 16S rDNA, part of genes of RPB2, TUB2, nuc rDNA 18S and 28S revealed that those strains represented five new species (i.e. Spissiomyces aggregatus, S. ramosus, Rupestriomyces sinensis, R. ampulliformis, R. torulosus). They were described, illustrated and compared with similar taxa based on morphological characteristics and phylogenetic relationships. The results of this paper provides insight into the richness and diversity of rock-inhibiting fungi in nature.
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Affiliation(s)
- Lei Su
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Liyun Guo
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Yang Hao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 Park 1, Beichen West Road, Chaoyang District, Beijing 100101, China
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Wäli PP, Huhtinen S, Pino-Bodas R, Stenroos S. Three common bryophilous fungi with meristematic anamorphs and phylogenetic alliance to Teratosphaeriaceae, Capnodiales. Fungal Biol 2014; 118:956-69. [DOI: 10.1016/j.funbio.2014.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 08/22/2014] [Accepted: 08/26/2014] [Indexed: 01/16/2023]
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Selbmann L, Zucconi L, Isola D, Onofri S. Rock black fungi: excellence in the extremes, from the Antarctic to space. Curr Genet 2014; 61:335-45. [PMID: 25381156 DOI: 10.1007/s00294-014-0457-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 01/05/2023]
Abstract
This work focuses on rock-inhabiting fungi (RIF) of Antarctic rocky deserts, considered the closest to a possible Martian habitat, as the best example of adaptation to the extremes. The study of RIF ecophysiology, resistance and adaptation provides tools that shed light on the evolution of extremophily. These studies also help define the actual limits for life and provide insight for investigating its existence beyond our planet. The scientific results obtained from over 20 years of research on the biodiversity, phylogeny and evolution toward extremotolerance reviewed here demonstrate how these fascinating organisms can withstand conditions well beyond those in their natural environment. A final focus is given on results and perspectives arising from a recent proteomic approach, and from astrobiological experiments and their significance for future space exploration. These studies demonstrate that Antarctic RIF offer an excellent opportunity to investigate many basic, but also applicative areas of research on extremophily.
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Affiliation(s)
- Laura Selbmann
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy,
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Noack-Schönmann S, Bus T, Banasiak R, Knabe N, Broughton WJ, Den Dulk-Ras H, Hooykaas PJJ, Gorbushina AA. Genetic transformation of Knufia petricola A95 - a model organism for biofilm-material interactions. AMB Express 2014; 4:80. [PMID: 25401079 PMCID: PMC4230810 DOI: 10.1186/s13568-014-0080-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/15/2014] [Indexed: 11/26/2022] Open
Abstract
We established a protoplast-based system to transfer DNA to Knufia petricola strain A95, a melanised rock-inhabiting microcolonial fungus that is also a component of a model sub-aerial biofilm (SAB) system. To test whether the desiccation resistant, highly melanised cell walls would hinder protoplast formation, we treated a melanin-minus mutant of A95 as well as the type-strain with a variety of cell-degrading enzymes. Of the different enzymes tested, lysing enzymes from Trichoderma harzianum were most effective in producing protoplasts. This mixture was equally effective on the melanin-minus mutant and the type-strain. Protoplasts produced using lysing enzymes were mixed with polyethyleneglycol (PEG) and plasmid pCB1004 which contains the hygromycin B (HmB) phosphotransferase (hph) gene under the control of the Aspergillus nidulans trpC. Integration and expression of hph into the A95 genome conferred hygromycin resistance upon the transformants. Two weeks after plating out on selective agar containing HmB, the protoplasts developed cell-walls and formed colonies. Transformation frequencies were in the range 36 to 87 transformants per 10 μg of vector DNA and 106 protoplasts. Stability of transformation was confirmed by sub-culturing the putative transformants on selective agar containing HmB as well as by PCR-detection of the hph gene in the colonies. The hph gene was stably integrated as shown by five subsequent passages with and without selection pressure.
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Gessler NN, Egorova AS, Belozerskaya TA. Melanin pigments of fungi under extreme environmental conditions (Review). APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814020094] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Egidi E, de Hoog GS, Isola D, Onofri S, Quaedvlieg W, de Vries M, Verkley GJM, Stielow JB, Zucconi L, Selbmann L. Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-013-0277-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Zakharova K, Tesei D, Marzban G, Dijksterhuis J, Wyatt T, Sterflinger K. Microcolonial fungi on rocks: a life in constant drought? Mycopathologia 2013; 175:537-47. [PMID: 23073825 PMCID: PMC3669513 DOI: 10.1007/s11046-012-9592-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/07/2012] [Indexed: 02/05/2023]
Abstract
Black microcolonial fungi (MCF) and black yeasts are among the most stress-resistant eukaryotic organisms known on Earth. They mainly inhabit bare rock surfaces in hot and cold deserts of all regions of the Earth, but some of them have a close phylogenetic relation to human pathogenic black fungi which makes them important model organisms also with respect to clinical mycology. The environment of those fungi is especially characterized by extreme changes from humidity to long periods of desiccation and extreme temperature differences. A key to the understanding of MCF ecology is the question about metabolic activity versus dormancy in the natural environments. In this study, the time lag from the desiccated state to rehydration and full metabolic activity and growth was measured and defined in accordance with simulated environmental conditions. The ability to survive after desiccation and the speed of rehydration as well as changes of the whole cell protein pattern are demonstrated. Whereas both mesophilic strains--Exophiala jeanselmei and Knufia perforans (=Coniosporium perforans)--show a clear reaction toward desiccation by production of small proteins, Cryomyces antarcticus--the extremotolerant MCF--does not show any response to desiccation but seems just to down-regulate its metabolism. Data on intracellular sugar suggest that both trehalose and mannitol might play a cell protective role in those fungi.
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Affiliation(s)
- Kristina Zakharova
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Gorji Marzban
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Jan Dijksterhuis
- CBS Fungal Biodiversity Center, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Timon Wyatt
- CBS Fungal Biodiversity Center, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Katja Sterflinger
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
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