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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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2
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Purahong W, Ji L, Wu YT. Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing. MICROBIAL ECOLOGY 2024; 87:66. [PMID: 38700528 PMCID: PMC11068674 DOI: 10.1007/s00248-024-02372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/31/2024] [Indexed: 05/06/2024]
Abstract
Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.
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Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
| | - Li Ji
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
- School of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan.
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
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3
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Kipping L, Jehmlich N, Moll J, Noll M, Gossner MM, Van Den Bossche T, Edelmann P, Borken W, Hofrichter M, Kellner H. Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species. THE ISME JOURNAL 2024; 18:wrae050. [PMID: 38519103 PMCID: PMC11022342 DOI: 10.1093/ismejo/wrae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/19/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.
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Affiliation(s)
- Lydia Kipping
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research—UFZ GmbH, 04318 Leipzig, Germany
- Institute for Bioanalysis, University of Applied Sciences Coburg, 96450 Coburg, Germany
| | - Nico Jehmlich
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research—UFZ GmbH, 04318 Leipzig, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research—UFZ GmbH, 06120 Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, University of Applied Sciences Coburg, 96450 Coburg, Germany
- Department of Soil Ecology, University of Bayreuth, 95448 Bayreuth, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, 8092 Zürich, Switzerland
| | - Tim Van Den Bossche
- VIB—UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Pascal Edelmann
- Department of Ecology and Ecosystem Management, Center of School of Life and Food Sciences Weihenstephan, TU München, 85354 Freising, Germany
| | - Werner Borken
- Department of Soil Ecology, University of Bayreuth, 95448 Bayreuth, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, International Institute Zittau, TU Dresden, 02763 Zittau, Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, International Institute Zittau, TU Dresden, 02763 Zittau, Germany
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4
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Verrone V, Gupta A, Laloo AE, Dubey RK, Hamid NAA, Swarup S. Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167757. [PMID: 37852479 DOI: 10.1016/j.scitotenv.2023.167757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.
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Affiliation(s)
- Valeria Verrone
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Abhishek Gupta
- Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore.
| | - Andrew Elohim Laloo
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore
| | - Rama Kant Dubey
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Nur Ashikin Abdul Hamid
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Sanjay Swarup
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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5
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Zou JY, Cadotte MW, Bässler C, Brandl R, Baldrian P, Borken W, Stengel E, Luo YH, Müller J, Seibold S. Wood decomposition is increased by insect diversity, selection effects, and interactions between insects and microbes. Ecology 2023; 104:e4184. [PMID: 37787980 DOI: 10.1002/ecy.4184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/03/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Biodiversity drives ecosystem processes, but its influence on deadwood decomposition is poorly understood. To test the effects of insect diversity on wood decomposition, we conducted a mesocosm experiment manipulating the species richness and functional diversity of beetles. We applied a novel approach using computed tomography scanning to quantify decomposition by insects and recorded fungal and bacterial communities. Decomposition rates increased with both species richness and functional diversity of beetles, but the effects of functional diversity were linked to beetle biomass, and to the presence of one large-bodied species in particular. This suggests that mechanisms behind observed biodiversity effects are the selection effect, which is linked to the occurrence probability of large species, and the complementarity effect, which is driven by functional differentiation among species. Additionally, beetles had significant indirect effects on wood decomposition via bacterial diversity, fungal community composition, and fungal biomass. Our experiment shows that wood decomposition is driven by beetle diversity and its interactions with bacteria and fungi. This highlights that both insect and microbial biodiversity are critical to maintaining ecosystem functioning.
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Affiliation(s)
- Jia-Yun Zou
- School of Life Sciences, Ecosystem Dynamics and Forest Management Research Group, Technical University of Munich, Freising, Germany
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Marc W Cadotte
- Biological Sciences, University of Toronto-Scarborough, Toronto, Ontario, Canada
| | - Claus Bässler
- Bavarian Forest National Park, Grafenau, Germany
- Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Ecology of Fungi, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Roland Brandl
- Faculty of Biology, Department of Ecology, Animal Ecology, Philipps-Universität Marburg, Marburg, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Werner Borken
- Department of Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | - Elisa Stengel
- Field Station Fabrikschleichach, Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jörg Müller
- Bavarian Forest National Park, Grafenau, Germany
- Field Station Fabrikschleichach, Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sebastian Seibold
- School of Life Sciences, Ecosystem Dynamics and Forest Management Research Group, Technical University of Munich, Freising, Germany
- Technische Universität Dresden, Forest Zoology, Tharandt, Germany
- Berchtesgaden National Park, Berchtesgaden, Germany
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6
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Gemmellaro MD, Lorusso NS, Domke R, Kovalska KM, Hashim A, Arevalo Mojica M, O’Connor AJ, Patel U, Pate O, Raise G, Shumskaya M. Assessment of Fungal Succession in Decomposing Swine Carcasses ( Sus scrofa L.) Using DNA Metabarcoding. J Fungi (Basel) 2023; 9:866. [PMID: 37754974 PMCID: PMC10532525 DOI: 10.3390/jof9090866] [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: 07/17/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
The decomposition of animal bodies is a process defined by specific stages, described by the state of the body and participation of certain guilds of invertebrates and microorganisms. While the participation of invertebrates in decomposing is well-studied and actively used in crime scene investigations, information on bacteria and fungi from the scene is rarely collected or used in the identification of important factors such as estimated time of death. Modern molecular techniques such as DNA metabarcoding allow the identification and quantification of the composition of microbial communities. In this study, we used DNA metabarcoding to monitor fungal succession during the decomposition of juvenile pigs in grasslands of New Jersey, USA. Our findings show that decomposition stages differ in a diversity of fungal communities. In particular, we noted increased fungal species richness in the more advanced stages of decomposition (e.g., bloat and decay stages), with unique fungal taxa becoming active with the progression of decay. Overall, our findings improve knowledge of how fungi contribute to forensically relevant decomposition and could help with the assessment of crime scenes.
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Affiliation(s)
| | | | - Rachel Domke
- Department of Biology, Kean University, Union, NJ 07083, USA
| | | | - Ayesha Hashim
- Department of Biology, Kean University, Union, NJ 07083, USA
| | | | | | - Urvi Patel
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Olivia Pate
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Gloria Raise
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Maria Shumskaya
- Department of Biology, Kean University, Union, NJ 07083, USA
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Crequer E, Ropars J, Jany J, Caron T, Coton M, Snirc A, Vernadet J, Branca A, Giraud T, Coton E. A new cheese population in Penicillium roqueforti and adaptation of the five populations to their ecological niche. Evol Appl 2023; 16:1438-1457. [PMID: 37622099 PMCID: PMC10445096 DOI: 10.1111/eva.13578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/26/2023] [Accepted: 06/22/2023] [Indexed: 08/26/2023] Open
Abstract
Domestication is an excellent case study for understanding adaptation and multiple fungal lineages have been domesticated for fermenting food products. Studying domestication in fungi has thus both fundamental and applied interest. Genomic studies have revealed the existence of four populations within the blue-cheese-making fungus Penicillium roqueforti. The two cheese populations show footprints of domestication, but the adaptation of the two non-cheese populations to their ecological niches (i.e., silage/spoiled food and lumber/spoiled food) has not been investigated yet. Here, we reveal the existence of a new P. roqueforti population, specific to French Termignon cheeses, produced using small-scale traditional practices, with spontaneous blue mould colonisation. This Termignon population is genetically differentiated from the four previously identified populations, providing a novel source of genetic diversity for cheese making. The Termignon population indeed displayed substantial genetic diversity, both mating types, horizontally transferred regions previously detected in the non-Roquefort population, and intermediate phenotypes between cheese and non-cheese populations. Phenotypically, the non-Roquefort cheese population was the most differentiated, with specific traits beneficial for cheese making, in particular higher tolerance to salt, to acidic pH and to lactic acid. Our results support the view that this clonal population, used for many cheese types in multiple countries, is a domesticated lineage on which humans exerted strong selection. The lumber/spoiled food and silage/spoiled food populations were not more tolerant to crop fungicides but showed faster growth in various carbon sources (e.g., dextrose, pectin, sucrose, xylose and/or lactose), which can be beneficial in their ecological niches. Such contrasted phenotypes between P. roqueforti populations, with beneficial traits for cheese-making in the cheese populations and enhanced ability to metabolise sugars in the lumber/spoiled food population, support the inference of domestication in cheese fungi and more generally of adaptation to anthropized environments.
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Affiliation(s)
- Ewen Crequer
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jeanne Ropars
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jean‐Luc Jany
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Thibault Caron
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Monika Coton
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Alodie Snirc
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jean‐Philippe Vernadet
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Antoine Branca
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Tatiana Giraud
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Emmanuel Coton
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
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8
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Huang W, Yu W, Yi B, Raman E, Yang J, Hammel KE, Timokhin VI, Lu C, Howe A, Weintraub-Leff SR, Hall SJ. Contrasting geochemical and fungal controls on decomposition of lignin and soil carbon at continental scale. Nat Commun 2023; 14:2227. [PMID: 37076534 PMCID: PMC10115774 DOI: 10.1038/s41467-023-37862-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Lignin is an abundant and complex plant polymer that may limit litter decomposition, yet lignin is sometimes a minor constituent of soil organic carbon (SOC). Accounting for diversity in soil characteristics might reconcile this apparent contradiction. Tracking decomposition of a lignin/litter mixture and SOC across different North American mineral soils using lab and field incubations, here we show that cumulative lignin decomposition varies 18-fold among soils and is strongly correlated with bulk litter decomposition, but not SOC decomposition. Climate legacy predicts decomposition in the lab, and impacts of nitrogen availability are minor compared with geochemical and microbial properties. Lignin decomposition increases with some metals and fungal taxa, whereas SOC decomposition decreases with metals and is weakly related with fungi. Decoupling of lignin and SOC decomposition and their contrasting biogeochemical drivers indicate that lignin is not necessarily a bottleneck for SOC decomposition and can explain variable contributions of lignin to SOC among ecosystems.
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Affiliation(s)
- Wenjuan Huang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Wenjuan Yu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Bo Yi
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Erik Raman
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Jihoon Yang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Kenneth E Hammel
- U.S. Forest Products Laboratory, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Vitaliy I Timokhin
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | - Chaoqun Lu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | | | - Steven J Hall
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
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9
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Perreault L, Forrester JA, Lindner DL, Jusino MA, Fraver S, Banik MT, Mladenoff DJ. Linking wood-decay fungal communities to decay rates: Using a long-term experimental manipulation of deadwood and canopy gaps. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101220] [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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10
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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11
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Fukasawa Y, Kaga K. Surface Area of Wood Influences the Effects of Fungal Interspecific Interaction on Wood Decomposition—A Case Study Based on Pinus densiflora and Selected White Rot Fungi. J Fungi (Basel) 2022; 8:jof8050517. [PMID: 35628772 PMCID: PMC9145481 DOI: 10.3390/jof8050517] [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: 04/26/2022] [Revised: 05/14/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023] Open
Abstract
Wood decomposer basidiomycetes are the major agents of lignocellulose decomposition in dead wood. As their interspecific interaction affects wood decomposition, difference in interaction area may alter the magnitude of the effects. This study examines the effects of wood surface area on decomposition by interacting basidiomycetes using laboratory incubation experiments with pine sapwood as a model. Two types of pine wood blocks with equal volume but identical surface area were prepared for colonization by one of four white rot basidiomycete species. The colonized wood blocks were then placed on agar media already colonized by the same strain or one of the other species, simulating fungal monoculture and interspecific interactions on wood surface. Results demonstrated that the decay rate of wood was greater in wood with larger surface, and wood decay was accelerated by the interaction of two fungal species in wood with larger surface but not in wood with smaller surface. In contrast, lignin decomposition was influenced by the competitor in wood with smaller surface but not in wood with larger surface. These results suggest that the observed promotion of decay by fungal interspecific interaction might not be attributable to the resource partitioning between fungal species but to the accelerated carbon of competition cost compensation in this case.
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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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Toapanta-Alban CE, Ordoñez ME, Blanchette RA. New Findings on the Biology and Ecology of the Ecuadorian Amazon Fungus Polyporus leprieurii var. yasuniensis. J Fungi (Basel) 2022; 8:jof8020203. [PMID: 35205957 PMCID: PMC8874993 DOI: 10.3390/jof8020203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
Polyporus leprieurii var. yasuniensis is a prolific wood-decay fungus inhabiting the forest floor of one of the most biodiverse places on earth, the Yasuní National Park in Ecuador. Basidiocarps and aerial rhizomorphs are commonly found growing on woody debris distributed along the floor of this forest ecosystem. Because of the extraordinary abundance of this fungus in the tropical rainforest, we carried out investigations to better understand the biological and ecological aspects contributing to its prolific distribution. Data on growth inhibition in paired competition studies with sixteen fungal isolates exemplifies defense mechanisms used to defend its territory, including pseudosclerotial plates and the development of a melanized rhizomorphic mat. Results of biomass loss on eleven types of tropical wood in microcosm experiments demonstrated the broad decay capacity of the fungus. In and ex situ observations provided information on how long rhizomorphs can prevail in highly competitive ecosystems as well as stressful conditions in the laboratory. Finally, high concentrations of metal ions occur on rhizomorphs as compared to colonized wood. Sequestration of metal ions from the environment by the melanized rhizomorphs may offer protection against competitors. The development of melanized rhizomorphs is key to find and colonize new substrates and resist changing environmental conditions.
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Affiliation(s)
| | - María E. Ordoñez
- Fungarium QCAM, Escuela de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador;
| | - Robert A. Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA;
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Abrego N. Wood-inhabiting fungal communities: Opportunities for integration of empirical and theoretical community ecology. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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15
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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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Fukasawa Y, Matsukura K, Stephan JG, Makoto K, Suzuki SN, Kominami Y, Takagi M, Tanaka N, Takemoto S, Kinuura H, Okano K, Song Z, Jomura M, Kadowaki K, Yamashita S, Ushio M. Patterns of community composition and diversity in latent fungi of living Quercus serrata trunks across a range of oak wilt prevalence and climate variables in Japan. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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