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Roy F, Ibayev O, Arnstadt T, Bässler C, Borken W, Groß C, Hoppe B, Hossen S, Kahl T, Moll J, Noll M, Purahong W, Schreiber J, Weisser WW, Hofrichter M, Kellner H. Nitrogen addition increases mass loss of gymnosperm but not of angiosperm deadwood without changing microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165868. [PMID: 37516186 DOI: 10.1016/j.scitotenv.2023.165868] [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: 03/07/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Enhanced nitrogen (N) deposition due to combustion of fossil fuels and agricultural fertilization is a global phenomenon which has severely altered carbon (C) and N cycling in temperate forest ecosystems in the northern hemisphere. Although deadwood holds a substantial amount of C in forest ecosystems and thus plays a crucial role in nutrient cycling, the effect of increased N deposition on microbial processes and communities, wood chemical traits and deadwood mass loss remains unclear. Here, we simulated high N deposition rates by adding reactive N in form of ammonium-nitrate (40 kg N ha-1 yr-1) to deadwood of 13 temperate tree species over nine years in a field experiment in Germany. Non-treated deadwood from the same logs served as control with background N deposition. Our results show that chronically elevated N levels alters deadwood mass loss alongside respiration, enzymatic activities and wood chemistry depending on tree clade and species. In gymnosperm deadwood, elevated N increased mass loss by +38 %, respiration by +37 % and increased laccase activity 12-fold alongside increases of white-rot fungal abundance +89 % (p = 0.03). Furthermore, we observed marginally significant (p = 0.06) shifts of bacterial communities in gymnosperm deadwood. In angiosperm deadwood, we did not detect consistent effects on mass loss, physico-chemical properties, extracellular enzymatic activity or changes in microbial communities except for changes in abundance of 10 fungal OTUs in seven tree species and 28 bacterial OTUs in 10 tree species. We conclude that N deposition alters decomposition processes exclusively in N limited gymnosperm deadwood in the long term by enhancing fungal activity as expressed by increases in respiration rate and extracellular enzyme activity with minor shifts in decomposing microbial communities. By contrast, deadwood of angiosperm tree species had higher N concentrations and mass loss as well as community composition did not respond to N addition.
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Affiliation(s)
- Friederike Roy
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Orkhan Ibayev
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Tobias Arnstadt
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Claus Bässler
- Institute for Ecology, Evolution and Diversity, Department of Conservation Biology, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany; National Park Bavarian Forest, Freyunger Str. 2, D-94481 Grafenau, Germany
| | - Werner Borken
- Institute for Soil Ecology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, D-95448 Bayreuth, Germany
| | - Christina Groß
- Institute for Soil Ecology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, D-95448 Bayreuth, Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11/12, D-38104 Braunschweig, Germany
| | - Shakhawat Hossen
- Institute for Bioanalysis, University of Applied Sciences Coburg, Friedrich-Streib-Straße 2, D-96450 Coburg, Germany
| | - Tiemo Kahl
- UNESCO-Biosphärenreservat Thüringer Wald, Schmiedefeld a. Rstg, Brunnenstraße 1, D-98528 Suhl, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Th.-Lieser- Str. 4, D-06120 Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, University of Applied Sciences Coburg, Friedrich-Streib-Straße 2, D-96450 Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Th.-Lieser- Str. 4, D-06120 Halle (Saale), Germany
| | - Jasper Schreiber
- Institute for Ecology, Evolution and Diversity, Department of Conservation Biology, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany
| | - Wolfgang W Weisser
- Terrestrial Ecology Research Group, Technical University of Munich, D-85354 Freising, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany.
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Cristini V, Nop P, Zlámal J, Vand MH, Šeda V, Tippner J. Fomes fomentarius and F. inzengae—A Comparison of Their Decay Patterns on Beech Wood. Microorganisms 2023; 11:microorganisms11030679. [PMID: 36985251 PMCID: PMC10056366 DOI: 10.3390/microorganisms11030679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Wood-decaying fungi are responsible for the degradation of wood and the alteration in its material properties. Fomes fomentarius (L.) Fr. is one of the most common white-rot fungi colonising coarse wood and standing trees. In recent years, according to their genetic, physiological, and morphological differences, Fomes inzengae (Ces. and De Not.) Lécuru was identified as an independent species. This article aimed to compare the impact of the degradation caused by both species on the anatomical, physical, and mechanical properties of beech wood. When comparing the degradation caused by different strains of both species, no statistically significant difference was found in mass loss (ML) or moisture content (MC). A relevant correlation between ML and MC was confirmed for both species. Variabilities in the density distribution of the degraded and intact bending samples were found to be statistically different. No relevant difference was observed in the modulus of rupture (MOR) between the two species after each exposure period. A strong linear relationship between the MOR and the dynamic modulus of elasticity was revealed for both species. Both species showed decay patterns typical for simultaneous white rot and soft rot. According to the presented results, the impact of both species on the investigated material properties of wood cannot be considered significantly different.
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Affiliation(s)
- Valentino Cristini
- Department of Wood Science and Technology, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Patrik Nop
- Department of Wood Science and Technology, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Jan Zlámal
- Department of Wood Science and Technology, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Mojtaba Hassan Vand
- Department of Wood Science and Technology, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Vít Šeda
- Department of Wood Science and Technology, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Jan Tippner
- Department of Wood Science and Technology, Mendel University in Brno, 613 00 Brno, Czech Republic
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Pylkkänen R, Werner D, Bishoyi A, Weil D, Scoppola E, Wagermaier W, Safeer A, Bahri S, Baldus M, Paananen A, Penttilä M, Szilvay GR, Mohammadi P. The complex structure of Fomes fomentarius represents an architectural design for high-performance ultralightweight materials. SCIENCE ADVANCES 2023; 9:eade5417. [PMID: 36812306 PMCID: PMC9946349 DOI: 10.1126/sciadv.ade5417] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
High strength, hardness, and fracture toughness are mechanical properties that are not commonly associated with the fleshy body of a fungus. Here, we show with detailed structural, chemical, and mechanical characterization that Fomes fomentarius is an exception, and its architectural design is a source of inspiration for an emerging class of ultralightweight high-performance materials. Our findings reveal that F. fomentarius is a functionally graded material with three distinct layers that undergo multiscale hierarchical self-assembly. Mycelium is the primary component in all layers. However, in each layer, mycelium exhibits a very distinct microstructure with unique preferential orientation, aspect ratio, density, and branch length. We also show that an extracellular matrix acts as a reinforcing adhesive that differs in each layer in terms of quantity, polymeric content, and interconnectivity. These findings demonstrate how the synergistic interplay of the aforementioned features results in distinct mechanical properties for each layer.
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Affiliation(s)
- Robert Pylkkänen
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Daniel Werner
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, D-14476 Potsdam, Germany
| | - Ajit Bishoyi
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Dominik Weil
- KLA-Tencor GmbH, Moritzburger Weg 67, Dresden 01109, Germany
| | - Ernesto Scoppola
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, D-14476 Potsdam, Germany
| | - Wolfgang Wagermaier
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, D-14476 Potsdam, Germany
| | - Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Salima Bahri
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Arja Paananen
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Géza R. Szilvay
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
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4
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Haq IU, Hillmann B, Moran M, Willard S, Knights D, Fixen KR, Schilling JS. Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms. ISME COMMUNICATIONS 2022; 2:26. [PMID: 37938255 PMCID: PMC9723729 DOI: 10.1038/s43705-022-00108-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/11/2023]
Abstract
Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth's woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.
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Affiliation(s)
- Irshad Ul Haq
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Molly Moran
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
| | - Samuel Willard
- Department of Life Sciences, Imperial College London, London, UK
| | - Dan Knights
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA.
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.
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5
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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6
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Angst Š, Baldrian P, Harantová L, Cajthaml T, Frouz J. Different twig litter (Salix caprea) diameter does affect microbial community activity and composition but not decay rate. FEMS Microbiol Ecol 2019; 94:5046416. [PMID: 29961854 DOI: 10.1093/femsec/fiy126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/23/2018] [Indexed: 12/21/2022] Open
Abstract
Small twigs represent a substantial input of organic carbon into forest soils, but potential influencing factors on their decomposition have rarely been investigated. Here, we studied potential effects of twig size on decomposition and associated composition and activity of microbial communities during decomposition. Because the surface area for microbial colonization and the volume of accessible substrate increases with decreasing twig size, we hypothesized that twig size affects both microbial community and decomposition rate. Litterbags with twigs (Salix caprea) of two different diameters were placed within the litter layer and consecutively collected over a seven-year period. We determined the mass loss and microbial measures after each sampling event. The observed microbial parameters suggested a faster microbial colonization of thin twigs, where the proportion of bacteria was higher than in thick twigs. The development of the microbial community in thick twigs was more gradual and the proportion of fungi was higher. Despite this differential and successional development of microbial communities (and against our hypothesis), the mass loss among different twig diameters did not differ after our seven-year experiment, indicating that surface-to-volume ratios, though a primary control on microbial succession, may have limited predictive power for twig decomposition rates.
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Affiliation(s)
- Šárka Angst
- Biology Centre of the Czech Academy of Sciences, v. v. i., SoWa Research Infrastructure & Institute of Soil Biology, Na Sádkách 7, CZ 37005 Ceské Budejovice, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Vídenská 1083, CZ 14220 Praha, Czech Republic
| | - Lenka Harantová
- Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Vídenská 1083, CZ 14220 Praha, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Vídeňská 1083, CZ 14220 Praha, Czech Republic.,Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benátská 2, CZ 12800, Praha 2, Czech Republic
| | - Jan Frouz
- Biology Centre of the Czech Academy of Sciences, v. v. i., SoWa Research Infrastructure & Institute of Soil Biology, Na Sádkách 7, CZ 37005 České Budějovice, Czech Republic.,Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benátská 2, CZ 12800, Praha 2, Czech Republic
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7
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Zhou S, Zhang J, Ma F, Tang C, Tang Q, Zhang X. Investigation of lignocellulolytic enzymes during different growth phases of Ganoderma lucidum strain G0119 using genomic, transcriptomic and secretomic analyses. PLoS One 2018; 13:e0198404. [PMID: 29852018 PMCID: PMC5979026 DOI: 10.1371/journal.pone.0198404] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/20/2018] [Indexed: 12/13/2022] Open
Abstract
Ganoderma lucidum is a medicinal mushroom that is well known for its ability to enhance human health, and products made from this fungus have been highly profitable. The substrate-degrading ability of G. lucidum could be related to its growth. CAZy proteins were more abundant in its genome than in the other white rot fungi models. Among these CAZy proteins, changes in lignocellulolytic enzymes during growth have not been well studied. Using genomic, transcriptomic and secretomic analyses, this study focuses on the lignocellulolytic enzymes of G. lucidum strain G0119 to determine which of these degradative enzymes contribute to its growth. From the genome sequencing data, genes belonging to CAZy protein families, especially genes involved in lignocellulose degradation, were investigated. The gene expression, protein abundance and enzymatic activity of lignocellulolytic enzymes in mycelia over a growth cycle were analysed. The overall expression cellulase was higher than that of hemicellulase and lignin-modifying enzymes, particularly during the development of fruiting bodies. The cellulase and hemicellulase abundances and activities increased after the fruiting bodies matured, when basidiospores were produced in massive quantities till the end of the growth cycle. Additionally, the protein abundances of the lignin-modifying enzymes and the expression of their corresponding genes, including laccases and lignin-degrading heme peroxidases, were highest when the mycelia fully spread in the compost bag. Type I cellobiohydrolase was observed to be the most abundant extracellular lignocellulolytic enzyme produced by the G. lucidum strain G0119. The AA2 family haem peroxidases were the dominant lignin-modifying enzyme expressed during the mycelial growth phase, and several laccases might play roles during the formation of the primordium. This study provides insight into the changes in the lignocellulose degradation ability of G. lucidum during its growth and will facilitate the discovery of new approaches to accelerate the growth of G. lucidum in culture.
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Affiliation(s)
- Shuai Zhou
- Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China.,National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China
| | - Jingsong Zhang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China
| | - Fuying Ma
- Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Chuanhong Tang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China
| | - Qingjiu Tang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China
| | - Xiaoyu Zhang
- Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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8
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Navrátilová D, Větrovský T, Baldrian P. Spatial heterogeneity of cellulolytic activity and fungal communities within individual decomposing Quercus petraea leaves. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2016.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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9
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Baldrian P, Zrůstová P, Tláskal V, Davidová A, Merhautová V, Vrška T. Fungi associated with decomposing deadwood in a natural beech-dominated forest. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.07.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Štursová M, Bárta J, Šantrůčková H, Baldrian P. Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil. FEMS Microbiol Ecol 2016; 92:fiw185. [PMID: 27604254 DOI: 10.1093/femsec/fiw185] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2016] [Indexed: 11/13/2022] Open
Abstract
Forests are recognised as spatially heterogeneous ecosystems. However, knowledge of the small-scale spatial variation in microbial abundance, community composition and activity is limited. Here, we aimed to describe the heterogeneity of environmental properties, namely vegetation, soil chemical composition, fungal and bacterial abundance and community composition, and enzymatic activity, in the topsoil in a small area (36 m2) of a highly heterogeneous regenerating temperate natural forest, and to explore the relationships among these variables. The results demonstrated a high level of spatial heterogeneity in all properties and revealed differences between litter and soil. Fungal communities had substantially higher beta-diversity than bacterial communities, which were more uniform and less spatially autocorrelated. In litter, fungal communities were affected by vegetation and appeared to be more involved in decomposition. In the soil, chemical composition affected both microbial abundance and the rates of decomposition, whereas the effect of vegetation was small. Importantly, decomposition appeared to be concentrated in hotspots with increased activity of multiple enzymes. Overall, forest topsoil should be considered a spatially heterogeneous environment in which the mean estimates of ecosystem-level processes and microbial community composition may confound the existence of highly specific microenvironments.
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Affiliation(s)
- Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Jiří Bárta
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Hana Šantrůčková
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
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11
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Johnston SR, Boddy L, Weightman AJ. Bacteria in decomposing wood and their interactions with wood-decay fungi. FEMS Microbiol Ecol 2016; 92:fiw179. [PMID: 27559028 DOI: 10.1093/femsec/fiw179] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 01/02/2023] Open
Abstract
The fungal community within dead wood has received considerable study, but far less attention has been paid to bacteria in the same habitat. Bacteria have long been known to inhabit decomposing wood, but much remains underexplored about their identity and ecology. Bacteria within the dead wood environment must interact with wood-decay fungi, but again, very little is known about the form this takes; there are indications of both antagonistic and beneficial interactions within this fungal microbiome. Fungi are hypothesised to play an important role in shaping bacterial communities in wood, and conversely, bacteria may affect wood-decay fungi in a variety of ways. This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats. It aims to identify key knowledge gaps and pressing questions for future research.
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Affiliation(s)
- Sarah R Johnston
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Lynne Boddy
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Andrew J Weightman
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
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12
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Purahong W, Arnstadt T, Kahl T, Bauhus J, Kellner H, Hofrichter M, Krüger D, Buscot F, Hoppe B. Are correlations between deadwood fungal community structure, wood physico-chemical properties and lignin-modifying enzymes stable across different geographical regions? FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.01.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Glumac M, Pejin B, Karaman M, Mojović M, Matavulj M. Lignicolous fungi hydrodistilled extracts may represent a promising source of natural phenolics. Nat Prod Res 2016; 31:104-107. [DOI: 10.1080/14786419.2016.1212036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Miodrag Glumac
- Faculty of Sciences, Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Boris Pejin
- Department of Life Sciences, University of Belgrade, Institute for Multidisciplinary Research – IMSI, Belgrade, Serbia
| | - Maja Karaman
- Faculty of Sciences, Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Miloš Mojović
- Faculty of Physical Chemistry, University of Belgrade, Belgrade, Serbia
| | - Milan Matavulj
- Faculty of Sciences, Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
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Kubartová A, Ottosson E, Stenlid J. Linking fungal communities to wood density loss after 12 years of log decay. FEMS Microbiol Ecol 2015; 91:fiv032. [DOI: 10.1093/femsec/fiv032] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2015] [Indexed: 11/12/2022] Open
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15
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Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2014.08.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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17
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Müller J, Jarzabek-Müller A, Bussler H, Gossner MM. Hollow beech trees identified as keystone structures for saproxylic beetles by analyses of functional and phylogenetic diversity. Anim Conserv 2013. [DOI: 10.1111/acv.12075] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- J. Müller
- Bavarian Forest National Park; Grafenau Germany
- Terrestrial Ecology Research Group; Department of Ecology and Ecosystem Management; Center for Food and Life Sciences Weihenstephan; Technische Universität München; Freising Germany
| | | | - H. Bussler
- Am Greifenkeller 1b; Feuchtwangen Germany
| | - M. M. Gossner
- Terrestrial Ecology Research Group; Department of Ecology and Ecosystem Management; Center for Food and Life Sciences Weihenstephan; Technische Universität München; Freising Germany
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18
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van der Wal A, Geydan TD, Kuyper TW, de Boer W. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiol Rev 2013; 37:477-94. [DOI: 10.1111/1574-6976.12001] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/02/2012] [Accepted: 08/21/2012] [Indexed: 12/24/2022] Open
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19
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Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi. ISME JOURNAL 2013; 7:1696-709. [PMID: 23575372 DOI: 10.1038/ismej.2013.61] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 03/07/2013] [Accepted: 03/13/2013] [Indexed: 11/09/2022]
Abstract
Before the recent revolution in molecular biology, field studies on fungal communities were mostly confined to fruit bodies, whereas mycelial interactions were studied in the laboratory. Here we combine high-throughput sequencing with a fruit body inventory to study simultaneously mycelial and fruit body occurrences in a community of fungi inhabiting dead wood of Norway spruce. We studied mycelial occurrence by extracting DNA from wood samples followed by 454-sequencing of the ITS1 and ITS2 regions and an automated procedure for species identification. In total, we detected 198 species as mycelia and 137 species as fruit bodies. The correlation between mycelial and fruit body occurrences was high for the majority of the species, suggesting that high-throughput sequencing can successfully characterize the dominating fungal communities, despite possible biases related to sampling, PCR, sequencing and molecular identification. We used the fruit body and molecular data to test hypothesized links between life history and population dynamic parameters. We show that the species that have on average a high mycelial abundance also have a high fruiting rate and produce large fruit bodies, leading to a positive feedback loop in their population dynamics. Earlier studies have shown that species with specialized resource requirements are rarely seen fruiting, for which reason they are often classified as red-listed. We show with the help of high-throughput sequencing that some of these species are more abundant as mycelium in wood than what could be expected from their occurrence as fruit bodies.
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Větrovský T, Baldrian P, Gabriel J. Extracellular enzymes of the white-rot fungus Fomes fomentarius and purification of 1,4-β-glucosidase. Appl Biochem Biotechnol 2012; 169:100-9. [PMID: 23149715 DOI: 10.1007/s12010-012-9952-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/31/2012] [Indexed: 01/24/2023]
Abstract
Production of the lignocellulose-degrading enzymes endo-1,4-β-glucanase, 1,4-β-glucosidase, cellobiohydrolase, endo-1,4-β-xylanase, 1,4-β-xylosidase, Mn peroxidase, and laccase was characterized in a common wood-rotting fungus Fomes fomentarius, a species able to efficiently decompose dead wood, and compared to the production in eight other fungal species. The main aim of this study was to characterize the 1,4-β-glucosidase produced by F. fomentarius that was produced in high quantities in liquid stationary culture (25.9 U ml(-1)), at least threefold compared to other saprotrophic basidiomycetes, such as Rhodocollybia butyracea, Hypholoma fasciculare, Irpex lacteus, Fomitopsis pinicola, Pleurotus ostreatus, Piptoporus betulinus, and Gymnopus sp. (between 0.7 and 7.9 U ml(-1)). The 1,4-β-glucosidase enzyme was purified to electrophoretic homogeneity by both anion-exchange and size-exclusion chromatography. A single 1,4-β-glucosidase was found to have an apparent molecular mass of 58 kDa and a pI of 6.7. The enzyme exhibited high thermotolerance with an optimum temperature of 60 °C. Maximal activity was found in the pH range of 4.5-5.0, and K (M) and V (max) values were 62 μM and 15.8 μmol min(-1) l(-1), respectively, when p-nitrophenylglucoside was used as a substrate. The enzyme was competitively inhibited by glucose with a K (i) of 3.37 mM. The enzyme also acted on p-nitrophenylxyloside, p-nitrophenylcellobioside, p-nitrophenylgalactoside, and p-nitrophenylmannoside with optimal pH values of 6.0, 3.5, 5.0, and 4.0-6.0, respectively. The combination of relatively low molecular mass and low K (M) value make the 1,4-β-glucosidase a promising enzyme for biotechnological applications.
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Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 14220 Praha 4, Czech Republic
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21
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Hahn F, Ullrich R, Hofrichter M, Liers C. Experimental approach to follow the spatiotemporal wood degradation in fungal microcosms. Biotechnol J 2012; 8:127-32. [DOI: 10.1002/biot.201200183] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/14/2012] [Accepted: 07/10/2012] [Indexed: 11/06/2022]
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