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Simpson HJ, Andrew C, Skrede I, Kauserud H, Schilling JS. Global field collection data confirm an affinity of brown rot fungi for coniferous habitats and substrates. THE NEW PHYTOLOGIST 2024; 242:2775-2786. [PMID: 38567688 DOI: 10.1111/nph.19723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
Unlike 'white rot' (WR) wood-decomposing fungi that remove lignin to access cellulosic sugars, 'brown rot' (BR) fungi selectively extract sugars and leave lignin behind. The relative frequency and distribution of these fungal types (decay modes) have not been thoroughly assessed at a global scale; thus, the fate of one-third of Earth's aboveground carbon, wood lignin, remains unclear. Using c. 1.5 million fungal sporocarp and c. 30 million tree records from publicly accessible databases, we mapped and compared decay mode and tree type (conifer vs angiosperm) distributions. Additionally, we mined fungal record metadata to assess substrate specificity per decay mode. The global average for BR fungi proportion (BR/(BR + WR records)) was 13% and geographic variation was positively correlated (R2 = 0.45) with conifer trees proportion (conifer/(conifer + angiosperm records)). Most BR species (61%) were conifer, rather than angiosperm (22%), specialists. The reverse was true for WR (conifer: 19%; angiosperm: 62%). Global BR proportion patterns were predicted with greater accuracy using the relative distributions of individual tree species (R2 = 0.82), rather than tree type. Fungal decay mode distributions can be explained by tree type and, more importantly, tree species distributions, which our data suggest is due to strong substrate specificities.
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Affiliation(s)
- Hunter J Simpson
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, MN, 55108, USA
| | - Carrie Andrew
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Blindernveien 31, 0316, Oslo, Norway
- Natural History Museum, University of Oslo, Sars' gate 1, 0562, Oslo, Norway
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Blindernveien 31, 0316, Oslo, Norway
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2
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Isola D, Lee HJ, Chung YJ, Zucconi L, Pelosi C. Once upon a Time, There Was a Piece of Wood: Present Knowledge and Future Perspectives in Fungal Deterioration of Wooden Cultural Heritage in Terrestrial Ecosystems and Diagnostic Tools. J Fungi (Basel) 2024; 10:366. [PMID: 38786721 PMCID: PMC11122135 DOI: 10.3390/jof10050366] [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: 02/28/2024] [Revised: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Wooden Cultural Heritage (WCH) represents a significant portion of the world's historical and artistic heritage, consisting of immovable and movable artefacts. Despite the expertise developed since ancient times to enhance its durability, wooden artefacts are inevitably prone to degradation. Fungi play a pivotal role in the deterioration of WCH in terrestrial ecosystems, accelerating its decay and leading to alterations in color and strength. Reviewing the literature of the last 25 years, we aimed to provide a comprehensive overview of fungal diversity affecting WCH, the biochemical processes involved in wood decay, and the diagnostic tools available for fungal identification and damage evaluation. Climatic conditions influence the occurrence of fungal species in threatened WCH, characterized by a prevalence of wood-rot fungi (e.g., Serpula lacrymans, Coniophora puteana) in architectural heritage in temperate and continental climates and Ascomycota in indoor and harsh environments. More efforts are needed to address the knowledge fragmentation concerning biodiversity, the biology of the fungi involved, and succession in the degradative process, which is frequently centered solely on the main actors. Multidisciplinary collaboration among engineers, restorers, and life sciences scientists is vital for tackling the challenges posed by climate change with increased awareness. Traditional microbiology and culture collections are fundamental in laying solid foundations for a more comprehensive interpretation of big data.
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Affiliation(s)
- Daniela Isola
- Department of Economics, Engineering, Society and Business Organization (DEIM), University of Tuscia, Largo dell’Università Snc, 01100 Viterbo, Italy;
| | - Hyun-Ju Lee
- Institute of Preventive Conservation for Cultural Heritage, Korea National University of Cultural Heritage, Buyeo 33115, Republic of Korea;
| | - Yong-Jae Chung
- Department of Heritage Conservation and Restoration, Graduate School of Cultural Heritage, Korea National University of Cultural Heritage, Buyeo 33115, Republic of Korea;
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell’Università Snc, 01100 Viterbo, Italy;
| | - Claudia Pelosi
- Department of Economics, Engineering, Society and Business Organization (DEIM), University of Tuscia, Largo dell’Università Snc, 01100 Viterbo, Italy;
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3
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Okmane L, Fitkin L, Sandgren M, Ståhlberg J. The first crystal structure of a family 45 glycoside hydrolase from a brown-rot fungus, Gloeophyllum trabeum GtCel45A. FEBS Open Bio 2024; 14:505-514. [PMID: 38311343 PMCID: PMC10909974 DOI: 10.1002/2211-5463.13774] [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: 08/31/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Here we describe the first crystal structure of a beta-1,4-endoglucanase from a brown-rot fungus, Gloeophyllum trabeum GtCel45A, which belongs to subfamily C of glycoside hydrolase family 45 (GH45). GtCel45A is ~ 18 kDa in size and the crystal structure contains 179 amino acids. The structure is refined at 1.30 Å resolution and Rfree 0.18. The enzyme consists of a single catalytic module folded into a six-stranded double-psi beta-barrel domain surrounded by long loops. GtCel45A is very similar in sequence (82% identity) and structure to PcCel45A from the white-rot fungus Phanerochaete chrysosporium. Surprisingly though, initial hydrolysis of barley beta-glucan was almost twice as fast in GtCel45A as compared to PcCel45A.
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Affiliation(s)
- Laura Okmane
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Louise Fitkin
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Mats Sandgren
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Jerry Ståhlberg
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
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4
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Flores-Moreno H, Yatsko AR, Cheesman AW, Allison SD, Cernusak LA, Cheney R, Clement RA, Cooper W, Eggleton P, Jensen R, Rosenfield M, Zanne AE. Shifts in internal stem damage along a tropical precipitation gradient and implications for forest biomass estimation. THE NEW PHYTOLOGIST 2024; 241:1047-1061. [PMID: 38087814 DOI: 10.1111/nph.19417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/03/2023] [Indexed: 01/12/2024]
Abstract
Woody biomass is a large carbon store in terrestrial ecosystems. In calculating biomass, tree stems are assumed to be solid structures. However, decomposer agents such as microbes and insects target stem heartwood, causing internal wood decay which is poorly quantified. We investigated internal stem damage across five sites in tropical Australia along a precipitation gradient. We estimated the amount of internal aboveground biomass damaged in living trees and measured four potential stem damage predictors: wood density, stem diameter, annual precipitation, and termite pressure (measured as termite damage in downed deadwood). Stem damage increased with increasing diameter, wood density, and termite pressure and decreased with increasing precipitation. High wood density stems sustained less damage in wet sites and more damage in dry sites, likely a result of shifting decomposer communities and their differing responses to changes in tree species and wood traits across sites. Incorporating stem damage reduced aboveground biomass estimates by > 30% in Australian savannas, compared to only 3% in rainforests. Accurate estimates of carbon storage across woody plant communities are critical for understanding the global carbon budget. Future biomass estimates should consider stem damage in concert with the effects of changes in decomposer communities and abiotic conditions.
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Affiliation(s)
- Habacuc Flores-Moreno
- Department of Biological Sciences, George Washington University, Washington, DC, 20007, USA
- CSIRO Health and Biosecurity, GPO Box 2583, Brisbane, Qld, 4001, Australia
| | - Abbey R Yatsko
- Biology Department, University of Miami, Miami, FL, 33146, USA
| | - Alexander W Cheesman
- College of Science and Engineering, James Cook University, Cairns, Qld, 4878, Australia
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4QE, UK
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Earth System Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Lucas A Cernusak
- College of Science and Engineering, James Cook University, Cairns, Qld, 4878, Australia
| | - Rose Cheney
- Department of Biological Sciences, George Washington University, Washington, DC, 20007, USA
| | - Rebecca A Clement
- Department of Biological Sciences, George Washington University, Washington, DC, 20007, USA
| | - Wendy Cooper
- Australian Tropical Herbarium, James Cook University, Cairns, Qld, 4878, Australia
| | - Paul Eggleton
- Life Sciences Department, The Natural History Museum, London, SW7 5BD, UK
| | - Rigel Jensen
- Australian Wildlife Conservancy, Malanda, Qld, 4885, Australia
| | - Marc Rosenfield
- Department of Biological Sciences, George Washington University, Washington, DC, 20007, USA
| | - Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, 20007, USA
- Biology Department, University of Miami, Miami, FL, 33146, USA
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5
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Min B, Ahrendt S, Lipzen A, Toapanta CE, Blanchette RA, Cullen D, Hibbett DS, Grigoriev IV. Transcriptomics of Temporal- versus Substrate-Specific Wood Decay in the Brown-Rot Fungus Fibroporia radiculosa. J Fungi (Basel) 2023; 9:1029. [PMID: 37888285 PMCID: PMC10608345 DOI: 10.3390/jof9101029] [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: 09/13/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Brown-rot fungi lack many enzymes associated with complete wood degradation, such as lignin-attacking peroxidases, and have developed alternative mechanisms for rapid wood breakdown. To identify the effects of culture conditions and wood substrates on gene expression, we grew Fibroporia radiculosa in submerged cultures containing Wiley milled wood (5 days) and solid wood wafers (30 days), using aspen, pine, and spruce as a substrate. The comparative analysis revealed that wood species had a limited effect on the transcriptome: <3% of genes were differentially expressed between different wood species substrates. The comparison between gene expression during growth on milled wood and wood wafer conditions, however, indicated that the genes encoding plant cell wall-degrading enzymes, such as glycoside hydrolases and peptidases, were activated during growth on wood wafers, confirming previous reports. On the other hand, it was shown for the first time that the genes encoding Fenton chemistry enzymes, such as hydroquinone biosynthesis enzymes and oxidoreductases, were activated during submerged growth on ground wood. This illustrates the diversity of wood-decay reactions encoded in fungi and activated at different stages of this process.
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Affiliation(s)
- Byoungnam Min
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (B.M.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (B.M.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (B.M.)
| | | | | | - Dan Cullen
- USDA Forest Products Laboratory, Madison, WI 53726, USA
| | | | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (B.M.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Grace Barrios-Gutiérrez S, Inés Vélez-Mercado M, Rodrigues Ortega J, da Silva Lima A, Luiza da Rocha Fortes Saraiva A, Leila Berto G, Segato F. Oxidative Machinery of basidiomycetes as potential enhancers in lignocellulosic biorefineries: A lytic polysaccharide monooxygenases approach. BIORESOURCE TECHNOLOGY 2023; 386:129481. [PMID: 37437815 DOI: 10.1016/j.biortech.2023.129481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
Basidiomycetes are renowned as highly effective decomposers of plant materials, due to their extensive array of oxidative enzymes, which enable them to efficiently break down complex lignocellulosic biomass structures. Among the oxidative machinery of industrially relevant basidiomycetes, the role of lytic polysaccharide monooxygenases (LPMO) in lignocellulosic biomass deconstruction is highlighted. So far, only a limited number of basidiomycetes LPMOs have been identified and heterologously expressed. These LPMOs have presented activity on cellulose and hemicellulose, as well as participation in the deconstruction of lignin. Expanding on this, the current review proposes both enzymatic and non-enzymatic mechanisms of LPMOs for biomass conversion, considering the significance of the Carbohydrate-Binding Modules and other C-terminal regions domains associated with their structure, which is involved in the deconstruction of lignocellulosic biomass.
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Affiliation(s)
- Solange Grace Barrios-Gutiérrez
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Martha Inés Vélez-Mercado
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Júlia Rodrigues Ortega
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Awana da Silva Lima
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Ana Luiza da Rocha Fortes Saraiva
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Gabriela Leila Berto
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Fernando Segato
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil.
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7
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Embacher J, Zeilinger S, Kirchmair M, Rodriguez-R LM, Neuhauser S. Wood decay fungi and their bacterial interaction partners in the built environment – A systematic review on fungal bacteria interactions in dead wood and timber. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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8
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Zhao H, Dai YC, Wu F, Liu XY, Maurice S, Krutovsky KV, Pavlov IN, Lindner DL, Martin FM, Yuan Y. Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia. Genome Biol Evol 2023; 15:evad136. [PMID: 37498334 PMCID: PMC10410303 DOI: 10.1093/gbe/evad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/01/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023] Open
Abstract
To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.
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Affiliation(s)
- Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yu-Cheng Dai
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Fang Wu
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Sundy Maurice
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research, George-August University of Göttingen, Göttingen, Germany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Forest Genomics, Department of Genomics and Bioinformatics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Scientific and Methodological Center, G. F. Morozov Voronezh State University of Forestry and Technologies, Voronezh, Russia
| | - Igor N Pavlov
- Mycology and Plant Pathology, V.N. Sukachev Institute of Forest SB RAS, Krasnoyarsk, Russia
- Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, Russia
| | | | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Champenoux, France
| | - Yuan Yuan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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Yu J, Lai J, Neal BM, White BJ, Banik MT, Dai SY. Genomic Diversity and Phenotypic Variation in Fungal Decomposers Involved in Bioremediation of Persistent Organic Pollutants. J Fungi (Basel) 2023; 9:418. [PMID: 37108874 PMCID: PMC10145412 DOI: 10.3390/jof9040418] [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: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Fungi work as decomposers to break down organic carbon, deposit recalcitrant carbon, and transform other elements such as nitrogen. The decomposition of biomass is a key function of wood-decaying basidiomycetes and ascomycetes, which have the potential for the bioremediation of hazardous chemicals present in the environment. Due to their adaptation to different environments, fungal strains have a diverse set of phenotypic traits. This study evaluated 320 basidiomycetes isolates across 74 species for their rate and efficiency of degrading organic dye. We found that dye-decolorization capacity varies among and within species. Among the top rapid dye-decolorizing fungi isolates, we further performed genome-wide gene family analysis and investigated the genomic mechanism for their most capable dye-degradation capacity. Class II peroxidase and DyP-type peroxidase were enriched in the fast-decomposer genomes. Gene families including lignin decomposition genes, reduction-oxidation genes, hydrophobin, and secreted peptidases were expanded in the fast-decomposer species. This work provides new insights into persistent organic pollutant removal by fungal isolates at both phenotypic and genotypic levels.
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Affiliation(s)
- Jiali Yu
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Jingru Lai
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Brian M. Neal
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Bert J. White
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
| | - Mark T. Banik
- USDA Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, WI 53726, USA
| | - Susie Y. Dai
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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10
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A Laccase Gene Reporting System That Enables Genetic Manipulations in a Brown Rot Wood Decomposer Fungus Gloeophyllum trabeum. Microbiol Spectr 2023; 11:e0424622. [PMID: 36651769 PMCID: PMC9927100 DOI: 10.1128/spectrum.04246-22] [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] [Indexed: 01/19/2023] Open
Abstract
Brown rot fungi are primary decomposers of wood and litter in northern forests. Relative to other microbes, these fungi have evolved distinct mechanisms that rapidly depolymerize and metabolize cellulose and hemicellulose without digesting the more recalcitrant lignin. Its efficient degradative system has therefore attracted considerable attention for the development of sustainable biomass conversion technologies. However, there has been a significant lack of genetic tools in brown rot species by which to manipulate genes for both mechanistic studies and engineering applications. To advance brown rot genetic studies, we provided a gene-reporting system that can facilitate genetic manipulations in a model fungus Gloeophyllum trabeum. We first optimized a transformation procedure in G. trabeum, and then transformed the fungus into a constitutive laccase producer with a well-studied white rot laccases gene (from Trametes versicolor). With this, we built a gene reporting system based on laccase gene's expression and its rapid assay using an 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) indicator dye. The laccase reporter system was validated robust enough to allow us to test the effects of donor DNA's formats, protoplast viability, and gene regulatory elements on transformation efficiencies. Going forward, we anticipate the toolset provided in this work would expedite phenotyping studies and genetic engineering of brown rot species. IMPORTANCE One of the most ubiquitous types of decomposers in nature, brown rot fungi, has lacked robust genetic tools by which to manipulate genes and understand its biology. Brown rot fungi are primary decomposers in northern forests helping recycle the encased carbons in trees back to ecosystem. Relative to other microbes, these fungi employ distinctive mechanisms to disrupt and consume the lignified polysaccharides in wood. Its decay mechanism allows fast, selective carbohydrate catabolization, but without digesting lignin-a barren component that produces least energy trade back for fungal metabolisms. Thus, its efficient degradative system provides a great platform for developing sustainable biotechnologies for biomass conversions. However, progress has been hampered by the lack genetic tools facilitating mechanistic studies and engineering applications. Here, the laccase reporter system provides a genetic toolset for genetic manipulations in brown rot species, which we expect would advance relevant genetic studies for discovering and harnessing the unique fungal degradative mechanisms.
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11
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Phylogenetic relationships and taxonomy of Grifola (Polyporales). Mycol Prog 2023. [DOI: 10.1007/s11557-022-01857-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Kalntremtziou M, Papaioannou IA, Vangalis V, Polemis E, Pappas KM, Zervakis GI, Typas MA. Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics. Front Microbiol 2023; 14:1121993. [PMID: 36922966 PMCID: PMC10008878 DOI: 10.3389/fmicb.2023.1121993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/28/2023] Open
Abstract
The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.
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Affiliation(s)
- Maria Kalntremtziou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis A Papaioannou
- Zentrum für Molekulare Biologie der Universität Heidelberg, ZMBH, University of Heidelberg, Heidelberg, Germany
| | - Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Elias Polemis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios I Zervakis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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13
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Metabolomics Highlights Different Life History Strategies of White and Brown Rot Wood-Degrading Fungi. mSphere 2022; 7:e0054522. [PMID: 36468887 PMCID: PMC9769625 DOI: 10.1128/msphere.00545-22] [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] [Indexed: 12/10/2022] Open
Abstract
White and brown rot fungi efficiently deconstruct lignocellulose in wood, Earth's largest pool of aboveground biotic carbon and an important natural resource. Despite its vital importance, little is known about the metabolomic signatures among fungal species and nutritional modes (rot types). In this study, we used GC-MS metabolomics in solid wood substrates (in planta) to compare brown rot fungi (Rhodonia placenta and Gloeophylum trabeum) and white rot fungi (Trametes versicolor and Pleurotus ostreatus) at two decay stages (earlier and later), finding identifiable patterns for brown rot fungi at later decay stages. These patterns occurred in highly reducing environments that were not observed in white rot fungi. Metabolomes measured among the two white rot fungi were notably different, but we found a potential biomarker compound, galactitol, that was characteristic to white rot taxa. In addition, we found that white rot fungi were more efficient at catabolizing phenolic compounds that were originally present in wood. Collectively, white rot fungi were characterized by measured sugar release relative to higher carbohydrate solubilization by brown rot fungi, a distinction in soluble sugar availability that might shape success in the face of "cheater" competitors. This need to protect excess free sugars may explain the differentially high brown rot fungal production of pyranones and furanones, likely linked to an expansion of polyketide synthase genes. IMPORTANCE Despite the ecological and economic importance of wood-degrading fungi, little is known about the array of metabolites that fungi produce during wood decomposition. This study provides an in-depth insight into the wood decomposition process by analyzing and comparing the changes of >100 compounds produced by fungi with metabolic distinct nutritional modes (white and brown rot fungi) at different decay stages. We found a unique pattern of metabolites that correlated well with brown rot (carbohydrate selective mode) in later decay. These compounds were in line with some of the physiochemical and genetic features previously seen in these fungi such as a faster sugar release, lower pH, and the expansion of polyketide-synthase genes compared to white rot fungi (lignin-degrading mode). This study provides spatiotemporally resolved mechanism insights as well as critical groundwork that will be valuable for studies in basic biology and ecology, as well as applied biomass deconstruction and bioremediation.
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14
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Hennicke F, Fleckenstein L, Bässler C, Krah FS. Organic Nitrogen Supplementation Increases Vegetative and Reproductive Biomass in a Versatile White Rot Fungus. J Fungi (Basel) 2022; 9:jof9010007. [PMID: 36675828 PMCID: PMC9865380 DOI: 10.3390/jof9010007] [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: 10/28/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The Black Poplar Mushroom Cyclocybe aegerita (syn. Agrocybe aegerita) is a white-rot fungus that naturally fruits from woody substrates, including buried wood. It is known for its substrate versatility and is equipped with a respective carbohydrate-active enzyme repertoire being intermediate between typical white-rot fungi and plant litter decomposers. Given relative nitrogen scarcity in wood, mobilization of nitrogen from surrounding litter is known as a way to meet nitrogen requirements for cellular homeostasis and reproduction of wood decay fungi. However, the effect of added nitrogen on vegetative and reproductive biomass has not yet been studied in a uniform minimalistic laboratory setup. For C. aegerita, such a growth and fruiting setup has been developed. In the present study, this white-rot fungus has been grown with and without additional β-adenosine, an organic nitrogen source present in plant litter. Elevated β-adenosine levels increased aerial mycelium weight by 30% (1 × β-adenosine) and 55% (10 × β-adenosine), reproductive biomass by 75% (1 × β-adenosine) and by 100% (10 × β-adenosine), number of primordia by 127% (10 × β-adenosine) and accelerated primordium formation by 1.6 days (10 × β-adenosine), compared to the control treatment. These findings imply that C. aegerita invests additional organic nitrogen resources into direct vegetative and reproductive biomass build-up at the same time. Colonization of niches with accessory nitrogen sources, like buried wood, which is near the plant litter layer, may thus provide an evolutionary fitness advantage. Globally anthropogenically altered nitrogen dynamics may affect hyphal-driven processes as well as fruit body-driven food webs.
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Affiliation(s)
- Florian Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum (RUB), 44801 Bochum, Germany
- Correspondence: (F.H.); (F.-S.K.)
| | - Lena Fleckenstein
- Conservation Biology, Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, 60323 Frankfurt am Main, Germany
| | - Claus Bässler
- Conservation Biology, Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, 60323 Frankfurt am Main, Germany
- Bavarian Forest National Park, 94481 Grafenau, Germany
| | - Franz-Sebastian Krah
- Conservation Biology, Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, 60323 Frankfurt am Main, Germany
- Correspondence: (F.H.); (F.-S.K.)
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15
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Kapitsa EA, Kuznetsov AN, Kuznetsova SP, Lopes de Gerenyu VO, Kaganov VV, Kurganova IN, Kushnevskaya YV, Shorohova EV. Coarse Woody Debris in Monsoon Tropical Forests of Vietnam. CONTEMP PROBL ECOL+ 2022. [DOI: 10.1134/s1995425522070125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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16
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Combined Biological and Chemical/Physicochemical Pretreatment Methods of Lignocellulosic Biomass for Bioethanol and Biomethane Energy Production—A Review. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Lignocellulosic biomass is a low-cost and environmentally-friendly resource that can be used to produce biofuels such as bioethanol and biogas, which are the leading candidates for the partial substitution of fossil fuels. However, the main challenge of using lignocellulosic materials for biofuel production is the low accessibility to cellulose for hydrolysis of enzymes and microorganisms, which can be overcome by pretreatment. Biological and chemical pretreatments have their own disadvantages, which could be reduced by combining the two methods. In this article, we review biological–chemical combined pretreatment strategies for biogas and bioethanol production. The synergy of fungal/enzyme–NaOH pretreatment is the only biological–chemical combination studied for biogas production and has proven to be effective. The use of enzyme, which is relatively expensive, has the advantage of hydrolysis efficiency compared to fungi. Nonetheless, there is vast scope for research and development of other chemical–biological combinations for biogas production. With respect to ethanol production, fungal–organosolv combination is widely studied and can achieve a maximum of 82% theoretical yield. Order of pretreatment is also important, as fungi may reduce the accessibility of cellulose made available by prior chemical strategies and suppress lignin degradation. The biofuel yield of similarly pretreated biomass can vary depending on the downstream process. Therefore, new strategies, such as bioaugmentation and genetically engineered strains, could help to further intensify biofuel yields.
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17
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Zhao H, Zhou M, Liu XY, Wu F, Dai YC. Phylogeny, Divergence Time Estimation and Biogeography of the Genus Onnia (Basidiomycota, Hymenochaetaceae). Front Microbiol 2022; 13:907961. [PMID: 35875515 PMCID: PMC9301299 DOI: 10.3389/fmicb.2022.907961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Species of Onnia are important tree pathogens and play a crucial role in forest ecosystems. The species diversity and distribution of Onnia have been studied, however, its evolutionary history is poorly understood. In this study, we reconstructed the phylogeny of Onnia using internal transcribed spacers (ITS) and large subunit (LSU) rDNA sequence data. Molecular clock analyses developed the divergence times of Onnia based on a dataset (ITS + LSU rDNA + rpb1 + rpb2 + tef1α). Reconstruct Ancestral State in Phylogenies (RASP) was used to reconstruct the historical biogeography for the genus Onnia with a Dispersal Extinction Cladogenesis (DEC) model. Here, we provide a robust phylogeny of Onnia, with a description of a new species, Onnia himalayana from Yunnan Province, China. Molecular clock analyses suggested that the common ancestor of Onnia and Porodaedalea emerged in the Paleogene period with full support and a mean stem age of 56.9 Mya (95% highest posterior density of 35.9–81.6 Mya), and most species occurred in the Neogene period. Biogeographic studies suggest that Asia, especially in the Hengduan-Himalayan region, is probably the ancestral area. Five dispersals and two vicariances indicate that species of Onnia were rapidly diversified. Speciation occurred in the Old World and New World due to geographic separation. This study is the first inference of the divergence times, biogeography, and speciation of the genus Onnia.
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Affiliation(s)
- Heng Zhao
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Meng Zhou
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Fang Wu
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- *Correspondence: Fang Wu,
| | - Yu-Cheng Dai
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- Yu-Cheng Dai,
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18
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Purahong W, Tanunchai B, Muszynski S, Maurer F, Wahdan SFM, Malter J, Buscot F, Noll M. Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay. Proc Biol Sci 2022; 289:20220130. [PMID: 35538788 PMCID: PMC9091849 DOI: 10.1098/rspb.2022.0130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and 15N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N2 fixation. The latter were governed by the genus Sphingomonas, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and 15N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.
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Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany
| | - Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany.,Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440, Bayreuth, Germany
| | - Sarah Muszynski
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - Florian Maurer
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany.,Department of Botany, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Jonas Malter
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440, Bayreuth, Germany.,Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
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19
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Bebber DP, Chaloner TM. Specialists, generalists and the shape of the ecological niche in fungi. THE NEW PHYTOLOGIST 2022; 234:345-349. [PMID: 35092019 PMCID: PMC9303431 DOI: 10.1111/nph.18005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/21/2022] [Indexed: 05/26/2023]
Affiliation(s)
| | - Thomas M. Chaloner
- Department of BiosciencesUniversity of ExeterExeterEX4 4QDUK
- CABIWallingfordOX10 8DEUK
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20
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Zhang R, Shi XF, Liu PG, Wilson AW, Mueller GM. Host Shift Speciation of the Ectomycorrhizal Genus Suillus (Suillineae, Boletales) and Biogeographic Comparison With Its Host Pinaceae. Front Microbiol 2022; 13:831450. [PMID: 35432238 PMCID: PMC9009389 DOI: 10.3389/fmicb.2022.831450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Suillus is a genus of ectomycorrhizal fungi associated almost exclusively with Pinaceae. Lack of sample collections in East Asia and unresolved basal phylogenetic relationships of the genus are the major obstacles for better understanding the Suillus evolution. A resolved phylogeny of Suillus representing global diversity was achieved by sequencing multiple nuclear ribosomal and protein coding genes and extensive samples collected in East Asia. Fungal fossils are extremely rare, and the Eocene ectomycorrhizal symbiosis (ECM) fossil of Pinus root has been widely used for calibration. This study explored an alternative calibration scenario of the ECM fossil for controversy. Ancestral host associations of Suillus were estimated by maximum likelihood and Bayesian Markov chain Monte Carlo (MCMC) analyses, inferred from current host information from root tips and field observation. Host shift speciation explains the diversification of Suillus major clades. The three basal subgenera of Suillus were inferred to be associated with Larix, and diverged in early Eocene or Upper Cretaceous. In the early Oligocene or Paleocene, subgenus Suillus diverged and switched host to Pinus subgenus Strobus, and then switched to subgenus Pinus four times. Suillus subgenus Douglasii switched host from Larix to Pseudotsuga in Oligocene or Eocene. Increased species diversity occurred in subgenus Suillus after it switched host to Pinus but no associated speciation rate shifts were detected. Ancestral biogeographic distributions of Suillus and Pinaceae were estimated under the Dispersal Extinction Cladogenesis (DEC) model. Ancestral distribution patterns of Suillus and Pinaceae are related but generally discordant. Dispersals between Eurasia and North America explain the prevalence of disjunct Suillus taxa.
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Affiliation(s)
- Rui Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
| | - Xiao-fei Shi
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
| | - Pei-gui Liu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
| | - Andrew W. Wilson
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Sam Mitchel Herbarium of Fungi, Denver Botanic Garden, Denver, CO, United States
| | - Gregory M. Mueller
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
- Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
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21
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Maillard F, Jusino MA, Andrews E, Moran M, Vaziri GJ, Banik MT, Fanin N, Trettin CC, Lindner DL, Schilling JS. Wood-decay type and fungal guild dominance across a North American log transplant experiment. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Shorohova E, Kapitsa E, Kuznetsov A, Kuznetsova S, Lopes de Gerenyu V, Kaganov V, Kurganova I. Coarse woody debris density and carbon concentration by decay classes in mixed montane wet tropical forests. Biotropica 2022. [DOI: 10.1111/btp.13077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ekaterina Shorohova
- Forest Research Institute of the Karelian Research Centre Russian Academy of Sciences Petrozavodsk Russia
- Saint‐Petersburg State Forest Technical University Saint‐Petersburg Russia
- Natural Resources Institute Finland (Luke) Helsinki Finland
| | - Ekaterina Kapitsa
- Saint‐Petersburg State Forest Technical University Saint‐Petersburg Russia
| | - Andrey Kuznetsov
- Joint Russian‐Vietnamese Tropical Scientific and Technological Center Hanoi Vietnam
- Institute of Ecology and Evolution of the Russian Academy of Sciences Moscow Russia
| | - Svetlana Kuznetsova
- Joint Russian‐Vietnamese Tropical Scientific and Technological Center Hanoi Vietnam
- Institute of Ecology and Evolution of the Russian Academy of Sciences Moscow Russia
| | - Valentin Lopes de Gerenyu
- Institute of Physicochemical and Biological Problems of Soil Science of the Russian Academy of Sciences Pushchino Russia
| | - Vladimir Kaganov
- Center for Forest Ecology and Productivity of the Russian Academy of Sciences (CEPF RAS) Moscow Russia
| | - Irina Kurganova
- Institute of Physicochemical and Biological Problems of Soil Science of the Russian Academy of Sciences Pushchino Russia
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23
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Wang XW, Jiang JH, Liu SL, Gafforov Y, Zhou LW. Species Diversification of the Coniferous Pathogenic Fungal Genus Coniferiporia (Hymenochaetales, Basidiomycota) in Association with Its Biogeography and Host Plants. PHYTOPATHOLOGY 2022; 112:404-413. [PMID: 34170760 DOI: 10.1094/phyto-05-21-0181-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Coniferiporia, belonging to Hymenochaetaceae and now segregated from Phellinidium, is a wood-inhabiting fungal genus with three species, each having a specific geographic distribution and a strong host specificity as a forest pathogen of coniferous trees. In this study, the species diversity of Coniferiporia is further clarified with the aid of a wider sampling and multilocus-based phylogenetic analysis, which reveals a new species Coniferiporia uzbekistanensis. The molecular clock and ancestral geographic origin analyses indicate that the ancestor of Coniferiporia emerged in one of the Pinaceae and Cupressaceae, then jumped to the other plant family originated in eastern Eurasia 17.01 million years ago (Mya; 95% highest posterior density: 9.46 to 25.86 Mya), and later extended its distribution to western North America, Central Asia, and eastern Europe. Coniferiporia sulphurascens speciated on Pinaceae in eastern Eurasia 8.78 Mya (9.46 to 25.86 Mya) and then extended its distribution to western North America and eastern Europe. Coniferiporia qilianensis and C. uzbekistanensis speciated on Juniperus przewalskii in eastern Eurasia 3.67 Mya (0.36 to 8.02 Mya) and on Juniperus polycarpos in Central Asia 4.35 Mya (0.94 to 8.37 Mya), respectively. The speciation event of Coniferiporia weirii occurred 4.45 Mya (0.77 to 9.33 Mya) right after the emergence of its host, the endemic Cupressaceae species Thuja plicata, and soon after, this fungus evolved to also inhabit another endemic Cupressaceae species Calocedrus decurrens. In summary, this study for the first time unambiguously clarified and timed the adaptive evolutionary event of Coniferiporia in association with its biogeography and host plants.
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Affiliation(s)
- Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Hang Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shi-Liang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yusufjon Gafforov
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent 100125, Uzbekistan
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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24
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Wu G, Miyauchi S, Morin E, Kuo A, Drula E, Varga T, Kohler A, Feng B, Cao Y, Lipzen A, Daum C, Hundley H, Pangilinan J, Johnson J, Barry K, LaButti K, Ng V, Ahrendt S, Min B, Choi IG, Park H, Plett JM, Magnuson J, Spatafora JW, Nagy LG, Henrissat B, Grigoriev IV, Yang ZL, Xu J, Martin FM. Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales. THE NEW PHYTOLOGIST 2022; 233:1383-1400. [PMID: 34767630 DOI: 10.1111/nph.17858] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.
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Affiliation(s)
- Gang Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (USC1408), INRAE, Marseille, 13009, France
| | - Torda Varga
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Bang Feng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Yang Cao
- Yunnan Institute of Tropic Crops, Jinghong, Yunnan, 666100, China
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Christopher Daum
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Hope Hundley
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Steven Ahrendt
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Byoungnam Min
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 02841, Seoul, Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 02841, Seoul, Korea
| | - Hongjae Park
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Jon Magnuson
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (USC1408), INRAE, Marseille, 13009, France
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13009, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Zhu-Liang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
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Wainhouse M, Boddy L. Making hollow trees: Inoculating living trees with wood-decay fungi for the conservation of threatened taxa - A guide for conservationists. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2021.e01967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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26
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Fukasawa Y. Ecological impacts of fungal wood decay types: A review of current knowledge and future research directions. Ecol Res 2021. [DOI: 10.1111/1440-1703.12260] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Fukasawa
- Graduate School of Agricultural Science Tohoku University Osaki Miyagi Japan
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27
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Abstract
Brown rot fungi release massive amounts of carbon from forest deadwood, particularly at high latitudes. These fungi degrade wood by generating small reactive oxygen species (ROS) to loosen lignocellulose, to then selectively remove carbohydrates. The ROS mechanism has long been considered the key adaptation defining brown rot wood decomposition, but recently, we found preliminary evidence that fungal glycoside hydrolases (GHs) implicated in early cell wall loosening might have been adapted to tolerate ROS stress and to synergize with ROS to loosen woody lignocellulose. In the current study, we found more specifically that side chain hemicellulases that help in the early deconstruction of the lignocellulosic complex are significantly more tolerant of ROS in the brown rot fungus Rhodonia placenta than in a white rot fungus (Trametes versicolor) and a soft rot fungus (Trichoderma reesei). Using proteomics to understand the extent of tolerance, we found that significant oxidation of secreted R. placenta proteins exposed to ROS was less than half of the oxidation observed for T. versicolor or T. reesei. The principal oxidative modifications observed in all cases were monooxidation and dioxidation/trioxidation (mainly in methionine and tryptophan residues), some of which were critical for enzyme activity. At the peptide level, we found that GHs in R. placenta were the least ROS affected among our tested fungi. These results confirm and describe underlying mechanisms of tolerance in early-secreted brown rot fungal hemicellulases. These enzymatic adaptations may have been as important as nonenzymatic ROS pathway adaptations in brown rot fungal evolution.
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Caseys C, Shi G, Soltis N, Gwinner R, Corwin J, Atwell S, Kliebenstein DJ. Quantitative interactions: the disease outcome of Botrytis cinerea across the plant kingdom. G3 (BETHESDA, MD.) 2021; 11:jkab175. [PMID: 34003931 PMCID: PMC8496218 DOI: 10.1093/g3journal/jkab175] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/28/2021] [Indexed: 11/12/2022]
Abstract
Botrytis cinerea is a fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. How B. cinerea interacts with such extensive host diversity remains largely unknown. To address this question, we generated an infectivity matrix of 98 strains of B. cinerea on 90 genotypes representing eight host plants. This experimental infectivity matrix revealed that the disease outcome is largely explained by variations in either the host resistance or pathogen virulence. However, the specific interactions between host and pathogen account for 16% of the disease outcome. Furthermore, the disease outcomes cluster among genotypes of a species but are independent of the relatedness between hosts. When analyzing the host specificity and virulence of B. cinerea, generalist strains are predominant. In this fungal necrotroph, specialization may happen by a loss in virulence on most hosts rather than an increase of virulence on a specific host. To uncover the genetic architecture of Botrytis host specificity and virulence, a genome-wide association study (GWAS) was performed and revealed up to 1492 genes of interest. The genetic architecture of these traits is widespread across the B. cinerea genome. The complexity of the disease outcome might be explained by hundreds of functionally diverse genes putatively involved in adjusting the infection to diverse hosts.
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Affiliation(s)
- Celine Caseys
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Gongjun Shi
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, USA
| | - Nicole Soltis
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California, Davis, Davis, CA 95616 USA
| | - Raoni Gwinner
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- Embrapa Amazonia Ocidental, Manaus 69010-970, Brazil
| | - Jason Corwin
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Ecology and Evolution Biology, University of Colorado, Boulder, CO 80309-0334, USA
| | - Susanna Atwell
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- DynaMo Center of Excellence, University of Copenhagen, Frederiksberg C DK-1871, Denmark
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29
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Ruiz-Dueñas FJ, Barrasa JM, Sánchez-García M, Camarero S, Miyauchi S, Serrano A, Linde D, Babiker R, Drula E, Ayuso-Fernández I, Pacheco R, Padilla G, Ferreira P, Barriuso J, Kellner H, Castanera R, Alfaro M, Ramírez L, Pisabarro AG, Riley R, Kuo A, Andreopoulos W, LaButti K, Pangilinan J, Tritt A, Lipzen A, He G, Yan M, Ng V, Grigoriev IV, Cullen D, Martin F, Rosso MN, Henrissat B, Hibbett D, Martínez AT. Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity. Mol Biol Evol 2021; 38:1428-1446. [PMID: 33211093 PMCID: PMC8480192 DOI: 10.1093/molbev/msaa301] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.
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Affiliation(s)
| | - José M Barrasa
- Life Sciences Department, Alcalá University, Alcalá de Henares, Spain
| | | | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | | | - Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Rashid Babiker
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
| | | | - Remedios Pacheco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Guillermo Padilla
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Patricia Ferreira
- Biochemistry and Molecular and Cellular Biology Department and BIFI, Zaragoza University, Zaragoza, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Harald Kellner
- International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Alan Kuo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - William Andreopoulos
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Andrew Tritt
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Cullen
- Forest Products Laboratory, US Department of Agriculture, Madison, WI, USA
| | - Francis Martin
- INRAE, Laboratory of Excellence ARBRE, Champenoux, France
| | - Marie-Noëlle Rosso
- INRAE, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, USA
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
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30
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Romero-Olivares AL, Morrison EW, Pringle A, Frey SD. Linking Genes to Traits in Fungi. MICROBIAL ECOLOGY 2021; 82:145-155. [PMID: 33483845 PMCID: PMC8282587 DOI: 10.1007/s00248-021-01687-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/06/2021] [Indexed: 05/31/2023]
Abstract
Fungi are mediators of the nitrogen and carbon cycles in terrestrial ecosystems. Examining how nitrogen uptake and organic matter decomposition potential differs in fungi can provide insight into the underlying mechanisms driving fungal ecological processes and ecosystem functioning. In this study, we assessed the frequency of genes encoding for specific enzymes that facilitate nitrogen uptake and organic matter decomposition in 879 fungal genomes with fungal taxa grouped into trait-based categories. Our linked gene-trait data approach revealed that gene frequencies vary across and within trait-based groups and that trait-based categories differ in trait space. We present two examples of how this linked gene-trait approach can be used to address ecological questions. First, we show that this type of approach can help us better understand, and potentially predict, how fungi will respond to environmental stress. Specifically, we found that trait-based categories with high nitrogen uptake gene frequency increased in relative abundance when exposed to high soil nitrogen enrichment. Second, by comparing frequencies of nitrogen uptake and organic matter decomposition genes, we found that most ectomycorrhizal fungi in our dataset have similar gene frequencies to brown rot fungi. This demonstrates that gene-trait data approaches can shed light on potential evolutionary trajectories of life history traits in fungi. We present a framework for exploring nitrogen uptake and organic matter decomposition gene frequencies in fungal trait-based groups and provide two concise examples on how to use our framework to address ecological questions from a mechanistic perspective.
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Affiliation(s)
- A L Romero-Olivares
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA.
- Department of Biology, New Mexico State University, Las Cruces, NM, 88001, USA.
| | - E W Morrison
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
| | - A Pringle
- Department of Botany and Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - S D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
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31
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From lignocellulose to plastics: Knowledge transfer on the degradation approaches by fungi. Biotechnol Adv 2021; 50:107770. [PMID: 33989704 DOI: 10.1016/j.biotechadv.2021.107770] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/04/2021] [Accepted: 05/08/2021] [Indexed: 01/21/2023]
Abstract
In this review, we argue that there is much to be learned by transferring knowledge from research on lignocellulose degradation to that on plastic. Plastic waste accumulates in the environment to hazardous levels, because it is inherently recalcitrant to biological degradation. Plants evolved lignocellulose to be resistant to degradation, but with time, fungi became capable of utilising it for their nutrition. Examples of how fungal strategies to degrade lignocellulose could be insightful for plastic degradation include how fungi overcome the hydrophobicity of lignin (e.g. production of hydrophobins) and crystallinity of cellulose (e.g. oxidative approaches). In parallel, knowledge of the methods for understanding lignocellulose degradation could be insightful such as advanced microscopy, genomic and post-genomic approaches (e.g. gene expression analysis). The known limitations of biological lignocellulose degradation, such as the necessity for physiochemical pretreatments for biofuel production, can be predictive of potential restrictions of biological plastic degradation. Taking lessons from lignocellulose degradation for plastic degradation is also important for biosafety as engineered plastic-degrading fungi could also have increased plant biomass degrading capabilities. Even though plastics are significantly different from lignocellulose because they lack hydrolysable C-C or C-O bonds and therefore have higher recalcitrance, there are apparent similarities, e.g. both types of compounds are mixtures of hydrophobic polymers with amorphous and crystalline regions, and both require hydrolases and oxidoreductases for their degradation. Thus, many lessons could be learned from fungal lignocellulose degradation.
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32
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Palacio M, Drechsler Dos Santos ER, Menolli N, da Silveira RMB. An overview of Favolus from the Neotropics, including four new species. Mycologia 2021; 113:759-775. [PMID: 33945432 DOI: 10.1080/00275514.2021.1878797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Favolus is a monophyletic genus of polypores that causes white rot of various woody plants. The genus has a worldwide distribution and is ecologically and economically important. Several taxa have been described or reported from the Neotropics, and F. brasiliensis, described originally from Brazil, is the type species for the genus. Based on molecular investigations, F. brasiliensis is now known to represent a species complex. The species is morphologically and phylogenetically circumscribed and epitypified here, and F. rugulosus is proposed as a new related species. Favolus grammocephalus and Polyporus philippinensis, initially described from Asia, have also recently been recorded from the Neotropics, so these taxa were included in this investigation employing morphological and multigene (mitochondrial, ribosomal, and protein-coding regions) phylogenetic analyses. These latter two species do not occur in the Neotropics, but the misapplied names actually represent three new species: F. pseudogrammocephalus, F. radiatifibrillosus, and F. yanomami. Nine species of Favolus are documented now for the Neotropics. Detailed descriptions of F. brasiliensis and all new taxa are provided, along with comments, illustrations, a map of potential distribution, and a key for neotropical species of Favolus.
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Affiliation(s)
- Melissa Palacio
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43.433, Campus do Vale, Agronomia, 91501-970, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Nelson Menolli
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Rua Pedro Vicente 625, 01109-010, São Paulo, SP, Brazil.,Instituto de Botânica, Núcleo de Pesquisa em Micologia, Caixa Postal 3005, 01031-970, São Paulo, SP, Brazil
| | - Rosa Mara Borges da Silveira
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43.433, Campus do Vale, Agronomia, 91501-970, Porto Alegre, Rio Grande do Sul, Brazil
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Enhanced Lignocellulolytic Enzyme Activities on Hardwood and Softwood during Interspecific Interactions of White- and Brown-Rot Fungi. J Fungi (Basel) 2021; 7:jof7040265. [PMID: 33807430 PMCID: PMC8065597 DOI: 10.3390/jof7040265] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/23/2022] Open
Abstract
Wood decomposition is a sophisticated process where various biocatalysts act simultaneously and synergistically on biopolymers to efficiently break down plant cell walls. In nature, this process depends on the activities of the wood-inhabiting fungal communities that co-exist and interact during wood decay. Wood-decaying fungal species have traditionally been classified as white-rot and brown-rot fungi, which differ in their decay mechanism and enzyme repertoire. To mimic the species interaction during wood decomposition, we have cultivated the white-rot fungus, Bjerkandera adusta, and two brown-rot fungi, Gloeophyllum sepiarium and Antrodia sinuosa, in single and co-cultivations on softwood and hardwood. We compared their extracellular hydrolytic carbohydrate-active and oxidative lignin-degrading enzyme activities and production profiles. The interaction of white-rot and brown-rot species showed enhanced (hemi)cellulase activities on birch and spruce-supplemented cultivations. Based on the enzyme activity profiles, the combination of B. adusta and G. sepiarium facilitated birch wood degradation, whereas B. adusta and A. sinuosa is a promising combination for efficient degradation of spruce wood, showing synergy in β-glucosidase (BGL) and α-galactosidase (AGL) activity. Synergistic BGL and AGL activity was also detected on birch during the interaction of brown-rot species. Our findings indicate that fungal interaction on different woody substrates have an impact on both simultaneous and sequential biocatalytic activities.
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Aylward FO. The coevolutionary history of the microbial planet. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:12-14. [PMID: 32939975 DOI: 10.1111/1758-2229.12888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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35
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Hess J, Balasundaram SV, Bakkemo RI, Drula E, Henrissat B, Högberg N, Eastwood D, Skrede I. Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans. THE ISME JOURNAL 2021; 15:592-604. [PMID: 33077886 PMCID: PMC8027034 DOI: 10.1038/s41396-020-00799-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/26/2020] [Accepted: 09/25/2020] [Indexed: 11/21/2022]
Abstract
Ecological niche breadth and the mechanisms facilitating its evolution are fundamental to understanding adaptation to changing environments, persistence of generalist and specialist lineages and the formation of new species. Woody substrates are structurally complex resources utilized by organisms with specialized decay machinery. Wood-decaying fungi represent ideal model systems to study evolution of niche breadth, as they vary greatly in their host range and preferred decay stage of the substrate. In order to dissect the genetic basis for niche specialization in the invasive brown rot fungus Serpula lacrymans, we used phenotyping and integrative analysis of phylogenomic and transcriptomic data to compare this species to wild relatives in the Serpulaceae with a range of specialist to generalist decay strategies. Our results indicate specialist species have rewired regulatory networks active during wood decay towards decreased reliance on enzymatic machinery, and therefore nitrogen-intensive decay components. This shift was likely accompanied with adaptation to a narrow tree line habitat and switch to a pioneer decomposer strategy, both requiring rapid colonization of a nitrogen-limited substrate. Among substrate specialists with narrow niches, we also found evidence for pathways facilitating reversal to generalism, highlighting how evolution may move along different axes of niche space.
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Affiliation(s)
- Jaqueline Hess
- Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, UFZ, Halle (Saale), Germany.
| | | | | | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nils Högberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Daniel Eastwood
- Department of Biosciences, University of Swansea, Swansea, UK
| | - Inger Skrede
- Department of Biosciences, University of Oslo, Oslo, Norway
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36
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Kendig AE, Spear ER, Daws SC, Flory SL, Mordecai EA. Native perennial and non-native annual grasses shape pathogen community composition and disease severity in a California grassland. THE JOURNAL OF ECOLOGY 2021; 109:900-912. [PMID: 34158675 PMCID: PMC8215988 DOI: 10.1111/1365-2745.13515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/23/2020] [Indexed: 06/13/2023]
Abstract
The densities of highly competent plant hosts (i.e. those that are susceptible to and successfully transmit a pathogen) may shape pathogen community composition and disease severity, altering disease risk and impacts. Life history and evolutionary history can influence host competence; longer lived species tend to be better defended than shorter lived species and pathogens adapt to infect species with which they have longer evolutionary histories. It is unclear, however, how the densities of species that differ in competence due to life and evolutionary histories affect plant pathogen community composition and disease severity.We examined foliar fungal pathogens of two host groups in a California grassland: native perennial and non-native annual grasses. We first characterized pathogen community composition and disease severity of the two host groups to approximate differences in competence. We then used observational and manipulated gradients of native perennial and non-native annual grass densities to assess the effects of each host group on pathogen community composition and disease severity in 1-m2 plots.Native perennial and non-native annual grasses hosted distinct pathogen communities but shared generalist pathogens. Native perennial grasses experienced 26% higher disease severity than non-native annuals. Only the observational gradient of native perennial grass density affected disease severity; there were no other significant relationships between host group density and either disease severity or pathogen community composition.Synthesis. The life and evolutionary histories of grasses likely influence their competence for different pathogen species, exemplified by distinct pathogen communities and differences in disease severity. However, there was limited evidence that the density of either host group affected pathogen community composition or disease severity. Therefore, competence for different pathogens likely shapes pathogen community composition and disease severity but may not interact with host density to alter disease risk and impacts at small scales.
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Affiliation(s)
- Amy E. Kendig
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Erin R. Spear
- Smithsonian Tropical Research Institute, Panama City, Panama
| | | | - S. Luke Flory
- Agronomy Department, University of Florida, Gainesville, FL, USA
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Abstract
Unharvested hardwoods are abundant in eastern Canada, due to the low quality of their fiber and the absence of outlets in conventional wood transformation industries. The objective of this study was to assess the biochemical and thermochemical energy conversion potential of decaying hardwoods and compare their relationships with external and internal indicators of tree degradation. We characterized how wood-decay processes altered the physical and chemical properties of these woods and affected their digestibility yield and their performance according to indexes of stability and efficiency of combustion. DNA analysis on wood samples was also performed to determine the relative abundance of white-rot fungi compared to that of other saprotrophs. All properties stayed within the range of variations allowing the wood to remain suitable for conversion into bioenergy, even with increased decay. We found no significant differences in the physical and chemical properties that are crucial for energy production between wood from externally-assessed live and decayed trees. However, the proportion of wood area affected by rot was significantly associated with increased digestibility yield, and with decreased combustion reactivity. We could not detect any specific effect associated with increased relative abundance of white-rot fungi. These results suggest that the utilization of biomass from decayed hardwoods instead of live trees for bioenergy production should not alter the conversion efficiency and even potentially increase the performance of biochemical pathways, and hence, support their use as feedstock for bioenergy production.
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Transcriptome analysis of the brown rot fungus Gloeophyllum trabeum during lignocellulose degradation. PLoS One 2020; 15:e0243984. [PMID: 33315957 PMCID: PMC7735643 DOI: 10.1371/journal.pone.0243984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/01/2020] [Indexed: 11/24/2022] Open
Abstract
Brown rot fungi have great potential in biorefinery wood conversion systems because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. Some studies have shown that wood degradation mechanisms of brown rot fungi have diversity in their substrate selectivity. Gloeophyllum trabeum, one of the most studied brown rot species, has broad substrate selectivity and even can degrade some grasses. However, the basis for this broad substrate specificity is poorly understood. In this study, we performed RNA-seq analyses on G. trabeum grown on media containing glucose, cellulose, or Japanese cedar (Cryptomeria japonica) as the sole carbon source. Comparison to the gene expression on glucose, 1,129 genes were upregulated on cellulose and 1,516 genes were upregulated on cedar. Carbohydrate Active enZyme (CAZyme) genes upregulated on cellulose and cedar media by G. trabeum included glycoside hyrolase family 12 (GH12), GH131, carbohydrate esterase family 1 (CE1), auxiliary activities family 3 subfamily 1 (AA3_1), AA3_2, AA3_4 and AA9, which is a newly reported expression pattern for brown rot fungi. The upregulation of both terpene synthase and cytochrome P450 genes on cedar media suggests the potential importance of these gene products in the production of secondary metabolites associated with the chelator-mediated Fenton reaction. These results provide new insights into the inherent wood degradation mechanism of G. trabeum and the diversity of brown rot mechanisms.
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Abstract
Wood durability researchers have long described fungal decay of timber using the starkly simple terms of white, brown and soft rot, along with the less destructive mold and stain fungi. These terms have taken on an almost iconic meaning but are only based upon the outward appearance of the damaged timber. Long-term deterioration studies, as well as the emerging genetic tools, are showing the fallacy of simplifying the decay process into such broad groups. This paper briefly reviews the fundamentals of fungal decay, staining and mold processes, then uses these fundamentals as the basis for a discussion of fungal attack of wood in light of current knowledge about these processes. Biotechnological applications of decay fungi are reviewed, and an overview is presented on how fungi surmount the protective barriers that coatings provide on surfaces. Advances in biochemical analyses have, in some cases, radically altered our perceptions of how wood is degraded, and even the relationships between fungal species, while other new findings have reinforced traditional perspectives. Suggestions for future research needs in the coatings field relative to enhanced fungal and environmental protection are presented.
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Kutszegi G, Siller I, Dima B, Merényi Z, Varga T, Takács K, Turcsányi G, Bidló A, Ódor P. Revealing hidden drivers of macrofungal species richness by analyzing fungal guilds in temperate forests, West Hungary. COMMUNITY ECOL 2020. [DOI: 10.1007/s42974-020-00031-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
AbstractWe explored the most influential stand-scaled drivers of ectomycorrhizal, terricolous saprotrophic, and wood-inhabiting (main functional groups) macrofungal species richness in mixed forests by applying regression models. We tested 67 potential explanatory variables representing tree species composition, stand structure, soil and litter conditions, microclimate, landscape structure, and management history. Within the main functional groups, we formed and modeled guilds and used their drivers to more objectively interpret the drivers of the main functional groups. Terricolous saprotrophic fungi were supported by air humidity and litter mass. Ectomycorrhizal fungi were suppressed by high soil nitrogen content and high air temperature. Wood saprotrophs were enhanced by litter pH (deciduous habitats), deadwood cover, and beech proportion. Wood saprotrophic guilds were determined often by drivers with hidden effects on all wood saprotrophs: non-parasites: total deadwood cover; parasites: beech proportion; white rotters: litter pH; brown rotters: air temperature (negatively); endophytes: beech proportion; early ruderals: deciduous stands that were formerly meadows; combative invaders: deciduous tree taxa; heart rotters: coarse woody debris; late stage specialists: deciduous deadwood. Terricolous saprotrophic cord formers positively responded to litter mass. Studying the drivers of guilds simultaneously, beech was a keystone species to maintain fungal diversity in the region, and coniferous stands would be more diverse by introducing deciduous tree species. Guilds were determined by drivers different from each other underlining their different functional roles and segregated substrate preferences. Modeling guilds of fungal species with concordant response to the environment would be powerful to explore and understand the functioning of fungal communities.
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Rueda AM, López de los Santos Y, Vincent AT, Létourneau M, Hernández I, Sánchez CI, Molina V. D, Ospina SA, Veyrier FJ, Doucet N. Genome sequencing and functional characterization of a Dictyopanus pusillus fungal enzymatic extract offers a promising alternative for lignocellulose pretreatment of oil palm residues. PLoS One 2020; 15:e0227529. [PMID: 32730337 PMCID: PMC7392265 DOI: 10.1371/journal.pone.0227529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/18/2020] [Indexed: 12/15/2022] Open
Abstract
The pretreatment of biomass remains a critical requirement for bio-renewable fuel production from lignocellulose. Although current processes primarily involve chemical and physical approaches, the biological breakdown of lignin using enzymes and microorganisms is quickly becoming an interesting eco-friendly alternative to classical processes. As a result, bioprospection of wild fungi from naturally occurring lignin-rich sources remains a suitable method to uncover and isolate new species exhibiting ligninolytic activity. In this study, wild species of white rot fungi were collected from Colombian forests based on their natural wood decay ability and high capacity to secrete oxidoreductases with high affinity for phenolic polymers such as lignin. Based on high activity obtained from solid-state fermentation using a lignocellulose source from oil palm as matrix, we describe the isolation and whole-genome sequencing of Dictyopanus pusillus, a wild basidiomycete fungus exhibiting ABTS oxidation as an indication of laccase activity. Functional characterization of a crude enzymatic extract identified laccase activity as the main enzymatic contributor to fungal extracts, an observation supported by the identification of 13 putative genes encoding for homologous laccases in the genome. To the best of our knowledge, this represents the first report of an enzymatic extract exhibiting laccase activity in the Dictyopanus genera, offering means to exploit this species and its enzymes for the delignification process of lignocellulosic by-products from oil palm.
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Affiliation(s)
- Andrés M. Rueda
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
- Instituto de Biotecnología, Universidad Nacional de Colombia, Bogotá, Colombia
- Centro de Estudios e Investigaciones Ambientales, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Yossef López de los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Antony T. Vincent
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Inés Hernández
- Centro de Estudios e Investigaciones Ambientales, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Clara I. Sánchez
- Centro de Estudios e Investigaciones Ambientales, Universidad Industrial de Santander, Bucaramanga, Colombia
- Escuela de Microbiología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Daniel Molina V.
- Escuela de Química, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Sonia A. Ospina
- Instituto de Biotecnología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Frédéric J. Veyrier
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
- PROTEO, Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
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Presley GN, Zhang J, Purvine SO, Schilling JS. Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms. Front Microbiol 2020; 11:1646. [PMID: 32849338 PMCID: PMC7399148 DOI: 10.3389/fmicb.2020.01646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/24/2020] [Indexed: 01/06/2023] Open
Abstract
Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.
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Affiliation(s)
- Gerald N Presley
- Department of Wood Science and Engineering, Oregon State University, Corvallis, OR, United States
| | - Jiwei Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, United States
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States
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Zhu Y, Plaza N, Kojima Y, Yoshida M, Zhang J, Jellison J, Pingali SV, O’Neill H, Goodell B. Nanostructural Analysis of Enzymatic and Non-enzymatic Brown Rot Fungal Deconstruction of the Lignocellulose Cell Wall †. Front Microbiol 2020; 11:1389. [PMID: 32670241 PMCID: PMC7326796 DOI: 10.3389/fmicb.2020.01389] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
Brown rot (BR) decay mechanisms employ carbohydrate-active enzymes (CAZymes) as well as a unique non-enzymatic chelator-mediated Fenton (CMF) chemistry to deconstruct lignocellulosic materials. Unlike white rot fungi, BR fungi lack peroxidases for lignin deconstruction, and also lack some endoglucanase/cellobiohydrolase activities. The role that the CMF mechanism plays in "opening up" the wood cell wall structure in advance of enzymatic action, and any interaction between CMF constituents and the selective CAZyme suite that BRs possess, is still unclear. Expression patterns for CMF redox metabolites and lytic polysaccharide monooxygenase (LPMO-AA9 family) genes showed that some LPMO isozymes were upregulated with genes associated with CMF at early stages of brown rot by Gloeophyllum trabeum. In the structural studies, wood decayed by the G. trabeum was compared to CMF-treated wood, or CMF-treated wood followed by treatment with either the early-upregulated LPMO or a commercial CAZyme cocktail. Structural modification of decayed/treated wood was characterized using small angle neutron scattering. CMF treatment produced neutron scattering patterns similar to that of the BR decay indicating that both systems enlarged the nanopore structure of wood cell walls to permit enzyme access. Enzymatic deconstruction of cellulose or lignin in raw wood samples was not achieved via CAZyme cocktail or LPMO enzyme action alone. CMF treatment resulted in depolymerization of crystalline cellulose as attack progressed from the outer regions of individual crystallites. Multiple pulses of CMF treatment on raw wood showed a progressive increase in the spacing between the cellulose elementary fibrils (EFs), indicating the CMF eroded the matrix outside the EF bundles, leading to less tightly packed EFs. Peracetic acid delignification treatment enhanced subsequent CMF treatment effects, and allowed both enzyme systems to further increase spacing of the EFs. Moreover, even after a single pulse of CMF treatment, both enzymes were apparently able to penetrate the cell wall to further increase EF spacing. The data suggest the potential for the early-upregulated LPMO enzyme to work in association with CMF chemistry, suggesting that G. trabeum may have adopted mechanisms to integrate non-enzymatic and enzymatic chemistries together during early stages of brown rot decay.
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Affiliation(s)
- Yuan Zhu
- School of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Nayomi Plaza
- Forest Products Laboratory, USDA Forest Service, Madison, WI, United States
| | - Yuka Kojima
- Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Makoto Yoshida
- Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Jiwei Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, United States
| | - Jody Jellison
- Center for Agriculture, Food and the Environment, University of Massachusetts, Amherst, MA, United States
| | - Sai Venkatesh Pingali
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hugh O’Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Barry Goodell
- Department of Microbiology, Morrill Science Center IV-N, University of Massachusetts, Amherst, MA, United States
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45
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Investigating Wood Decaying Fungi Diversity in Central Siberia, Russia Using ITS Sequence Analysis and Interaction with Host Trees. SUSTAINABILITY 2020. [DOI: 10.3390/su12062535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Wood-decay fungi (WDF) play a significant role in recycling nutrients, using enzymatic and mechanical processes to degrade wood. Designated as a biodiversity hot spot, Central Siberia is a geographically important region for understanding the spatial distribution and the evolutionary processes shaping biodiversity. There have been several studies of WDF diversity in Central Siberia, but identification of species was based on morphological characteristics, lacking detailed descriptions and molecular data. Thus, the aim of this study was to identify WDF in Central Siberia, regarding the degradation of host trees based on both morphological and molecular analyses. We collected 106 WDF samples from Krasnoyarsk and the Republic of Khakassia in 2014 and 2017, and identified a total of 52 fungal species from six main host tree genera. In order to assess the host preference of the WDF, we examined previous literature, and data from this study. We confirmed a division in host preference of WDF between gymnosperms and angiosperms. DNA-based identification and host preference assessment of the WDF provide preliminary data on WDF diversity and their role in nutrient cycles in the ecosystem of Central Siberia. To fully understand WDF diversity in Central Siberia, continuous long-term surveys, including DNA sequence data, are needed.
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46
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Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens. J Biotechnol 2020; 308:35-39. [PMID: 31778732 DOI: 10.1016/j.jbiotec.2019.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/18/2019] [Accepted: 11/23/2019] [Indexed: 11/23/2022]
Abstract
Heterologous production of fungal ligninolytic cocktails is challenging due to the low yields of catalytically active lignin modifying peroxidases. Production using a natural system, such as a wood-rotting fungus, is a promising alternative if specific or preferential induction of the ligninolytic activities could be achieved. Using transcriptomics, gene expression of the white-rot Dichomitus squalens during growth on mixtures of aromatic compounds, with ring structures representing the two major lignin sub-units, was compared to a wood substrate. Most of the genes encoding lignin modifying enzymes (laccases and peroxidases) categorised as highly or moderately expressed on wood were expressed similarly on aromatic compounds. Higher expression levels of a subset of manganese and versatile peroxidases was observed on di- compared to mono-methoxylated aromatics. The expression of polysaccharide degrading enzymes was lower on aromatic compounds compared to wood, demonstrating that the induction of lignin modifying enzymes became more specific. This study suggests potential for aromatic waste streams, e.g. from lignocellulose pretreatment, to produce a lignin-specific enzyme cocktail from D. squalens or other white-rot fungi.
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Zanne AE, Abarenkov K, Afkhami ME, Aguilar-Trigueros CA, Bates S, Bhatnagar JM, Busby PE, Christian N, Cornwell WK, Crowther TW, Flores-Moreno H, Floudas D, Gazis R, Hibbett D, Kennedy P, Lindner DL, Maynard DS, Milo AM, Nilsson RH, Powell J, Schildhauer M, Schilling J, Treseder KK. Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biol Rev Camb Philos Soc 2019; 95:409-433. [PMID: 31763752 DOI: 10.1111/brv.12570] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022]
Abstract
Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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Affiliation(s)
- Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, U.S.A
| | - Carlos A Aguilar-Trigueros
- Freie Universität-Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
| | - Scott Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, IN, 46391, U.S.A
| | | | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97330, U.S.A
| | - Natalie Christian
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, U.S.A.,Department of Biology, University of Louisville, Louisville, KY 40208, U.S.A
| | - William K Cornwell
- Evolution & Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Habacuc Flores-Moreno
- Department of Ecology, Evolution, and Behavior, and Department of Forest Resources, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Dimitrios Floudas
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Romina Gazis
- Department of Plant Pathology, Tropical Research & Education Center, University of Florida, Homestead, FL, 33031, U.S.A
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, 01610, U.S.A
| | - Peter Kennedy
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, Wisconsin, WI, 53726, U.S.A
| | - Daniel S Maynard
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Amy M Milo
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Rolf Henrik Nilsson
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30, Göteborg, Sweden
| | - Jeff Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Mark Schildhauer
- National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa Barbara, CA, 93101, U.S.A
| | - Jonathan Schilling
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, U.S.A
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Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens. Appl Environ Microbiol 2019; 85:AEM.01828-19. [PMID: 31585998 DOI: 10.1128/aem.01828-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/22/2019] [Indexed: 12/15/2022] Open
Abstract
The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of plant biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant biomass would benefit from derepressed or constitutively CAZyme-expressing strains.IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant biomass utilization in the white-rot fungus Dichomitus squalens This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.
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49
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Moiseenko KV, Glazunova OA, Shakhova NV, Savinova OS, Vasina DV, Tyazhelova TV, Psurtseva NV, Fedorova TV. Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum. Microorganisms 2019; 7:E527. [PMID: 31694151 PMCID: PMC6921079 DOI: 10.3390/microorganisms7110527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022] Open
Abstract
Steccherinum ochraceum is a white rot basidiomycete with wide ecological amplitude. It occurs in different regions of Russia and throughout the world, occupying different climatic zones. S. ochraceum colonizes stumps, trunks, and branches of various deciduous (seldom coniferous) trees. As a secondary colonizing fungus, S. ochraceum is mainly observed at the late decay stages. Here, we present the de novo assembly and annotation of the genome of S. ochraceum, LE-BIN 3174. This is the 8th published genome of fungus from the residual polyporoid clade and the first from the Steccherinaceae family. The obtained genome provides a first glimpse into the genetic and enzymatic mechanisms governing adaptation of S. ochraceum to an ecological niche of pre-degraded wood. It is proposed that increased number of carbohydrate-active enzymes (CAZymes) belonging to the AA superfamily and decreased number of CAZymes belonging to the GH superfamily reflects substrate preferences of S. ochraceum. This proposition is further substantiated by the results of the biochemical plate tests and exoproteomic study, which demonstrates that S. ochraceum assumes the intermediate position between typical primary colonizing fungi and litter decomposers or humus saprotrophs. Phylogenetic analysis of S. ochraceum laccase and class II peroxidase genes revealed the distinct evolutional origin of these genes in the Steccherinaceae family.
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Affiliation(s)
- Konstantin V. Moiseenko
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Olga A. Glazunova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Natalia V. Shakhova
- Komarov Botanical Institute of the Russian Academy of Sciences, Professor Popov St. 2, St. Petersburg 197376, Russia;
| | - Olga S. Savinova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Daria V. Vasina
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Tatiana V. Tyazhelova
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119071, Russia;
| | - Nadezhda V. Psurtseva
- Komarov Botanical Institute of the Russian Academy of Sciences, Professor Popov St. 2, St. Petersburg 197376, Russia;
| | - Tatiana V. Fedorova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
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Peintner U, Kuhnert-Finkernagel R, Wille V, Biasioli F, Shiryaev A, Perini C. How to resolve cryptic species of polypores: an example in Fomes. IMA Fungus 2019; 10:17. [PMID: 32647621 PMCID: PMC7325651 DOI: 10.1186/s43008-019-0016-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/27/2019] [Indexed: 01/02/2023] Open
Abstract
Species that cannot be easily distinguished based on morphology, but which form distinct phylogenetic lineages based on molecular markers, are often referred to as cryptic species. They have been proposed in a number of fungal genera, including the basidiomycete genus Fomes. The main aim of this work was to test new methods for species delimitation in cryptic lineages of polypores, and to define useful characters for species identification. A detailed examination of a number of different Fomes strains that had been collected and isolated from different habitats in Italy and Austria confirmed the presence of distinct lineages in the Fomes fomentarius clade. Our zero hypothesis was that the Mediterranean strains growing on Quercus represent a species which can be delimited based on morphological and physiological characters when they are evaluated in statistically relevant numbers. This hypothesis was tested based on phylogenetic analysis of the rDNA ITS region, morphological characters of basidiomes and pure cultures, growth rates and optimum growth temperature experiments, mycelial confrontation tests, enzyme activity tests and volatile organic compound (VOC) production. The Mediterranean lineage can unambiguously be delimited from F. fomentarius. A syntype of an obscure and previously synonymized name, Polyporus inzengae, represents the Mediterranean lineage that we recognize as Fomes inzengae, a distinct species. The rDNA ITS region is useful for delimitation of Fomes species. Moreover, also a variety of morphological characters including hymenophore pore size, basidiospore size, and diameter of skeletal hyphae are useful delimiting characters. The ecology is also very important, because the plant host appears to be a central factor driving speciation. Physiological characters turned also out to be species-specific, e.g. daily mycelial growth rates or the temperature range of pure cultures. The production of VOCs can be considered as a very promising tool for fast and reliable species delimitation in the future.
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Affiliation(s)
- Ursula Peintner
- University Innsbruck, Institute of Microbiology, Technikerstr. 25, 6020 Innsbruck, Austria
| | | | - Viana Wille
- University Innsbruck, Institute of Microbiology, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Franco Biasioli
- Food Quality and Nutrition Department, Edmund Mach Foundation, Via Edmund Mach 1, 38010 San Michele all’ Adige, Italy
| | - Anton Shiryaev
- Vegetation & Mycobiota Diversity Department, Institute of Plant and Animal Ecology (IPAE), Ural Branch of the Russian Academy of Sciences (UrB RAS), 8 March str., 202/3, 620144 Ekaterinburg, Russia
| | - Claudia Perini
- Department of Life Sciences, University Siena, 53100 Siena, Italy
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